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WO2018078142A1 - Means and methods for determining efficacy of fluorouracil (5-fu) in colorectal cancer (crc) therapy - Google Patents

Means and methods for determining efficacy of fluorouracil (5-fu) in colorectal cancer (crc) therapy Download PDF

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WO2018078142A1
WO2018078142A1 PCT/EP2017/077693 EP2017077693W WO2018078142A1 WO 2018078142 A1 WO2018078142 A1 WO 2018078142A1 EP 2017077693 W EP2017077693 W EP 2017077693W WO 2018078142 A1 WO2018078142 A1 WO 2018078142A1
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transcript variant
gene
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PCT/EP2017/077693
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French (fr)
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Marie-Laure Yaspo
Thomas Risch
Christine JANDRASITS
Hans Lehrach
Bodo Lange
Moritz SCHÜTTE
Jens Hoffmann
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MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V.
Alacris Theranostics Gmbh
Experimentelle Pharmakologie Und Onkologie (Epo) Berlin-Buch Gmbh
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Publication of WO2018078142A1 publication Critical patent/WO2018078142A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to a method for determining the susceptibility/responsiveness of (a) cancer cell(s), preferably (a) colorectal cancer cell(s), to the treatment with fluorouracil (5- FU). Further, the present invention relates to a method of selecting (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) of colorectal cancer (CRC) with susceptibility to fluorouracil (5-FU).
  • an in vitro method for the identification of a responder for or a subject, preferably a human patient, suffering from colorectal cancer (CRC) to fluorouracil (5-FU) is disclosed.
  • the present invention also relates to a method of monitoring the efficacy of a treatment of the colorectal cancer (CRC) with fluorouracil (5-FU).
  • Colorectal cancer represents the third most frequent cancer worldwide. The five-year survival rate of patients diagnosed with metastasis is below 10%. CRC is refractory to most chemotherapeutic agents. Only fluorouracil (5-FU), irinotecan and oxaliplatin have documented responses in metastatic diseases such as colorectal cancer (CRC). Antibodies targeting the epidermal growth factor receptor (EGFR), such as cetuximab offer therapeutic options for a fraction of metastatic colorectal cancers (CRCs) but have failed in the adjuvant setting (Nelson V.M. et al. Gastrointest Oncol. 4(3) (2013), 245-252).
  • EGFR epidermal growth factor receptor
  • Regorafenib monotherapy a multi tyrosine kinase inhibitor
  • CRC metastatic colorectal cancer
  • Colorectal cancers are heterogeneous tumors which can be classified within characteristic molecular groups, however the clinical utility of this classification has not been demonstrated so far (De Sousa E.M.F. et al. Nat Med 19 (2013), 614-618; Guinney J. et al, Nat Med 21 (2015), 1350-1356; Marisa L. et al, PLoS Med 10 (2013), el 001453; Sadanandam A.
  • WO-A2 2008/115419 discloses marker gene(s) and methods for prediction of patient response to fluorouracil (5-FU); see also WO-A1 2007/147877; WO-A2 2006/015742; WO-A1 2009/114836; WO-A1 2014/197543; Ju et al, Journal of Cellular Biochemistry 116(2) (2015), 277-286.
  • fluorouracil 5-FU
  • the technical problem underlying the present invention is the provision of means and methods for the evaluation of (a) cell(s), in particular (a) cancer cell(s), (a) cancer tissue or tumor sample(s) obtained from a subject suffering from cancer, for their susceptibility or responsiveness to the treatment with an anti-cancer treatment.
  • the present invention relates to a method for determining the susceptibility or responsiveness of (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), comprising (a) obtaining (a) cancer cell(s), cancer tissue(s) or tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said cancer cell(s), cancer tissue(s) or tumor sample(s), wherein said expression level is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5-FU).
  • the present invention is based on the unexpected finding that by determining the expression of one or more gene(s) shown in Table 1 ( Figure 1), more preferably by determining the expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) it is possible to predict in a reliable manner whether or not a subject suffering from colorectal cancer (CRC) is susceptible or responsive to a treatment with fluorouracil (5-FU).
  • the methods of the present invention allow the prediction or determination of the responsiveness or susceptibility to a treatment with fluorouracil (5-FU) in a subject suffering from colorectal cancer (CRC).
  • the present invention generally relates to a method of selecting (a) subject(s) suffering from colorectal cancer (CRC) with susceptibility or responsiveness to fluorouracil (5-FU), comprising the steps of: (a) determining the expression level of one or more gene(s) shown in Table 1 ( Figure 1), more preferably determining the expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) of said subject; and (b) selecting (a) subject(s)/patient(s) suffering from colorectal cancer (CRC) characterized by a differential expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably characterized by a differential expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the method may additionally comprise (i) contacting (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) with fluorouracil (5-FU) and (ii) evaluating susceptibility or responsiveness of said cancer cell(s), cancer tissue(s) or tumor sample(s) contacted with fluorouracil (5-FU). It is of note that steps (i) and (ii) may be performed prior to step (a) but also after step (a) or, optionally, after step (b). Said steps (i) and (ii) may in particular serve as further experimental proof that the selected subject(s) is responsive or susceptible in its viability to fluorouracil (5-FU).
  • cancer cell(s), cancer tissue(s) or tumor sample(s) is not only limited to (an) isolated cell(s), (a) tissue(s), (a) tumor sample(s) and cell culture(s) from a carcinogenic tissue, preferably from colorectal cancer (CRC), but also comprises the use of (a) sample(s), i.e. (a) biological, medical or pathological sample(s) that consist of fluids such as blood, ascites, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots and comprise such (a) carcinogenic cell(s) or parts, fragments of carcinogenic cell(s).
  • sample(s) i.e.
  • biological, medical or pathological sample(s) that consist of fluids such as blood, ascites, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots and comprise such (a) carcinogenic cell(s) or parts, fragments of carcinogenic cell(s).
  • the gist of the present invention lies in the fact that a method is provided that allows the determination of the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) for the anti-cancer or anti-proliferative treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • 5-FU fluorouracil
  • the present invention provides a method for selecting (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) which are susceptible or responsive to fluorouracil (5-FU), but also for an in vitro method for assessing a subject suffering from colorectal cancer (CRC), i.e.
  • the present invention provides not only the possibility to select (a) cell(s), (a) cancer tissue(s), (a) tumor sample(s) that are susceptible or responsive to the treatment with fluorouracil (5-FU) but also for a method to evaluate whether a given subject, preferably a subject suffering from colorectal cancer (CRC), is a responder or non-responder for a fluorouracil (5-FU) treatment.
  • a given subject preferably a subject suffering from colorectal cancer (CRC)
  • CRC colorectal cancer
  • the present invention relates to a method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) which comprises the step of: (a) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 is determined. Accordingly, in the herein described method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) the activity or expression of one or more gene(s), preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.
  • DDX43 NCBI accession no.:
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NMJ300146; version no.: NM 000146.3; GL56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_02450
  • the selection method of an fluorouracil (5-FU) responding cell or a responding subject, preferably a human patient comprises the steps of (a) obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably determining the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU) comprises the step of obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject suffering from CRC with (a) differential gene expression of 1 , 2, 3,
  • the present invention relates in particular to a method for determining the responsiveness or susceptibility of colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s) obtained from a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), said method comprises determining the gene expression level of one or more gene(s) shown in Table 1 ( Figure 1), preferably of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the gene(s) as shown in Table 3 ( Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s), wherein said gene expression level is indicative of whether the cell is likely to respond or is responsive to the fluorouracil (5-FU) treatment.
  • Table 1 Figure 1
  • Figure 3 preferably of 1 , 2, 3, 4, 5, 6,
  • Such a determination may take place on (an) individual, isolated tumor cell(s). Such an evaluation may also be carried out on biological/medical/pathological sample(s), like body fluids, isolated body tissue samples and the like, wherein said sample(s) preferably comprise cells or cell debris to be analyzed.
  • Subject of the present invention is a method for diagnosing a subject/patient suffering from colorectal cancer (CRC) who is to be subjected to or is being subjected to an anti-cancer treatment or an anti-proliferative treatment to assess the responsiveness or susceptibility to fluorouracil (5-FU) prior, during and/or after fluorouracil (5-FU) treatment which comprises the steps of (a) detection of the gene expression level of one or more gene(s) as shown in Table 1 ( Figure 1), preferably of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 gene(s) as shown in Table 3 ( Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in (a) biological/medical/pathological sample(s) wherein the differential gene expression level of at least one of said gene(s) is (are) indicative for the responsiveness or susceptibility to fluorouracil (5-FU), treatment prior, during and/or after treatment with flu
  • the invention provides for the first time markers in (a) subject(s) suffering from colorectal cancer (CRC) which can predict the outcome of an anti-cancer/anti-proliferative treatment with fluorouracil (5-FU) prior to the treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • the presence of (a) differential expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) was identified as a marker/predictor for responsiveness or susceptibility to the treatment of a subject suffering from colorectal cancer (CRC) with 5 -fluorouracil (5-FU).
  • fluorouracil is to be administered to a subject/patient after determination of the expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably after the determination of the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) in a cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from said patient/subject.
  • the present invention solves the above identified technical problem since, as documented herein below and in the appended Examples, it was surprisingly found that the presence of (a) differential gene expression of one or more gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) in (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from colorectal cancer (CRC) is predictive for susceptibility of said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU).
  • 5-FU fluorouracil
  • marker for responsiveness to the treatment with fluorouracil (5-FU) and “predictor for responsiveness to the treatment with fluorouracil (5-FU)” can be used interchangeably and refer to (a) gene amplification(s) of said gene(s), whereby the amplification status is indicative for susceptibility or responsiveness to fluorouracil (5-FU).
  • the expression level(s) of the gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2) , Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3) are indicative for the susceptibility or responsiveness of (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) to the treatment with fluorouracil (5- FU).
  • a differential gene expression level is defined herein as an expression level of the gene above or below a corresponding reference expression level.
  • the differential gene expression level is defined as the up- or down-regulation of the gene(s) as determined in (a sample from) a subject/patient (responder) compared to the gene expression level determined in (a sample from) a reference subject/patient (non- responder), wherein the extent of the difference between the gene expression determined in (a sample from) a subject/patient (responder) and said reference gene expression is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5- FU).
  • the term "responder” refers in this context to a subject/patient which responds/is responsive/is susceptible to the treatment with fluorouracil (5-FU).
  • non-responder refers in this context to a subject/patient which does not respond/is not responsive/is not susceptible to the treatment with fluorouracil (5-FU). Whether a subject/patient is classified as a "responder” or “non-responder” with respect to the gene expression analysis can be evaluated by the skilled person on the basis of the read per kilo-base per million (RPKM) value/cut off value.
  • RPKM read per kilo-base per million
  • a “responder” may be, for example, a subject/patient characterized by (i) a down regulated expression level of the genes DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH5197; version no.: NM_015197.3; GI:341604746
  • a patient i.e. responder
  • a "non-responder” may be a subject/patient characterized by (i) an up regulated expression level of the genes DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), GATADl (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:3416047
  • the expression level(s) of the corresponding gene(s) is (are) disclosed in Table 1 , Table 2 and/or Table 3. Whether (a) gene(s) is (are) differentially expressed may be also determined by using bioinformatic approaches. A gene was considered differentially expressed if the False Discovery Rate (FDR) was equal or less than 1 % (0.01). Further, in the context of the present invention, different bioinformatic setups were used in order to identify differentially expressed genes. For setups a, b, c (as indicated in Table 1 ( Figure 1), Table 2 ( Figure 2) and/or Table 3 ( Figure 3)) the differential gene expression was determined by
  • the differential gene expression was determined by FDR ⁇ 0.01 and a dispersion of ⁇ 4.
  • a machine learning technique can be used in order to identify whether a patient is responsive or susceptible to the treatment with fluorouracil (5- FU).
  • a machine learning technique can be used in order to classify (a) sample(s) from a subject/patient into (a) patient(s)/subject(s) which is (are) responsive or susceptible to the treatment with fluorouracil (5-FU) (responder) or into (a) patient(s)/subject(s) which is (are) not responsive or susceptible to the treatment with fluorouracil (5-FU) (non-responder).
  • Machine learning techniques which can be used in the context of the present invention are known to the skilled person (see e.g., Larranaga, et al., Bioinform.
  • Machine learning involves training a machine learning algorithm to perform some task, rather than directly programming the system to perform the task.
  • the system observes some data, i.e. the expression level of one or more gen(s) as shown in Table 1 ( Figure 1), more preferably the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3) in (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from CRC, and automatically determines some structure of the data for the classification whether or not said patient(s) is (are) responsive or susceptible to the treatment with fluorouracil (5-FU).
  • 5-FU fluorouracil
  • SVM support vector machine
  • Bennet et al SIGKDD Explorations 2, (2000); Cortes et al., Machine Learning 20 (1995), 273-297). Additional details related to SVM-based prediction are provided below in the appended Examples. Briefly, the data set was randomly split into two respective training and independent test cohorts. Then differentially expressed genes were identified using an appropriate statistical test and a learning model was trained on the identified genes. Using this approach, the algorithm would learn to discriminate between the respective subtypes based on gene expression data in the given patient cohort.
  • the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,
  • the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90,
  • three normalization procedures can be applied: 1 ) After the determination of the expression profile, a single sample is positioned against the cohort that was used to train the classifier. The training cohort is used to calculate the mean and standard deviation of expression for each gene in the expression profile. The gene expression values of the single sample are normalized by calculating a z-score per gene, which is based on the mean and standard deviation values that are derived from the training cohort. If the established expression values do not follow a normal distribution, the expression values of the training cohort and the single sample need to be log-transformed before the normalization by taking the logarithm (e.g. base two). 2) The expression values are normalized against one or more reference genes that are established with the expression profile.
  • the training of the SVM comprises the steps: a) establishing the gene expression profile comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104
  • susceptibility to fluorouracil (5-FU) or responsiveness to the treatment with fluorouracil (5-FU) are well known in the art.
  • susceptibility to fluorouracil (5-FU)/responsiveness to fluorouracil (5-FU) may be determined by contacting (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) which are obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) with fluorouracil (5-FU) and determining the viability of said cell(s), cancer tissue(s), or tumor sample(s) after contacting.
  • CRC colorectal cancer
  • determining the susceptibility to fluorouracil (5-FU)/responsiveness to treatment with fluorouracil (5-FU) may, for example, comprise an evaluation/determination step, which may, for example, include determining the viability of the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) contacted with/exposed to fluorouracil (5- FU), or (a) colorectal cancer cell(s), colorectal cancer tissue(s) or colorectal tumor sample(s) treated with fluorouracil (5-FU).
  • an evaluation/determination step may, for example, include determining the viability of the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) contacted with/exposed to fluorouracil (5- FU), or (a) colorectal cancer cell(s), colorectal cancer tissue(
  • cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) described herein above may show decreased viability upon contacting/exposing/treating with fluorouracil (5- FU).
  • the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) may show an at least 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in viability compared to reference/control cell(s), cancer tissue(s) or tumor sample(s) obtained from a patient suffering from CRC not contacted/exposed/treated with fluorouracil (5-FU).
  • CRC colorectal cancer
  • the referece/control cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) will be identical to the cell(s), (a) cancer tissue(s) or tumor sample (s) to be tested as described herein with the only exception that the reference(s)/control(s) refer to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from a subject not suffering from CRC or to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from the subject suffering from CRC before treatment with fluorouracil (5-FU) has been started.
  • CRC colorectal cancer
  • cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) contacted/exposed/treated with fluorouracil (5-FU), and showing, for example, a decreased viability as described herein above, can be considered as being susceptible or responsible to fluorouracil (5-FU).
  • cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) as obtained from a subject suffering from CRC treated with fluorouracil (5-FU) showing such a decreased viability can be considered as responsive to treatment with fluorouracil (5-FU).
  • a reduction in viability may, for example, be reflected in a decreased proliferation, such as 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in proliferation compared to reference/control cancer cell(s), cancer tissue(s) or tumor sample(s) not contact ed/exposed/treated with fluorouracil (5-FU).
  • the decreased proliferation may be quantified, for example, by measuring the total cell volume, tissue volume or tumor sample volume using standard techniques.
  • the difference in proliferation between contacted/exposed/treated cancer cell(s), cancer tissue(s) or tumor sample(s) as obtained from a subject and corresponding references/controls as defined herein may, for example, be evaluated/determined by measuring the volume of the cancer cell(s), tissue(s) or cell culture(s) taking advantage of standard techniques.
  • Said evaluation/determination may be performed in various points in time, for example, 15 minutes, 30 minutes, 60 minutes, 2 hours, 5 hours, 18 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks and/or more than 4 weeks after contacting/treating said cell(s), tissue(s) or tumor sample(s) with fluorouracil (5-FU), or exposing said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU). It is envisaged herein that said evaluation/determination may be performed repeatedly, for example, at 15 minutes, 30 minutes and 60 minutes after said contacting/exposing/treating.
  • said cell(s), tissue(s) or tumor sample(s) may be contacted/treated not only once with fluorouracil (5-FU) or exposed to fluorouracil (5-FU) but several times (e.g. 2 times, 3 times, 5 times, 10 times or 20 times) under various conditions (e.g. same concentration of inhibitor, different concentration of inhibitor, inhibitor comprised in a composition with different stabilizers, diluents, and/or carriers and the like). Accordingly, said optionally repeated evaluation/determination may be performed after the final contacting/treating with or exposing to fluorouracil (5-FU) or in between said above-mentioned various contacting/exposing/treating steps.
  • a Patient Derived Xenograft from (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from said cancer, like in the present application CRC, are known to the skilled person (Fichtner et al., Eur J Cancer 40, 298-307 (2004)).
  • the Patient Derived Xenograft (PDX) models are known to be closely reflective of tumors or infections in patients for both their histopathological and genetic profiles.
  • PDX model(s) was (were) generated from tumor tissue of individuals of a population of 106 patients suffering from colorectal cancer, comprising 89 primary tumors (stages I to IV), and 27 metastases.
  • parameters of the subject may be considered as well for the prediction of the response, etc.
  • Such parameters in a multivariate model may include gender, age, histological evaluation, and other markers.
  • a Cox- Proportional-Hazard regression predicts the dependent variable based on one or more independent variables. These predictors can either be measured (as e.g. level of a biomarker) or categorical data.
  • diagnostic/predictive markers only give a certain degree of sensitivity and specificity, as also outlined herein.
  • different further parameters might be considered in order to increase both, like previous response of the patient to the drug.
  • the present invention provides (a) new and superior marker(s) for predicting the response as defined herein.
  • the presence of one or more further diagnostic/predictive markers for the response is detected in the sample.
  • fluorouracil (5-FU) and like expressions encompass within their meaning response to treatment comprising fluorouracil (5-FU) as monotherapy, or in combination with other agents, or as prodrugs, or together with local therapies such as surgery and radiation, or as adjuvant or neoadjuvant chemotherapy, or as part of a multimodal approach to the treatment of neoplastic disease.
  • the general mechanism of action of fluorouracil (5-FU) is its activity as a pyrimidine antimetabolite. In fluorouracil (5-FU), the smaller fluorine at position 5 allows the molecule to mimic uracil biochemically.
  • the fluorine-carbon bond is much tighter than that of C-H and prevents methylation of the 5 position of fluorouracil (5- FU) by thymidylate synthase.
  • the fluoropyrimidine locks the enzyme in an inhibited state and prevents the synthesis of thymidylate, a required DNA precursor.
  • a fluorouracil (5-FU) combination refers to a combination of fluorouracil (5-FU) and another agent.
  • a number of agents have been combined with fluorouracil (5-FU) to enhance the cytotoxic activity through biochemical modulation.
  • Addition of exogenous folate in the form of 5-formyl-tetrahydrofolate (leucovorin) sustains inhibition of thymidylate synthase.
  • Methotrexate by inhibiting purine synthesis and increasing cellular pools of certain substrates for reactivity with 5-FU, enhances the activation of fluorouracil (5-FU).
  • the combination of cisplatin and 5-FU increases the antitumor activity of fluorouracil (5-FU).
  • Oxaliplatin is commonly used with 5-FU and leucovorin for treating colorectal cancer, and it may inhibit catabolism of 5-FU, perhaps by inhibiting dihydropyrimidine dehydrogenase (the enzyme that is responsible for the catabolism of fluorouracil (5-FU)), and may also inhibit expression of thymidylate synthase.
  • the combination of fluorouracil (5-FU) and irinotecan, a topoisomerase-1 inhibitor is a treatment that combines fluorouracil (5-FU) with an agent that has a different mechanism of action.
  • Eniluracil which is an inactivator of dihydropyrimidine dehydrogenase, leads to another strategy for improving the efficacy of fluorouracil (5-FU).
  • fluorouracil (5-FU) prodrugs have been developed.
  • One is capecitabine (N4- pentoxycarbonyl-5'-deoxy-5-fluorcytidine). This orally administered agent is converted to 5'- deoxy-5-fluorcytidine by the ubiquitous enzyme cytidine deaminase.
  • the final step in its activation occurs when thymidine phosphorylase cleaves off the 5'-deoxy sugar, leaving intracellular fluorouracil (5-FU).
  • Capecitabine Xeloda(R)
  • Another fluoropyrimidine that acts as a prodrug for fluorouracil (5-FU) is ftorafur.
  • fluorouracil (5-FU) is applied intravenously.
  • fluorouracil (5-FU) and 5 -fluorouracil (5- FU) are used interchangeably.
  • HTS high throughput screening
  • cancer cell(s), cancer tissue(s) and/or tumor sample(s) obtained from a subject, preferably a patient, suffering from colorectal cancer (CRC) for responsiveness/sensitivity to fluorouracil (5-FU), preferably cetuximab.
  • CRC colorectal cancer
  • Suitable (HTS) approaches are known in the art. Screening-assays are usually performed in liquid phase, wherein for each cell/tissue/cell culture to be tested at least one reaction batch is made. Typical containers to be used are micro titer plates having, for example, 384, 1536, or 3456 wells (i.e. multiples of the "original" 96 reaction vessels).
  • Robotics, data processing and control software and sensitive detectors are further commonly used components of a HTS device.
  • robot system which transport micro titer plates from station to station for addition and mixing of sample(s) and reagent(s), incubating the reagents, and final readout (detection).
  • HTS can be used in the simultaneous preparation, incubation, and analysis of many plates.
  • the assay can be performed in a single reaction (which is usually preferred), may, however, also comprise washing and/or transfer steps. Detection can be performed taking advantage of radioactivity, luminescence or fluorescence, like fluorescence- resonance-energytransfer (FRET), fluorescence polarisation (FP) and the like.
  • FRET fluorescence- resonance-energytransfer
  • FP fluorescence polarisation
  • cellular assays and in vivo assays can be employed in HTS.
  • Cellular assays may also comprise cellular extracts, i.e. extracts from cells, tissues and the like.
  • preferred herein is the use of cancer cell(s), cancer tissue(s) or tumor sample(s) as biological sample (in particular a sample obtained from a patient/subject suffering or being prone to suffer from colorectal cancer (CRC)), whereas in vivo assays (wherein suitable animal models are employed, e.g. the herein described mouse models) are particularly useful in the validation/monitoring of the treatment with fluorouracil (5-FU).
  • follow up assays can be performed by re-running the experiment to collect further data on a narrowed set (e.g. samples found "positive" in the first assay), confirming and refining observations.
  • a suitable readout in animal (in vivo) models is tumor growth (or respectively the complete or partial inhibition of tumor growth and/or its remission).
  • the herein described HTS methods for the detection of copy number changes include but are not limited to sequencing technologies such as whole genome sequencing and exome sequencing.
  • the exome sequencing is a techniques for sequencing all the differentially expressed genes in a genome (known as the exome) of, e.g., extracts from cells, tissues or tumor samples obtained from a patient (responder and/or non- responder).
  • the meaning of the terms "cell(s)", “tissue(s)” and “sample(s)” is well known in the art and may, for example, be deduced from “The Cell” (Garland Publishing, Inc.).
  • the term “cell(s)” used herein refers to a single cell or a plurality of cells.
  • pluripotent cells means in the context of the present invention a group of cells comprising more than a single cell. Thereby, the cells out of said group of cells may have a similar function. Said cells may be connected cells and/or separate cells.
  • tissue in the context of the present invention particularly means a group of cells that perform a similar function.
  • sample refers in context of the present invention to all biological tissues, all fluids such as blood, ascites, sputum, broncho-alveolar lavage, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots. Tissues may be, e.g.
  • sample is collected from the patient or subjected to the method or treatment according to the invention.
  • a “tumor sample” is a sample of the tumor to be treated. Such sample may be for example taken from an excised tumor, for example, tumor tissue retrieved by surgery.
  • the cell(s), tissue(s) or tumor sample(s) to be selected comprise/are derived from or are (a) tumor cell(s), preferably (a) colorectal cancer cell(s).
  • the tumor cell(s) may, for example, be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from or being prone to suffering from colorectal cancer (CRC). It is preferred herein that said subject is a human.
  • the cancer cell(s) may be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from colorectal cancer (CRC)".
  • said tumor sample(s) or cancer cell(s) may be obtained from any biological source/organism, particularly any biological source/organism, suffering from or being prone to suffer from colorectal cancer (CRC).
  • the (tumor) cell(s) or (cancer) cell to be contacted is (are) obtained/derived from a subject, preferably a patient, suffering from colorectal cancer (CRC).
  • said tumor/cancer cell(s) may be (are) derived from an animal or mammal.
  • the meaning of the terms "animal” or “mammal” is well known in the art and can, for example, be deduced from Wehner und Gehring (1995; Thieme Verlag).
  • Non-limiting examples for mammals are even-toed ungulates such as sheep, cattle and pig, odd-toed angulates such as horses as well as carnivores such as cats and dogs.
  • DNA samples are derived from organisms that are economically, agronomically or scientifically important.
  • Scientifically or experimentally important organisms include, but are not limited to, mice, rats, rabbits, guinea pigs and pigs.
  • the tumor cell(s) may also be obtained carnivores such as cats or dogs or, for example, from primates which comprise dogs, cates, lemurs, monkeys and apes.
  • the meaning of the terms "dogs”, “cats”, “primate”, “lemur”, “monkey” and “ape” is known and may, for example, be deduced by an artisan from Wehner und Gehring (1995, Thieme Verlag).
  • the tumor or cancer cell(s) is (are) most preferably derived from a human being suffering from the above-mentioned colorectal cancer.
  • particular useful cells in particular tumor or cancer cells, are, accordingly, human cells. These cells can be obtained from e.g. biopsies or from biological samples but the term "cell” also relates to in vitro cultured cells.
  • the present invention relates to an in vitro method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising the following steps:
  • an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
  • the present invention relates to a method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising determining the gene expression of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), whereby an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
  • the present invention also relates to a method of monitoring the efficacy of a fluorouracil (5- FU) treatment of colorectal cancer (CRC) in a subject suffering from said disease comprising the steps of:
  • sample(s) may, for example, be obtained by (a) biopsy (biopsies).
  • said sample is obtained from a subject/patient suffering from colorectal cancer (CRC).
  • said sample is obtained from (a) tumor(s) and, accordingly, is (a) tumor cell(s) or (a) tumor tissue(s).
  • tumor sample(s) may be obtained from subjects/patients suffering from colorectal cancer (CRC).
  • Particularly preferred is the use of one or more gene(s) as shown in Table 1 ( Figure 1), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) as marker gene(s).
  • the gene expression/amplification status of at least one additional gene selected from the group of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) (as shown in Table 2 ( Figure 2)) is assessed or determined.
  • Exemplarily combination which may be determined in this context are FOS (NCBI accession no.: NM_005252; version no.: NM_005252.3; GI:254750707) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting iDDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ314860; version no
  • NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153 (as shown in Table 2) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: DDX43 (NCBI accession no.:
  • FOS NCBI accession no.: NM_005252; version no.: NM 005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153) and one, or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NMJD04367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos
  • “Expression” refers to transcription and translation occurring within a host cell.
  • the level of expression of a DNA molecule in a host cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of the protein encoded by the respective gene produced by the host cells. Further detail for the term “ • expression” within the context of the present invention can be obtained via a review of Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1 -9361 13-41-5.
  • the expression of said gene(s) is determined by determining RNA levels of the respective gene(s) or protein level(s) encoded by the respective gene(s).
  • the present invention has been exemplified by using the expression determination through determination of mRNA levels using RNA sequencing techniques. The skilled person will however acknowledge that the method may likewise be performed using different techniques and detection methods suited for determining the expression level of genes.
  • Methods for determining the expression level of a gene on the nucleic acid level, i.e. on RNA levels are known by those skilled in the art and include hybridization-based, PCR-based and sequencing-based methods, including next generation sequencing (NGS). Such methods are generally known by those skilled in the art.
  • the methods may be applied to detect the expression of one or more certain genes.
  • hybridization probes and/or primers are used to detect and/or amplify a certain nucleic acid sequence. It will be understood by the skilled person that it may be desirable to reverse transcribe the mRNA prior to detection. Reverse transcription using Reverse-Transcriptase is also commonly known (see inter alia Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1-936113-41 -5). Likewise there are kits and assays available allowing sequencing the entire genome or transcriptome. It may hence be preferred to sequence the entire transcriptome of a sample in order to gain information about the entire transcription levels. The assessment of certain expression levels, e.g.
  • RNAseq libraries may be prepared to include modifications preserving strand-specific information (Parkhomchuk D, et al., Nucleic Acids Res. 37(18) (2009), el23). Sequencing of the so generated libraries may be performed by common methods.
  • RNAseq libraries either prepared using TruSeq RNA Sample Prep Kit v2 (Illumina, set A: RS-122-2001 ; set B: RS-122-2002) with modifications preserving strand- specific information or using TruSeq Stranded mRNA Sample Prep Kit (Illumina, set A: RS- 122-2101 ; set B: RS- 122-2102).
  • TruSeq Stranded mRNA Sample Prep Kit Illumina, set A: RS- 122-2101 ; set B: RS- 122-2102.
  • Ribo-ZeroTM Magnetic Gold Kit Epicentre, MRZG 12324
  • Sequencing (2 51 bp) was performed on HiSeq 2000/2500 instruments with v3 chemistry. In the context of the present invention the use of those kits and assays is preferred.
  • Oligonucleotide primers and probes having the desired sequence may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods or automated embodiments thereof.
  • diethylophosphoramidites are used as starting materials and may be synthesized (see Beaucage et al, Tetrahedron Letters, 22 (1981), 1859-1862).
  • One method for synthesizing oligonucleotides on a modified solid support is described in US Bl 4,458,006. It is also possible to use a primer which has been isolated from a biological source (such as a restriction endonuclease digestion).
  • Preferred primers or hybridization probes have a length of from about 15-100, more preferably about 20-50, most preferably about 20-40 bases.
  • RNA reads may be first aligned to the sequences of a database to identify the gene(s). Such alignment may be for example performed against hgl9 (Kent et al, Genome Res. 12(6) (2002), 996-1006; Kent et al, Nature. 409(6822) (2001), 860-921 ) using BWA (Li et al, Bioinformatics 25 (2009), 1754-1760) and SAMtools (Li et al, Bioinformatics 25 (2009), 2078-2079). Mapped reads may be annotated, e.g. using Ensembl v70.
  • Gene expression levels may then be quantified by detecting the relative amount of an RNA of a certain gene, e.g. using reads per kilobase of exon model per million mapped reads (RPKM) as a measure (see Mortazavi A. et al, Nat Methods.5(7) (2008), 621-628).
  • RPKM per million mapped reads
  • RNA levels for example mRNA levels
  • the expression level of said gene(s) is determined by determining RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods, and RNA sequencing (RNAseq).
  • the expression level may, for example, be detected, assessed or evaluated by an in situ hybridization method, an in situ sequencing method, comparative genomic hybridisation and single-nucleotide polymorphism arrays.
  • exemplary in situ hybridisations are, inter alia, fluorescent in situ hybridisation (FISH), chromogenic in situ hybridisation (CISH) and silver in situ hybridisation (SISH).
  • FISH fluorescent in situ hybridisation
  • CISH chromogenic in situ hybridisation
  • SISH silver in situ hybridisation
  • the expression level of said gene(s) can be determined by the assessment, determination, detection or evaluation of the RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods and RNA sequencing.
  • the expression level may be determined by determining in the sample the amount of protein encoded by the gene. This may be performed using common techniques known by those skilled in the art. These techniques include immunoassays. Suitable immunoassays may be selected from the group of immunoprecipitation, enzyme immunoassay (EIA), enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), fluorescent immunoassay, a cytometric bead array (CBA), a chemiluminescent assay, an agglutination assay, nephelometric assay, turbidimetric assay, a Western Blot, a competitive immunoassay, a non-competitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay and a reporter assay such as a luciferase assay.
  • the immunoassay is an enzyme linked immunosorbent assay (ELISA)
  • the present invention also relates to a method of diagnosing (colorectal cancer (CRC)) in a subject/patient suspected of suffering from colorectal cancer or suspected of being prone to suffering from colorectal cancer (CRC) comprising the steps of a) determining in a cell or tumor sample obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the expression or activity of said at least one marker gene determined in a) with a reference gene expression level of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (healthy subject), wherein said colorectal cancer (CRC
  • the present invention also relates to a method of monitoring the efficacy of a treatment of a colorectal cancer (CRC) in a subject/patient suffering from said cancer or being prone to suffer from said cancer comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the gene expression or protein level of said one or more marker gene(s) determined in a) with a reference gene expression or protein level of said one or more marker gene(s), optionally determined in (a sample from)
  • the term "gene expression level" as used herein refers to the gene expression status as described elsewhere herein.
  • the method of monitoring the efficacy of a treatment of a cancer may comprise a step of determining in a cell or tissue sample obtained from a subject/patient suffering from colorectal cancer (CRC) (e.g. a biopsy) the gene expression status of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2).
  • CRC colorectal cancer
  • the present invention also relates to a method of predicting the efficacy of a treatment of a colorectal cancer (CRC) for a subject/patient suffering from said disease comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the expression of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the expression of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (responder and/or non-responder) in a) and said reference expression is indicative for the predicted efficacy of a treatment of a colore
  • the treatment of colorectal cancer may comprise the administration of fluorouracil (5- FU) as described herein.
  • the colorectal cancer (CRC) is a malignant tumor that arises from cells of the colon or the rectum.
  • CRC is classified into hypermutated or non-hypermutated, chromosomal instable tumors. Hypermutated case show either microsatellite instability (MSI) caused by defects in the mismatch repair mechanism or mutations in POLE or POLDl .
  • MSI microsatellite instability
  • Chromosomal instable CRC is characterized by extensive chromosomal rearrangements.
  • a recent attempt to define four consensus molecular subtypes in CRC was published by Guinney et al.
  • the patient/subject suffering from colorectal cancer may be a subject/patient characterized by having a colorectal cancer (CRC) which can be classified into hypermutated, non-hypermutated, and/or chromosomal instable tumors.
  • the subject/patient suffering from colorectal cancer may be a subject/patient characterized by having a colorectal cancer (CRC) which does not have (a) KRAS, BRAS and/or NRAS mutation(s) (see Gong J. et al.,. J. Gastrointest. Oncol. 7 (2016), 687-704).
  • the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s).
  • the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by having (a) KRAS, BRAS and/or NRAS mutation(s).
  • cell(s), tissue(s) or tumor sample(s) obtained from the patient/subject suffering from CRC which is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s).
  • the differential expression of one or more gene(s) as shown in Table 1 ( Figure 1 ), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) as disclosed herein act as markers/predictors for susceptibility to fluorouracil (5-FU).
  • a responder to fluorouracil (5-FU) or a subject/patient sensitive to fluorouracil (5-FU) may be identified in accordance with the present method.
  • the present invention provides the possibility to recognize changes of any one of the genes shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) immediately once they occur, for example, by determining the gene expression level of said marker gene(s).
  • the assessment/evaluation/detection of the expression status of any of the above marker genes is sufficient for determining whether a subject/patient is likely to respond to or is sensitive to fluorouracil (5- FU), whether a (tumor) cell of a colorectal cancer is likely to respond or is responsive to treatment with fluorouracil (5-FU).
  • the assessment/evaluation/detection of the expression status of any of the above marker genes (and their combinations) is also sufficient for diagnosing sensitivity to fluorouracil (5-FU).
  • the expression status alone of any of the above marker genes is indicative for a sensitivity/responsiveness to fluorouracil (5-FU) and the expression level/activity of the gene products of the above marker genes need not be determined in addition to the gene expression status.
  • the present invention relates to means, methods and uses which are based on the early recognition of (an) expression change(s) of one or more gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) and/or the protein level of the respective gene(s).
  • "early” particularly means prior to (the onset of) a (complete or partial) cytogenetic or hematological response or a response measured by any imaging technique and/or to the outbreak of colorectal cancer (CRC).
  • "early" monitoring the efficacy of a therapy/treatment of said colorectal cancer may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment and/or at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment (of the patient or control patient (responder)), wherein the longer periods are preferred.
  • "early” monitoring the efficacy of a therapy/treatment of said cancer may also be at most 1, at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of said cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said cancer at the day the therapy/treatment was initiated, i.e.
  • expression of one or more gene(s) as shown in Table 1 may be determined daily during the first week after initiation of the therapy/treatment, weekly during the first month of the therapy/treatment and, afterwards, monthly.
  • the reference activity/expression level may be taken at the day the therapy/treatment is initiated, from the subject/patient to be treated and/or from a corresponding reference/control subject/patient (responder/non-responder); see below.
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response to said therapy/treatment and/or at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment, wherein the longer periods are preferred.
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of the cancer defined herein, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said colorectal cancer (CRC) at the day the therapy/treatment was initiated, i.e.
  • CRC colorectal cancer
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after diagnosis of the cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already predict the efficacy of fluorouracil (5- FU) therapy/treatment of said colorectal cancer (CRC) at the day of diagnosis. As mentioned, the present invention is particularly useful for monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC) as defined herein. Corresponding means, uses and methods are provided herein.
  • monitoring the efficacy of a certain kind of a fluorouracil (5-FU) therapy/treatment is regularly applied in clinical routine.
  • the skilled person is aware of the meaning of monitoring the efficacy of a certain kind of fluorouracil (5-FU) therapy/treatment.
  • the meaning of the term “monitoring” encompasses the meaning of terms like “tracking”, “discovering” etc.
  • the term "monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of colorectal cancer (CRC) as used herein refers to monitoring whether a subject/patient suffering from said disease (or being prone to suffering from said cancer) responds at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond is (e.g. how fast/slow the respond is and/or to what extent the respond is).
  • the present invention is further useful for predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC) as defined herein.
  • CRC colorectal cancer
  • predicting the efficacy of a fluorouracil (5-FU) therapy/treatment is highly desired in clinical routine, since it allows for preventing the disease (colorectal cancer (CRC)) and/or increasing the efficiency of a fluorouracil (5-FU) therapy/treatment and hence, leads to savings in cost and time and to a higher lifespan/likelihood of survival or of 'Genesung' of the affected patient.
  • the term "predicting the efficacy of a therapy/treatment of colorectal cancer (CRC) for a subject/patient” is used in basically the same sense like determining whether, and/or to what extent, a subject/patient exhibits susceptibility to such a fluorouracil (5-FU) therapy/treatment, i.e. whether said subject/patient will or would respond at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond will or would be (e.g.
  • a subject/patient exhibits susceptibility to said colorectal cancer (CRC) in accordance with this invention, when its (amplified) activity/expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ) (and/or any other gene(s) as shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)) is differential.
  • said expression level is differential as defined herein.
  • the "predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC)" in accordance with this invention may be performed after initiation of the fluorouracil (5-FU) therapy/treatment, i.e. during the already ongoing fluorouracil (5-FU) therapy/treatment.
  • said "predicting” may be performed during the herein described monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer, preferably early after the beginning of said monitoring.
  • the predicting may be based on results from said monitoring obtained at a certain point in time of the ongoing fluorouracil (5-FU) therapy/treatment.
  • said point in time is an early point in time, like, for example that point in time, when a first result from said monitoring has been obtained.
  • predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC) as defined herein is performed during an already ongoing fluorouracil (5-FU) therapy/treatment, it refers to the following/subsequent efficacy of said fluorouracil (5-FU) therapy/treatment.
  • the "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC)” may be performed (immediately) after diagnosis but, however, prior to initiation of the fluorouracil (5-FU) therapy/treatment.
  • "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer (CRC)” refers to the efficacy of a fluorouracil (5-FU) therapy/treatment which has not yet been initiated (or has been initiated substantially at the same point in time when the "predicting" was performed).
  • one non-limiting example of a healthy reference/control subject/patient is one having, e.g. (a) non-amplified gene(s) as shown in Table 1 ( Figure 1) (and/or any other gene(s) shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)).
  • a non-amplified gene(s) as shown in Table 1 ( Figure 1) (and/or any other gene(s) shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)).
  • DDX43 NCBI accession no.: NM_018665; version no.: NMJD18665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: N _024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_00
  • the reference/control subject/patient is, in one embodiment, envisaged to be a subject/patient suffering from said cancer, i.e.
  • a subject/patient having, for example, an differential activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; Gl:399154168; (NCBI accession no.:
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; Gl:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM 024501
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NMJB 1409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_2450
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_ 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_
  • different, higher or lower means at least 1.0 fold, at least 1.5 fold, at least 2 fold, at least 2.5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold, at least 200 fold different, higher or lower, wherein the higher values are preferred. Whether, in which direction (i.e., in which direction (i.e., in which direction (i.e.
  • the reference/control subject/patient is subjected to the same fluorouracil (5-FU) treatment of the colorectal cancer (CRC) as the subject/patient suffering from colorectal cancer (CRC) described and defined herein.
  • Said reference/control subject/patient may be a responder (positive reference/control) or non- responder (negative reference/control) to this treatment.
  • a subject/patient is a "responder” or “non-responder” with respect to a colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy can be evaluated by the skilled person on the basis of his common general knowledge and/or the teaching provided herein, hi particular, a "responder” may be a subject/patient whose cytological/hematological parameters and/or (aberrant) DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript
  • a “responder” may be a subject/patient not suffering from one of the herein defined resistances.
  • a “non-responder” may be a subject/patient whose cytological/hematological parameters and/or (aberrant) activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.
  • CRC fluorouracil (5-FU) fluorouracil (5-FU) treatment/therapy if the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GF.544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 2450), HOXD1
  • DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148)
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_00524
  • a reduction in expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154
  • CRC colorectal cancer fluorouracil
  • DDX43 NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:2223521478
  • FTL NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM 024501
  • a person skilled in the art may also determine cytological/hematological parameters characteristic for a specific colorectal cancer (CRC) in order to assess whether a patient responds to a fluorouracil (5-FU) treatment/therapy.
  • CRC colorectal cancer
  • a patient who does not respond to a fluorouracil (5-FU) treatment/therapy does not show a reduced expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.:
  • one non-limiting example of a diseased reference/control subject/patient (responder and/or non-responder) suffering from a colorectal cancer (CRC) defined herein (or being prone to suffering from a susceptibility thereto) is one having an amplified DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF.222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ)04367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2;
  • the subject/patient is a "responder”. If the response of a subject/patient is as fast (or even faster) than the "typical/desired response", the subject/patient is a "responder". If the response of a subject/patient is slower than the "typical/desired response", the subject/patient is a "non-responder" (when no substantial response can be seen) or "weak-responder".
  • the efficacy of a cancer treatment/therapy can be determined taking account of the change in the activity/expression level of DDX43 (NCBI accession no.: NMJ) 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM _031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2;
  • a skilled person is able to assess the efficacy of a treatment by evaluating the activity/expression level of the above marker gene(s) at various points in time during the treatment (e.g. prior to the treatment, after start of the treatment, and subseqently in intervals during the treatment).
  • a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e. enhanced or decreased) activity or expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) is shifted back towards the "normal level" of a (healthy) reference/control subject/patient or to "normal level” of a defined responder ("positive control") due to/in consequence of said treatment of the cancer or susceptibility thereto.
  • a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e.
  • the efficacy of a treatment of the cancer defined herein is high, when the subject/patient (to be) treated responds as fast (or even faster) and as complete as a "responder”, i.e. exhibits a "typical/desired response".
  • the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response".
  • the efficacy is high, when the activity/expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said patient reach a "normal” activity/level as rapidly as in a "typical/desired response".
  • the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response".
  • the efficacy is high, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NMJ300146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJH4860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.
  • the efficacy of a fluorouracil (5-FU) treatment of the cancer defined herein is moderate/low, when the subject/patient (to be) treated responds not as fast and/or not as complete as a "responder”, i.e. does not exhibit a "typical/desired response".
  • the efficacy is low, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJM4860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM _24501.2; GI:399154168; (NCBI accession
  • DDX43 NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5
  • GI: 150417991 transcription variant 1
  • NCBI accession no.: NM_031409 version nos.: NM_031409.3
  • GI: 150417990 transcription variant 2
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM 014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168;
  • Such an "own" reference sample may be obtained prior to (or at the beginning of) the treatment/therapy.
  • the "reference/control subject/patient” would be the subject/patient to be treated itself.
  • the efficacy of the fluorouracil (5-FU) treatment would then be assessed on the basis of how the activity or expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.:
  • a fluorouracil (5-FU) treatment of the colorectal cancer is assessed in accordance with specific embodiments of this invention, on the basis that the activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos.
  • a fluorouracil (5-FU) treatment of the colorectal cancer is assessed based on the comparison of the activity/ expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 02
  • DDX43 NCBI accession no.: NM O 18665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960
  • CCR6 NCBI accession no.: NMJ304367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2
  • different, higher or lower means at least 1.5 fold, at least 2 fold, at least 2,5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold or at least 200 fold different, higher or lower, wherein the higher values are preferred.
  • a certain type of colorectal cancer can be associated with increased activity/expression level of any one of the above marker gene(s) or with a decreased increased activity/expression level of any one of the above marker gene(s). Since a skilled person will be aware of reference activity/expression levels of the marker gene(s) (e.g. in a healthy person), he will be readily in the position to determine whether the activity/expression level of any one of the above marker genes is increased or decreased when compared to the reference activity/expression level.
  • a responder shows expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM
  • a responder may show reduced or increased expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXDl (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.:
  • CRC colorectal cancer
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_02450
  • the cancer is characterised by a low expression level/activity of at least one of the marker gene(s) and if expression/ activity of DDX43 (NCBI accession no.: NMJM 8665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM _004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NMJ
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501 .2; GI
  • a reference/control sample can be obtained from a non-responder or can be obtained prior to/at the beginning of a therapy/treatment of a cancer. Accordingly, if the difference between the expression level/activity of DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM _031409; version nos.: NM 031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.
  • a responder shows a reduced expression level/activity of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 024501 ; version no.:
  • the reference activity/reference expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: X
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5;
  • GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.:
  • NM 014860 version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.:
  • NM_024501 version no.: NM 24501.2; GI:399154168; (NCBI accession no.:
  • XM 005246507 version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)
  • MRAP2 NCBI accession no.: NMJ38409; version no.: NM 138409.2; Gil 56523250
  • GATAD1 NCBI accession no.: NM 021167; version no.: NM_021167.4;
  • TNFSF13 NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM _024003; version no.: NM_024003.3;
  • CCR6 NCBI accession no.: NM_004367; version no.: NM 004367.5;
  • GL150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.:
  • NM_024501 version no.: NM_24501.2; GL399154168; (NCBI accession no.:
  • XM_005246507 version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
  • GATAD1 NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002
  • RHBDL2 NCBI accession no.: NMJH7821 ; version no.: NM_017821.4;
  • TNFSF13 NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • GI:341604746 MAGEA11 (NCBI accession no.: NM_ 005366; version no.: NM_005366.4), SLC9A8 (NCB1 accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 ( Figure 1), Table 2 ( Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)), for example with respect to the course of the therapy/treatment.
  • MAGEA11 NCBI accession no.: NM_ 005366; version no.: NM_005366.4
  • DDX43 NCBI accession no.: NM_018665; version no.: NM 018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NMJ304367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version
  • activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NMJH 8665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJD24501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507;
  • DDX43 activities/expression levels of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM
  • Non-limiting examples of schemes of determining activities/expression levels of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005
  • the present invention also relates to the use of a (transgenic) cell or a (transgenic) non-human animal having at least one gene marker/predictor as defined herein for screening and/or validation of a fluorouracil (5-FU) medicament for the treatment of colorectal cancer (CRC).
  • the term "cell" as used in this context may also comprise a plurality of cells as well as cells comprised in a tissue.
  • a cell to be used may, for example, be a primary tumor cell.
  • the tumor cell or cell to be used in the screening or validation method may be obtained from samples from a (transgenic) non-human animal suffering from colorectal cancer (CRC).
  • the tumor cell or cell may also be obtained from patient samples (e.g.
  • the tumor cell or cell may be a human tumor cell.
  • such a cell to be used in the present screening or validation methods may be comprised in a tissue or tissue sample, like in a sample biopsy.
  • the used non-human animal or cell may be transgenic or non transgenic.
  • Transgenic in this context particularly means that at least one of the marker gene(s) as described or defined herein is over- or under- expressed or has a higher or lower activity.
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5
  • GI: 150417991 transcription variant 1
  • NCBI accession no.: NM_031409 version nos.: NM_031409.3
  • GI: 150417990 transcription variant 2
  • SUPT7L NCBI accession no.: NM_ 014860; version no.: NM _014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM J24501.2; GI:399154168; (NCBI accession no.: X
  • Transgenic in this context may also mean that DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.:
  • XM_005246507 version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
  • GATAD1 NCBI accession no.: NM 021167; version no.: NM _021167.4;
  • GI:392307002 NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_ 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 ( Figure 1), Table 2 ( Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)) is over- or under-expressed, and/or that the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM 024501 ; version no.: M_24501.2; GI:399154168; (NCBI accession no.: XM_005246507
  • a preferred (transgenic) non-human animal or (transgenic) cell in context of the invention suffers from colorectal cancer (CRC) for the treatment of which the medicament is to be screened and/or validated.
  • CRC colorectal cancer
  • the (transgenic) non-human animal or (transgenic) cell is particularly intended to suffer from DDX4S (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 031409;
  • transgenic non-human animal or “transgenic cell” as used herein refers to a non- human animal or cell, not being a human that comprises genetic material different from the genetic material of a corresponding wild-type animal/cell.
  • Genetic material in this context may be any kind of a nucleic acid molecule, or analogues thereof, for example a nucleic acid molecule, or analogues thereof as defined herein.
  • “Different” in this context means additional or fewer genetic material with respect to the genome of the wild-type animal/cell and/or rearranged genetic material, i.e. genetic material present at a different locus of the genome with respect to the genome of the wild-type animal/cell.
  • the (transgenic) non-human animal or (transgenic) cell is or is derived from a mammal.
  • Non-limiting examples of the (transgenic) non-human animal or derived (transgenic) cell are selected from the group consisting of a mouse, a rat, a rabbit, a guinea pig and a Drosophila.
  • the (transgenic) cell in accordance with this invention may be an animal cell, for example, a non-human animal cell.
  • human cells are envisaged to be employed as cells in context of the present invention.
  • such cell may be an embryonic stem cell (ES cell), particularly a non- human animal ES, like, for example, a mouse or rat ES cell.
  • the (transgenic) cell as described herein, particularly the ES cell, may also be used for generating the (transgenic) non-human animal as described herein.
  • the ES cell technology for generating transgenic animals is well known in the art and for example is described in Pirity et.al. (Methods Cell Biol, 1998, 57:279).
  • the (transgenic) cell may be a prokaryotic or eukaryotic cell.
  • the (transgenic) cell may be a bacterial, yeast, fungus, plant or animal cell.
  • the transformation or genetically engineering of a cell with a nucleic acid construct or vector can be carried out by standard methods, as for instance described in Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, NY, USA; Methods in Yeast Genetics, A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, 1990.
  • the (transgenic) non-human animal or (transgenic) cell as described or defined in context of this invention is particularly useful in methods for screening and/or validation of a medicament for the treatment of cancers as defined and described herein.
  • These screening methods may, in particular, performed in vivo using, for example, (transgenic) animals as described herein (e.g. rats, mice and the like) and/or animals comprising (a) colorectal cancer (CRC) cell(s), (a) tissue(s) or (a) cell culture(s).
  • Said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may, for example, be obtained/derived from (a) colorectal cancer (CRC) tumor cell(s)/tumor(s).
  • said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may be obtained from a subject/patient suffering from a CRC.
  • These in vivo screening methods may in particular comprise measuring and determining differences in tumor volume, for example, in the (transgenic) animals described herein above.
  • the present invention also relates to a method for screening and/or validation of a fluorouracil (5-FU) for the treatment of a colorectal cancer (CRC).
  • Said method may comprise the steps of
  • screening and/or validation of medicaments means, on the one hand, whether a given set of compounds comprises one or more compound(s) that can function as (a) medicament(s), and/or, on the other hand, whether (a) given compound(s) can function as (a) medicament(s). It is particularly intended that the medicaments to be screened and/or validated in context of this invention are medicaments for the treatment, prevention and/or amelioration of a cancer as defined herein.
  • the compound(s)/medicament(s) to be screened and/or validated may be administered to the non-human (transgenic) animal or cell described herein, and, afterwards (for example after a certain period of time sufficient to allow a compound to effect on a cancer as described herein), it is analyzed whether the cancer, or a symptom thereof, of said animal/cell is ameliorated.
  • the present invention also relates to a fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC) if (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1.
  • the present invention relates to fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC), wherein said fluorouracil (5-FU) is administered to the subject to be treated if (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) obtained from the subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1.
  • the subject to be treated has been predicted to be responsive or susceptible to the treatment with a fluorouracil (5-FU) in a method of the present invention.
  • the present invention also relates to a kit useful for carrying out the method or used of this invention.
  • said kit comprises oligonucleotides or polynucleotides capable of detecting the amplification status of at least one gene selected from the group of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GF56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version
  • said kit may comprise (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX4S (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI
  • the kit (to be prepared in context) of this invention is a diagnostic kit.
  • the kit (to be prepared in context) of this invention or the methods and uses of the invention may further comprise or be provided with (an) instruction manual(s).
  • said instruction manual(s) may guide the skilled person (how) to determine amplification status of at least one gene of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168;
  • the kit (to be prepared in context) of this invention may further comprise substances/chemicals and/or equipment suitable/required for carrying out the methods and uses of this invention.
  • substances/chemicals and/or equipment are solvents, diluents and/or buffers for stabilizing and/or storing (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7
  • the present invention also relates to the use of an oligo- or polynucleotide capable of detecting the expression level(s) of one or more of the gene(s) of Table 1 ( Figure 1) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • Figure 1 an oligo- or polynucleotide capable of detecting the expression level(s) of one or more of the gene(s) of Table 1 ( Figure 1) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • oligonucleotide(s) is (are) about 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 to 100 nucleotides in length.
  • the expression of at least 1 additional gene selected from the group consisting of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707), and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) is (are) detected for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • Figure 1 Novel fluorouracil (5-FU) sensitivity related genes (see Table 1).
  • EIR expression in responders
  • a RPKM expression level
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • logFC log 2 normalized fold change.
  • FDR false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d.
  • EER expression in responders indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models.
  • a RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff”.
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • logFC - log2 normalized fold change.
  • FDR false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d.
  • Figure 3 14-gene mini-classifier (see Table 3). Selection of fluorouracil (5-FU) sensitivity related genes.
  • EIR expression in responders indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models.
  • a RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff'.
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • FDR false discovery rate (Benjamini-Hochberg procedure). Please see the methods for further details on setups a-d and the selection of the genes using SVM.
  • FIG. 4 Response to fluorouracil (5-FU) in xenografts (PDXs): Heatmap of genes that correlate in their expression to fluorouracil (5-FU) sensitivity.
  • PDX samples and genes are clustered using hierarchical clustering. The drug sensitivity is determined by a treatment in comparison to control (T/C) (as illustrated in a continuous grey scale color code) in PDX: black - strongly responding models, grey - resistant models
  • T/C control
  • Heatmap includes genes that are not reported to be associated with fluorouracil (5-FU) sensitivity (236 genes)
  • Heatmap includes genes known to be associated with fluorouracil (5-FU) sensitivity.
  • FIG. 5 Performance range of the downsized sub-signatures of the 14-gene mini- classifier.
  • the plot shows the upper range of the balanced accuracy for sub- signatures with a signature size of two up to 13 genes. Sub-signatures were randomly generated out of the 14-gene mini-classifier. For each signature size 120 unique sub-signatures were generated. Hyperparameter fitting and and SVM training was performed on the OncoTrack PDX cohort as described. The upper bound shows the maximum of balanced accuracy. The lower bound shows the median of balanced accuracy. The small vertical line marks the 75% quartile of balanced accuracy. The balanced accuracy of the downsized sub- signatures was evaluated on the OncoTrack PDX cohort and plotted over the signature size. The mini-gene classifier accuracy is stable or stays in an acceptable range, i.e. the performance of the 14-gene mini-classifier is more or less independent of the number of applied genes.
  • tissue samples were used to generate a collection of pre-clinical patient-derived experimental models.
  • the genomes, exomes and transcriptomes of the donor cohort as well as of the matched untreated PDX models were sequenced.
  • RNA reads were aligned to hgl 9 (GCA_000001405.1) using BWA and SAMtools. Mapped reads were annotated using Ensembl v70. Gene expression levels were quantified in reads per kilobase of exon per million mapped reads (RPKM) (Mortazavi A. et al, Nat Methods. 5(7) (2008), 621 -8).
  • DNA reads were aligned to the human reference genome hgl 9 using BWA (Li H. et al, Bioinformatics 25 (2009), 1754-1760) (bwa0.7.7-r441-mem for 75/101bp, bwa0.5.9-rl6-aln for 51bp reads).
  • BWA Li H. et al, Bioinformatics 25 (2009), 1754-1760
  • PDX xenograft
  • Somatic SNVs were detected using established pipelines based on VarScan2 (Koboldt D.C. et al, Genome Res 22 (2012), 568-576) combined with RNAseq data and functional annotation of the variants based on Ensembl v.70. Somatic indels were detected using SAMtools and Dindel (Albers C.A. et al, Genome Res 21 (2011), 961- 973). Development and characterization of patient derived xenografts (PDX)
  • Resected tumor tissues were transplanted to immunodeficient mice (NMRI nude or NOG, Taconic, Bomholdtgard, DK- Tac:NMRI-Foxnlnu, females, 6-8 weeks at start of transplantation) using previously described methods by Fichtner et al. (Fichtner I. et ah, Eur J Cancer 40 (2004), 298-307). Animal experiments were carried out in accordance with the United Kingdom Coordinating Committee on Cancer Research regulations for the Welfare of Animals and of the German Animal Protection Law and approved by the local responsible authorities. Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO) strictly follows the EU guideline European convention for the protection of vertebrate animals used for experimental and other scientific purposes.
  • mice were monitored 3 times weekly for tumor engraftment for up to 3 month. Engrafted tumors at a size of about 1cm 3 were surgically excised and smaller fragments re-transplanted to naive NMRI nu/nu mice for further passage. Within passage 1 to 3 numerous samples were cryo-conserved (DMSO-medium) for further experiments. Tumors were passaged not more than 6 times. For confirmation of tumor histology, tumor tissue was formalin fixed and paraffin embedded (FFPE) and 5 ⁇ sections were prepared. Samples were stained according to a standard protocol for hematoxilin, eosin and Ki67 to ensure xenograft comparability to the original specimen. Cases with changed histological pattern were sent for pathological review and outgrowth of lymphoproliferative diseases was excluded. In this study, no blinding was done.
  • FFPE paraffin embedded
  • mice were randomized to treatment or control groups consisting of 5-6 animals each. Doses and schedules were chosen according to previous experience in animal experiments and represent maximum tolerated or efficient doses.
  • the applied schedule for 5-FU was as follows: Application route: i.p. (intraperitoneal injection); Schedule: Once per week; Day: Monday; number of cycles: 4; Dose: 100 mg/kg. The injection volume was 0.1-0.2 ml/20 g body weight.
  • Treatment was continued over a period of four weeks (4 cycles) or till tumor size exceeded 1 cm 3 or animals showed loss of >15% body weight. From the first treatment day onwards the tumor volumes and body weights were recorded twice weekly. At the end of the treatment period animals were sacrificed, blood and tumor samples collected, and stored in liquid nitrogen immediately.
  • RTV relative tumor volume
  • xenograft samples of the 52 xenografts (PDX) that derived from one colorectal carcinoma (CRC) (150 MET1) shared highly similar global expression profiles. They were merged into one artificial single sample to avoid analysis bias by taking an average of the reads per kilobase of exon per million mapped (RPKM) (Mortazavi A, et al, Nat Methods 5 (2008), 621 -628)-values and of the T/C -values per gene or drug, i.e. 5-FU. Taking the artificial sample for 150JVIET1 into account 48 PDX were included into the drug response analysis. Drug response related gene signatures in xenografts (PDX)
  • DGE analysis using the R package edgeR (Robinson MD et al., Bioinformatics 26 (2010), 139-140) to identify signatures associated with drug, i.e. 5-FU, response results in form of T/C values for PDX: strong, moderate, minor, resistant (see the above section 6).
  • DGE analysis was applied in different setups as follows: a) combined strong+moderate vs combined minor+resistant, b) combined strong+moderate+minor vs. resistant, and c): 20 most sensitive vs. 20 least sensitive PDX. Genes were filtered by a false discovery rate (FDR) ⁇ 0.01,
  • FDR false discovery rate
  • the IC 50 or T/C values as phenotype vector in a general linear model (GLM) provided by the edgeR package was used.
  • Genes were filtered by FDR ⁇ 0.01 and dispersion ⁇ 4.
  • Gene signatures associated with a given drug response were generated by combining results from setups a-d.
  • Low expressed genes were filtered by an expression > 1 RPKM in minimum five PDX and by a mean expression > 0.8 RPKM. In total 253 genes correlate in their expression with the response to 5-FU. Building drug response classifiers for 5-FU
  • SVM linear support vector machine
  • samples can be classified into groups (Bennet K.P. et al., SIGBCDD Explorations 2 (2000); Cortes et al, Machine Learning 20 (1995), 273-297).
  • An important factor for a proper classification is the selection of features (genes) that define the data space and the SVM learns from. From the preselected genes that are associated to drug response, the SVM itself was used to rank features and the probably most important one were selected. The application of the SVM is described in further details below.
  • a class weighted SVM was used and the hyperparameter C was tuned for each of classes resistance and response ⁇ C res i S , C resp ).
  • the feature (gene) selection included feature ranking and feature size selection.
  • SVM- RFE SVM recursive feature elimination
  • a SVM-RFE includes following steps: 1) hyperparameter tuning, 2) train multiple SVMs on subsamples of the original training set, 3) calculate a ranking score per feature based on the trained SVMs, 4) note the relative position in the final ranking vector of m features with the lowest ranking score, 5) eliminate m features with the lowest ranking score from the feature space, 6) repeat step 1 -5 until all features are ranked in the final ranking vector.
  • the bootstrap was separately applied on the responder and resistance set with a sample size of 13 and 31 , respectively.
  • the performance of a hyperparameter set was evaluated using the Fi- score.
  • For the leave-n-out resampling two and five samples of the responder and resistance set were left out from the training set, respectively.
  • the calculation of the ranking score was based on the weight vector w of a linear SVM and not w 2 as described from Duan et al.
  • the 5-FU mini classifier (14 genes) was cross-validated on the OT PDX cohort via a 100 times repeated 10-fold cross-validation. Performance values were averaged over the repeats. The performance of the classifier was estimated from the number of true positive (TP), false positive (FP), true negative (TN) and false negative (FN) predictions as well as the sensitivity, specificity and balanced accuracy. Additional information

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Abstract

The present invention relates to a method for determining the susceptibility/responsiveness of (a) cancer cell(s), preferably (a) colorectal cancer cell(s), to the treatment with fluorouracil (5-FU). Further, the present invention relates to a method of selecting (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) of colorectal cancer (CRC) with susceptibility to fluorouracil (5-FU). Furthermore, an in vitro method for the identification of a responder for or a subject, preferably a human patient, suffering from colorectal cancer (CRC) to fluorouracil (5-FU) is disclosed. The present invention also relates to a method of monitoring the efficacy of a treatment of the colorectal cancer (CRC) with fluorouracil (5-FU).

Description

MEANS AND METHODS FOR DETERMINING EFFICACY OF FLUOROURACIL (5-FU) IN COLORECTAL CANCER (CRC) THERAPY The present invention relates to a method for determining the susceptibility/responsiveness of (a) cancer cell(s), preferably (a) colorectal cancer cell(s), to the treatment with fluorouracil (5- FU). Further, the present invention relates to a method of selecting (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) of colorectal cancer (CRC) with susceptibility to fluorouracil (5-FU). Furthermore, an in vitro method for the identification of a responder for or a subject, preferably a human patient, suffering from colorectal cancer (CRC) to fluorouracil (5-FU) is disclosed. The present invention also relates to a method of monitoring the efficacy of a treatment of the colorectal cancer (CRC) with fluorouracil (5-FU).
Colorectal cancer (CRC) represents the third most frequent cancer worldwide. The five-year survival rate of patients diagnosed with metastasis is below 10%. CRC is refractory to most chemotherapeutic agents. Only fluorouracil (5-FU), irinotecan and oxaliplatin have documented responses in metastatic diseases such as colorectal cancer (CRC). Antibodies targeting the epidermal growth factor receptor (EGFR), such as cetuximab offer therapeutic options for a fraction of metastatic colorectal cancers (CRCs) but have failed in the adjuvant setting (Nelson V.M. et al. Gastrointest Oncol. 4(3) (2013), 245-252). Regorafenib monotherapy, a multi tyrosine kinase inhibitor, has been recently approved for previously treated metastatic colorectal cancer (CRC) (Grothey et al, Lancet 381(9863) (2013), 303- 312). Colorectal cancers (CRCs) are heterogeneous tumors which can be classified within characteristic molecular groups, however the clinical utility of this classification has not been demonstrated so far (De Sousa E.M.F. et al. Nat Med 19 (2013), 614-618; Guinney J. et al, Nat Med 21 (2015), 1350-1356; Marisa L. et al, PLoS Med 10 (2013), el 001453; Sadanandam A. et al, Nat Med 19 (2013), 619-625; Schlicker A. et al, BMC Med Genomics 5 (2012), 66). WO-A2 2008/115419 discloses marker gene(s) and methods for prediction of patient response to fluorouracil (5-FU); see also WO-A1 2007/147877; WO-A2 2006/015742; WO-A1 2009/114836; WO-A1 2014/197543; Ju et al, Journal of Cellular Biochemistry 116(2) (2015), 277-286. However, there is still an unmet need to identify effective biomarkers predicting the cancer treatment outcomes. In particular, a major challenge in cancer treatment remains to select subjects/patients for specific treatment regimens based on pathogenetic and/or genetic markers in order to optimize the anti-cancer treatment outcome. It would, therefore, be helpful to know and better understand which subject(s)/patient(s) is (are) able to respond to an intended anti-cancer treatment.
Thus, the technical problem underlying the present invention is the provision of means and methods for the evaluation of (a) cell(s), in particular (a) cancer cell(s), (a) cancer tissue or tumor sample(s) obtained from a subject suffering from cancer, for their susceptibility or responsiveness to the treatment with an anti-cancer treatment.
This need is addressed by the present invention by providing the embodiments as defined in the claims. The present invention relates to a method for determining the susceptibility or responsiveness of (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), comprising (a) obtaining (a) cancer cell(s), cancer tissue(s) or tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 (Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) in said cancer cell(s), cancer tissue(s) or tumor sample(s), wherein said expression level is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5-FU). The present invention is based on the unexpected finding that by determining the expression of one or more gene(s) shown in Table 1 (Figure 1), more preferably by determining the expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) it is possible to predict in a reliable manner whether or not a subject suffering from colorectal cancer (CRC) is susceptible or responsive to a treatment with fluorouracil (5-FU). In particular, it was found that the methods of the present invention allow the prediction or determination of the responsiveness or susceptibility to a treatment with fluorouracil (5-FU) in a subject suffering from colorectal cancer (CRC). Accordingly, the present invention generally relates to a method of selecting (a) subject(s) suffering from colorectal cancer (CRC) with susceptibility or responsiveness to fluorouracil (5-FU), comprising the steps of: (a) determining the expression level of one or more gene(s) shown in Table 1 (Figure 1), more preferably determining the expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3) in (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) of said subject; and (b) selecting (a) subject(s)/patient(s) suffering from colorectal cancer (CRC) characterized by a differential expression level of one or more gene(s) as shown in Table 1 (Figure 1), more preferably characterized by a differential expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3). The method may additionally comprise (i) contacting (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) with fluorouracil (5-FU) and (ii) evaluating susceptibility or responsiveness of said cancer cell(s), cancer tissue(s) or tumor sample(s) contacted with fluorouracil (5-FU). It is of note that steps (i) and (ii) may be performed prior to step (a) but also after step (a) or, optionally, after step (b). Said steps (i) and (ii) may in particular serve as further experimental proof that the selected subject(s) is responsive or susceptible in its viability to fluorouracil (5-FU).
As used herein, the term "cancer cell(s), cancer tissue(s) or tumor sample(s)" is not only limited to (an) isolated cell(s), (a) tissue(s), (a) tumor sample(s) and cell culture(s) from a carcinogenic tissue, preferably from colorectal cancer (CRC), but also comprises the use of (a) sample(s), i.e. (a) biological, medical or pathological sample(s) that consist of fluids such as blood, ascites, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots and comprise such (a) carcinogenic cell(s) or parts, fragments of carcinogenic cell(s). Accordingly, the gist of the present invention lies in the fact that a method is provided that allows the determination of the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) for the anti-cancer or anti-proliferative treatment with fluorouracil (5-FU). As detailed in the appended Examples, it was surprisingly found that a panel of genes, i.e. the genes as shown in Table 1 (Figure 1) and/or Table 3 (Figure 3), that are differentially expressed among the cancer cell(s), cancer tissue(s), tumor tissue(s) of a subject suffering from colorectal cancer (CRC) is attributed to the response to the treatment of fluorouracil (5- FU). In particular, as shown in the appended Examples, it was surprisingly found that the determination of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 ges as shown in Table 3 (Figure 3), that are differentially expressed among the cancer cell(s), cancer tissue(s), tumor tissue(s) of a subject suffering from colorectal cancer (CRC) is attributed to the response to the of fluorouracil (5-FU). Therefore, the present invention provides a method for selecting (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) which are susceptible or responsive to fluorouracil (5-FU), but also for an in vitro method for assessing a subject suffering from colorectal cancer (CRC), i.e. a human or animal patient, for its potential susceptibility or responsiveness to an anti-cancer or anti-proliferate treatment with fluorouracil (5-FU). The present invention provides not only the possibility to select (a) cell(s), (a) cancer tissue(s), (a) tumor sample(s) that are susceptible or responsive to the treatment with fluorouracil (5-FU) but also for a method to evaluate whether a given subject, preferably a subject suffering from colorectal cancer (CRC), is a responder or non-responder for a fluorouracil (5-FU) treatment.
Accordingly, the present invention relates to a method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) which comprises the step of: (a) determining the expression level of one or more gene(s) as shown in Table 1 (Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3). In the context of the present invention the expression level of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 , 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129, 130, 131 , 132, 133, 134, 135, 136, 137, 138, 139, 140, 141 , 142, 143, 144, 145, 146, 147, 148, 149, 150, 151 , 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171 , 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235 or 236 gene(s) as shown in Table 1 (Figure 1) may be determined. In a more preferred embodiment of the present invention the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3) is determined. Accordingly, in the herein described method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) the activity or expression of one or more gene(s), preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF1S (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_ 015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ) and/or Table 2 (Figure 2)) is (are) determined. Also preferred in the context of the present invention is the determination of the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NMJ300146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_ 138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_ 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NMJ)15266.2; GL386781491), and L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) in combination with 1 or 2 genes as shown in Table 2 (Figure 2).
The selection method of an fluorouracil (5-FU) responding cell or a responding subject, preferably a human patient, comprises the steps of (a) obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 (Figure 1), more preferably determining the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3). Accordingly, in the context of the present invention the method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU) comprises the step of obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject suffering from CRC with (a) differential gene expression of 1 , 2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30,
31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79,
80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 ,
122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140,
141 , 142, 143, 144, 145, 146, 147, 148, 149, 150, 151 , 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171 , 172, 173, 174, 175, 176, 177,
178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 211 , 212, 213, 214, 215, 216, 217, 218, 219, 220, 221 , 222, 223, 224, 225, 226, 227, 228, 229, 230, 231 , 232, 233, 234, 235 or 236 gene(s) as shown in Table 1 (Figure 1 ) (and/or any other gene(s) as shown in Table 2 (Figure 2)) is (are) determined. Said differential gene expression level(s) of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 ,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 , 122,
123, 124, 125, 126, 127, 128, 129, 130, 131 , 132, 133, 134, 135, 136, 137, 138, 139, 140, 141,
142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178,
179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 211 , 212, 213, 214, 215, 216, 217, 218, 219, 220, 221 , 222, 223, 224, 225, 226, 227, 228, 229, 230, 231 , 232, 233, 234, 235 or 236 gene(s) as shown in Table 1 (Figure 1) (and/or any other gene(s) as shown in Table 2 (Figure 2)), preferably of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 gene(s) as shown in Table 3 (Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) is (are) indicative for susceptibility or responsiveness to fluorouracil (5- FU). As pointed out above, the present invention relates in particular to a method for determining the responsiveness or susceptibility of colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s) obtained from a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), said method comprises determining the gene expression level of one or more gene(s) shown in Table 1 (Figure 1), preferably of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the gene(s) as shown in Table 3 (Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) in said colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s), wherein said gene expression level is indicative of whether the cell is likely to respond or is responsive to the fluorouracil (5-FU) treatment. Such a determination may take place on (an) individual, isolated tumor cell(s). Such an evaluation may also be carried out on biological/medical/pathological sample(s), like body fluids, isolated body tissue samples and the like, wherein said sample(s) preferably comprise cells or cell debris to be analyzed.
As pointed out in the technical problem above, there is a need in the art for markers which can predict the outcome of an anti-cancer therapy with fluorouracil (5-FU) prior to and being during treatment. There is a need for stratification of subjects/patients who are to be subjected to or being subjected to an anti-cancer therapy with fluorouracil (5-FU) and distinguishing between fluorouracil (5-FU) "responder" and "non-responder" subjects/patients.
Subject of the present invention is a method for diagnosing a subject/patient suffering from colorectal cancer (CRC) who is to be subjected to or is being subjected to an anti-cancer treatment or an anti-proliferative treatment to assess the responsiveness or susceptibility to fluorouracil (5-FU) prior, during and/or after fluorouracil (5-FU) treatment which comprises the steps of (a) detection of the gene expression level of one or more gene(s) as shown in Table 1 (Figure 1), preferably of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 gene(s) as shown in Table 3 (Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) in (a) biological/medical/pathological sample(s) wherein the differential gene expression level of at least one of said gene(s) is (are) indicative for the responsiveness or susceptibility to fluorouracil (5-FU), treatment prior, during and/or after treatment with fluorouracil (5-FU); and (b) sorting the subject suffering from colorectal cancer (CRC) into a responder or a non-responder based on detection of said gene expression level of one or more of said gene(s).
Thus, the invention provides for the first time markers in (a) subject(s) suffering from colorectal cancer (CRC) which can predict the outcome of an anti-cancer/anti-proliferative treatment with fluorouracil (5-FU) prior to the treatment with fluorouracil (5-FU). Accordingly, the presence of (a) differential expression level of one or more gene(s) as shown in Table 1 (Figure 1 ), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 (Figure 3) was identified as a marker/predictor for responsiveness or susceptibility to the treatment of a subject suffering from colorectal cancer (CRC) with 5 -fluorouracil (5-FU). Accordingly, in the context of the present invention, fluorouracil (5-FU) is to be administered to a subject/patient after determination of the expression level of one or more gene(s) as shown in Table 1 (Figure 1 ), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably after the determination of the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 (Figure 3) in a cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from said patient/subject.
The present invention solves the above identified technical problem since, as documented herein below and in the appended Examples, it was surprisingly found that the presence of (a) differential gene expression of one or more gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 (Figure 3) in (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from colorectal cancer (CRC) is predictive for susceptibility of said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU).
In the present invention, the presence of (a) differential expression level of one or more gene(s) as shown in Table 1 (Figure 1 ), Table 2 (Figure 2), Table 3, and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3) (Figure 3) was surprisingly identified as a marker/predictor for responsiveness or susceptibility to the treatment of a subject suffering from colorectal cancer (CRC) with fluorouracil (5-FU). The terms "marker for responsiveness to the treatment with fluorouracil (5-FU)" and "predictor for responsiveness to the treatment with fluorouracil (5-FU)" can be used interchangeably and refer to (a) gene amplification(s) of said gene(s), whereby the amplification status is indicative for susceptibility or responsiveness to fluorouracil (5-FU). As outlined herein, the expression level(s) of the gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2) , Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3) are indicative for the susceptibility or responsiveness of (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) to the treatment with fluorouracil (5- FU). A differential gene expression level is defined herein as an expression level of the gene above or below a corresponding reference expression level. In the context of the present invention, the differential gene expression level is defined as the up- or down-regulation of the gene(s) as determined in (a sample from) a subject/patient (responder) compared to the gene expression level determined in (a sample from) a reference subject/patient (non- responder), wherein the extent of the difference between the gene expression determined in (a sample from) a subject/patient (responder) and said reference gene expression is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5- FU). The term "responder" refers in this context to a subject/patient which responds/is responsive/is susceptible to the treatment with fluorouracil (5-FU). The term "non-responder" refers in this context to a subject/patient which does not respond/is not responsive/is not susceptible to the treatment with fluorouracil (5-FU). Whether a subject/patient is classified as a "responder" or "non-responder" with respect to the gene expression analysis can be evaluated by the skilled person on the basis of the read per kilo-base per million (RPKM) value/cut off value. The term "RPKM" value is indicated in Table 1 (Figure 1), Table 2 (Figure 2) and/or Table 3 (Figure 3). A "responder" may be, for example, a subject/patient characterized by (i) a down regulated expression level of the genes DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH5197; version no.: NM_015197.3; GI:341604746), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM _024003.3; GL497239882) and (ii) a up regulated expression expression level of the genes CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416) and/or MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4). In particular such a patient, i.e. responder, would be characterized by having a RPKM value which is below 0.01 for the gene DDX43, by a RPKM value which is below 1232.50 for the gene FTL, by a RPKM value which is above 0.75 for the gene CCR6, by a RPKM value which is below 9.02 for the gene SUPT7L, by a RPKM value which is above 0.26 for the gene HOXD1, by a RPKM value which is above 2.36 for the gene MRAP2, by a RPKM value which is below 18.45 for the gene GATADl, by a RPKM value which is above 5.63 for the gene RHBDL2, by a RPKM value which is above 19.45 for the gene TNFSF13, by a RPKM value which is below 0.49 for the gene MYRIP, by a RPKM value which is below 5.78 for the gene PACS2, by a RPKM value which is above 1.91 for the gene MAGEA11, by a RPKM value which is below 4.76 for the gene SLC9A8 and/or by a RPKM value which is below 0.83 for the gene LI CAM (see Table 3). Consequently, a "non-responder" may be a subject/patient characterized by (i) an up regulated expression level of the genes DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), GATADl (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) and (ii) a down regulated expression expression level of the genes CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM l 38409; version no.: NMJ38409.2; GI156523250), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416) and/or MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4). Accordingly, the expression level(s) of the corresponding gene(s) is (are) disclosed in Table 1 , Table 2 and/or Table 3. Whether (a) gene(s) is (are) differentially expressed may be also determined by using bioinformatic approaches. A gene was considered differentially expressed if the False Discovery Rate (FDR) was equal or less than 1 % (0.01). Further, in the context of the present invention, different bioinformatic setups were used in order to identify differentially expressed genes. For setups a, b, c (as indicated in Table 1 (Figure 1), Table 2 (Figure 2) and/or Table 3 (Figure 3)) the differential gene expression was determined by |log2(FC)|≥log2(1.0) (fold change) and FDR < 0.01. For setup d (as indicated in Table 1 (Figure 1), Table 2 (Figure 2) and/or Table 3 (Figure 3)) the differential gene expression was determined by FDR < 0.01 and a dispersion of < 4. In the context of the present invention a machine learning technique can be used in order to identify whether a patient is responsive or susceptible to the treatment with fluorouracil (5- FU). Accordingly, in the context of the present invention a machine learning technique can be used in order to classify (a) sample(s) from a subject/patient into (a) patient(s)/subject(s) which is (are) responsive or susceptible to the treatment with fluorouracil (5-FU) (responder) or into (a) patient(s)/subject(s) which is (are) not responsive or susceptible to the treatment with fluorouracil (5-FU) (non-responder). Machine learning techniques which can be used in the context of the present invention are known to the skilled person (see e.g., Larranaga, et al., Bioinform. 7 (2006), 86-112; Libbrecht and Noble, Nat Rev Genet 16 (2015), 321-332) Machine learning involves training a machine learning algorithm to perform some task, rather than directly programming the system to perform the task. The system observes some data, i.e. the expression level of one or more gen(s) as shown in Table 1 (Figure 1), more preferably the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3) in (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from CRC, and automatically determines some structure of the data for the classification whether or not said patient(s) is (are) responsive or susceptible to the treatment with fluorouracil (5-FU). One particular type of learning machine is a support vector machine (SVM). SVMs are well known in the art, for example as described in (see e.g., Bennet et al, SIGKDD Explorations 2, (2000); Cortes et al., Machine Learning 20 (1995), 273-297). Additional details related to SVM-based prediction are provided below in the appended Examples. Briefly, the data set was randomly split into two respective training and independent test cohorts. Then differentially expressed genes were identified using an appropriate statistical test and a learning model was trained on the identified genes. Using this approach, the algorithm would learn to discriminate between the respective subtypes based on gene expression data in the given patient cohort. Having learned the expression features of these classes, the algorithm could recognize new samples as class members based on the expression patterns. Accordingly, the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 , 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129, 130, 131 , 132, 133, 134, 135, 136, 137, 138, 139, 140, 141 , 142, 143, 144, 145, 146, 147, 148, 149, 150, 151 , 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211 , 212, 213, 214, 215, 216, 217, 218, 219, 220, 221 , 222, 223, 224, 225, 226, 227, 228, 229, 230, 231 , 232, 233, 234, 235, 236, 237 or 238 genes as shown in Table 1 (Figure 1) and Table 2 (Figure 2) in said cell(s), cancer tissue(s) or tumor sample(s); and b) applying a SVM trained with the genes determined in step a). This method may optionally comprise the step of normalizing the gene expression levels of the genes determined in the above step a).
Accordingly, the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129, 130, 131 , 132, 133, 134, 135, 136, 137, 138, 139, 140, 141 , 142, 143, 144, 145, 146, 147, 148, 149, 150, 151 , 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171 , 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 211 , 212, 213, 214, 215, 216, 217, 218, 219, 220, 221 , 222, 223, 224, 225, 226, 227, 228, 229, 230, 231 , 232, 233, 234, 235, 236, 237 or 238 genes as shown in Table 1 (Figure 1 ) and Table 2 (Figure 2) in said cell(s), cancer tissue(s) or tumor sample(s); b) normalizing the gene expression levels; and c) applying a SVM trained with the genes determined in step a). In the context of the present invention, three normalization procedures can be applied: 1 ) After the determination of the expression profile, a single sample is positioned against the cohort that was used to train the classifier. The training cohort is used to calculate the mean and standard deviation of expression for each gene in the expression profile. The gene expression values of the single sample are normalized by calculating a z-score per gene, which is based on the mean and standard deviation values that are derived from the training cohort. If the established expression values do not follow a normal distribution, the expression values of the training cohort and the single sample need to be log-transformed before the normalization by taking the logarithm (e.g. base two). 2) The expression values are normalized against one or more reference genes that are established with the expression profile. This implies that the expression profile of the training cohort was established and normalized in the same way. 3) The expression values are normalized against one or more spike-in controls that integrated into establishment of the expression profile. This implies that the expression profile of the training cohort was established and normalized in the same way.
Accordingly, in the context of the present invention the training of the SVM comprises the steps: a) establishing the gene expression profile comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 , 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129, 130, 131 , 132, 133, 134, 135, 136, 137, 138, 139, 140, 141 , 142, 143, 144, 145, 146, 147, 148, 149, 150, 151 , 152, 153, 154, 155, 156, 157, 158, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 211 , 212, 213, 214, 215, 216, 217, 218, 219, 220, 221 , 222, 223, 224, 225, 226, 227, 228, 229, 230, 231 , 232, 233, 234, 235, 236, 237 or 238 genes as shown in Table 1 (Figure 1 ) and Table 2 (Figure 2) from a cohort of cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a patient suffering from CRC or from a cohort of a CRC tumor derived model treated with fluorouracil (5-FU); b) fitting of the SVM parameter on the expression profiles of the cohort in step a) using the response information of the cohort; and c) training of the SVM to classify a CRC tumor or derived model into responders or non-responders using the expression profiles of the cohort in step a) and the response information of the cohort. On the basis of the genes as shown in Table 1, a mini- classifier of 14 genes (Table 3) were built by following the bioinformatic approaches described above.
The identification of (a) differential gene expression of one or more genes as shown in Table 1 (Figure 1), preferably of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the genes shown in Table 3 (Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 of the genes shown in Table 3 (Figure 3) as markers for susceptibility or responsiveness of colorectal cancer cell(s), cancer tissue(s) or tumor sample(s) to fluorouracil (5-FU) allows for the first time a reliable identification of subjects/patients suffering from colorectal cancer (CRC) which can be specifically and efficiently treated with fluorouracil (5-FU).
The terms "susceptibility to fluorouracil (5-FU)" and "responsiveness to treatment with fluorouracil (5-FU)" are used interchangeably in context of the present invention. Any explanations given herein in respect to "susceptibility to fluorouracil (5-FU)" also apply to "responsiveness to treatment with fluorouracil (5-FU)", mutatis mutandis, and vice versa.
Methods for determining the susceptibility to fluorouracil (5-FU) or responsiveness to the treatment with fluorouracil (5-FU), are well known in the art. For example, susceptibility to fluorouracil (5-FU)/responsiveness to fluorouracil (5-FU) may be determined by contacting (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) which are obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) with fluorouracil (5-FU) and determining the viability of said cell(s), cancer tissue(s), or tumor sample(s) after contacting. These above-mentioned methods for determining the susceptibility to fluorouracil (5-FU)/responsiveness to treatment with fluorouracil (5-FU), may, for example, comprise an evaluation/determination step, which may, for example, include determining the viability of the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) contacted with/exposed to fluorouracil (5- FU), or (a) colorectal cancer cell(s), colorectal cancer tissue(s) or colorectal tumor sample(s) treated with fluorouracil (5-FU). For example, (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) described herein above may show decreased viability upon contacting/exposing/treating with fluorouracil (5- FU). Preferably, the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) may show an at least 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in viability compared to reference/control cell(s), cancer tissue(s) or tumor sample(s) obtained from a patient suffering from CRC not contacted/exposed/treated with fluorouracil (5-FU). Preferably, the referece/control cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) will be identical to the cell(s), (a) cancer tissue(s) or tumor sample (s) to be tested as described herein with the only exception that the reference(s)/control(s) refer to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from a subject not suffering from CRC or to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from the subject suffering from CRC before treatment with fluorouracil (5-FU) has been started. Thus (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) contacted/exposed/treated with fluorouracil (5-FU), and showing, for example, a decreased viability as described herein above, can be considered as being susceptible or responsible to fluorouracil (5-FU). Correspondingly, (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) as obtained from a subject suffering from CRC treated with fluorouracil (5-FU) showing such a decreased viability can be considered as responsive to treatment with fluorouracil (5-FU).
A reduction in viability may, for example, be reflected in a decreased proliferation, such as 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in proliferation compared to reference/control cancer cell(s), cancer tissue(s) or tumor sample(s) not contact ed/exposed/treated with fluorouracil (5-FU). The decreased proliferation may be quantified, for example, by measuring the total cell volume, tissue volume or tumor sample volume using standard techniques. The difference in proliferation between contacted/exposed/treated cancer cell(s), cancer tissue(s) or tumor sample(s) as obtained from a subject and corresponding references/controls as defined herein may, for example, be evaluated/determined by measuring the volume of the cancer cell(s), tissue(s) or cell culture(s) taking advantage of standard techniques. Said evaluation/determination may be performed in various points in time, for example, 15 minutes, 30 minutes, 60 minutes, 2 hours, 5 hours, 18 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks and/or more than 4 weeks after contacting/treating said cell(s), tissue(s) or tumor sample(s) with fluorouracil (5-FU), or exposing said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU). It is envisaged herein that said evaluation/determination may be performed repeatedly, for example, at 15 minutes, 30 minutes and 60 minutes after said contacting/exposing/treating. It is of note that said cell(s), tissue(s) or tumor sample(s) may be contacted/treated not only once with fluorouracil (5-FU) or exposed to fluorouracil (5-FU) but several times (e.g. 2 times, 3 times, 5 times, 10 times or 20 times) under various conditions (e.g. same concentration of inhibitor, different concentration of inhibitor, inhibitor comprised in a composition with different stabilizers, diluents, and/or carriers and the like). Accordingly, said optionally repeated evaluation/determination may be performed after the final contacting/treating with or exposing to fluorouracil (5-FU) or in between said above-mentioned various contacting/exposing/treating steps.
The explanations given herein above with respect of the exemplarily determination/evaluation step, comprising determination the proliferation of the cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC), contacted with/exposed to fluorouracil (5-FU) also apply to the use of a patient derived xenograft (PDX) model of colorectal cancer (CRC). The gene expression of one or more gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2) or Table 3 (Figure 3) in the PDX model may be determined by those skilled in the art. Methods for the generation of a Patient Derived Xenograft (PDX) from (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from said cancer, like in the present application CRC, are known to the skilled person (Fichtner et al., Eur J Cancer 40, 298-307 (2004)). The Patient Derived Xenograft (PDX) models are known to be closely reflective of tumors or infections in patients for both their histopathological and genetic profiles. As explained in the appended Examples, in the context of the present invention, (a) PDX model(s) was (were) generated from tumor tissue of individuals of a population of 106 patients suffering from colorectal cancer, comprising 89 primary tumors (stages I to IV), and 27 metastases.
Furthermore, in the methods of the present invention further parameters of the subject may be considered as well for the prediction of the response, etc. Such parameters in a multivariate model may include gender, age, histological evaluation, and other markers. A Cox- Proportional-Hazard regression predicts the dependent variable based on one or more independent variables. These predictors can either be measured (as e.g. level of a biomarker) or categorical data. The skilled person is aware of the fact that diagnostic/predictive markers only give a certain degree of sensitivity and specificity, as also outlined herein. The skilled person knows that different further parameters might be considered in order to increase both, like previous response of the patient to the drug. Nevertheless, the present invention provides (a) new and superior marker(s) for predicting the response as defined herein. In the context of the methods of the invention, the presence of one or more further diagnostic/predictive markers for the response is detected in the sample.
Reference to fluorouracil (5-FU) and like expressions encompass within their meaning response to treatment comprising fluorouracil (5-FU) as monotherapy, or in combination with other agents, or as prodrugs, or together with local therapies such as surgery and radiation, or as adjuvant or neoadjuvant chemotherapy, or as part of a multimodal approach to the treatment of neoplastic disease. The general mechanism of action of fluorouracil (5-FU) is its activity as a pyrimidine antimetabolite. In fluorouracil (5-FU), the smaller fluorine at position 5 allows the molecule to mimic uracil biochemically. However, the fluorine-carbon bond is much tighter than that of C-H and prevents methylation of the 5 position of fluorouracil (5- FU) by thymidylate synthase. Instead, in the presence of the physiological co factor 5, 10- methylene tetrahydrofolate, the fluoropyrimidine locks the enzyme in an inhibited state and prevents the synthesis of thymidylate, a required DNA precursor.
A fluorouracil (5-FU) combination refers to a combination of fluorouracil (5-FU) and another agent. A number of agents have been combined with fluorouracil (5-FU) to enhance the cytotoxic activity through biochemical modulation. Addition of exogenous folate in the form of 5-formyl-tetrahydrofolate (leucovorin) sustains inhibition of thymidylate synthase. Methotrexate, by inhibiting purine synthesis and increasing cellular pools of certain substrates for reactivity with 5-FU, enhances the activation of fluorouracil (5-FU). The combination of cisplatin and 5-FU increases the antitumor activity of fluorouracil (5-FU). Oxaliplatin is commonly used with 5-FU and leucovorin for treating colorectal cancer, and it may inhibit catabolism of 5-FU, perhaps by inhibiting dihydropyrimidine dehydrogenase (the enzyme that is responsible for the catabolism of fluorouracil (5-FU)), and may also inhibit expression of thymidylate synthase. The combination of fluorouracil (5-FU) and irinotecan, a topoisomerase-1 inhibitor, is a treatment that combines fluorouracil (5-FU) with an agent that has a different mechanism of action. Eniluracil, which is an inactivator of dihydropyrimidine dehydrogenase, leads to another strategy for improving the efficacy of fluorouracil (5-FU). A number of fluorouracil (5-FU) prodrugs have been developed. One is capecitabine (N4- pentoxycarbonyl-5'-deoxy-5-fluorcytidine). This orally administered agent is converted to 5'- deoxy-5-fluorcytidine by the ubiquitous enzyme cytidine deaminase. The final step in its activation occurs when thymidine phosphorylase cleaves off the 5'-deoxy sugar, leaving intracellular fluorouracil (5-FU). Capecitabine (Xeloda(R)) is approved by the FDA for certain treatments including colorectal cancer. Another fluoropyrimidine that acts as a prodrug for fluorouracil (5-FU) is ftorafur.
In the context of the present invention fluorouracil (5-FU) is applied intravenously. In the context of the present invention, the terms fluorouracil (5-FU) and 5 -fluorouracil (5- FU) are used interchangeably.
Also the use of high throughput screening (HTS) is envisaged in context of the present invention, in particular the screening methods of cancer cell(s), cancer tissue(s) and/or tumor sample(s) obtained from a subject, preferably a patient, suffering from colorectal cancer (CRC) for responsiveness/sensitivity to fluorouracil (5-FU), preferably cetuximab. Suitable (HTS) approaches are known in the art. Screening-assays are usually performed in liquid phase, wherein for each cell/tissue/cell culture to be tested at least one reaction batch is made. Typical containers to be used are micro titer plates having, for example, 384, 1536, or 3456 wells (i.e. multiples of the "original" 96 reaction vessels). Robotics, data processing and control software and sensitive detectors are further commonly used components of a HTS device. Often robot system are used which transport micro titer plates from station to station for addition and mixing of sample(s) and reagent(s), incubating the reagents, and final readout (detection). Usually, HTS can be used in the simultaneous preparation, incubation, and analysis of many plates. The assay can be performed in a single reaction (which is usually preferred), may, however, also comprise washing and/or transfer steps. Detection can be performed taking advantage of radioactivity, luminescence or fluorescence, like fluorescence- resonance-energytransfer (FRET), fluorescence polarisation (FP) and the like. The tumor samples described herein can also be used in such a context. In particular cellular assays and in vivo assays can be employed in HTS. Cellular assays may also comprise cellular extracts, i.e. extracts from cells, tissues and the like. However, preferred herein is the use of cancer cell(s), cancer tissue(s) or tumor sample(s) as biological sample (in particular a sample obtained from a patient/subject suffering or being prone to suffer from colorectal cancer (CRC)), whereas in vivo assays (wherein suitable animal models are employed, e.g. the herein described mouse models) are particularly useful in the validation/monitoring of the treatment with fluorouracil (5-FU). Depending on the results of a first assay, follow up assays can be performed by re-running the experiment to collect further data on a narrowed set (e.g. samples found "positive" in the first assay), confirming and refining observations. A suitable readout in animal (in vivo) models is tumor growth (or respectively the complete or partial inhibition of tumor growth and/or its remission).
In the context of the present invention, the herein described HTS methods for the detection of copy number changes include but are not limited to sequencing technologies such as whole genome sequencing and exome sequencing. The exome sequencing is a techniques for sequencing all the differentially expressed genes in a genome (known as the exome) of, e.g., extracts from cells, tissues or tumor samples obtained from a patient (responder and/or non- responder). The meaning of the terms "cell(s)", "tissue(s)" and "sample(s)" is well known in the art and may, for example, be deduced from "The Cell" (Garland Publishing, Inc.). Generally, the term "cell(s)" used herein refers to a single cell or a plurality of cells. The term "plurality of cells" means in the context of the present invention a group of cells comprising more than a single cell. Thereby, the cells out of said group of cells may have a similar function. Said cells may be connected cells and/or separate cells. The term "tissue" in the context of the present invention particularly means a group of cells that perform a similar function. The term "sample" refers in context of the present invention to all biological tissues, all fluids such as blood, ascites, sputum, broncho-alveolar lavage, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots. Tissues may be, e.g. epithelial tissue, connective tissue such as bone or blood, muscle tissue such as visceral or smooth muscle and skeletal muscle, as well as nervous tissue. The "sample" is collected from the patient or subjected to the method or treatment according to the invention. A "tumor sample" is a sample of the tumor to be treated. Such sample may be for example taken from an excised tumor, for example, tumor tissue retrieved by surgery.
Preferably, the cell(s), tissue(s) or tumor sample(s) to be selected comprise/are derived from or are (a) tumor cell(s), preferably (a) colorectal cancer cell(s). The tumor cell(s) may, for example, be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from or being prone to suffering from colorectal cancer (CRC). It is preferred herein that said subject is a human. As described herein above in respect of "cell(s)", "tissue(s)" and "tumor sample(s)" the cancer cell(s) may be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from colorectal cancer (CRC)". Generally, said tumor sample(s) or cancer cell(s) may be obtained from any biological source/organism, particularly any biological source/organism, suffering from or being prone to suffer from colorectal cancer (CRC).
Preferably, the (tumor) cell(s) or (cancer) cell to be contacted is (are) obtained/derived from a subject, preferably a patient, suffering from colorectal cancer (CRC). In the context of the present invention, said tumor/cancer cell(s) may be (are) derived from an animal or mammal. The meaning of the terms "animal" or "mammal" is well known in the art and can, for example, be deduced from Wehner und Gehring (1995; Thieme Verlag). Non-limiting examples for mammals are even-toed ungulates such as sheep, cattle and pig, odd-toed angulates such as horses as well as carnivores such as cats and dogs. In the context of this invention, it is particularly envisaged that DNA samples are derived from organisms that are economically, agronomically or scientifically important. Scientifically or experimentally important organisms include, but are not limited to, mice, rats, rabbits, guinea pigs and pigs. The tumor cell(s) may also be obtained carnivores such as cats or dogs or, for example, from primates which comprise dogs, cates, lemurs, monkeys and apes. The meaning of the terms "dogs", "cats", "primate", "lemur", "monkey" and "ape" is known and may, for example, be deduced by an artisan from Wehner und Gehring (1995, Thieme Verlag). As mentioned above, the tumor or cancer cell(s) is (are) most preferably derived from a human being suffering from the above-mentioned colorectal cancer. In context of this invention particular useful cells, in particular tumor or cancer cells, are, accordingly, human cells. These cells can be obtained from e.g. biopsies or from biological samples but the term "cell" also relates to in vitro cultured cells.
Further, the present invention relates to an in vitro method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising the following steps:
(a) obtaining a sample from a subject suffering from colorectal cancer (CRC); and
(b) determining the gene expression of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2);
whereby an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
Accordingly, the present invention relates to a method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising determining the gene expression of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), whereby an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
The present invention also relates to a method of monitoring the efficacy of a fluorouracil (5- FU) treatment of colorectal cancer (CRC) in a subject suffering from said disease comprising the steps of:
(a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject suffering from CRC the expression level of one or more genes as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2; and
(b) comparing the expression level of said one or more gene(s) determined in a) with a reference expression level of said one or more gene(s), optionally determined in a sample from a reference/control subject, wherein the extend of the difference between said expression level determined in a) and said reference expression level is indicative for the efficacy of a treatment of colorectal cancer (CRC). Said sample(s) may, for example, be obtained by (a) biopsy (biopsies). Preferably, said sample is obtained from a subject/patient suffering from colorectal cancer (CRC). It is preferred herein that said sample is obtained from (a) tumor(s) and, accordingly, is (a) tumor cell(s) or (a) tumor tissue(s). Preferably, (a) tumor sample(s) may be obtained from subjects/patients suffering from colorectal cancer (CRC).
Particularly preferred is the use of one or more gene(s) as shown in Table 1 (Figure 1), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2) as marker gene(s). In the context of the present invention, in the present method the gene expression/amplification status of at least one additional gene selected from the group of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) (as shown in Table 2 (Figure 2)) is assessed or determined. Exemplarily combination which may be determined in this context are FOS (NCBI accession no.: NM_005252; version no.: NM_005252.3; GI:254750707) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting iDDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ314860; version no.: NM_014860.2; GI.-544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and ZJC4 (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1)). Also preferred is the determination of S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153) (as shown in Table 2) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_ 005246507.3; GI: 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NMJM 7821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM _005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and ZJG4 (NCBI accession no.: NM__024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 )). Also preferred, in the context of the present invention, is the determination of FOS (NCBI accession no.: NM_005252; version no.: NM 005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153) and one, or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NMJD04367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSFJ3 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NMJD15266.2; GI:386781491), and L1CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 )). In the context of the present invention, the expression of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14, more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 gene(s) selected from the group consisting of DDX43 (NCBI accession no.: NM _018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ)14860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_ 021167.4; GT.392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and LI CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ) and/or Table 2 (Figure 2)) is determined. "Expression" refers to transcription and translation occurring within a host cell. The level of expression of a DNA molecule in a host cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of the protein encoded by the respective gene produced by the host cells. Further detail for the term "•expression" within the context of the present invention can be obtained via a review of Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1 -9361 13-41-5.
Accordingly, in the context of the present invention the expression of said gene(s) is determined by determining RNA levels of the respective gene(s) or protein level(s) encoded by the respective gene(s). In the appended Examples, the present invention has been exemplified by using the expression determination through determination of mRNA levels using RNA sequencing techniques. The skilled person will however acknowledge that the method may likewise be performed using different techniques and detection methods suited for determining the expression level of genes. Methods for determining the expression level of a gene on the nucleic acid level, i.e. on RNA levels are known by those skilled in the art and include hybridization-based, PCR-based and sequencing-based methods, including next generation sequencing (NGS). Such methods are generally known by those skilled in the art. The methods may be applied to detect the expression of one or more certain genes. In such hybridization probes and/or primers are used to detect and/or amplify a certain nucleic acid sequence. It will be understood by the skilled person that it may be desirable to reverse transcribe the mRNA prior to detection. Reverse transcription using Reverse-Transcriptase is also commonly known (see inter alia Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1-936113-41 -5). Likewise there are kits and assays available allowing sequencing the entire genome or transcriptome. It may hence be preferred to sequence the entire transcriptome of a sample in order to gain information about the entire transcription levels. The assessment of certain expression levels, e.g. of the gene(s) inventive diagnostic panels herein may then be conducted based on the information on the entire transcriptome. Whole transcriptome sequencing may preferably be performed by preparing an RNAseq library. The library may be prepared to include modifications preserving strand-specific information (Parkhomchuk D, et al., Nucleic Acids Res. 37(18) (2009), el23). Sequencing of the so generated libraries may be performed by common methods. The exemplified method of the Examples used RNAseq libraries either prepared using TruSeq RNA Sample Prep Kit v2 (Illumina, set A: RS-122-2001 ; set B: RS-122-2002) with modifications preserving strand- specific information or using TruSeq Stranded mRNA Sample Prep Kit (Illumina, set A: RS- 122-2101 ; set B: RS- 122-2102). For five total RNA samples Ribo-Zero™ Magnetic Gold Kit (Epicentre, MRZG 12324) used. Sequencing (2 51 bp) was performed on HiSeq 2000/2500 instruments with v3 chemistry. In the context of the present invention the use of those kits and assays is preferred. Oligonucleotide primers and probes having the desired sequence, e.g. for sequence specific detection and/or amplification may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods or automated embodiments thereof. In one such automated embodiment diethylophosphoramidites are used as starting materials and may be synthesized (see Beaucage et al, Tetrahedron Letters, 22 (1981), 1859-1862). One method for synthesizing oligonucleotides on a modified solid support is described in US Bl 4,458,006. It is also possible to use a primer which has been isolated from a biological source (such as a restriction endonuclease digestion). Preferred primers or hybridization probes have a length of from about 15-100, more preferably about 20-50, most preferably about 20-40 bases.
When using RNAseq methods the expression level may be determined using the amount of reads in the sequencing. To this end, RNA reads may be first aligned to the sequences of a database to identify the gene(s). Such alignment may be for example performed against hgl9 (Kent et al, Genome Res. 12(6) (2002), 996-1006; Kent et al, Nature. 409(6822) (2001), 860-921 ) using BWA (Li et al, Bioinformatics 25 (2009), 1754-1760) and SAMtools (Li et al, Bioinformatics 25 (2009), 2078-2079). Mapped reads may be annotated, e.g. using Ensembl v70. Gene expression levels may then be quantified by detecting the relative amount of an RNA of a certain gene, e.g. using reads per kilobase of exon model per million mapped reads (RPKM) as a measure (see Mortazavi A. et al, Nat Methods.5(7) (2008), 621-628).
Notwithstanding the above, further methods for determining the RNA levels, for example mRNA levels, of a gene may be applied for expression level analysis. In the context of the present invention the expression level of said gene(s) is determined by determining RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods, and RNA sequencing (RNAseq).
Accordingly, the expression level may, for example, be detected, assessed or evaluated by an in situ hybridization method, an in situ sequencing method, comparative genomic hybridisation and single-nucleotide polymorphism arrays. Exemplary in situ hybridisations are, inter alia, fluorescent in situ hybridisation (FISH), chromogenic in situ hybridisation (CISH) and silver in situ hybridisation (SISH). Further, in the context of the present invention the expression level of said gene(s) can be determined by the assessment, determination, detection or evaluation of the RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods and RNA sequencing.
Furthermore, the expression level may be determined by determining in the sample the amount of protein encoded by the gene. This may be performed using common techniques known by those skilled in the art. These techniques include immunoassays. Suitable immunoassays may be selected from the group of immunoprecipitation, enzyme immunoassay (EIA), enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), fluorescent immunoassay, a cytometric bead array (CBA), a chemiluminescent assay, an agglutination assay, nephelometric assay, turbidimetric assay, a Western Blot, a competitive immunoassay, a non-competitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay and a reporter assay such as a luciferase assay. Preferably herein the immunoassay is an enzyme linked immunosorbent assay (ELISA).
The present invention also relates to a method of diagnosing (colorectal cancer (CRC)) in a subject/patient suspected of suffering from colorectal cancer or suspected of being prone to suffering from colorectal cancer (CRC) comprising the steps of a) determining in a cell or tumor sample obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2); and b) comparing the expression or activity of said at least one marker gene determined in a) with a reference gene expression level of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (healthy subject), wherein said colorectal cancer (CRC) is diagnosed when said activity determined in a) differs from said reference activity. The present invention also relates to a method of monitoring the efficacy of a treatment of a colorectal cancer (CRC) in a subject/patient suffering from said cancer or being prone to suffer from said cancer comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2); and b) comparing the gene expression or protein level of said one or more marker gene(s) determined in a) with a reference gene expression or protein level of said one or more marker gene(s), optionally determined in (a sample from) a reference/control subject/patient (responder and/or non-responder),wherein the extent of the difference between said activity determined in a) and said reference gene expression or protein level is indicative for said efficacy of a treatment of a colorectal cancer.
The term "gene expression level" as used herein refers to the gene expression status as described elsewhere herein. The method of monitoring the efficacy of a treatment of a cancer may comprise a step of determining in a cell or tissue sample obtained from a subject/patient suffering from colorectal cancer (CRC) (e.g. a biopsy) the gene expression status of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2).
The present invention also relates to a method of predicting the efficacy of a treatment of a colorectal cancer (CRC) for a subject/patient suffering from said disease comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the expression of one or more gene(s) as shown in Table 1 (Figure 1), optionally in combination the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2); and b) comparing the expression of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (responder and/or non-responder) in a) and said reference expression is indicative for the predicted efficacy of a treatment of a colorectal cancer (CRC). The treatment of colorectal cancer (CRC) may comprise the administration of fluorouracil (5- FU) as described herein. The colorectal cancer (CRC) is a malignant tumor that arises from cells of the colon or the rectum. At the genomic level, CRC is classified into hypermutated or non-hypermutated, chromosomal instable tumors. Hypermutated case show either microsatellite instability (MSI) caused by defects in the mismatch repair mechanism or mutations in POLE or POLDl . Chromosomal instable CRC is characterized by extensive chromosomal rearrangements. A recent attempt to define four consensus molecular subtypes in CRC was published by Guinney et al. Accordingly, in the context of the present invention, the patient/subject suffering from colorectal cancer (CRC) may be a subject/patient characterized by having a colorectal cancer (CRC) which can be classified into hypermutated, non-hypermutated, and/or chromosomal instable tumors. Further, the subject/patient suffering from colorectal cancer may be a subject/patient characterized by having a colorectal cancer (CRC) which does not have (a) KRAS, BRAS and/or NRAS mutation(s) (see Gong J. et al.,. J. Gastrointest. Oncol. 7 (2016), 687-704). Thus, in the context of the present invention, the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s). Alternatively, in the context of the present invention, the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by having (a) KRAS, BRAS and/or NRAS mutation(s). In the context of the present invention, it is preferred to use cell(s), tissue(s) or tumor sample(s) obtained from the patient/subject suffering from CRC which is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s).
It has been described in the context of the present invention that the differential expression of one or more gene(s) as shown in Table 1 (Figure 1 ), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2) as disclosed herein act as markers/predictors for susceptibility to fluorouracil (5-FU). In particular, a responder to fluorouracil (5-FU) or a subject/patient sensitive to fluorouracil (5-FU) may be identified in accordance with the present method. Accordingly, the present invention provides the possibility to recognize changes of any one of the genes shown in Table 1 (Figure 1), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2) immediately once they occur, for example, by determining the gene expression level of said marker gene(s).
It is of note that the assessment/evaluation/detection of the expression status of any of the above marker genes (and their various combinations described herein) is sufficient for determining whether a subject/patient is likely to respond to or is sensitive to fluorouracil (5- FU), whether a (tumor) cell of a colorectal cancer is likely to respond or is responsive to treatment with fluorouracil (5-FU). The assessment/evaluation/detection of the expression status of any of the above marker genes (and their combinations) is also sufficient for diagnosing sensitivity to fluorouracil (5-FU). In other words, in particular in these methods described and provided in the present invention, the expression status alone of any of the above marker genes is indicative for a sensitivity/responsiveness to fluorouracil (5-FU) and the expression level/activity of the gene products of the above marker genes need not be determined in addition to the gene expression status. Accordingly, the present invention relates to means, methods and uses which are based on the early recognition of (an) expression change(s) of one or more gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) and/or the protein level of the respective gene(s). The possibility of recognizing changes of one or more (amplified) gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3) and/or the protein level of the respective gene(s) early, provides several advantages, like a higher lifespan/likelihood of survival of the subject/patient (for example due to the notice of possible treatment failures and a corresponding change of the treatment regimen and the possibility of a more efficient therapy or for example due to the possibility to avoid/recognize treatment failures early and, hence, to correspondingly change the fluorouracil (5-FU) treatment regimen early in therapy, i.e. to timely switch to a more suited treatment, to discontinue an ineffective treatment after diagnosis and to pot for alternative therapy). In the context of the present invention, "early" particularly means prior to (the onset of) a (complete or partial) cytogenetic or hematological response or a response measured by any imaging technique and/or to the outbreak of colorectal cancer (CRC). For example, "early" monitoring the efficacy of a therapy/treatment of said colorectal cancer may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment and/or at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment (of the patient or control patient (responder)), wherein the longer periods are preferred.
Alternatively, "early" monitoring the efficacy of a therapy/treatment of said cancer may also be at most 1, at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of said cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said cancer at the day the therapy/treatment was initiated, i.e. once the (amplified) activity/expression level of one or more genes as shown in Table 1 (Figure 1) (and/or any other gene(s) as shown in Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3)) changes upon said therapy/treatment.
In the following, an example of a scheme for (early) monitoring the efficacy of a therapy/treatment of the colorectal cancer (CRC) defined herein in accordance with this invention is provided:
• When monitoring the therapy/treatment of said cancer (for example therapy/treatment based on fluorouracil (5-FU) as described herein, expression of one or more gene(s) as shown in Table 1 , more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional expression of 1 or 2 gene(s) as shown in Table 2 (Figure 2), may be determined daily during the first week after initiation of the therapy/treatment, weekly during the first month of the therapy/treatment and, afterwards, monthly. • The reference activity/expression level may be taken at the day the therapy/treatment is initiated, from the subject/patient to be treated and/or from a corresponding reference/control subject/patient (responder/non-responder); see below.
• If a rise in marker levels is observed in two consecutive samples, or if decrease in marker level is not fast enough (for example not as fast as that of responder or not sufficiently faster than that of a non-responder), change of treatment regimen may be considered.
It is of note that this example is in no way limiting. The skilled person is readily in the position to adapt this scheme to the particular requirements relevant for each individual case, based on the teaching provided herein an on his common general knowledge.
For example, "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response to said therapy/treatment and/or at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment, wherein the longer periods are preferred.
Alternatively, "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of the cancer defined herein, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said colorectal cancer (CRC) at the day the therapy/treatment was initiated, i.e. once the (amplified) activity/expression level of one or more gene(s) as shown in Table 1 (Figure 1) (and/or any other gene(s) as shown in Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) changes upon said therapy/treatment.
Furthermore, "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after diagnosis of the cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already predict the efficacy of fluorouracil (5- FU) therapy/treatment of said colorectal cancer (CRC) at the day of diagnosis. As mentioned, the present invention is particularly useful for monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC) as defined herein. Corresponding means, uses and methods are provided herein. In general, monitoring the efficacy of a certain kind of a fluorouracil (5-FU) therapy/treatment is regularly applied in clinical routine. Hence, the skilled person is aware of the meaning of monitoring the efficacy of a certain kind of fluorouracil (5-FU) therapy/treatment. In context of this invention, the meaning of the term "monitoring" encompasses the meaning of terms like "tracking", "discovering" etc. In particular, the term "monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of colorectal cancer (CRC) as used herein refers to monitoring whether a subject/patient suffering from said disease (or being prone to suffering from said cancer) responds at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond is (e.g. how fast/slow the respond is and/or to what extent the respond is).
The present invention is further useful for predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC) as defined herein. Corresponding means, uses and methods are also provided herein. In general, predicting the efficacy of a fluorouracil (5-FU) therapy/treatment is highly desired in clinical routine, since it allows for preventing the disease (colorectal cancer (CRC)) and/or increasing the efficiency of a fluorouracil (5-FU) therapy/treatment and hence, leads to savings in cost and time and to a higher lifespan/likelihood of survival or of 'Genesung' of the affected patient. The definitions given with respect to the term "efficacy of a therapy/treatment of colorectal cancer (CRC)" provided herein apply here, mutatis mutandis. In context of this invention, the term "predicting the efficacy of a therapy/treatment of colorectal cancer (CRC) for a subject/patient" is used in basically the same sense like determining whether, and/or to what extent, a subject/patient exhibits susceptibility to such a fluorouracil (5-FU) therapy/treatment, i.e. whether said subject/patient will or would respond at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond will or would be (e.g. how fast/slow the respond is and/or to what extent the respond is). In particular, a subject/patient exhibits susceptibility to said colorectal cancer (CRC) in accordance with this invention, when its (amplified) activity/expression level of one or more gene(s) as shown in Table 1 (Figure 1 ) (and/or any other gene(s) as shown in Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is differential. In this context, said expression level is differential as defined herein.
In the context of the present invention, the "predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC)" in accordance with this invention may be performed after initiation of the fluorouracil (5-FU) therapy/treatment, i.e. during the already ongoing fluorouracil (5-FU) therapy/treatment. In particular, said "predicting" may be performed during the herein described monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer, preferably early after the beginning of said monitoring. Thereby, the predicting may be based on results from said monitoring obtained at a certain point in time of the ongoing fluorouracil (5-FU) therapy/treatment. Preferably, said point in time is an early point in time, like, for example that point in time, when a first result from said monitoring has been obtained. In cases where the "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC)" as defined herein is performed during an already ongoing fluorouracil (5-FU) therapy/treatment, it refers to the following/subsequent efficacy of said fluorouracil (5-FU) therapy/treatment.
In the context of the present invention, the "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC)" may be performed (immediately) after diagnosis but, however, prior to initiation of the fluorouracil (5-FU) therapy/treatment. In such cases, "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer (CRC)" refers to the efficacy of a fluorouracil (5-FU) therapy/treatment which has not yet been initiated (or has been initiated substantially at the same point in time when the "predicting" was performed).
In context of the invention, one non-limiting example of a healthy reference/control subject/patient is one having, e.g. (a) non-amplified gene(s) as shown in Table 1 (Figure 1) (and/or any other gene(s) shown in Table 2 (Figure 2), Table 3 (Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). This is in contrast to an amplification leading to an differential activity/expression of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 gene(s), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJH4860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021 167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ) and/or Table 2 (Figure 2)).
In accordance with the above, the "reference activity" of DDX43 (NCBI accession no.: NM_018665; version no.: NMJD18665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: N _024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: M_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) or the "reference expression level" of said marker gene(s), with respect to the means, methods and uses of monitoring the efficacy of a fluorouracil (5-FU) treatment of a colorectal cancer (CRC) defined herein, is that "reference activity/reference expression level" determined in (a sample of) the corresponding healthy reference/control subject, i.e. is the "normal" activity/expression level.
It is to be understood that the activity of amplified DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM__004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJM4860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GL211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) described herein is different from the above described "reference activity/reference expression level" of "normal" DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GL211938416), MYRIP (NCBI accession no.: NMJ) 15460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM 015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). In particular with respect to the herein disclosed means, methods and uses of monitoring/predicting the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) as defined herein, the reference/control subject/patient is, in one embodiment, envisaged to be a subject/patient suffering from said cancer, i.e. a subject/patient having, for example, an differential activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; Gl:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: ΝΜ_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_ 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NMJH 5197; version no.: NM_015197.3; GI:341604746), MAGEAll (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM _015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) and, hence, not a "normal" activity or "normal expression level" of DDX43 (NCBI accession no.: NM_018665; version no.: NMJH 8665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ)04367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021 167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJM7821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GL211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NMJD15460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NMJH5197.3; GL341604746), MAGEAll (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) as described in accordance with this invention. Thereby, "different" or "differential" means and comprises "higher" or "lower", depending on whether the cancer defined and described herein comes along with an up- or down-regulated activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; Gl:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GL211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM 015266.2; GL386781491 ) and/or L1CAM (NCBI accession no.: NMJD24003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). In this context, "different", "differential", "higher" or "lower" means different, higher or lower than the normal (range of) activity of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NMJB 1409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM l 38409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJH5460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LICAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) activity. As far as the "expression level" of said marker gene(s) is concerned, "different", "differential", "higher" or "lower" means different, higher or lower than the normal (range of) expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_ 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_ 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GL211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LICAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). For example, different, higher or lower means at least 1.0 fold, at least 1.5 fold, at least 2 fold, at least 2.5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold, at least 200 fold different, higher or lower, wherein the higher values are preferred. Whether, in which direction (i.e. higher or lower) and/or to which extent the activity and/or the expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_ 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NMJH5266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) differs from its corresponding reference activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NMJ)31409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_ 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM_005366; version no.: NM__005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), can easily be deduced by the skilled person based on the teaching provided herein and the common general knowledge. It is preferred and envisaged in this context that the reference/control subject/patient is subjected to the same fluorouracil (5-FU) treatment of the colorectal cancer (CRC) as the subject/patient suffering from colorectal cancer (CRC) described and defined herein. Said reference/control subject/patient may be a responder (positive reference/control) or non- responder (negative reference/control) to this treatment. Whether a subject/patient is a "responder" or "non-responder" with respect to a colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy can be evaluated by the skilled person on the basis of his common general knowledge and/or the teaching provided herein, hi particular, a "responder" may be a subject/patient whose cytological/hematological parameters and/or (aberrant) DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJM4860.2; GI.-544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021 167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NMJ) 17821.4; GL754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI: 548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NMJD05366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) activity/expression level (and hence the corresponding marker gene expression level(s))/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI: 754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or L1CAM (NCBI accession no.: NM_ 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) change towards the their "normal" activity/( expression) level(s) (in a sufficient manner) upon the colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy. In one specific embodiment, a "responder" may be a subject/patient not suffering from one of the herein defined resistances. In particular, a "non-responder" may be a subject/patient whose cytological/hematological parameters and/or (aberrant) activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos. : NM 031409.3 ; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NMJ317821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 015197.3; GI:341604746), MAGEAU (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) (and hence the corresponding marker gene expression level(s)) do not change towards the "normal" (expression) level(s) (in a sufficient manner) upon the cancer fluorouracil (5-FU) treatment/therapy. In one specific embodiment, a "non-responder" may be a subject/patient suffering from one of the herein defined resistances.
Accordingly, the patient responds to colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy, if the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GF.544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_ 138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NMJD21167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:21 1938416), MYR1P (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is reduced upon said treatment/therapy. Preferably, the expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_ 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is reduced to reference/control expression level/activity (e.g. determined in a sample obtained from a person not suffering from said cancer). In other words, a reduction in expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM_ 138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_ 003808; version no.: NM_ 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1) and/or Table 2 (Figure 2)) is indicative for a successful fluorouracil (5-FU) treatment/therapy. A skilled person is readily in the position to determine whether a patient responds to colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy by evaluation of the expression/ activity of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM 021 167.4; Gl:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEAll (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GL386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: M_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). In addition to the evaluation of said expression level/activity, a person skilled in the art may also determine cytological/hematological parameters characteristic for a specific colorectal cancer (CRC) in order to assess whether a patient responds to a fluorouracil (5-FU) treatment/therapy.
In contrast, a patient who does not respond to a fluorouracil (5-FU) treatment/therapy does not show a reduced expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM _015197.3; GI:341604746), MAGEAll (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or LI CAM (NCBI accession no.: NM_ 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) upon said treatment/therapy as defined herein above in context of responders/responding patients.
In context of the invention, one non-limiting example of a diseased reference/control subject/patient (responder and/or non-responder) suffering from a colorectal cancer (CRC) defined herein (or being prone to suffering from a susceptibility thereto) is one having an amplified DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF.222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ)04367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NMJ)05366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJ315266; version no.: NM 015266.2; GL386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) leading to a different expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM 017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEAll (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). The skilled person is aware of how a typical/desired response to a known fluorouracil (5-FU) therapy/treatment of colorectal cancer (CRC) should proceed or is intended to proceed. Moreover, the skilled person can consider how a typical/desired response to a (unknown) fluorouracil (5-FU) therapy/treatment of a colorectal cancer proceeds or is intended to proceed. Based on this knowledge, the means, methods and uses of this invention referring to the efficacy of a fluorouracil (5-FU) therapy/treatment of such a cancer can, for example, also be carried out without employing (a sample of) a particular reference/control subject/patient, i.e. without comparing the activity or expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM__005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBl accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; Gl:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) with a "reference activity" or "reference expression level" of DDX43 (NCBI accession no.: NM_018665; version no.: NM _018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_ 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI.T034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), for example in (a sample from) a reference/control subject/patient. Simply by comparing the course of the determined "activity" ore expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ) 14860; version no.: NM_014860.2; GI: 544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM _005246507; version nos.: XM 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NMJ) 15460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH5197; version no.: NMJH5197.3; GL341604746), MAGEAU (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) during the therapy/treatment of a colorectal cancer (CRC) with the above- mentioned known "typical/desired response", the skilled person is able to consider about the efficacy of the fluorouracil (5-FU) therapy/treatment monitored/predicted. If the response of a subject/patient is as fast (or even faster) than the "typical/desired response", the subject/patient is a "responder". If the response of a subject/patient is slower than the "typical/desired response", the subject/patient is a "non-responder" (when no substantial response can be seen) or "weak-responder".
Accordingly, the efficacy of a cancer treatment/therapy can be determined taking account of the change in the activity/expression level of DDX43 (NCBI accession no.: NMJ) 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM _031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) during the treatment/therapy. Thus, a skilled person is able to assess the efficacy of a treatment by evaluating the activity/expression level of the above marker gene(s) at various points in time during the treatment (e.g. prior to the treatment, after start of the treatment, and subseqently in intervals during the treatment). In this particular case, it may not be necessary to compare the activity/expression level with reference values (reference/control values) as indicated above in order to assess the efficacy of the fluorouracil (5-FU) treatment. Instead it may suffice to detect the change in the activity/expression level of the marker gene(s) in samples obtained from a treated patient after start of the treatment. In general, a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e. enhanced or decreased) activity or expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3) is shifted back towards the "normal level" of a (healthy) reference/control subject/patient or to "normal level" of a defined responder ("positive control") due to/in consequence of said treatment of the cancer or susceptibility thereto. For example a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e. enhanced or decreased) activity or expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJ)24501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM l 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_ 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is shifted back towards the "normal level" of a (healthy) reference/control subject/patient or to "normal level" of a defined responder ("positive control") due to/in consequence of said treatment of the cancer or susceptibility thereto.
In context of this invention, the efficacy of a treatment of the cancer defined herein is high, when the subject/patient (to be) treated responds as fast (or even faster) and as complete as a "responder", i.e. exhibits a "typical/desired response". This means that said subject/patient reaches the "normal" level of the relevant cytological/hematological parameters and/or DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM l 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM _017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2). and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) activity (and hence of the corresponding marker gene expression level(s)) of a healthy subject/patient as fast as a "responder", i.e. in the same manner as in a "typical/desired response".
Accordingly, the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response". In other words, the efficacy is high, when the activity/expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3) in said patient reach a "normal" activity/level as rapidly as in a "typical/desired response". For example, the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response". In other words, the efficacy is high, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NMJ300146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJH4860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NMJH7821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJ315460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEAU (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_ 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2). and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in said patient reach a "normal" activity/level as rapidly as in a "typical/desired response".
In context of this invention, the efficacy of a fluorouracil (5-FU) treatment of the cancer defined herein is moderate/low, when the subject/patient (to be) treated responds not as fast and/or not as complete as a "responder", i.e. does not exhibit a "typical/desired response". This means that said subject/patient does not reach the "normal" level of the relevant cytological/hematological parameters and/or activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ)04367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_ 005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NMJH7821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) (and hence of the corresponding marker gene expression level(s)) of a healthy subject/patient as complete and/or as fast as a "responder", i.e. not in the same manner as in a "typical/desired response". Accordingly, the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer is low, if the patient treated does not show a "typical/desired response". In other words, the efficacy is low, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJM4860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM _24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM 015197.3; GI:341604746), MAGEAU (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJM 5266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in said patient reaches a "normal" activity/level slower than in a "typical/desired response".
In context of this invention, there is no efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) at all, when the subject/patient (to be) treated does not respond at all. Particularly, when the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) as monitored/predicted in context of this invention is moderate/low or when there is no such efficacy, a change of the (planned) fluorouracil (5-FU) therapy/treatment might be and should be considered.
In an alternative embodiment, of the herein disclosed means, methods and uses of monitoring/predicting, the reference activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NMJH7821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ) and/or Table 2 (Figure 2)) of a "reference/control subject/patient" can be replaced by a "own" reference activity or expression level sample of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJ324501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM__005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJH7821 ; version no.: NMJH7821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NMJH5460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) from the subject/patient to be treated itself. Such an "own" reference sample may be obtained prior to (or at the beginning of) the treatment/therapy. In this specific case, the "reference/control subject/patient" would be the subject/patient to be treated itself. The efficacy of the fluorouracil (5-FU) treatment would then be assessed on the basis of how the activity or expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM_ 138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NMJH7821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE A 11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) changes during fluorouracil (5-FU) treatment/therapy compared with said particular "reference activity/ expression level" of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; Gl:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJM 5460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NMJH5197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). The more significant and/or faster said change is, the more efficacious is the fluorouracil (5-FU) treatment/therapy.
As mentioned above, the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is assessed in accordance with specific embodiments of this invention, on the basis that the activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos. : NM_031409.3 ; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_ 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM _005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is different from a certain or given "reference activity/reference expression level" of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM _014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XMJ305246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM _017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJH5460; version no.: NMJ315460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM _015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). Thereby, it is clear that "different" means higher or lower, depending on whether the cancer comes along with an up- or down-regulated activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJH4860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM l 38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_ 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)).
In accordance with the above, the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is assessed based on the comparison of the activity/ expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_ 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJH5460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM _005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a sample obtained from a patient with a reference (control) activity/expression level.
In this context, "different", "higher" or "lower" means different, higher or lower than the normal (range of) activity/expression level of DDX43 (NCBI accession no.: NM O 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960), CCR6 (NCBI accession no.: NMJ304367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_ 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GL386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). For example, different, higher or lower means at least 1.5 fold, at least 2 fold, at least 2,5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold or at least 200 fold different, higher or lower, wherein the higher values are preferred.
Whether, in which direction (i.e. higher or lower) and/or to which extend the activity/expression level of DDX43 (NCBI accession no.: NM O 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATADl (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJH7821 ; version no.: NMJH7821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NMJH5197.3; GL341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM _024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2). and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) described herein differs from its corresponding "reference activity/reference expression level", can easily be deduced by the skilled person based on the teaching provided herein and the common general knowledge. Accordingly, it is possible to assess for each marker gene particularly described herein, whether a given difference between the reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM _018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM _014860; version no.: NM 014860.2; GI: 544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATADl (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH 5197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a subject/patient to be assessed in accordance with this invention exists. This diagnostic assessment may be, in accordance with this invention the diagnostic for a colorectal cancer (CRC).
As explained above, a certain type of colorectal cancer (CRC) can be associated with increased activity/expression level of any one of the above marker gene(s) or with a decreased increased activity/expression level of any one of the above marker gene(s). Since a skilled person will be aware of reference activity/expression levels of the marker gene(s) (e.g. in a healthy person), he will be readily in the position to determine whether the activity/expression level of any one of the above marker genes is increased or decreased when compared to the reference activity/expression level.
As mentioned, in context of the means, methods and uses of monitoring/predicting as disclosed herein, the extent of the difference between the activity/expression level of DDX43 (NCBI accession no.: NMJH 8665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:21 1938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM _015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NMJ)05366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1) and/or Table 2 (Figure 2)) and corresponding reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NMJ331409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NMJD05366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is indicative for the (predicted) efficacy of the fluorouracil (5-FU) therapy/treatment of a the colorectal cancer (to be) performed.
For example, if the reference/control subject/patient is a responder, or the activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; Gl: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM _005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJU5460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is evaluated on the basis of a "typical/desired response", a low difference (at a certain point in time) indicates a high efficacy.
Accordingly, a responder shows expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM _015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) similar to a typical/desired response, wherein a typical/desired response is indicative for a successful fluorouracil (5-FU) treatment/therapy. As explained herein above, a responder may show reduced or increased expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXDl (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM _005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), depending on the type of cancer.
If the colorectal cancer (CRC) is, for example, characterised by a high expression level/activity of at least one of the marker gene(s) and if expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NMJD21167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJ317821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NMJH5460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), is reduced in a responder to a similar extent as in a typical/desired response, the cancer treatment/therapy can be considered successful. Vice versa, if the cancer is characterised by a low expression level/activity of at least one of the marker gene(s) and if expression/ activity of DDX43 (NCBI accession no.: NMJM 8665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM _004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NMJ24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM l 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GL211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2)), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2), is increased in a responder to a similar extent as in a typical/desired response, the fiuorouracil (5-FU) treatment/therapy can be considered successful.
In other words, if the difference between the expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NMJH7821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NMJH5197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a responder and in a typical/desired response is low, such a low difference indicates a successful fluorouracil (5- FU) treatment/therapy (i.e. a high efficacy in the fluorouracil (5-FU) treatment/therapy).
For example, if the reference/control subject/patient is a non-responder, or the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501 .2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021 167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is evaluated on the basis of a reference activity/reference expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXDl (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM _015266; version no.: NM 015266.2; GL386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) obtained from the subject to be treated prior to/at the beginning of a therapy/treatment of colorectal cancer (CRC), a high difference (at a certain point in time) indicates a high efficacy. As explained above, a reference/control sample can be obtained from a non-responder or can be obtained prior to/at the beginning of a therapy/treatment of a cancer. Accordingly, if the difference between the expression level/activity of DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM _031409; version nos.: NM 031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI.T 034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJ317821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NMJ303808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a responder (or similarly in a typical/desired response) compared to said reference/control is high, such a high difference indicates a successful fluorouracil (5-FU) treatment/therapy (i.e. a high efficacy in the fluorouracil (5-FU) treatment/therapy). In other words, a responder shows a reduced expression level/activity of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJ)15266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) compared to high expression level/activity DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM _ 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI.-392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM _015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: N _015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a reference/control, when the cancer is associated with such a high expression level/activity. In this context, the difference between the expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM _003808.3; GL211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in a responder and the reference/control should be high. The same explanations apply mutatis mutandis in context of the treatment of cancer associated with a low expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM _005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM Ol 5460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), wherein the expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI.T50417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM _021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NMJH 5197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is increased in a responder compared to a reference/control.
As can be deduced from the above, the reference activity/reference expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJM7821 ; version no.: NM_017821.4; GT754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM 003808.3; GL211938416), MYRIP (NCBI accession no.: NMJH 5460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_ 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) may be taken at the day of diagnosis, once the therapy/treatment is initiated, in between and/or during therapy/treatment, either from the subject/patient to be treated itself or from a corresponding reference/control subject/patient (healthy/responder/non-responder). The reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2;
GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3;
GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5;
GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.:
NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.:
NM_024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.:
XM 005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM 138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4;
GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4;
GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3;
GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 01 460.3;
GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_ 015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4),
SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM _024003; version no.: NM_024003.3;
GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1) and/or Table 2 (Figure
2)) may be determined at the same or at a different point in time than the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2;
GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3;
GI.-56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5;
GL150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.:
NM _031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.:
NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.:
XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJH7821 ; version no.: NM_017821.4;
GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3;
GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3;
GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3;
GI:341604746), MAGEA11 (NCBI accession no.: NM_ 005366; version no.: NM_005366.4), SLC9A8 (NCB1 accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), for example with respect to the course of the therapy/treatment.
Accordingly, the reference activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ304367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM _021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH 5197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) can be determined in a reference/control sample obtained from a patient (healthy tissue) or healthy person at the same time or at a different time when the cancer sample is obtained from said patient.
If the reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: M_031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM 024003; version no.: NM 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is obtained from a reference/control subject/patient different from the subject/patient to be treated, it is preferred that the reference activity/reference expression level of DDX43 (NCBI accession no.: NM O 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM O 17821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GL386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NMJ324003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is determined at the same point in time during therapy/treatment. In particular, if the reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NMJ)00146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM _031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NMJ303808; version no.: NM 003808.3; GL211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NMJH5197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NMJ)05366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH 5266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is obtained from the subject/patient to be treated itself, the reference activity/reference expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; Gl:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM J38409; version no.: NM 138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NMJ321167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI.-211938416), MYRIP (NCBI accession no.: NMJ) 15460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH 5197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) should be determined at a different point in time during therapy/treatment to allow comparison, for example, at the beginning of (or prior to) the therapy/treatment.
In general, activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NMJH 8665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJD24501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 21167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NMJ) 17821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 03808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM 15197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJH5266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) as described herein can be determined once or, preferably, several times. For example, activities/expression levels of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM _005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; Gl:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or L1CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) can be determined on a daily, weekly, monthly or yearly basis during therapy/treatment. Commonly, the requirements of corresponding studies would be met, if the frequency of determining activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2; GI156523250), GATADl (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NMJH 7821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM _015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) decreases during process of the fluorouracil (5-FU) therapy/treatment. Non-limiting examples of schemes of determining activities/expression levels of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; GI156523250), GATADl (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM _003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM _015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_ 015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) gene(s) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in accordance with this invention are provided herein. It is of note that the skilled person is readily in the position to elect (a) suitable reference/control patient(s)/subject(s) and the point(s) in time when the (reference) activity/(reference) expression levels of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GL386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) are determined for each individual setup of the means, methods and uses provided.
The present invention also relates to the use of a (transgenic) cell or a (transgenic) non-human animal having at least one gene marker/predictor as defined herein for screening and/or validation of a fluorouracil (5-FU) medicament for the treatment of colorectal cancer (CRC). The term "cell" as used in this context may also comprise a plurality of cells as well as cells comprised in a tissue. A cell to be used may, for example, be a primary tumor cell. The tumor cell or cell to be used in the screening or validation method may be obtained from samples from a (transgenic) non-human animal suffering from colorectal cancer (CRC). The tumor cell or cell may also be obtained from patient samples (e.g. biopsies), in particular a biopsy/biopsies from a patient/subject suffering from colorectal cancer. Accordingly, the tumor cell or cell may be a human tumor cell. Again, such a cell to be used in the present screening or validation methods may be comprised in a tissue or tissue sample, like in a sample biopsy.
The used non-human animal or cell may be transgenic or non transgenic. "Transgenic" in this context particularly means that at least one of the marker gene(s) as described or defined herein is over- or under- expressed or has a higher or lower activity. For example, if a variant of a fluorouracil (5-FU) is to be screened and/or validated, it is preferred that such marker gene(s) as DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: M_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246 07.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GT392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: M_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM 003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGE All (NCBI accession no.: NM_005366; version no.: NM__005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) are under-expressed or have a decreased activity. It is also envisaged in the context of the present invention that the DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_ 014860; version no.: NM _014860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM J24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; Gil 56523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJ317821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEAU (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NMJH5266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) are over-expressed or have an increased activity.
"Transgenic" in this context may also mean that DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.:
NM_ 004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM _014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.:
XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
Gil 56523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM _021167.4;
GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3;
GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3;
GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3;
GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4),
SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_ 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is over- or under-expressed, and/or that the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: M_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM l 38409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GI:341604746), MAGEAI1 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM _015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in the transgenic non-human animal or a transgenic cell is enhanced or decreased. It is also envisaged in this context that DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: M_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GF.754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NMJ315197; version no.: NM 015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) is under-expressed, and/or that the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM _004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XMJD05246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; G1156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM 021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NMJM5460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or LI CAM (NCBI accession no.: NM 024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) activity in the transgenic non-human animal or a transgenic cell is decreased. A preferred (transgenic) non-human animal or (transgenic) cell in context of the invention suffers from colorectal cancer (CRC) for the treatment of which the medicament is to be screened and/or validated. For example, if a medicament for CRC is to be screened and/or validated, the (transgenic) non-human animal or (transgenic) cell is particularly intended to suffer from DDX4S (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJD24501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507; version nos.: XM 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NMJ317821 ; version no.: NM 017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_ 015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NMJ)24003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), i.e. to have, for example, an decreased DDX43 (NCBI accession no.: NMJH 8665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM J24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBl accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1) and/or Table 2 (Figure 2)) activity and/or increased expression level of, for example, DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NMJB 1409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXDl (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM _005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEAll (NCBI accession no.: NM 005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GL386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NMJ324003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)).
The term "transgenic non-human animal" or "transgenic cell" as used herein refers to a non- human animal or cell, not being a human that comprises genetic material different from the genetic material of a corresponding wild-type animal/cell. "Genetic material" in this context may be any kind of a nucleic acid molecule, or analogues thereof, for example a nucleic acid molecule, or analogues thereof as defined herein. "Different" in this context means additional or fewer genetic material with respect to the genome of the wild-type animal/cell and/or rearranged genetic material, i.e. genetic material present at a different locus of the genome with respect to the genome of the wild-type animal/cell. An overview of examples of different expression systems to be used for generating transgenic cell/animal is, for instance, contained in Methods in Enzymology 153 (1987), 385-516, in Bitter et al. (Methods in Enzymology 153 (1987), 516-544) and in Sawers et al. (Applied Microbiology and Biotechnology 46 (1996), 1 -9), Billman-Jacobe (Current Opinion in Biotechnology 7 (1996), 500-4), Hockney (Trends in Biotechnology 12 (1994), 456-463), Griffiths et al, (Methods in Molecular Biology 75 (1997), 427-440).
In a preferred embodiment, the (transgenic) non-human animal or (transgenic) cell is or is derived from a mammal. Non-limiting examples of the (transgenic) non-human animal or derived (transgenic) cell are selected from the group consisting of a mouse, a rat, a rabbit, a guinea pig and a Drosophila. Preferably, the (transgenic) cell in accordance with this invention may be an animal cell, for example, a non-human animal cell. However, also human cells are envisaged to be employed as cells in context of the present invention. In a non limiting example, such cell may be an embryonic stem cell (ES cell), particularly a non- human animal ES, like, for example, a mouse or rat ES cell. The (transgenic) cell as described herein, particularly the ES cell, may also be used for generating the (transgenic) non-human animal as described herein. The ES cell technology for generating transgenic animals is well known in the art and for example is described in Pirity et.al. (Methods Cell Biol, 1998, 57:279). Generally, the (transgenic) cell may be a prokaryotic or eukaryotic cell. For example, the (transgenic) cell, may be a bacterial, yeast, fungus, plant or animal cell. In general, the transformation or genetically engineering of a cell with a nucleic acid construct or vector can be carried out by standard methods, as for instance described in Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, NY, USA; Methods in Yeast Genetics, A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, 1990. The (transgenic) non-human animal or (transgenic) cell as described or defined in context of this invention is particularly useful in methods for screening and/or validation of a medicament for the treatment of cancers as defined and described herein.
These screening methods may, in particular, performed in vivo using, for example, (transgenic) animals as described herein (e.g. rats, mice and the like) and/or animals comprising (a) colorectal cancer (CRC) cell(s), (a) tissue(s) or (a) cell culture(s). Said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may, for example, be obtained/derived from (a) colorectal cancer (CRC) tumor cell(s)/tumor(s). In particular, said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may be obtained from a subject/patient suffering from a CRC. These in vivo screening methods may in particular comprise measuring and determining differences in tumor volume, for example, in the (transgenic) animals described herein above.
Accordingly, the present invention also relates to a method for screening and/or validation of a fluorouracil (5-FU) for the treatment of a colorectal cancer (CRC). Said method may comprise the steps of
a) administering to a (transgenic) non-human animal or (transgenic) cell as defined herein said medicament to be screened/ validated;
b) determining in (a sample from) said animal or cell the activity or expression level of the DDX43 (NCBI accession no.: NM_018665; version no.: NM O 18665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GL544186059), HOXD1 (NCBI accession no.: NM _024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_ 015197.3; GI:341604746), MAGEAll (NCBI accession no.: NMJ305366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NMJ315266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) in accordance with this invention;
comparing the activity or expression level of said at least one marker gene determined in b) with a reference activity or reference expression level of the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NMJ315460; version no.: NM _015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM__024003; version no.: NM 024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), said activity or said expression level optionally determined in (a sample from) a reference/control (transgenic) non-human animal or (transgenic) cell as defined herein to which said medicament to be screened has not been administered; and d) selecting said medicament when said activity/expression level of the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM _015197.3; GI:341604746), MAGE All (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)) determined in b) differs from said reference activity/expression level determined in c).
The corresponding definitions and descriptions provided above, for example with respect to "marker gene", "therapy/treatment", "efficacy", "CRC" "susceptibility" thereto, "(reference/control) subject/patient", "(transgenic) non-human animal" or "(transgenic) cell", "expression level", "reference expression level" etc., apply here, mutatis mutandis. Particularly the relevant definitions and descriptions provided above with respect to "reference/control subject/patient" also apply to the "reference/control (transgenic) non- human animal" or "(transgenic) cell", mutatis mutandis. In context of this invention, "screening and/or validation of medicaments" means, on the one hand, whether a given set of compounds comprises one or more compound(s) that can function as (a) medicament(s), and/or, on the other hand, whether (a) given compound(s) can function as (a) medicament(s). It is particularly intended that the medicaments to be screened and/or validated in context of this invention are medicaments for the treatment, prevention and/or amelioration of a cancer as defined herein.
The skilled person is readily in the position to put this embodiment of the present invention into practice. For example, by doing so, the compound(s)/medicament(s) to be screened and/or validated may be administered to the non-human (transgenic) animal or cell described herein, and, afterwards (for example after a certain period of time sufficient to allow a compound to effect on a cancer as described herein), it is analyzed whether the cancer, or a symptom thereof, of said animal/cell is ameliorated. The present invention also relates to a fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC) if (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1. Accordingly, the present invention relates to fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC), wherein said fluorouracil (5-FU) is administered to the subject to be treated if (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) obtained from the subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1.
The corresponding definitions and descriptions provided above, for example with respect to "subject", "therapy/treatment", "efficacy", "colorectal cancer (CRC)" "fluorouracil (5-FU)", "expression", etc., apply here, mutatis mutandis. Particularly, the subject to be treated has been predicted to be responsive or susceptible to the treatment with a fluorouracil (5-FU) in a method of the present invention. The present invention also relates to a kit useful for carrying out the method or used of this invention. In a preferred embodiment, said kit comprises oligonucleotides or polynucleotides capable of detecting the amplification status of at least one gene selected from the group of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GF56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GL341604746), MAGEAU (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). For example, said kit may comprise (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX4S (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM l 38409; version no.: NM_138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NMJ303808; version no.: NM_ 003808.3; GL211938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM 015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491 ) and/or LI CAM (NCBI accession no.: NMJ)24003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). In a preferred embodiment, the kit (to be prepared in context) of this invention is a diagnostic kit. In a particularly preferred embodiment of the present invention, the kit (to be prepared in context) of this invention or the methods and uses of the invention may further comprise or be provided with (an) instruction manual(s). For example, said instruction manual(s) may guide the skilled person (how) to determine amplification status of at least one gene of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_ 005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM _021167; version no.: NM 021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM _015460.3; GI: 548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEAU (NCBI accession no.: NMJ305366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 (Figure 1 ), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)), i.e. (how) to diagnose the susceptibility to fluorouracil (5-FU). Particularly, said instruction manual(s) may comprise guidance to use or apply the herein provided methods or uses.
The kit (to be prepared in context) of this invention may further comprise substances/chemicals and/or equipment suitable/required for carrying out the methods and uses of this invention. For example, such substances/chemicals and/or equipment are solvents, diluents and/or buffers for stabilizing and/or storing (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:211938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM 015266; version no.: NM_015266.2; GL386781491) and/or LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 (Figure 1), Table 2 (Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 (Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 (Figure 2)). The present invention also relates to the use of an oligo- or polynucleotide capable of detecting the expression level(s) of one or more of the gene(s) of Table 1 (Figure 1) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU). In the context of the present invention preferably 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the gene(s) shown in Table 3 (Figure 3), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the genes shown in Table 3 (Figure 3) is (are) detected in order to predict the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU). Preferably, the oligonucleotide(s) is (are) about 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 to 100 nucleotides in length. In the context of the present invention, the expression of at least 1 additional gene selected from the group consisting of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707), and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) is (are) detected for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU). A person skilled in the art is, based on his general knowledge and the teaching provided herein, easily in the position to identify and/or prepare (a) an oligo- or polynucleotide capable of detecting one or more gene(s) as shown in Table 1 (Figure 1), Table 2 (Figure 2) and/or Table 3 (Figure 3). The Figures show
Figure 1: Novel fluorouracil (5-FU) sensitivity related genes (see Table 1). The column "EIR" (expression in responders) indicates if a certain gene is up or down regulated in responding PDX models compared to non -responding PDX models. A RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff'. Down regulated genes indicate likelihood for response to cetuximab below the cutoff. Up regulated genes indicate likelihood for response to cetuximab above the cutoff. logFC - log2 normalized fold change. FDR - false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d.
Figure 2: Fluorouracil (5-FU) sensitivity related genes (see Table 2). The column
"EER" (expression in responders) indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models. A RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff". Down regulated genes indicate likelihood for response to cetuximab below the cutoff. Up regulated genes indicate likelihood for response to cetuximab above the cutoff. logFC - log2 normalized fold change. FDR - false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d. Figure 3: 14-gene mini-classifier (see Table 3). Selection of fluorouracil (5-FU) sensitivity related genes. The column "EIR" (expression in responders) indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models. A RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff'. Down regulated genes indicate likelihood for response to cetuximab below the cutoff. Up regulated genes indicate likelihood for response to cetuximab above the cutoff. logFC - log2 normalized fold change. FDR - false discovery rate (Benjamini-Hochberg procedure). Please see the methods for further details on setups a-d and the selection of the genes using SVM.
Figure 4: Response to fluorouracil (5-FU) in xenografts (PDXs): Heatmap of genes that correlate in their expression to fluorouracil (5-FU) sensitivity. 48 PDX samples and genes are clustered using hierarchical clustering. The drug sensitivity is determined by a treatment in comparison to control (T/C) (as illustrated in a continuous grey scale color code) in PDX: black - strongly responding models, grey - resistant models (a) Heatmap includes genes that are not reported to be associated with fluorouracil (5-FU) sensitivity (236 genes), (b) Heatmap includes genes known to be associated with fluorouracil (5-FU) sensitivity.
Figure 5: Performance range of the downsized sub-signatures of the 14-gene mini- classifier. The plot shows the upper range of the balanced accuracy for sub- signatures with a signature size of two up to 13 genes. Sub-signatures were randomly generated out of the 14-gene mini-classifier. For each signature size 120 unique sub-signatures were generated. Hyperparameter fitting and and SVM training was performed on the OncoTrack PDX cohort as described. The upper bound shows the maximum of balanced accuracy. The lower bound shows the median of balanced accuracy. The small vertical line marks the 75% quartile of balanced accuracy. The balanced accuracy of the downsized sub- signatures was evaluated on the OncoTrack PDX cohort and plotted over the signature size. The mini-gene classifier accuracy is stable or stays in an acceptable range, i.e. the performance of the 14-gene mini-classifier is more or less independent of the number of applied genes.
The following Examples illustrate the invention
1. Patient cohort
From a prospective CRC cohort of 106 patients a total of 116 resected tissue samples with matched blood samples, comprising 89 primary tumours (ranging from stage I to IV) and 27 metastases were collected. The tissue samples were used to generate a collection of pre-clinical patient-derived experimental models. 52 xenografts (PDX), established from 48 patient samples, were that were utilized for in vivo drug response testing. The genomes, exomes and transcriptomes of the donor cohort as well as of the matched untreated PDX models were sequenced.
RNA data processing
RNA reads were aligned to hgl 9 (GCA_000001405.1) using BWA and SAMtools. Mapped reads were annotated using Ensembl v70. Gene expression levels were quantified in reads per kilobase of exon per million mapped reads (RPKM) (Mortazavi A. et al, Nat Methods. 5(7) (2008), 621 -8).
DNA data processing
DNA reads were aligned to the human reference genome hgl 9 using BWA (Li H. et al, Bioinformatics 25 (2009), 1754-1760) (bwa0.7.7-r441-mem for 75/101bp, bwa0.5.9-rl6-aln for 51bp reads). For xenograft (PDX) samples, the human and mouse DNA reads were deconvoluted after mapping to references from human hgl9 and mouse mm9 genome versions.
Somatic SNVs
Somatic SNVs were detected using established pipelines based on VarScan2 (Koboldt D.C. et al, Genome Res 22 (2012), 568-576) combined with RNAseq data and functional annotation of the variants based on Ensembl v.70. Somatic indels were detected using SAMtools and Dindel (Albers C.A. et al, Genome Res 21 (2011), 961- 973). Development and characterization of patient derived xenografts (PDX)
Resected tumor tissues were transplanted to immunodeficient mice (NMRI nude or NOG, Taconic, Bomholdtgard, DK- Tac:NMRI-Foxnlnu, females, 6-8 weeks at start of transplantation) using previously described methods by Fichtner et al. (Fichtner I. et ah, Eur J Cancer 40 (2004), 298-307). Animal experiments were carried out in accordance with the United Kingdom Coordinating Committee on Cancer Research regulations for the Welfare of Animals and of the German Animal Protection Law and approved by the local responsible authorities. Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO) strictly follows the EU guideline European convention for the protection of vertebrate animals used for experimental and other scientific purposes. (EST 123)" and "German Animal Protection law -Version July 2014" (Tierschutzgesetz: zuletzt geandert durch Art. 3 G v. 28.7.2014 I 1308). Further the animals were handled according to Regulation on the protection of experimental scientific purposes or other Purposes used animals (Tierschutz- Versuchstierverordnung- TierSchVersV: Geandert durch Art. 6 V v. 12.12.2013 I 4145). Compliance with the above rules and regulations is monitored by the Landesamt fur Gesundheit und Soziales (LAGeSo) which is the responsible regulatory authority monitoring the animal husbandry based on the German Animal Welfare Act, last revised in 2014. Approval was given after careful inspection of the site including bedding, feeding & water, ventilation, temperature and humidity, cleaning and hygiene concepts. Mice were monitored 3 times weekly for tumor engraftment for up to 3 month. Engrafted tumors at a size of about 1cm3 were surgically excised and smaller fragments re-transplanted to naive NMRI nu/nu mice for further passage. Within passage 1 to 3 numerous samples were cryo-conserved (DMSO-medium) for further experiments. Tumors were passaged not more than 6 times. For confirmation of tumor histology, tumor tissue was formalin fixed and paraffin embedded (FFPE) and 5 μηι sections were prepared. Samples were stained according to a standard protocol for hematoxilin, eosin and Ki67 to ensure xenograft comparability to the original specimen. Cases with changed histological pattern were sent for pathological review and outgrowth of lymphoproliferative diseases was excluded. In this study, no blinding was done.
In vivo drug response testing of the xenografts Response to 5-FU was evaluated in early passages using the design of a preclinical phase II study. Tumor fragments of similar size were transplanted subcutaneously to a large cohort of mice. At palpable tumor size (50-200 mm3), mice were randomized to treatment or control groups consisting of 5-6 animals each. Doses and schedules were chosen according to previous experience in animal experiments and represent maximum tolerated or efficient doses. The applied schedule for 5-FU was as follows: Application route: i.p. (intraperitoneal injection); Schedule: Once per week; Day: Monday; number of cycles: 4; Dose: 100 mg/kg. The injection volume was 0.1-0.2 ml/20 g body weight. Treatment was continued over a period of four weeks (4 cycles) or till tumor size exceeded 1 cm3 or animals showed loss of >15% body weight. From the first treatment day onwards the tumor volumes and body weights were recorded twice weekly. At the end of the treatment period animals were sacrificed, blood and tumor samples collected, and stored in liquid nitrogen immediately.
Animal welfare was controlled twice daily. Tumor volume was calculated from the length and width of subcutaneous tumors (V = (length x [width]2)/2). Sensitivity to the tested compounds was determined as tumor growth inhibition by treatment in comparison to the control (T/C) on each measurement point. Efficacy of the tested drugs in PDX models was classified by end-point T/C (treated/control) values expressing tumor growth delay of treated versus untreated (control) mice, with the following categories: T/C < 10% as strong tumor growth delay, T/C 11-25% as moderate tumor growth delay, T/C 26-50%) as minor tumor growth delay, and T/C >50% as resistant. Tumors with a T/C <25%> can be considered to represent sensitivity in terms of (partial) tumor regression or stable disease.
For comparison, treatment response was in parallel evaluated using the adopted, stringent clinical response criteria (RECIST) (Eisenhauer E.A. et ai, Eur J Cancer 45 (2009), 228-247). The relative tumor volume (RTV) was calculated as the ratio of the tumor volume at the end of treatment / tumor volume at the start of treatment.
The revised clinical response (RECIST) criteria taking as reference the baseline sum diameters define:
- Complete Response (CR): Disappearance of all target lesions. RTV = 0
- Partial Response (PR): At least a 30%> decrease in the sum of diameters of target lesions (RTV < 0.7)
- Progressive Disease (PD): At least a 20%> increase in the sum of diameters of target lesions. (RTV > 1.2) - Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD. (RTV 0.7-1.2). Preprocessing for drug response analysis
Five xenograft samples of the 52 xenografts (PDX) that derived from one colorectal carcinoma (CRC) (150 MET1) shared highly similar global expression profiles. They were merged into one artificial single sample to avoid analysis bias by taking an average of the reads per kilobase of exon per million mapped (RPKM) (Mortazavi A, et al, Nat Methods 5 (2008), 621 -628)-values and of the T/C -values per gene or drug, i.e. 5-FU. Taking the artificial sample for 150JVIET1 into account 48 PDX were included into the drug response analysis. Drug response related gene signatures in xenografts (PDX)
Differential gene expression (DGE) analysis using the R package edgeR (Robinson MD et al., Bioinformatics 26 (2010), 139-140) to identify signatures associated with drug, i.e. 5-FU, response results in form of T/C values for PDX: strong, moderate, minor, resistant (see the above section 6). DGE analysis was applied in different setups as follows: a) combined strong+moderate vs combined minor+resistant, b) combined strong+moderate+minor vs. resistant, and c): 20 most sensitive vs. 20 least sensitive PDX. Genes were filtered by a false discovery rate (FDR) < 0.01, |log2FC| > 1 and RPKM difference > 1. In addition, in setup d the IC50 or T/C values as phenotype vector in a general linear model (GLM) provided by the edgeR package was used. Genes were filtered by FDR < 0.01 and dispersion < 4. Gene signatures associated with a given drug response were generated by combining results from setups a-d. Low expressed genes were filtered by an expression > 1 RPKM in minimum five PDX and by a mean expression > 0.8 RPKM. In total 253 genes correlate in their expression with the response to 5-FU. Building drug response classifiers for 5-FU
Based on the gene signature associated with 5-FU response, a 14-gene classifier was built that predict the outcome of 5-FU treatment (response or resistance). Genes that showed lower mean expression between highly correlated gene pairs (Pearson correlation > 0.8) were excluded in two iterations. For the drug response classifier a linear support vector machine (SVM) implemented in the R package "el 071" (Dimitriadou E. et al., The Lancet el071 Package (2005)) was trained on 48 PDX of the OT cohort (14 responding and 34 resistant PDX). A SVM is a supervised machine learning method that is used to find the best separation between two groups in a given space by one or a set of hyperplanes. Based on the found hyperplane, samples can be classified into groups (Bennet K.P. et al., SIGBCDD Explorations 2 (2000); Cortes et al, Machine Learning 20 (1995), 273-297). An important factor for a proper classification is the selection of features (genes) that define the data space and the SVM learns from. From the preselected genes that are associated to drug response, the SVM itself was used to rank features and the probably most important one were selected. The application of the SVM is described in further details below. To address the imbalance of the training set, a class weighted SVM was used and the hyperparameter C was tuned for each of classes resistance and response {CresiS, Cresp). The feature (gene) selection included feature ranking and feature size selection. In order to avoid overfitting of the SVM, a SVM recursive feature elimination (SVM- RFE) was used for feature ranking, similar to the approach of Duan et al. (Duan K.B. et al., IEEE transactions on nanobioscience 4 (2005), 228-234)). To describe briefly the procedure proposed by Duan et al, a SVM-RFE includes following steps: 1) hyperparameter tuning, 2) train multiple SVMs on subsamples of the original training set, 3) calculate a ranking score per feature based on the trained SVMs, 4) note the relative position in the final ranking vector of m features with the lowest ranking score, 5) eliminate m features with the lowest ranking score from the feature space, 6) repeat step 1 -5 until all features are ranked in the final ranking vector. In each recursive step of our adaptation of the procedure, the hyperparameter Cresis and Cresp were tuned via grid search with a stratified bootstrap (C = 2~s, 2'7, ... , 212; 100 iterations), the ranking scores were calculated based on a stratified leave-n-out resampling (200 iterations) and m=4 features were eliminated. The bootstrap was separately applied on the responder and resistance set with a sample size of 13 and 31 , respectively. The performance of a hyperparameter set was evaluated using the Fi- score. For the leave-n-out resampling two and five samples of the responder and resistance set were left out from the training set, respectively. The calculation of the ranking score was based on the weight vector w of a linear SVM and not w2 as described from Duan et al. For the final classifier, the hyperparameter Cresis and Cresp as well as the features size of the top ranked features were tuned using a grid search as described above (C = [10"4, 104], features size = 2, 4, ... , 38). The parameter set for the 14-gene classifier with third highest Fi -score was taken as optimal solution, since it showed the highest sensitivity among the top three: CreSiS= 0.007, Cresp= 0.02, feature size = 14. Validation of the 5-FU response classifier
The 5-FU mini classifier (14 genes) was cross-validated on the OT PDX cohort via a 100 times repeated 10-fold cross-validation. Performance values were averaged over the repeats. The performance of the classifier was estimated from the number of true positive (TP), false positive (FP), true negative (TN) and false negative (FN) predictions as well as the sensitivity, specificity and balanced accuracy. Additional information
The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115234 (OncoTrack), resources of which are composed of financial contributions from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies' in-kind contribution (www.imi.europa.eu).

Claims

1. A method for determining the susceptibility or responsiveness of (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), said method comprising determining the expression level of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NM_138409.2; GI156523250), GATADl (NCBI accession no.: NMJ321 167; version no.: NM_021 167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GI:21 1938416), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NMJH5197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM _015266.2; GL386781491), and LICAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GL497239882) in said cancer cell(s), cancer tissue(s) or tumor sample(s), wherein said expression level is indicative of whether said patient is responsive or susceptible to the treatment with a fluorouracil (5-FU).
2. A method for the identification of a responder to or a subject sensitive to fluorouracil (5-FU), wherein said method comprising determining the expression level of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NMJH 8665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_ 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM__004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ314860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: M_024501 ; version no.: M_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ 38409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021 167; version no.: NM_021 167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_OO3808.3; GI:211938416), MYRIP (NCBI accession no.: NMJM 5460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ), and L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) on (a) cancer cell(s), cancer tissue(s) or tumor sample(s) from a subject suffering from colorectal cancer (CRC), whereby a expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5- FU).
3. A method of monitoring the efficacy of a fluorouracil (5-FU) treatment of colorectal cancer (CRC) in a subject suffering from said disease comprising the steps of:
(a) determining in (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from said subject the expression level of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NMJ)00146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM _031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM O 14860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XMJ305246507; version nos.: XM 005246507.3; GL 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021 167; version no.: NM 021 167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:21 1938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM 015197; version no.: NM_015197.3; GL341604746), MAGEAll (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM 015266.2; GI:386781491), and LI CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882); and
(b) comparing the expression level of said one or more gene(s) determined in a) with a reference expression level of said one or more gene(s), optionally determined in a sample from a reference subject, wherein the extend of the difference between said expression level determined in a) and said reference expression level is indicative for the efficacy of a treatment of colorectal cancer (CRC).
4. The method according to any one of claims 1 to 3, wherein the expression of at least 1 additional gene selected from the group consisting of FOS (NCBI accession no.: NM _005252; version no.: NM_005252.3; GI:254750707), and S100A2 (NCBI accession no.: NM 005978; version no.: NM 005978.3; GI:45269153) is determined.
5. The method according to any one of claims 1 to 4, wherein the expression level of said genes is determined by an in situ hybridization method, an in situ sequencing method or by determining RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods and RNA sequencing.
6. Fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC) if (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject to be treated exhibits expression of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NMJH 8665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM_138409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM 021 167; version no.: NM_021167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM _017821 ; version no.: NMJH7821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:21 1938416), MYRIP (NCBI accession no.: NM _015460; version no.: NM_015460.3; GL548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM 005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NMJH 5266.2; GI:386781491), and L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GL497239882).
The fluorouracil (5-FU) for use according to claim 6, wherein the subject to be treated has been predicted to be responsive or susceptible to the treatment with said fluorouracil (5-FU) in a method according to any one of claims 1 , 2, 4 and 5.
A kit for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), comprising oligonucleotides or polynucleotides capable of detecting the expression level of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NMJU 8665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM J24501.2; GI:399154168; (NCBI accession no.: XM 005246507; version nos.: XM_005246507.3; GI:1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NMJ 38409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021 167; version no.: NM_021 167.4; GI:392307002), RHBDL2 (NCBI accession no.: NM 017821 ; version no.: NM_017821.4; GL754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM 003808.3; GL21 1938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GL341604746), MAGEA11 (NCBI accession no.: NM_005366; version no.: NM_005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and LI CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GI:497239882), and optionally further comprising oligonucleotides or polynucleotides capable of detecting the expression level of at least one gene selected from the group consisting of FOS (NCBI accession no.: NM_005252; version no.: NM_005252.3; GL254750707), and S100A2 (NCBI accession no.: NM 005978; version no.: NM__005978.3; GI:45269153).
9. Use of an oligonucleotide or polynucleotide capable of detecting the expression level of at least 2 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM_005246507; version nos.: XM 005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NMJ38409; version no.: NM 138409.2; GI156523250), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021 167.4; GL392307002), RHBDL2 (NCBI accession no.: NM_017821 ; version no.: NM_017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3; GI:21 1938416), MYRIP (NCBI accession no.: NM_015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJ315197; version no.: NM_015197.3; GI:341604746), MAGEA11 (NCBI accession no.: NM 005366; version no.: NM _005366.4), SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491), and L1CAM (NCBI accession no.: NM_024003; version no.: NM 024003.3; GL497239882) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
10. The use of claim 9, wherein the expression of at least 1 additional gene selected from the group consisting of FOS (NCBI accession no.: NM_005252; version no.: NM_005252.3; GI:254750707), and S100A2 (NCBI accession no.: NM_005978; version no.: NM 005978.3; GI:45269153) is detected.
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