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EP1177285A1 - Erythropoietinpolypeptide und dafür kodierende nukleinsäuren von schimpansen - Google Patents

Erythropoietinpolypeptide und dafür kodierende nukleinsäuren von schimpansen

Info

Publication number
EP1177285A1
EP1177285A1 EP00928879A EP00928879A EP1177285A1 EP 1177285 A1 EP1177285 A1 EP 1177285A1 EP 00928879 A EP00928879 A EP 00928879A EP 00928879 A EP00928879 A EP 00928879A EP 1177285 A1 EP1177285 A1 EP 1177285A1
Authority
EP
European Patent Office
Prior art keywords
chepo
seq
amino acid
polypeptide
acid sequence
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00928879A
Other languages
English (en)
French (fr)
Inventor
Frederic Desauvage
Dennis J. Henner
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Genentech Inc
Original Assignee
Genentech Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US09/552,265 external-priority patent/US6555343B1/en
Application filed by Genentech Inc filed Critical Genentech Inc
Publication of EP1177285A1 publication Critical patent/EP1177285A1/de
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/475—Growth factors; Growth regulators
    • C07K14/505—Erythropoietin [EPO]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A61P7/06—Antianaemics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates generally to the identification and isolation of novel chimpanzee erythropoietin polypeptides, nucleic acid molecules encoding those polypeptides and to the recombinant production of those polypeptides.
  • Erythropoiesis the production of red blood ceils, occurs continuously throughout the human life span to offset cell destruction. Er ⁇ thropoiesis is a very precisely controlled physiological mechanism enabling sufficient numbers of red blood cells to be available in the blood for proper tissue oxygenation, but not so many that the cells would impede circulation. The formation of red blood cells occurs in the bone marrow and is under control of the hormone, erythropoietin.
  • Erythropoietin an acidic gl ⁇ coprotein is approximately 34,000 dalton molecular weight, may occur in three forms: alpha, beta and asialo.
  • the alpha and beta forms different slightly in carbohydrate components have the same potency, biological activity and molecular weight.
  • the asialo form is an alpha or beta form with the terminal carbohydrate (sialic acid) removed.
  • Erythropoietin is present in a very low concentrations in plasma when the body is in a healthy state wherein tissues receive sufficient oxygenation from the existing number of er ⁇ throc ⁇ tes. Tbis normal low concentration is enough to stimulate replacement of red blood cells which are lost normally through aging.
  • the amount of erythropoietin in the circulation is increased under conditions of hypoxia when oxygen transport by blood cells in the circulation is reduced.
  • Hypoxia may be caused by loss of large amounts of blood through hemorrhage, destruction of red blood cells by over-exposure to radiation, reduction in oxygen intake due to high altitudes or prolonged unconsciousness, or various forms of anemia.
  • erythropoietin will increase red blood cell production by stimulating the conversion of primitive precursor ceils in the bone marrow into proerythroblasts which subsequently mature, synthesize hemoglobin and are released into the circulation as red blood cells.
  • the number of red blood cells in circulation is greater than needed for normal tissue oxygen requirements, erythropoietin in circulation is decreased.
  • erythropoietin is essential in the process of red blood cell formation, the hormone has potential useful application in both the diagnosis and treatment of blood disorders characterized by low or defective red blood cell production. See, generally, Pennathur-Das, et al., Blood 63(5):1168-71 (1984) and Haddy, Am. Jour. Ped. Hematol. Oncol., 4:191-196 (1982) relating to erythropoietin in possible therapies for sickle cell disease, and Eschbach et al., J. Cli ⁇ . Invest.
  • the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes a CHEPO polypeptide.
  • the isolated nucleic acid molecule comprises a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81 % nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91 % nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nu
  • the isolated nucleic acid molecule comprises (a) a nucieotide sequence encoding a CHEPO polypeptide having the sequence of amino acid residues from about 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N0S:2 and 5), or (b) the complement of the nucleotide sequence of (a).
  • the isolated nucleic acid molecule comprises a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81 % nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91 % nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nu
  • the isolated nucleic acid molecule comprises (a) the nucleotide sequence of from about 1 or about 82 to about 579, inclusive, of Figure 2 (SEQ ID N0:3), or (b) the complement of the nucleotide sequence of (a).
  • the invention concerns an isolated nucleic acid molecule which encodes an active CHEPO polypeptide as defined below comprising a nucleotide sequence that hybridizes to the complement of a nucleic acid sequence that encodes ammo acids 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N0S:2 and 5)
  • hybridization occurs under stringent hybridization and wash conditions.
  • the invention concerns an isolated nucleic acid molecule which encodes an active CHEPO polypeptide as defined below comprising a nucleotide sequence that hybridizes to the complement of the nucleic acid sequence between about nucleotides 1 or about 82 and about 579, inclusive, of Figure 2 (SEQ ID N0:3).
  • hybridization occurs under stringent hybridization and wash conditions.
  • the invention concerns an isolated nucleic acid molecule which is produced by hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a CHEPO polypeptide having the sequence of ammo acid residues from about 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N0S:2 and 5), or (b) the complement of the DNA molecule of (a), and, if the test DNA molecule has at least about an 80% nucleic acid sequence identity, alternatively at least about 81 % nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity
  • the invention concerns an isolated nucleic acid molecule comprising (a) a nucleotide sequence encoding a polypeptide scoring at least about 80% positives, alternatively at least about 81% positives, alternatively at least about 82% positives, alternatively at least about 83% positives, alternatively at least about 84% positives, alternatively at least about 85% positives, alternatively at least about 86% positives, alternatively at least about 87% positives, alternatively at least about 88% positives, alternatively at least about 89% positives, alternatively at least about
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a CHEPO polypeptide without the N-terminal signal sequence and/or the initiating methionine, or is complementary to such encoding nucleic acid molecule.
  • the signal peptide has been tentatively identified as extending from about amino acid position 1 to about amino acid position 27 in the sequence of Figure 3 (SEQ ID N0S:2 and 5).
  • the C-terminal boundary of the signal peptide may vary, but most likely by no more than about 5 amino acids on either side of the signal peptide C-terminal boundary as initially identified herein, wherein the C-terminal boundary of the signal peptide may be identified pursuant to criteria routinely employed in the art for identifying that type of amino acid sequence element (e.g.,
  • the signal peptide of the CHEPO polypeptide shown in Figure 3 extends from amino acids 1 to X of Figure 3 (SEQ ID N0S:2 and 5), wherein X is any amino acid from 23 to 32 of Figure 3 (SEQ ID N0S:2 and 5). Therefore, mature forms of the CHEPO polypeptide which are encompassed by the present invention include those comprising amino acids X to 193 of Figure 3 (SEQ I0 N0S:2 and 5), wherein X is any amino acid from 23 to 32 of Figure 3 (SEQ ID N0S:2 and 5) and variants thereof as described below.
  • Isolated nucleic acid molecules encoding these polypeptides are also contemplated.
  • Another embodiment is directed to fragments of a CHEPO polypeptide coding sequence that may find use as, for example, hybridization probes or for encoding fragments of a CHEPO polypeptide that may optionally encode a polypeptide comprising a binding site for an anti-CHEPO antibody.
  • nucleic acid fragments are usually at least about 20 nucleotides in length, alternatively at least about 30 nucleotides in length, alternatively at least about 40 nucleotides in length, alternatively at least about 50 nucleotides in length, alternatively at least about 60 nucleotides in length, alternatively at least about 70 nucleotides in length, alternatively at least about 80 nucleotides in length, alternatively at least about 90 nucleotides in length, alternatively at least about 100 nucleotides in length, alternatively at least about 110 nucleotides in length, alternatively at least about 120 nucleotides in length, alternatively at least about 130 nucleotides in length, alternatively at least about 140 nucleotides in length, alternatively at least about 150 nucleotides in length, alternatively at least about 160 nucleotides in length, alternatively at least about 170 nucleotides in length, alternatively at least about 180 nucleotides in length, alternatively at least about 190 nucle
  • the nucleotide sequence fragment is derived from any coding region of the nucleotide sequence shown in Figure 1 (SEQ ID N0:1). It is noted that novel fragments of a CHEPO polypeptide-encoding nucleotide sequence may be determined in a routine manner by aligning the CHEPO polypeptide-encodi ⁇ g nucleotide sequence with other known nucleotide sequences using any of a number of well known sequence alignment programs and determining which CHEPO polypeptide-encoding nucleotide sequence fragment(s) are novel. All of such CHEPO polypeptide-encoding nucleotide sequences are contemplated herein and can be determined without undue experimentation. Also contemplated are the CHEPO polypeptide fragments encoded by these nucleotide molecule fragments, preferably those CHEPO polypeptide fragments that comprise a binding site for an a ⁇ ti-CHEPO antibody.
  • the invention provides a vector comprising a nucleotide sequence encoding CHEPO or its variants.
  • the vector may comprise any of the isolated nucleic acid molecules hereinabove identified.
  • a host cell comprising such a vector is also provided.
  • the host cells may be CHO cells, £ coli, or yeast.
  • a process for producing CHEPO polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of CHEPO and recovering CHEPO from the cell culture.
  • the invention provides isolated CHEPO polypeptide encoded by any of the isolated nucleic acid sequences hereinabove identified.
  • the invention provides isolated native sequence CHEPO polypeptide, which in certain embodiments, includes an amino acid sequence comprising residues from about 1 or about 28 to about 193 of Figure 3 (SEQ ID N0S:2 and 5).
  • the invention concerns an isolated CHEPO polypeptide, comprising an amino acid sequence having at least about 80% amino acid sequence identity, alternatively at least about 81 % amino acid sequence identity, alternatively at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% amino acid sequence identity, alternatively at least about 87% amino acid sequence identity, alternatively at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91 % amino acid sequence identity, alternatively at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity and alternatively at
  • the invention concerns an isolated CHEPO polypeptide comprising an amino acid sequence scoring at least about 80% positives, alternatively at least about 81 % positives, alternatively at least about 82% positives, alternatively at least about 83% positives, alternatively at least about 84% positives, alternatively at least about 85% positives, alternatively at least about 86% positives, alternatively at least about 87% positives, alternatively at least about 88% positives, alternatively at least about 89% positives, alternatively at least about 90% positives, alternatively at least about 91 % positives, alternatively at least about 92% positives, alternatively at least about 93% positives, alternatively at least about 94% positives, alternatively at least about 95% positives, alternatively at least about 96% positives, alternatively at least about 97% positives, alternatively at least about 98% positives and alternatively at least about 99% positives when compared with the amino acid sequence of residues from about 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N)
  • the invention provides an isolated CHEPO polypeptide without the N-terminai signal sequence and/or the initiating methionine and is encoded by a nucleotide sequence that encodes such an amino acid sequence as hereinbefore described.
  • Processes for producing the same are also herein described, wherein those processes comprise culturing a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the CHEPO polypeptide and recovering the CHEPO polypeptide from the ceil culture.
  • the invention concerns an isolated CHEPO polypeptide, comprising the sequence of amino acid residues from about 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N0S:2 and 5), or a fragment thereof which is biologically active or sufficient to provide a binding site for an anti-CHEPO antibody, wherein the identification of CHEPO polypeptide fragments that possess biological activity or provide a binding site for an anti-CHEPO antibody may be accomplished in a routine manner using techniques which are well known in the art.
  • the CHEPO fragment retains a qualitative biological activity of a native CHEPO polypeptide.
  • the invention provides a polypeptide produced by (i) hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a CHEPO polypeptide having the sequence of amino acid residues from about 1 or about 28 to about 193, inclusive, of Figure 3 (SEQ ID N0S:2 and 5), or (b) the complement of the DNA molecule of (a), and if the test DNA molecule has at least about an 80% nucleic acid sequence identity, alternatively at least about 81 % nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least at least about 80%
  • the invention provides chimeric molecules comprising a CHEPO polypeptide fused to a heterologous polypeptide or amino acid sequence, wherein the CHEPO polypeptide may comprise any CHEPO polypeptide, variant or fragment thereof as hereinbefore described.
  • a chimeric molecule comprises a CHEPO polypeptide fused to an epitope tag sequence or a Fc region of an immunoglobulin.
  • the invention provides an antibody as defined below which specifically binds to a CHEPO polypeptide as hereinbefore described.
  • the antibody is a monoclonal antibody, an antibody fragment or a single chain antibody.
  • the invention concerns agonists and antagonists of a native CHEPO polypeptide as defined below.
  • the agonist or antagonist is an anti-CHEPO antibody or a small molecule.
  • the invention concerns a method of identifying agonists or antagonists to a CHEPO polypeptide which comprise contacting the CHEPO polypeptide with a candidate molecule and monitoring a biological activity mediated by said CHEPO polypeptide.
  • the CHEPO polypeptide is a native CHEPO polypeptide.
  • the invention concerns a composition of matter comprising a CHEPO polypeptide, or an agonist or antagonist of a CHEPO polypeptide as herein described, or an anti-CHEPO antibody, in combination with a carrier.
  • the carrier is a pharmaceutically acceptable carrier.
  • Another embodiment of the present invention is directed to the use of a CHEPO polypeptide, or an agonist or antagonist thereof as herein described, or an anti-CHEPO antibody, for the preparation of a medicament useful in the treatment of a condition which is responsive to the CHEPO polypeptide, an agonist or antagonist thereof or an anti-CHEPO antibody.
  • Yet another embodiment of the present invention is directed to CHEPO polypeptides having altered glycosylation patterns in one or more regions of the polypeptide as compared to the native sequence CHEPO polypeptide, preferably in the region surrounding and/or including amino acid position 84 in the CHEPO amino acids sequence shown in Figure 3 (SEQ ID N0S:2 and 5).
  • CHEPO variant polypeptides are prepared using well known techniques so as to create an N- or O-linked glycosylation site at or near amino acid position 84 in the CHEPO polypeptide sequence.
  • CHEPO polypeptides contemplated by the present invention include those where (a) amino acids 81-84 of the CHEPO amino acid sequence shown in Figure 3 (SEQ ID N0S:2 and 5) (i.e., Met-Glu-Val-Arg; SEQ ID N0:6) are replaced by the amino acid sequence Asn-X-Ser-X (SEQ ID N0:7) or Asn-X-Thr-X (SEQ ID N0:8), where X is any amino acid except for Pro; (b) amino acids 82-85 of the CHEPO amino acid sequence shown in Figure 3 (SEQ ID N0S:2 and 5) (i.e., Glu-Val-Arg- Gin; SEQ ID N0:9) are replaced by the amino acid sequence Asn-X-Ser-X (SEQ ID N0:7) or Asn-X-Thr-X (SEQ ID N0:8), where X is any amino acid except for Pro; (c) amino acids 83-86 of the CHEPO amino acid sequence shown in Figure 3 (
  • Figures 1 A C show a nucleotide sequence (SEQ ID N0:1) of an isolated genomic DNA molecule containing a nucleotide sequence (nucleotides 134-146, 667-812, 1071-1157, 1760-1939 and 2074-2226, exclusive of others) encoding native sequence CHEPO. Also presented in the ge ⁇ omic sequence are the locations of the start codon, exons and introns as well as the amino acid sequence (SEQ ID N0:2) encoded by the coding sequence of SEQ ID N0:1.
  • Figure 2 shows the cDNA sequence of the CHEPO molecule (SEQ ID N0:3) and the amino acid sequence encoded thereby (SEQ ID N0:2).
  • Figure 3 shows a comparison of the human erythropoietin amino acid sequence (human) (SEQ ID N0:4) and that of the chimp erythropoietin (chepo) described herein, wherein the amino acid designated X at amino acid position 142 of the CHEPO sequence is either glutamine (SEQ ID N0:2) or lysine (SEQ ID N0:5).
  • CHEPO polypeptide when used herein encompass native sequence CHEPO and CHEPO polypeptide variants (which are further defined herein).
  • the CHEPO polypeptide may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant and/or synthetic methods.
  • a "native sequence CHEPO” comprises a polypeptide having the same amino acid sequence as a CHEPO derived from nature. Such native sequence CHEPO can be isolated from nature or can be produced by recombinant and/or synthetic means.
  • native sequence CHEPO specifically encompasses naturally-occurring truncated or secreted forms (e.g., an extracellular domain sequence), naturally-occurring variant forms (e.g., alternatively spliced forms) and naturally- occurring allelic variants of the CHEPO.
  • the native sequence CHEPO is a mature or full-length native sequence CHEPO comprising amino acids 1 to 193 of Figure 3 (SEQ ID N0S:2 and 5).
  • CHEPO polypeptides disclosed in Figure 3 (SEQ ID N0S:2 and 5) is shown to begin with the methionine residue designated herein as amino acid position 1, it is conceivable and possible that another methionine residue located either upstream or downstream from amino acid position 1 in Figure 3 (SEQ ID N0S:2 and 5) may be employed as the starting amino acid residue for the CHEPO polypeptide.
  • CHEPO variant polypeptide means an active CHEPO polypeptide as defined below having at least about 80% amino acid sequence identity with the amino acid sequence of (a) residues 1 or about 28 to 193 of the CHEPO polypeptide shown in Figure 3 (SEQ ID N0S:2 and 5), (b) X to 193 of the CHEPO polypeptide shown in Figure 3 (SEQ ID N0S:2 and 5), wherein X is any amino acid residue from 23 to 32 of Figure 3 (SEQ ID N0S:2 and 5) or (c) another specifically derived fragment of the amino acid sequence shown in Figure 3 (SEQ ID N0S:2 and 5).
  • Such CHEPO variant polypeptides include, for instance, CHEPO polypeptides wherein one or more amino acid residues are added, or deleted, at the N- and/or C- terminus, as well as within one or more internal domains, of the sequence of Figure 3 (SEQ ID N0S:2 and 5).
  • a CHEPO variant polypeptide will have at least about 80% amino acid sequence identity, alternatively at least about 81 % amino acid sequence identity, alternatively at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% amino acid sequence identity, alternatively at least about 87% amino acid sequence identity, alternatively at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91 % amino acid sequence identity, alternatively at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity and alternatively at least about 99% amino acid sequence identity
  • CHEPO variant polypeptides do not encompass the native CHEPO polypeptide sequence.
  • CHEPO variant polypeptides are at least about 10 amino acids in length, alternatively at least about 20 amino acids in length, alternatively at least about 30 amino acids in length, alternatively at least about 40 amino acids in length, alternatively at least about 50 amino acids in length, alternatively at least about 60 amino acids in length, alternatively at least about 70 amino acids in length, alternatively at least about 80 amino acids in length, alternatively at least about 90 amino acids in length, alternatively at least about 100 amino acids in length, alternatively at least about 150 amino acids in length, alternatively at least about 200 amino acids in length, alternatively at least about 300 amino acids in length, or more.
  • Percent (%) amino acid sequence identity with respect to the CHEPO polypeptide sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a CHEPO sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software.
  • ALIGN-2 sequence comparison computer program
  • Table 1 sequence comparison computer program
  • the ALIGN-2 sequence comparison computer program was authored by Gene ⁇ tech, Inc. and the source code shown in Table 1 has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087.
  • the ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.
  • the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows: 100 times the fraction X/Y
  • % amino acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program.
  • % amino acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)).
  • NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov or otherwise obtained from the National Institute of Health, Bethesda, MD.
  • % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • CHEPO variant polynucleotide or CHEPO variant nucleic acid sequence means a nucleic acid molecule which encodes an active CHEPO polypeptide as defined below and which has at least about 80% nucleic acid sequence identity with either (a) a nucleic acid sequence which encodes residues 1 or about 28 to 193 of the CHEPO polypeptide shown in
  • Figure 3 (SEQ ID N0S:2 and 5), (b) a nucleic acid sequence which encodes residues X to 193 of the CHEPO polypeptide shown in Figure 3 (SEQ ID N0S:2 and 5), wherein X is any amino acid residue from 23 to 32 of Figure 3 (SEQ ID N0S:2 and 5) or (c) a nucleic acid sequence which encodes another specifically derived fragment of the amino acid sequence shown in Figure 3 (SEQ ID N0S:2 and 5).
  • a CHEPO variant polynucleotide will have at least about 80% nucleic acid sequence identity, alternatively at least about 81 % nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91 % nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid
  • nucleotides in length alternatively at least about 90 nucleotides in length, alternatively at least about 120 nucleotides in length, alternatively at least about 150 nucleotides in length, alternatively at least about 180 nucleotides in length, alternatively at least about 210 nucleotides in length, alternatively at least about 240 nucleotides in length, alternatively at least about 270 nucleotides in length, alternatively at least about 300 nucleotides in length, alternatively at least about 450 nucleotides in length, alternatively at least about 600 nucleotides in length, alternatively at least about 900 nucleotides in length, or more.
  • Percent (%) nucleic acid sequence identity with respect to the CHEPO polypeptide-encoding nucleic acid sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in a CHEPO polypeptide-encoding nucleic acid sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software.
  • ALIGN-2 sequence comparison computer program
  • Table 1 complete source code for the ALIGN-2 program is provided in Table 1.
  • the ALIGN-2 sequence comparison computer program was authored by Genentech, Inc. and the source code shown in Table 1 has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087.
  • the ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.
  • % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D is calculated as follows:
  • % nucleic acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program. However, % nucleic acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nim.nih.gov or otherwise obtained from the National Institute of Health, Bethesda, MD.
  • % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D is calculated as follows:
  • CHEPO variant polynucleotides are nucleic acid molecules that encode an active CHEPO polypeptide and which are capable of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding the full-length CHEPO polypeptide shown in Figure 3 (SEQ ID N0S:2 and 5).
  • CHEPO variant polypeptides may be those that are encoded by a CHEPO variant polynucleotide.
  • amino acid residues in the sequences compared that are not only identical, but also those that have similar properties are those that are either identical to the amino acid residue of interest or are a preferred substitution (as defined in Table 6 below) of the amino acid residue of interest.
  • the % value of positives of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • isolated when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Preferably, the isolated polypeptide is free of association with all components with which it is naturally associated. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other protei ⁇ aceous or non-protei ⁇ aceous solutes.
  • the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup seque ⁇ ator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the CHEPO natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • An "isolated" nucleic acid molecule encoding a CHEPO polypeptide is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the CHEPO-e ⁇ coding nucleic acid. Preferably, the isolated nucleic is free of association with all components with which it is naturally associated.
  • An isolated CHEPO-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the CHEPO-encoding nucleic acid molecule as it exists in natural cells.
  • an isolated nucleic acid molecule encoding a CHEPO polypeptide includes CHEPO-encoding nucleic acid molecules contained in cells that ordinarily express CHEPO where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotei ⁇ that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
  • antibody is used in the broadest sense and specifically covers, for example, single anti-CHEPO monoclonal antibodies (including agonist, antagonist, and neutralizing antibodies), anti-CHEPO antibody compositions with polyepitopic specificity, single chain anti-CHEPO antibodies, and fragments of anti-CHEPO antibodies (see below).
  • monoclonal antibody refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homolog ⁇ between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al.. Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).
  • “Stringent conditions” or “high stringency conditions”, as defined herein, may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1 % sodium dodecyl sulfate at 50 C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1 % bovine serum albumin/0.1 % Ficoll/0.1 % po!y in ⁇ lp ⁇ rrolidone/50mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42 C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCI, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1 % sodium pyrophosphate, 5 x Denhardt s solution, sonicated salmon sperm DNA (50 g/ml), 0.1 % SDS
  • Modely stringent conditions may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and %SDS) less stringent that those described above.
  • washing solution and hybridization conditions e.g., temperature, ionic strength and %SDS
  • moderately stringent conditions is overnight incubation at 37 C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCI, 15 mM t ⁇ sodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt s solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50 C.
  • a solution comprising: 20% formamide, 5 x SSC (150 mM NaCI, 15 mM t ⁇ sodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt s solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50 C.
  • 5 x SSC 150 mM NaCI, 15 mM t ⁇ sodium citrate
  • epitope tagged when used herein refers to a chimeric polypeptide comprising a CHEPO polypeptide fused to a "tag polypeptide".
  • the tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the polypeptide to which it is fused.
  • the tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes.
  • Suitable tag polypeptides generally have at least six ammo acid residues and usually between about 8 and 50 ammo acid residues (preferably, between about 10 and 20 ammo acid residues).
  • immunoadhesin designates antibody-like molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains.
  • the immunoadhesins comprise a fusion of an ammo acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is "heterologous"), and an immunoglobulin constant domain sequence.
  • the adhesin part of an immunoadhesin molecule typically is a contiguous ammo acid sequence comprising at least the binding site of a receptor or a ligand.
  • the immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG 1 , lgG-2, lgG-3, or lgG-4 subtypes, IgA (including lgA-1 and lgA-2), IgE, IgD or IgM.
  • immunoglobulin such as IgG 1 , lgG-2, lgG-3, or lgG-4 subtypes, IgA (including lgA-1 and lgA-2), IgE, IgD or IgM.
  • Activity refers to form(s) of CHEPO which retain a biological and/or an immunological activity of native or naturally-occurring CHEPO, wherein biological activity refers to a biological function (either inhibitory or stimulatory) caused by a native or naturally-occurring CHEPO other than the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring CHEPO and an immunological activity refers to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring CHEPO.
  • Preferred biological activities includes, for example, the ability to regulate red blood ceil production, to bind to receptors on the surface of committed progenitor cells of the bone marrow and/or other hematopoietic tissues and/or to induce proliferation and/or terminal maturation of erythroid cells.
  • antagonist is used in the broadest sense, and includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native CHEPO polypeptide disclosed herein.
  • agonist is used in the broadest sense and includes any molecule that mimics a biological activity of a native CHEPO polypeptide disclosed herein.
  • Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments or ammo acid sequence variants of native CHEPO polypeptides, peptides, small organic molecules, etc.
  • Methods for identifying agonists or antagonists of a CHEPO polypeptide may comprise contacting a CHEPO polypeptide with a candidate agonist or antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the CHEPO polypeptide.
  • Treatment refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
  • Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
  • Chronic administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to maintain the initial therapeutic effect (activity) for an extended period of time. Intermittent administration is treatment that is not consecutively done without interruption, but rather is cyclic in nature.
  • “Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc. Preferably, the mammal is human.
  • Administration "in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
  • Carriers as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution.
  • physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxida ⁇ ts including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunogiobulins; hydrophilic polymers such as polyvinyipyrrolido ⁇ e; amino acids such as glycine, glutamine, asparagine, argi ⁇ ine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN , polyethylene glycol (PEG), and PLURONICS .
  • buffers such as phosphate, citrate, and other organic acids
  • antioxida ⁇ ts including ascorbic acid
  • Antibody fragments comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody.
  • antibody fragments include Fab, Fab', F(ab') 2 , and Fv fragments; diabodies; linear antibodies (Zapata et al., Protein Enq. 8(10): 1057-1062 [1995]); single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual "Fc” fragment, a designation reflecting the ability to crystallize readily.
  • Pepsin treatment yields an F(ab') 2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
  • Fv is the minimum antibody fragment which contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the V H -V L dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain.
  • Fab fragments differ from Fab fragments by the addition of a few residues at the carbox ⁇ terminus of the heavy chain CH1 domain including one or more cystei ⁇ es from the antibody hinge region.
  • Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab') antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • the "light chains" of antibodies (immunogiobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino acid sequences of their constant domains.
  • immunogiobulins can be assigned to different classes. There are five major classes of immunogiobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isot ⁇ pes), e.g., lgG1, lgG2, lgG3, lgG4, IgA, and lgA2.
  • Single-chain Fv or “sFv” antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain.
  • the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding.
  • diabodies refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH - VL).
  • VH heavy-chain variable domain
  • VL light-chain variable domain
  • an "isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1 ) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or no ⁇ reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • label when used herein refers to a detectable compound or composition which is conjugated directly or indirectly to the antibody so as to generate a “labeled” antibody.
  • the label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable.
  • solid phase is meant a non-aqueous matrix to which the antibody of the present invention can adhere.
  • solid phases encompassed herein include those formed partially or entirely of glass (e.g., controlled pore glass), polysaccharides (e.g., agarose), polyacryiamides, polystyrene, polyvinyl alcohol and siiicones.
  • the solid phase can comprise the well of an assay plate; in others it is a purification column (e.g., an affinity chromatography column).
  • This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S. Patent No. 4,275,149.
  • a “liposome” is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug (such as a CHEPO polypeptide or antibody thereto) to a mammal.
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.
  • a small molecule is defined herein to have a molecular weight below about 500 Daltons.
  • B is average of ND match with stop is _M; stop-stop - 0; J (joker) match - 0
  • Max file length is 65535 (limited by unsigned short x in the jmp struct)
  • the program may create a tmp file in /tmp to hold info about traceback.
  • prog - av[0]; if(ac!- 3) ⁇ fpri ⁇ tf(stderr, "usage: %s filel file2 ⁇ n", prog); fprintf(stderr,”where filel and file2 are two dna or two protein sequences. ⁇ n”); fpri ⁇ tf(stderr,"The sequences can be in upper- or lower-case ⁇ n”); fpri ⁇ tf(stderr,”Any lines beginning with ';' or ' ⁇ ' are ignored “); fprintf(stderr,"Output is in the file ⁇ "align.out ⁇ " ⁇ n”); exitd); ⁇ namex[0] - av[1]; namex[1] - av[2]; seqx[0] - getseq(namex[0], &lenO); seqx[1] getseq(namex[1], &le ⁇ 1); xbm - (d
  • nw() fill in the matrix, get the possible jmps * / readjmpsO; / * get the actual jmps * / printO; / * print stats, alignment * /
  • ⁇ fprintfffx " ⁇ first sequence: %s (length - %d) ⁇ n", namex[0], lenO); fprintflfx, " ⁇ second sequence: %s (length - %d) ⁇ n", namex[1], lenl); olen - 60; Ix - lenO; ly - lenl; firstgap - lastgap - 0; if (dmax ⁇ lenl - 1) ⁇ / * leading gap in x */ pp[0].spc - firstgap - lenl - dmax - 1; ly-- pp[0].spc;
  • static nm matches in core -- for checking */ static Imax; / * lengths of stripped file names */ static ij[2]; /* jmp index for a path */ static nc[2]; / * number at start of current line */ static ni[2]; / * current elem number -- for gapping static siz[2]; static char * ps[2]; / * ptr to current element * / static char po[2]; / * ptr to next output char slot * static char out[2][P_LINE]; / * output line * / static char startPJJNE]; / * set by starsO * /
  • * ps[i] toupper( * ps[i]); po[i] + +; ps[i]++;
  • * py++ toupper( * px); if(index("ATGCU", * (py-1))) natgc ++; ⁇ ⁇
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred o in the present application as CHEPO.
  • DNA encoding a CHEPO polypeptide has been identified and isolated, as disclosed in further detail in the Examples below.
  • CHEPO variants can be prepared.
  • CHEPO variants can be prepared by introducing appropriate nucleotide changes into the CHEPO DNA, and/or by synthesis of the desired CHEPO polypeptide.
  • amino acid changes may alter post-translational processes of the CHEPO, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.
  • Variations in the native full-length sequence CHEPO or in various domains of the CHEPO described herein can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Patent No. 5,364,934.
  • Variations may be a substitution, deletion or insertion of one or more codons encoding the CHEPO that results in a change in the amino acid sequence of the CHEPO as compared with the native sequence CHEPO.
  • the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of the CHEPO.
  • Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the CHEPO with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements.
  • Insertions or deletions may optionally be in the range of about 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the full-length or mature native sequence.
  • CHEPO polypeptide fragments are provided herein. Such fragments may be truncated at the N-terminus or C- terminus, or may lack internal residues, for example, when compared with a full length native protein. Certain fragments lack amino acid residues that are not essential for a desired biological activity of the CHEPO polypeptide.
  • CHEPO fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized.
  • An alternative approach involves generating CHEPO fragments by enzymatic digestion, e.g., by treating the protein with an enzyme known to cleave proteins at sites defined by particular amino acid residues, or by digesting the DNA with suitable restriction enzymes and isolating the desired fragment.
  • Yet another suitable technique involves isolating and amplifying a DNA fragment encoding a desired polypeptide fragment, by polymerase chain reaction (PCR). Oligonucleotides that define the desired termini of the DNA fragment are employed at the 5' and 3' primers in the PCR.
  • CHEPO polypeptide fragments share at least one biological and/or immunological activity with the native CHEPO polypeptides shown in Figure 3 (SEQ ID N0S:2 and 5).
  • conservative substitutions of interest are shown in Table 6 under the heading of preferred substitutions. If such substitutions result in a change in biological activity, then more substantial changes, denominated exemplary substitutions in Table 6, or as further described below in reference to amino acid classes, are introduced and the products screened.
  • Substantial modifications in function or immunological identity of the CHEPO polypeptide are accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • Naturally occurring residues are divided into groups based on common side-chain properties:
  • hydrophobic norleucine, met, ala, val, leu, ile
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Such substituted residues also may be introduced into the conservative substitution sites or, more preferably, into the remaining
  • the variations can be made using methods known in the art such as oligo ⁇ ucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis [Carter et al., Nucl. Acids Res., 3:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)]
  • cassette mutagenesis [Wells et al., Gene, 34:315 (1985)]
  • restriction selection mutagenesis [Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)] or other known techniques can be performed on the cloned DNA to produce the CHEPO variant DNA.
  • Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence.
  • preferred scanning amino acids are relatively small, neutral amino acids.
  • amino acids include alanine, glycine, serine, and cysteine.
  • Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant
  • Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions [Creighton, The Proteins, (W.H.
  • Covalent modifications of CHEPO are included within the scope of this invention.
  • One type of covalent modification includes reacting targeted amino acid residues of a CHEPO polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the CHEPO.
  • Derivatization with bifunctional agents is useful, for instance, for crosslinking CHEPO to a water-insoluble support matrix or surface for use in the method for purifying anti-CHEPO antibodies, and vice-versa.
  • crosslinking agents include, e.g., 1,1 - bis(diazoacetyl)-2-phen ⁇ lethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disucci ⁇ imidyl esters such as 3,3'-dithiobis(succi ⁇ imidylpropionate), bifunctional maleimides such as bis-N-maleimido-1 ,8-octane and agents such as methyl-3 [(p-azidophenyl)dithio]propioimidate.
  • 1,1 - bis(diazoacetyl)-2-phen ⁇ lethane glutaraldehyde
  • N-hydroxysuccinimide esters for example, esters with 4-azidosalicylic acid
  • homobifunctional imidoesters including disucci ⁇ imidyl esters such as 3,3'-di
  • Another type of covalent modification of the CHEPO polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide.
  • "Altering the native glycosylation pattern" is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence CHEPO (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence CHEPO.
  • the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.
  • Addition of glycosylation sites to the CHEPO polypeptide may be accomplished by altering the amino acid sequence.
  • the alteration may be made, for example, by the addition of, or substitution by, one or more serine or threo ⁇ ine residues to the native sequence CHEPO (for O-linked glycosylation sites).
  • the CHEPO amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the CHEPO polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.
  • Another means of increasing the number of carbohydrate moieties on the CHEPO polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330 published 11 September 1987, and in Aplin and Wriston, CRC Crit. Rev. Biochem.. pp. 259-306 ( 1981 ).
  • Removal of carbohydrate moieties present on the CHEPO polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation.
  • Chemical deglycosyiation techniques are known in the art and described, for instance, by Hakimuddi ⁇ , et al., Arch. Biochem. Biophvs., 259:52 (1987) and by Edge et al., Anal. Biochem., 118:131 (1981).
  • Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al., Meth. Enzvmol., 138:350 (1987).
  • Another type of covalent modification of CHEPO comprises linking the CHEPO polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.
  • the CHEPO of the present invention may also be modified in a way to form a chimeric molecule comprising
  • such a chimeric molecule comprises a fusion of the CHEPO with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind.
  • the epitope tag is generally placed at the amino- or carboxyl- terminus of the CHEPO.
  • the presence of such epitope-tagged forms of the CHEPO can be detected using an antibody against the tag polypeptide.
  • provision of the epitope tag enables the CHEPO to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
  • tag polypeptides and their respective antibodies are well known in the art.
  • poly-histidine poly-his
  • poly-his-giycine poly-his-gly
  • flu HA tag polypeptide and its antibody 12CA5 [Field et al dislike Mol. Cell. Biol., 8:2159- 2165 (1988)]
  • the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto [Evan et al., Molecular and Cellular Biology, 5:3610-3616 (1985)]
  • gD Herpes Simplex virus glycoprotein D
  • tag polypeptides include the Flag-peptide [Hopp et al., BioTech ⁇ olo ⁇ v. 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin et al., Science, 255:192-194 (1992)]; an -tubulin epitope peptide [Skinner et al., J. Biol. Chem.. 266:15163-15166 (1991)]; and the T7 gene 10 protein peptide tag [Lutz- Freyermuth et al., Proc. Natl. Acad. Sci. USA. 87:6393-6397 (1990)].
  • the chimeric molecule may comprise a fusion of the CHEPO with an immunoglobulin or a particular region of an immunoglobulin.
  • an immunoglobulin also referred to as an immunoadhesin
  • a fusion could be to the Fc region of an IgG molecule.
  • the Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a CHEPO polypeptide in place of at least one variable region within an Ig molecule.
  • the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3 regions of an IgG 1 molecule.
  • CHEPO sequence or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al., Solid-Phase Peptide Synthesis. W.H. Freeman Co., San Francisco, CA (1969); Merrifield, J. Am. Chem. Soc, 85:2149-2154 (1963)]. In vitro protein synthesis may be performed using manual techniques or by automation.
  • Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City, CA) using manufacturer's instructions.
  • Various portions of the CHEPO may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length CHEPO.
  • DNA encoding CHEPO may be obtained from a cDNA library prepared from tissue believed to possess the CHEPO mRNA and to express it at a detectable level. Accordingly, human CHEPO DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as described in the Examples.
  • the CHEPO-encoding gene may also be obtained from a ge ⁇ omic library or by known synthetic procedures (e.g., automated nucleic acid synthesis).
  • Probes such as antibodies to the CHEPO or oligonucleotides of at least about 20-
  • Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., Molecular
  • the oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized.
  • the oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 32 P-labeled ATP, biotin ⁇ lation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra.
  • Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined using methods known in the art and as described herein.
  • Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
  • Host cells are transfected or transformed with expression or cloning vectors described herein for CHEPO production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the culture conditions such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of ceil cultures can be found in Mammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991 ) and Sambrook et al., supra.
  • Methods of eukaryotic cell transf ection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCI 2 , CaP0 4 , liposome-mediated and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes.
  • Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published 29 June 1989.
  • DNA into cells such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact ceils, or polycations, e.g., polybrene, polyornithine, may also be used.
  • polycations e.g., polybrene, polyornithine.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells.
  • Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as £ coli.
  • Various £ coli strains are publicly available, such as £ coli K12 strain MM294 (ATCC 31,446); £ «?// X1776 (ATCC 31,537); £ coli strain W3110 (ATCC 27,325) and K5 772 (ATCC 53,635).
  • suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g., £ coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41 P disclosed in DD 266,710 published 12 April 1989), Pseudomonas such as P. aeruginosa, and Streptomyces. These examples are illustrative rather than limiting.
  • Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations.
  • the host cell secretes minimal amounts of proteoiytic enzymes.
  • strain W3110 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including £ c ⁇ // W3110 strain 1 A2, which has the complete genotype to ⁇ A ; £ co//W3110 strain 9E4, which has the complete genotype tonA ptr3; £ coli W3110 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3phoA El 5 (argF-lac)1B9 degP ompTkari; £ c ⁇ //W3110 strain 37D6, which has the complete genotype tonA ptr3 phoA El 5 (argFlac)1B9 degP ompT rbs7 ilvG kari; £
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for CHEPO-encoding vectors.
  • Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.
  • Others include Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 [1981]; EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Patent No.4,943,529; Fleer eta/., Bio/Technology, 9: 968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 737 [1983]), K. fragilis (ATCC
  • Penicillium, Tolypocladium (W0 91 /00357 published 10 January 1991 ), and Aspergillus hosts such as A. nidulans (Ballance et a/., Biochem. Biophvs. Res. Commun., 112: 284-289 [1983]; Tilburn et a/., Gene, 26: 205-221 [1983]; Yelton et a/., Proc. Natl. Acad. Sci. USA. 81 1470-1474 [1984]) and A. niger (Kelly and Hynes, EMBO J.. 4: 475-479 [1985]).
  • Meth ⁇ lotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula.
  • yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula.
  • yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula.
  • a list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).
  • Suitable host cells for the expression of glycosylated CHEPO are derived from multicellular organisms.
  • invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf 9, as well as plant cells.
  • useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol., 36:59 (1977)); Chinese hamster ovary cells/ DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA.
  • mice sertoli ceils TM4, Mather, Biol. Reprod., 23:243-251 (1980)
  • human lung cells W138, ATCC CCL 75
  • human liver cells Hep G2, HB 8065
  • mouse mammary tumor MMT 060562, ATCC CCL51 .
  • the selection of the appropriate host cell is deemed to be within the skill in the art.
  • the nucleic acid (e.g., cDNA or genomic DNA) encoding CHEPO may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression.
  • a replicable vector for cloning (amplification of the DNA) or for expression.
  • the vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage.
  • the appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art.
  • Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan.
  • the CHEPO may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N- terminus of the mature protein or polypeptide.
  • a heterologous polypeptide which may be a signal sequence or other polypeptide having a specific cleavage site at the N- terminus of the mature protein or polypeptide.
  • the signal sequence may be a component of the vector, or it may be a part of the CHEPO-encoding DNA that is inserted into the vector.
  • the signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin
  • yeast secretion the signal sequence may be, e.g., the yeast i ⁇ vertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces -factor leaders, the latter described in U.S. Patent No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179 published 4 April 1990), or the signal described in WO 90/13646 published 15 November 1990.
  • mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host ceils. Such sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampiciliin, ⁇ eomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • antibiotics or other toxins e.g., ampiciliin, ⁇ eomycin, methotrexate, or tetracycline
  • suitable selectable markers for mammalian ceils are those that enable the identification of cells competent to take up the CHEPO-encoding nucleic acid, such as DHFR or thymidine kinase.
  • DHFR DHFR activity
  • yeast plasmid YRp7 yeast plasmid YRp7
  • the trp ⁇ gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
  • Expression and cloning vectors usually contain a promoter operably linked to the CHEPO-encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the -lactamase and lactose promoter systems [Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281 :544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding
  • Suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzema ⁇ et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv. Enzyme Reg.,
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isoc ⁇ tochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionei ⁇ , glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
  • CHEPO transcription from vectors in mammalian host ceils is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211 ,504 published 5 July 1989), adenovirus (such as
  • Adenovirus 2 bovine papilloma virus, avian sarcoma virus, c ⁇ tomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the acti ⁇ promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription.
  • Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, -fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus.
  • Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the CHEPO coding sequence, but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding CHEPO.
  • Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein.
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • Gene expression may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product.
  • Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence CHEPO polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to CHEPO DNA and encoding a specific antibody epitope.
  • CHEPO may be recovered from culture medium or from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Trito ⁇ -X 100) or by enzymatic cleavage. Cells employed in expression of CHEPO can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or ceil lysing agents. It may be desired to purify CHEPO from recombinant cell proteins or polypeptides.
  • a suitable detergent solution e.g. Trito ⁇ -X 100
  • Cells employed in expression of CHEPO can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or ceil lysing agents. It may be desired to purify CHEPO from recombinant cell proteins or polypeptides.
  • the following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanoi precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of the CHEPO.
  • CHEPO nucleotide sequences (or their complement) encoding CHEPO have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA.
  • CHEPO nucleic acid will also be useful for the preparation of CHEPO polypeptides by the recombinant techniques described herein.
  • the full-length native sequence CHEPO cDNA (SEQ ID N0:3), or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length CHEPO cDNA or to isolate still other cDNAs (for instance, those encoding naturally-occurring variants of CHEPO or CHEPO from other species) which have a desired sequence identity to the CHEPO sequence disclosed in Figure 2 (SEQ ID N0:3).
  • the length of the probes will be about 20 to about 50 bases.
  • the hybridization probes may be derived from at least partially novel regions of the nucleotide sequence of SEQ ID N0:3 wherein those regions may be determined without undue experimentation or from genomic sequences including promoters, enhancer elements and introns of native sequence CHEPO.
  • a screening method will comprise isolating the coding region of the CHEPO gene using the known DNA sequence to synthesize a selected probe of about 40 bases.
  • Hybridization probes may be labeled by a variety of labels, including radionucleotides such as 32 P or 35 S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidi ⁇ /biotin coupling systems.
  • Labeled probes having a sequence complementary to that of the CHEPO gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine which members of such libraries the probe hybridizes to. Hybridization techniques are described in further detail in the Examples below.
  • CHEPO nucleic acids include antisense or sense oligonucleotides comprising a singe-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target CHEPO mRNA (sense) or CHEPO
  • Antisense or sense oligonucleotides comprise a fragment of the coding region of CHEPO DNA. Such a fragment generally comprises at least about 14 nucleotides, preferably from about 14 to 30 nucleotides.
  • the ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, for example, Stein and Cohen (Cancer Res. 48:2659, 1988) and van der Krol et al. (Bio Techniques 6:958, 1988).
  • binding of antisense or sense oligonucleotides to target nucleic acid sequences results in the formation of duplexes that block transcription or translation of the target sequence by one of several means, including enhanced degradation of the duplexes, premature termination of transcription or translation, or by other means.
  • the antisense oligonucleotides thus may be used to block expression of CHEPO proteins.
  • Antisense or sense oligonucleotides further comprise oligonucleotides having modified sugar-phosphodiester backbones (or other sugar linkages, such as those described in WO 91/06629) and wherein such sugar linkages are resistant to endogenous nucleases.
  • Such oligonucleotides with resistant sugar linkages are stable in vivo (i.e., capable of resisting enzymatic degradation) but retain sequence specificity to be able to bind to target nucleotide sequences.
  • sense or antisense oligonucleotides include those oligonucleotides which are covalently linked to organic moieties, such as those described in WO 90/10048, and other moieties that increases affinity of the oligonucleotide for a target nucleic acid sequence, such as poiy-(L-lysine).
  • intercalating agents such as ellipticine, and alkylating agents or metal complexes may be attached to sense or antisense oligonucleotides to modify binding specificities of the antisense or sense oligonucleotide for the target nucleotide sequence.
  • Antisense or sense oligonucleotides may be introduced into a ceil containing the target nucleic acid sequence by any gene transfer method, including, for example, CaP0 4 -mediated DNA transf ection, electroporation, or by using gene transfer vectors such as Epstein-Barr virus.
  • an antisense or sense oligonucleotide is inserted into a suitable retroviral vector.
  • a cell containing the target nucleic acid sequence is contacted with the recombinant retroviral vector, either in vivo or ex vivo.
  • Suitable retroviral vectors include, but are not limited to, those derived from the murine retrovirus M-MuLV, N2 (a retrovirus derived from M-MuLV), or the double copy vectors designated DCT5A, DCT5B and DCT5C (see WO 90/13641 ).
  • Sense or antisense oligonucleotides also may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO 91/04753.
  • Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to ceil surface receptors.
  • conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell.
  • a sense or an antisense oligonucleotide may be introduced into a cell containing the target nucleic acid sequence by formation of an oligo ⁇ ucleotide-lipid complex, as described in WO 90/10448.
  • the sense or antisense oligonucieotide-lipid complex is preferably dissociated within the cell by an endogenous lipase.
  • the probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related CHEPO coding sequences.
  • Nucleotide sequences encoding a CHEPO can also be used to construct hybridization probes for mapping the gene which encodes that CHEPO and for the genetic analysis of individuals with genetic disorders.
  • the nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries.
  • the coding sequences for CHEPO encode a protein which binds to another protein (example, where the CHEPQ is a receptor)
  • the CHEPO can be used in assays to identify the other proteins or molecules involved in the binding interaction. By such methods, inhibitors of the receptor/iigand binding interaction can be identified.
  • Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.
  • the receptor CHEPO can be used to isolate correlative ligand(s).
  • Screening assays can be designed to find lead compounds that mimic the biological activity of a native CHEPO or a receptor for CHEPO. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates. Small molecules contemplated include synthetic organic or inorganic compounds.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art.
  • Nucleic acids which encode CHEPO or its modified forms can also be used to generate either transgenic animals or "knock out" animals which, in turn, are useful in the development and screening of therapeutically useful reagents.
  • a transgenic animal e.g., a mouse or rat
  • a transgenic animal is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage.
  • a transgene is a DNA which is integrated into the genome of a cell from which a transgenic animal develops.
  • cDNA encoding CHEPO can be used to clone genomic DNA encoding CHEPO in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding CHEPO.
  • Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009.
  • particular cells would be targeted for CHEPO transgene incorporation with tissue-specific enhancers.
  • Transgenic animals that include a copy of a transgene encoding CHEPO introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding CHEPO.
  • Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression.
  • an animal is treated with the reagent and a reduced incidence of the pathological condition, compared to untreated animals bearing the transgene, would indicate a potential therapeutic intervention for the pathological condition.
  • non-human homologues of CHEPO can be used to construct a CHEPO "knock out" animal which has a defective or altered gene encoding CHEPO as a result of homologous recombination between the endogenous gene encoding CHEPO and altered genomic DNA encoding CHEPO introduced into an embryonic stem ceil of the animal.
  • cDNA encoding CHEPO can be used to clone genomic DNA encoding CHEPO in accordance with established techniques.
  • a portion of the genomic DNA encoding CHEPO can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration.
  • flanking DNA typically, several kilobases of unaltered flanking DNA (both at the 5' and 3' ends) are included in the vector [see e.g., Thomas and Capecchi, Cell, 5 .:503 (1987) for a description of homologous recombination vectors].
  • the vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologousl ⁇ recombined with the endogenous DNA are selected [see e.g., Li et al., CeJL 69:915 (1992)].
  • the selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152].
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a "knock out" animal.
  • Progeny harboring the homologousl ⁇ recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA.
  • Knockout animals can be characterized for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the CHEPO polypeptide.
  • Nucleic acid encoding the CHEPO polypeptides may also be used in gene therapy.
  • genes are introduced into cells in order to achieve in vivo synthesis of a therapeutically effective genetic product, for example for replacement of a defective gene.
  • Gene therapy includes both conventional gene therapy where a lasting effect is achieved by a single treatment, and the administration of gene therapeutic agents, which involves the one time or repeated administration of a therapeutically effective DNA or mRNA.
  • Antisense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo. It has already been shown that short antisense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by their restricted uptake by the cell membrane.
  • oligonucleotides can be modified to enhance their uptake, e.g. by substituting their negatively charged phosphodiester groups by uncharged groups.
  • nucleic acids there are a variety of techniques available for introducing nucleic acids into viable cells.
  • the techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or in vivo in the cells of the intended host.
  • Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc.
  • the currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protei ⁇ - liposome mediated transfection (Dzau et al., Trends in Biotechnology H, 205-210 [1993]).
  • the nucleic acid source with an agent that targets the target cells, such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cell, etc.
  • an agent that targets the target cells such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cell, etc.
  • proteins which bind to a ceil surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g. capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half-life.
  • the technique of receptor-mediated endocytosis is described, for example, by Wu et al., 1 Biol. Chem.
  • CHEPO polypeptides described herein may also be employed as molecular weight markers for protein electrophoresis purposes.
  • the nucleic acid molecules encoding the CHEPO polypeptides or fragments thereof described herein are useful for chromosome identification.
  • Each CHEPO nucleic acid molecule of the present invention can be used as a chromosome marker.
  • the CHEPO polypeptides and nucleic acid molecules of the present invention may also be used for tissue typing, wherein the CHEPO polypeptides of the present invention may be differentially expressed in one tissue as compared to another.
  • CHEPO nucleic acid molecules will find use for generating probes for PCR, Northern analysis. Southern analysis and Western analysis.
  • the CHEPO polypeptides described herein may also be employed as therapeutic agents.
  • the CHEPO polypeptides of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby the CHEPO product hereof is combined in admixture with a pharmaceutically acceptable carrier vehicle.
  • Therapeutic formulations are prepared for storage by mixing the active ingredient having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the form of lyophilized formulations or aqueous solutions.
  • Acceptable carriers, excipients or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin or immunogiobulins; h ⁇ drophilic polymers such as polyvinyipyrrolidone, amino acids such as glycine, glutami ⁇ e, asparagine, arginine or lysine; monosaccharides, disaccharides and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as man ⁇ itol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM, PLURONICSTM or PEG.
  • buffers such as phosphate, citrate and other organic acids
  • antioxidants including ascorbic acid
  • compositions to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution.
  • Therapeutic compositions herein generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
  • the route of administration is in accord with known methods, e.g. injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial or intralesional routes, topical administration, or by sustained release systems.
  • Dosages and desired drug concentrations of pharmaceutical compositions of the present invention may vary depending on the particular use envisioned.
  • the determination of the appropriate dosage or route of administration is well within the skill of an ordinary physician. Animal experiments provide reliable guidance for the determination of effective doses for human therapy.
  • Interspecies scaling of effective doses can be performed following the principles laid down by Mordenti, J. and Chapped, W. "The use of interspecies scaling in toxicokinetics" jn Toxicokinetics and New Drug Development, Yacobi et al, Eds., Pergamon Press, New York 1989, pp. 42-96.
  • CHEPO polypeptide or agonist or antagonist thereof When in vivo administration of a CHEPO polypeptide or agonist or antagonist thereof is employed, normal dosage amounts may vary from about 10 ng/kg to up to 100 mg/kg of mammal body weight or more per day, preferably about 1 g/kg/day to 10 mg/kg/day, depending upon the route of administration.
  • Guidance as to particular dosages and methods of delivery is provided in the literature; see, for example, U.S. Pat. Nos. 4,657,760; 5,206,344; or 5,225,212. It is anticipated that different formulations will be effective for different treatment compounds and different disorders, that administration targeting one organ or tissue, for example, may necessitate delivery in a manner different from that to another organ or tissue.
  • microencapsulation of the CHEPO polypeptide is contemplated.
  • Microencapsulation of recombinant proteins for sustained release has been successfully performed with human growth hormone (rhGH), interferon- (rhlFN- ), interleukin-2, and MN rgp120. Johnson et al, Nat. Med.. 2: 795-799 (1996); Yasuda. Biomed. Ther.. Th 1221-1223 (1993); Hora et a/.,
  • the sustained-release formulations of these proteins were developed using poly-lactic-coglycoiic acid (PLGA) polymer due to its biocompatibility and wide range of biodegradable properties.
  • PLGA poly-lactic-coglycoiic acid
  • the degradation products of PLGA, lactic and glycolic acids, can be cleared quickly within the human body.
  • the degradability of this polymer can be adjusted from months to years depending on its molecular weight and composition.
  • Lewis “Controlled release of bioactive agents from lactide/glycolide polymer," in: M. Chasin and R. Langer (Eds.), Biodegradable Polymers as Drug Delivery
  • This invention encompasses methods of screening compounds to identify those that mimic the CHEPO polypeptide (agonists) or prevent the effect of the CHEPO polypeptide (antagonists).
  • Screening assays for antagonist drug candidates are designed to identify compounds that bind or complex with the CHEPO polypeptides encoded by the genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins.
  • Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassa ⁇ s, and cell-based assays, which are well characterized in the art. All assays for antagonists are common in that they call for contacting the drug candidate with a CHEPO polypeptide encoded by a nucleic acid identified herein under conditions and for a time sufficient to allow these two components to interact.
  • the interaction is binding and the complex formed can be isolated or detected in the reaction mixture.
  • the CHEPO polypeptide encoded by the gene identified herein or the drug candidate is immobilized on a solid phase, e.g., on a microtiter plate, by covalent or non-covending attachments.
  • Non-covalent attachment generally is accomplished by coating the solid surface with a solution of the CHEPO polypeptide and drying.
  • an immobilized antibody e.g., a monoclonal antibody, specific for the CHEPO polypeptide to be immobilized can be used to anchor it to a solid surface.
  • the assay is performed by adding the non-immobilized component, which may be labeled by a detectable label, to the immobilized component, e.g., the coated surface containing the anchored component.
  • the non-reacted components are removed, e.g., by washing, and complexes anchored on the solid surface are detected.
  • the detection of label immobilized on the surface indicates that complexing occurred.
  • complexing can be detected, for example, by using a labeled antibody specifically binding the immobilized complex.
  • the candidate compound interacts with but does not bind to a particular CHEPO polypeptide encoded by a gene identified herein, its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions.
  • assays include traditional approaches, such as, e.g., cross-linking, co-immunoprecipitation, and co- purification through gradients or chromatographic columns.
  • protein-protein interactions can be monitored by using a yeast-based genetic system described by Fields and co-workers (Fields and Song, Nature (London). 340: 245-246 (1989); Chie ⁇ eta/., Proc. Natl. Acad. Sci. USA.
  • yeast GAL4 consist of two physically discrete modular domains, one acting as the DNA-binding domain, the other one functioning as the transcription-activation domain.
  • the yeast expression system described in the foregoing publications (generally referred to as the "two-hybrid system") takes advantage of this property, and employs two hybrid proteins, one in which the target protein is fused to the DNA-binding domain of GAL4, and another, in which candidate activating proteins are fused to the activation domain.
  • GAL acZ reporter gene under control of a GAL4-activated promoter depends on reconstitutio ⁇ of GAL4 activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with a chromogenic substrate for -galactosidase.
  • a complete kit (MATCHMAKERTM) for identifying protein-protein interactions between two specific proteins using the two-hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions.
  • a reaction mixture is prepared containing the product of the gene and the intra- or extracellular component under conditions and for a time allowing for the interaction and binding of the two products.
  • a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound.
  • a placebo may be added to a third reaction mixture, to serve as positive control.
  • the binding (complex formation) between the test compound and the intra- or extracellular component present in the mixture is monitored as described hereinabove. The formation of a complex in the control reaction(s) but not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.
  • the CHEPO polypeptide may be added to a cell along with the compound to be screened for a particular activity and the ability of the compound to inhibit the activity of interest in the presence of the CHEPO polypeptide indicates that the compound is an antagonist to the CHEPO polypeptide.
  • antagonists may be detected by combining the CHEPO polypeptide and a potential antagonist with membrane-bound CHEPO polypeptide receptors or recombinant receptors under appropriate conditions for a competitive inhibition assay.
  • the CHEPO polypeptide can be labeled, such as by radioactivity, such that the number of CHEPO polypeptide molecules bound to the receptor can be used to determine the effectiveness of the potential antagonist.
  • the gene encoding the receptor can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. Coligan eta/., Current Protocols in Immun., 1(2): Chapter 5 (1991).
  • expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the CHEPO polypeptide and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the CHEPO polypeptide. Transfected cells that are grown on glass slides are exposed to labeled CHEPO polypeptide.
  • the CHEPO polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an interactive sub-pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.
  • labeled CHEPO polypeptide can be photoaffinity-iinked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro-sequencing. The amino acid sequence obtained from micro- sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.
  • mammalian cells or a membrane preparation expressing the receptor would be incubated with labeled CHEPO polypeptide in the presence of the candidate compound. The ability of the compound to enhance or block this interaction could then be measured.
  • potential antagonists include an oligonucleotide that binds to the fusions of immunoglobulin with CHEPO polypeptide, and, in particular, antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodies, anti-idiotypic antibodies, and chimeric or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments.
  • a potential antagonist may be a closely related protein, for example, a mutated form of the CHEPO polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the CHEPO polypeptide.
  • Another potential CHEPO polypeptide antagonist is an antisense RNA or DNA construct prepared using antisense technology, where, e.g., an antisense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation.
  • Antisense technology can be used to control gene expression through triple-helix formation or antisense DNA or RNA, both of which methods are based on binding of a polynucleotide to DNA or RNA.
  • the 5' coding portion of the polynucleotide sequence, which encodes the mature CHEPO polypeptides herein, is used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length.
  • a DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription (triple helix - see Lee et al., Nucl. Acids Res., 6: 3073 (1979); Coo ⁇ ey et al.. Science, 241: 456 (1988); Dervan et al., Science, 251: 1360 (1991 )), thereby preventing transcription and the production of the CHEPO polypeptide.
  • the antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into the CHEPO polypeptide (antisense - Okano, Neurochem., 56: 560 (1991); Oliqodeoxynucleotides as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton, FL, 1988).
  • the oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the CHEPO polypeptide.
  • antisense DNA is used.
  • oligodeox ⁇ ribonucleotides derived from the translation-initiation site e.g., between about -10 and + 10 positions of the target gene nucleotide sequence, are preferred.
  • Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the CHEPO polypeptide, thereby blocking the normal biological activity of the CHEPO polypeptide.
  • small molecules include, but are not limited to, small peptides or peptide-iike molecules, preferably soluble peptides, and synthetic no ⁇ -peptidyl organic or inorganic compounds.
  • Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see, e.g., Rossi, Current Biology, 4: 469-471 (1994), and PCT publication No. WO 97/33551 (published September 18, 1997).
  • Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single-stranded and composed of deoxynucleotides.
  • the base composition of these oligonucleotides is designed such that it promotes triple- helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex.
  • These small molecules can be identified by any one or more of the screening assays discussed hereinabove and/or by any other screening techniques well known for those skilled in the art.
  • the present invention further provides anti-CHEPO antibodies.
  • Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies.
  • the anti-CHEPO antibodies may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperito ⁇ eal injections.
  • the immunizing agent may include the CHEPO polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized.
  • immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine th ⁇ roglobulin, and soybean trypsin inhibitor.
  • adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicory ⁇ omycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.
  • the anti-CHEPO antibodies may, alternatively, be monoclonal antibodies.
  • Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975).
  • a hybridoma method a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vitro.
  • the immunizing agent will typically include the CHEPO polypeptide or a fusion protein thereof.
  • PBLs peripheral blood lymphocytes
  • spleen ceils or lymph node cells are used if non-human mammalian sources are desired.
  • the lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103].
  • Immortalized ceil lines are usually transformed mammalian ceils, particularly myeloma cells of rodent, bovine and human origin.
  • the hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unf used, immortalized cells.
  • a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unf used, immortalized cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances prevent the growth of HGPRT-deficient cells.
  • Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63].
  • the culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against CHEPO.
  • the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immu ⁇ oprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme- linked immunoabsorbent assay (ELISA).
  • RIA radioimmunoassay
  • ELISA enzyme- linked immunoabsorbent assay
  • the binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980).
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods [Goding, supra]. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.
  • the monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • the monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S.
  • DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies).
  • the hybridoma cells of the invention serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host ceils such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma ceils that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • the DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences [U.S. Patent No. 4,816,567; Morrison et al., supra] or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide.
  • a non- immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
  • the antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art.
  • one method involves recombinant expression of immunoglobulin light chain and modified heavy chain.
  • the heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking.
  • the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.
  • In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly. Fab fragments, can be accomplished using routine techniques known in the art.
  • the anti-CHEPO antibodies of the invention may further comprise humanized antibodies or human antibodies.
  • Humanized forms of non-human (e.g., murine) antibodies are chimeric immunogiobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab') 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • Humanized antibodies include human immunogiobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • CDR complementary determining region
  • Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992)].
  • Fc immunoglobulin constant region
  • a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import” variable domain. Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., Nature, 321:522- 525 (1986); Riechmann et al., Nature. 332:323-327 (1988); Verhoeyen et al., Science. 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • humanized antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.
  • humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, J. Mol. Biol.. 227:381 (1991); Marks et al., J. Mol. Biol.. 222:581 (1991)].
  • the techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol., 147(11:86-95 (1991)].
  • human antibodies can be made by introducing of human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire.
  • transgenic animals e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated.
  • human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire.
  • This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in the following scientific publications: Marks et al., Bio/Tech ⁇ oloov 10. 779-783 (1992); Lonberg et a/..
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens.
  • one of the binding specificities is for the CHEPO, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit.
  • bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heav ⁇ -chai ⁇ /light-chain pairs, where the two heavy chains have different specificities [Milstein and Cueilo, Nature, 305:537-539 (1983)]. Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991 ).
  • Antibody variable domains with the desired binding specificities can be fused to immunoglobulin constant domain sequences.
  • the fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions.
  • DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co-transfected into a suitable host organism.
  • the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture.
  • the preferred interface comprises at least a part of the CH3 region of an antibody constant domain.
  • one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan).
  • Compensatory cavities of identical or similar size to the large side chainfs) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threo ⁇ ine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
  • Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g. Ffab ) 2 bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared can be prepared using chemical linkage. Bren ⁇ an eta/., Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate Ffab ) 2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecuiar disulfide formation. The Fab fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
  • TAB thionitrobenzoate
  • One of the Fab -TNB derivatives is then reconverted to the Fab -thiol by reduction with mercaptoethylami ⁇ e and is mixed with an equimoiar amount of the other Fab -TNB derivative to form the bispecific antibody.
  • the bispecific antibodies produced can be used as agents for the selective immobilization of enzymes. Fab fragments may be directly recovered from £ coli and chemically coupled to form bispecific antibodies.
  • bispecific antibodies have been produced using leucine zippers.
  • the leucine zipper peptides from the Fos and Jun proteins were linked to the Fab portions of two different antibodies by gene fusion.
  • the antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
  • the fragments comprise a heavy-chain variable domain (V H ) connected to a light-chain variable domain (V L ) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the V H and V L domains of one fragment are forced to pair with the complementary V L and V H domains of another fragment, thereby forming two antigen-binding sites.
  • V H and V L domains of one fragment are forced to pair with the complementary V L and V H domains of another fragment, thereby forming two antigen-binding sites.
  • sFv single-chain Fv
  • Antibodies with more than two valencies are contemplated.
  • trispecific antibodies can be prepared. Tutt et a/.. l Immunol. 147:60 (1991).
  • Exemplary bispecific antibodies may bind to two different epitopes on a given CHEPO polypeptide herein.
  • an anti-CHEPO polypeptide arm may be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (Fc R), such as Fc Rl (CD64), Fc Rll (CD32) and Fc Rill (CD 16) so as to focus cellular defense mechanisms to the cell expressing the particular CHEPO polypeptide.
  • a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (Fc R), such as Fc Rl (CD64), Fc Rll (CD32) and Fc Rill (CD 16) so as to focus cellular defense mechanisms to the cell expressing the particular CHEPO polypeptide.
  • Bispecific antibodies may also be used to localize cytotoxic agents to cells which express a particular CHEPO polypeptide.
  • These antibodies possess a CHEPO-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA.
  • a cytotoxic agent or a radionuclide chelator such as EOTUBE, DPTA, DOTA, or TETA.
  • Another bispecific antibody of interest binds the CHEPO polypeptide and further binds tissue factor (TF).
  • Heteroconjugate antibodies are also within the scope of the present invention.
  • Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Patent No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP 03089].
  • the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents.
  • immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980.
  • cysteine residue(s) may be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region.
  • the homodimeric antibody thus generated may have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et a/., J. Exp Med.. 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992).
  • Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross- linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993).
  • an antibody can be engineered that has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989). 7. Immunoconiugates
  • the invention also pertains to immu ⁇ oconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, no ⁇ binding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites / ⁇ // proteins, dianthi ⁇ proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP S), momordica charantia inhibitor, curci ⁇ , crotin, sapaonaria officinaiis inhibitor, geloni ⁇ , mitogellin, restrictocin, pheno ycin, enomycin, and the tricothecenes.
  • a variety of radionuclides are available for the production of radioconjugated antibodies. Examples include 2,2 Bi, ,3,
  • Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succi ⁇ imidyl-3-(2-pyridyldithiol) propio ⁇ ate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p- diazoniumbe ⁇ zoyD-eth ⁇ ienediamine), diisoc ⁇ anates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene).
  • SPDP N-succ
  • a ricin immu ⁇ otoxin can be prepared as described in Vitetta eta/., Science, 238: 1098 (1987).
  • Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethyle ⁇ e tria inepentaacetic acid (MX- DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
  • the antibody may be conjugated to a "receptor" (such streptavidi ⁇ ) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand” (e.g., avidin) that is conjugated to a cytotoxic agent (e.g., a radionucleotide).
  • a "receptor” such streptavidi ⁇
  • a ligand e.g., avidin
  • cytotoxic agent e.g., a radionucleotide
  • the antibodies disclosed herein may also be formulated as immunoliposomes.
  • Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein eta/., Proc. Natl. Acad. Sci. USA. 82: 3688 (1985); Hwang eta/., Proc. Natl Acad. Sci. USA, 77: 4030 (1980); and U.S. Pat. Nos.4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Patent No. 5,013,556.
  • Particularly useful liposomes can be generated by the reverse-phase evaporation method with a lipid composition comprising phosphatidylcholi ⁇ e, cholesterol, and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter.
  • Fab 1 fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et a/., J. Biol. Chem.. 257: 286-288 (1982) via a disulfide-interchange reaction.
  • a chemotherapeutic agent such as Doxorubicin is optionally contained within the liposome.
  • Antibodies specifically binding a CHEPO polypeptide identified herein, as well as other molecules identified by the screening assays disclosed hereinbefore, can be administered for the treatment of various disorders in the form of pharmaceutical compositions.
  • CHEPO polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred.
  • pofectio ⁇ s or liposomes can also be used to deliver the antibody, or an antibody fragment, into cells.
  • the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred.
  • peptide molecules can be designed that retain the ability to bind the target protein sequence.
  • Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993).
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • the composition may comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent.
  • cytotoxic agent such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent.
  • Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, na ⁇ o-particles, and nanocapsules) or in macroemuisions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, na ⁇ o-particles, and nanocapsules
  • the formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, h ⁇ drogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(v ⁇ nylaicohol)), polylactides (U.S. Pat. No.
  • copolymers of L-glutamic acid and ethyl-L-glutamate non-degradable ethylene-vinyl acetate
  • degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT TM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate)
  • poly-D-(-)-3-hydrox ⁇ butyr ⁇ c acid While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods.
  • encapsulated antibodies When encapsulated antibodies remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37 C, resulting in a loss of biological activity and possible changes in immunogemcity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, iyophiiizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.
  • anti-CHEPO antibodies of the invention have various utilities.
  • anti-CHEPO antibodies may be used in diagnostic assays for CHEPO, e.g., detecting its expression in specific cells, tissues, or serum.
  • diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immu ⁇ oprecipitatio ⁇ assays conducted in either heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, inc. (1987) pp. 147-158].
  • the antibodies used in the diagnostic assays can be labeled with a detectable moiety.
  • the detectable moiety should be capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as 3 H, 14 C, 32 P, 35 S, or 125 l, a fluorescent or chemiluminescent compound, such as fluorescein isothiocya ⁇ ate, rhoda ine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144:945 (1962); David et al., Biochemistry, 13:1014 (1974); Pain et al., J. Immunol. Meth..40:219 (1981 ); and Nygren, J. Histochem. and Cvtochem.. 30:407 (1982).
  • Anti-CHEPO antibodies also are useful for the affinity purification of CHEPO from recombinant cell culture or natural sources, in this process, the antibodies against CHEPO are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art.
  • the immobilized antibody then is contacted with a sample containing the CHEPO to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the CHEPO, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the CHEPO from the antibody.
  • EXAMPLES Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, Manassas, VA. EXAMPLE 1 Isolation of Nucleic Acid Encoding CHEPO Genomic DNA was isolated from two chimpanzee cell lines (ATCC CRL1609 and CRL1857) using a Qiage ⁇ kit (cat#10262) as recommended by the manufacturer's instructions.
  • the chimp Epo gene was then obtained on 3 separate fragments by PCR using 1 g of genomic DNA as template and the following primer pairs: EPO.F: 5'-ACCGCGCCCCCTGGACAG-3' (SEQ ID N0:12) EP0.INT1.R: 5'-CATCCACTTCTCCGGCCAAACTTCA-3' (SEQ ID N0:13)
  • EP0.INT1 F 5'-TTTGGCCGGAGAAGTGGATGC-3' (SEQ ID N0:14)
  • EP0.INT4R 5'-TCACTCACTCACTCA ⁇ CATTCATTCATTCA-3' (SEQ ID N0:15)
  • EP0.INT4F 5'-GTTGAATGAATGATTGAATGAATGAGTGA-3" (SEQ ID NO: 16)
  • EPO.R 5'-GCACTGGAGTGTCCATGGGACAG-3' (SEQ ID N0:17)
  • Each PCR reaction contained 5 I of 10x PCR Buffer (Perkin Elmer), 1 1 dNTP (20mM), 1 g genomic DNA, 1 I of each primer, 1 1 of Taq polymerase (Clontech) and H 2 0 to bring the total volume to 50 I.
  • the reaction was first denatured for 4 min. at 94 C then amplified for 40 cycles of 1 in. at 94 C, 1 min. at 65 C or 66 C then extended for 1 min. at 72 C. A last extension step of 5 min. at 72 C was performed.
  • the reaction was then analyzed on agarose gel. PCR product of 500bp, 1200bp and 750bp were observed for each PCR product, respectively.
  • PCR reactions were then purified using a Wizard kit (Promega cat it A7170) then directly sequenced.
  • DNA sequencing of the PCR products was done using an Applied Bios ⁇ stems 377 DNA Sequencer (PE/Applied Biosystems, Foster City, CA).
  • the chemistry used was DYE Terminator Cycle Sequencing with dRhodamine and BIG DYE terminators (PE/Applied Biosystems, Foster City, CA). Sequence assembly and editing done with Sequencher software (Gene Codes, Ann Arbor, Ml).
  • the 5 coding exons were identified by homoiog ⁇ with the human erythropoietin sequence and assembled into a predicted full length cDNA.
  • the coding region of CHEPO cDNA is 579 nucleotides long ( Figure 1) and encodes a predicted protein of 193 amino acids ( Figure 3).
  • Figure 1 There are 3 putative signal cleavage sites predicted after amino acid residue 22, 24 and 27.
  • the latest one is likely to correspond to the cleavage site for chimp Epo.
  • the h ⁇ drophobic 27 amino acid signal peptide is followed by a 166 amino acid long mature protein containing 3 potential N-glycosylation sites.
  • a single nucleotide polymorphism is present in the predicted sequence obtained from CRL1609 and changes the protein sequence at amino acid position 142 from a Q to a K. Alignment of the chimp Epo protein with the human sequence indicates a single change at amino acid position 84 ( Figure 3).
  • EXAMPLE 2 Use of CHEPO cDNA as a hybridization probe
  • DNA comprising the coding sequence of full-length or mature CHEPO (as shown in Figure 2, SEQ ID N0:3) is employed as a probe to screen for homologous DNAs (such as those encoding naturally-occurring variants of CHEPO) in human tissue cDNA libraries or human tissue genomic libraries.
  • Hybridization and washing of filters containing either library DNAs is performed under the following high stringency conditions.
  • Hybridization of radiolabeled CHEPO-derived probe to the filters is performed in a solution of 50% formamide, 5x SSC, 0.1 % SDS, 0.1 % sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2x Denhardt's solution, and 10% dextran sulfate at 42"C for 20 hours. Washing of the filters is performed in an aqueous solution of 0.1 x SSC and
  • DNAs having a desired sequence identity with the DNA encoding full-length native sequence CHEPO can then be identified using standard techniques known in the art.
  • EXAMPLE 3 Expression of CHEPO in £ coli
  • the DNA sequence encoding CHEPQ (SEQ ID N0:3) is initially amplified using selected PCR primers.
  • the primers should contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector.
  • a variety of expression vectors may be employed.
  • An example of a suitable vector is pBR322 (derived from £ coir, see Bolivar et al., Gene, 2:95 (1977)) which contains genes for ampicillin and tetracycline resistance.
  • the vector is digested with restriction enzyme and dephosphor ⁇ lated.
  • the PCR amplified sequences are then ligated into the vector.
  • the vector will preferably include sequences which encode for an antibiotic resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the CHEPO coding region, lambda transcriptional terminator, and an argU gene.
  • the ligation mixture is then used to transform a selected £ coli strain using the methods described in Sambrook et al., supra. Transf ormants are identified by their ability to grow on LB plates and antibiotic resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.
  • Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics.
  • the overnight culture may subsequently be used to inoculate a larger scale culture.
  • the cells are then grown to a desired optical density, during which the expression promoter is turned on.
  • the cells After culturing the cells for several more hours, the cells can be harvested by centrifugation.
  • the ceil pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized CHEPO protein can then be purified using a metal chelating column under conditions that allow tight binding of the protein.
  • CHEPO may be expressed in £ coli ' m a poly-His tagged form, using the following procedure.
  • CHEPO is initially amplified using selected PCR primers.
  • the primers will contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector, and other useful sequences providing for efficient and reliable translation initiation, rapid purification on a metal chelation column, and proteolytic removal with enterokinase.
  • PCR-amplified, poly-His tagged sequences are then ligated into an expression vector, which is used to transform an £ c ⁇ // host based on strain 52 (W3110 fuhA(tonA) ion galE rpoHts(htpRts) clpP(laclq).
  • Transf ormants are first grown in LB containing 50 mg/mi carbenicilii ⁇ at 30 C with shaking until an 0.D.600 of 3-5 is reached.
  • Cultures are then diluted 50-100 fold into CRAP media (prepared by mixing 3.57 g (NH 4 ) 2 S0 4 , 0.71 g sodium citrate 2H20, 1.07 g KCI, 5.36 g Difco yeast extract, 5.36 g Sheffield hycase SF in 500 mL water, as well as 110 mM MPOS, pH 7.3, 0.55% (w/v) glucose and 7 mM MgS0 4 ) and grown for approximately 20-30 hours at 30 C with shaking. Samples are removed to verify expression by SDS-PAGE analysis, and the bulk culture is centrifuged to pellet the cells. Cell pellets are frozen until purification and refolding.
  • CRAP media prepared by mixing 3.57 g (NH 4 ) 2 S0 4 , 0.71 g sodium citrate 2H20, 1.07 g KCI, 5.36 g Difco yeast extract, 5.36 g Sheffield hycase SF in 500 mL water, as well as 110 mM MPOS, pH 7.3
  • £ coli paste from 0.5 to 1 L fermentations (6-10 g pellets) is resuspended in 10 volumes (w/v) in 7 M guanidine, 20 M Tris, pH 8 buffer.
  • Solid sodium sulfite and sodium tetrathionate is added to make final concentrations of 0.1 M and 0.02 M, respectively, and the solution is stirred overnight at 4 C. This step results in a denatured protein with all cysteine residues blocked by sulfitolization.
  • the solution is centrifuged at 40,000 rpm in a Beckman Ultracentifuge for 30 min.
  • the supernatant is diluted with 3-5 volumes of metal chelate column buffer (6 M guanidine, 20 mM Tris, pH 7.4) and filtered through 0.22 micron filters to clarify.
  • the clarified extract is loaded onto a 5 ml Qiagen Ni-NTA metal chelate column equilibrated in the metal chelate column buffer.
  • the column is washed with additional buffer containing 50 mM imidazole (Calbiochem, Utrol grade), pH 7.4.
  • the protein is eluted with buffer containing 250 mM imidazole. Fractions containing the desired protein are pooled and stored at 4 C. Protein concentration is estimated by its absorbance at 280 nm using the calculated extinction coefficient based on its amino acid sequence.
  • the proteins are refolded by diluting the sample slowly into freshly prepared refolding buffer consisting of: 20 mM Tris, pH 8.6, 0.3 M NaCI, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA. Refolding volumes are chosen so that the final protein concentration is between 50 to 100 micrograms/ml.
  • the refolding solution is stirred gently at 4 C for 12-36 hours.
  • the refolding reaction is quenched by the addition of TFA to a final concentration of 0.4% (pH of approximately 3).
  • the solution is filtered through a 0.22 micron filter and acetonitrile is added to 2-10% final concentration.
  • the refolded protein is chromatographed on a Poros R1/H reversed phase column using a mobile buffer of 0.1 % TFA with elution with a gradient of acetonitrile from 10 to 80%. Aliquots of fractions with A280 absorbance are analyzed on SOS polyacrylamide gels and fractions containing homogeneous refolded protein are pooled. Generally, the properly refolded species of most proteins are eluted at the lowest concentrations of acetonitrile since those species are the most compact with their hydrophobic interiors shielded from interaction with the reversed phase resin. Aggregated species are usually eluted at higher acetonitrile concentrations. In addition to resolving misfolded forms of proteins from the desired form, the reversed phase step also removes endotoxin from the samples.
  • the CHEPO DNA is ligated into pRK5 with selected restriction enzymes to allow insertion of the CHEPO DNA using ligation methods such as described in Sambrook et al., supra.
  • the resulting vector is called pRK5-CHEP0.
  • the selected host cells may be 293 cells.
  • Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics.
  • About 10 g pRK5-CHEP0 DNA is mixed with about 1 g DNA encoding the VA RNA gene [Thimmappaya et al., CeH, 31:543 (1982)] and dissolved in 500 I of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCI 2 .
  • the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 Ci/ml 35 S-cysteine and 200 Ci/ml 35 S-methioni ⁇ e.
  • culture medium alone
  • culture medium containing 200 Ci/ml 35 S-cysteine and 200 Ci/ml 35 S-methioni ⁇ e After a 12 hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of CHEPO polypeptide.
  • the cultures containing transfected cells may undergo further incubation (in serum free medium) and the medium is tested in selected bioassays.
  • CHEPO may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., Proc. Natl. Acad. Sci.. 12:7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 g pRK5-CHEP0 DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours.
  • the ceils are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culture medium, 5 g/ml bovine insulin and 0.1 g/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris. The sample containing expressed CHEPO can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.
  • CHEPO can be expressed in CHO cells.
  • the pRK5-CHEP0 can be transfected into CHO cells using known reagents such as CaP0 4 or DEAE-dextran.
  • the ceil cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as 35 S-methio ⁇ ine.
  • the culture medium may be replaced with serum free medium.
  • the cultures are incubated for about 6 days, and then the conditioned medium is harvested.
  • the medium containing the expressed CHEPO can then be concentrated and purified by any selected method.
  • Epitope-tagged CHEPO may also be expressed in host CHO cells.
  • the CHEPO may be subcloned out of the pRK5 vector.
  • the subcione insert can undergo PCR to fuse in frame with a selected epitope tag such as a poly-his tag into a Baculovirus expression vector.
  • the poly-his tagged CHEPO insert can then be subcloned into a SV40 driven vector containing a selection marker such as DHFR for selection of stable clones.
  • the CHO cells can be transfected (as described above) with the SV40 driven vector. Labeling may be performed, as described above, to verify expression.
  • the culture medium containing the expressed poly-His tagged CHEPO can then be concentrated and purified by any selected method, such as by Ni 2* -chelate affinity chromatography.
  • CHEPO may also be expressed in CHO and/or COS cells by a transient expression procedure or in CHO ceils by another stable expression procedure. Stable expression in CHO ceils is performed using the following procedure.
  • the proteins are expressed as an IgG construct (immunoadhesin), in which the coding sequences for the soluble forms (e.g. extracellular domains) of the respective proteins are fused to an IgGI constant region sequence containing the hinge, CH2 and CH2 domains and/or is a poly-His tagged form.
  • CHO expression vectors are constructed to have compatible restriction sites 5 and 3 of the DNA of interest to allow the convenient shuttling of cDNA s.
  • the vector used expression in CHO cells is as described in Lucas et al., Nucl. Acids Res. 24:9 (1774-1779 (1996), and uses the SV40 early promoter/enhancer to drive expression of the cDNA of interest and dihydrofolate reductase (DHFR).
  • DHFR expression permits selection for stable maintenance of the plasmid following transfection.
  • Twelve micrograms of the desired plasmid DNA is introduced into approximately 10 million CHO cells using commercially available transfection reagents Superfect (Quiagen), Dosper or Fuge ⁇ e (Boehringer Mannheim). The cells are grown as described in Lucas et al., supra. Approximately 3 x 10 7 cells are frozen in an ampule for further growth and production as described below. The ampules containing the plasmid DNA are thawed by placement into water bath and mixed by vortexing. The contents are pipetted into a centrifuge tube containing 10 mLs of media and centrifuged at 1000 rpm for 5 minutes.
  • the supernatant is aspirated and the cells are resuspe ⁇ ded in 10 mL of selective media (0.2 m filtered PS20 with 5% 0.2 m diafiltered fetal bovine serum).
  • the cells are then aliquoted into a 100 mL spinner containing 90 mL of selective media. After 1-2 days, the ceils are transferred into a 250 mL spinner filled with 150 mL selective growth medium and incubated at 37°C. After another 2-3 days, 250 mL, 500 mL and 2000 mL spinners are seeded with 3 x 10 5 cells/mL.
  • the cell media is exchanged with fresh media by centrifugation and resuspension in production medium.
  • a 3L production spinner is seeded at 1.2 x 10 6 cells/mL. On day 0, the cell number pH ie determined. On day 1, the spinner is sampled and sparging with filtered air is commenced. On day 2, the spinner is sampled, the temperature shifted to 33°C, and 30 mL of 500 g/L glucose and 0.6 mL of 10% antifoam (e.g., 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion) taken. Throughout the production, the pH is adjusted as necessary to keep it at around 7.2.
  • 10% antifoam e.g., 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion
  • the cell culture is harvested by centrifugation and filtering through a 0.22 m filter.
  • the filtrate was either stored at 4°C or immediately loaded onto columns for purification.
  • the proteins are purified using a Ni-NTA column (Qiagen).
  • imidazole is added to the conditioned media to a concentration of 5 mM.
  • the conditioned media is pumped onto a 6 ml Ni- NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCI and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4°C.
  • the column is washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole.
  • the highly purified protein is subsequently desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCI and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -80°C.
  • Immunoadhesin (Fc-contai ⁇ ing) constructs are purified from the conditioned media as follows.
  • the conditioned medium is pumped onto a 5 ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8.
  • the column After loading, the column is washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5.
  • the eluted protein is immediately neutralized by collecting 1 ml fractions into tubes containing 275 L of 1 M Tris buffer, pH 9.
  • the highly purified protein is subsequently desalted into storage buffer as described above for the poly-His tagged proteins.
  • the homogeneity is assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation.
  • EXAMPLE 5 Expression of CHEPQ in Yeast The following method describes recombinant expression of CHEPO in yeast.
  • yeast expression vectors are constructed for intracellular production or secretion of CHEPO from the ADH2/GAPDH promoter.
  • DNA encoding CHEPO and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of CHEPO.
  • DNA encoding CHEPO can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, a native CHEPO signal peptide or other mammalian signal peptide, or, for example, a yeast alpha-factor or invertase secretory signal/leader sequence, and linker sequences (if needed) for expression of CHEPQ.
  • yeast cells such as yeast strain AB110
  • yeast strain AB110 can then be transformed with the expression plasmids described above and cultured in selected fermentation media.
  • the transformed yeast supematants can be analyzed by precipitation with 10% trichioroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.
  • Recombinant CHEPO can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters.
  • the concentrate containing CHEPO may further be purified using selected column chromatography resins.
  • the following method describes recombinant expression of CHEPO in Baculovirus-infected insect cells.
  • the sequence coding for CHEPO is fused upstream of an epitope tag contained within a bacuiovirus expression vector.
  • epitope tags include poly-his tags and immunoglobulin tags (like Fc regions of IgG).
  • plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen).
  • sequence encoding CHEPO or the desired portion of the coding sequence of CHEPO such as the sequence encoding the extracellular domain of a transmembrane protein or the sequence encoding the mature protein if the protein is extracellular is amplified by PCR with primers complementary to the 5' and 3' regions.
  • the 5' primer may incorporate flanking (selected) restriction enzyme sites.
  • the product is then digested with those selected restriction enzymes and subcloned into the expression vector.
  • Recombinant bacuiovirus is generated by co-transfecting the above plasmid and BaculoGoldTM virus DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). After 4 - 5 days of incubation at 28°C, the released viruses are harvested and used for further amplifications. Viral infection and protein expression are performed as described by O'Reilley et al., Bacuiovirus expression vectors: A Laboratory Manual, Oxford: Oxford University Press (1994).
  • Expressed poly-his tagged CHEPO can then be purified, for example, by Ni 2+ -chelate affinity chromatography as follows. Extracts are prepared from recombinant virus-infected Sf 9 cells as described by Rupert et al., Nature, 362:175- 179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCI 2 ; 0.1 mM EDTA; 10% glycerol; 0.1 % NP-40; 0.4 M KCI), and sonicated twice for 20 seconds on ice.
  • sonication buffer 25 mL Hepes, pH 7.9; 12.5 mM MgCI 2 ; 0.1 mM EDTA; 10% glycerol; 0.1 % NP-40; 0.4 M KCI
  • the sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCI, 10% glycerol, pH 7.8) and filtered through a 0.45 m filter.
  • loading buffer 50 mM phosphate, 300 mM NaCI, 10% glycerol, pH 7.8
  • a Ni 2* -NTA agarose column (commercially available from Qiage ⁇ ) is prepared with a bed volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer.
  • the filtered cell extract is loaded onto the column at 0.5 mL per minute.
  • the column is washed to baseline A 280 with loading buffer, at which point fraction collection is started.
  • the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCI, 10% glycerol, pH 6.0), which elutes nonspecifically bound protein.
  • a secondary wash buffer 50 mM phosphate; 300 mM NaCI, 10% glycerol, pH 6.0
  • the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer.
  • One mL fractions are collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni 2* -NTA-conjugated to alkaline phosphatase (Qiage ⁇ ).
  • Fractions containing the eluted His 10 -tagged CHEPO are pooled and diaiyzed against loading buffer.
  • purification of the IgG tagged (or Fc tagged) CHEPO can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography.
  • the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, MT) and injected into the animal's hind foot pads.
  • MPL-TDM adjuvant Ribi Immunochemical Research, Hamilton, MT
  • the immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect anti- CHEPO antibodies.
  • the animals "positive" for antibodies can be injected with a final intravenous injection of CHEPO.
  • the mice Three to four days later, the mice are sacrificed and the spleen cells are harvested.
  • the spleen cells are then fused (using 35% polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597.
  • the fusions generate hybridoma cells which can then be plated in 96 well tissue culture plates containing HAT (hypoxanthine, aminopteri ⁇ , and thymidi ⁇ e) medium to inhibit proliferation of non- fused cells, myeloma hybrids, and spleen cell hybrids.
  • HAT hyperxanthine, aminopteri ⁇ , and thymidi ⁇ e
  • hybridoma cells will be screened in an ELISA for reactivity against CHEPO. Determination of "positive" hybridoma cells secreting the desired monoclonal antibodies against CHEPO is within the skill in the art.
  • the positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-CHEPO monoclonal antibodies.
  • the hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.
  • CHEPO Polypeptides may be purified by a variety of standard techniques in the art of protein purification. For example, pro-CHEPO polypeptide, mature CHEPO polypeptide, or pre-CHEPO polypeptide is purified by immunoaffi ⁇ ity chromatography using antibodies specific for the CHEPO polypeptide of interest. In general, an immunoaffinity column is constructed by covalently coupling the anti-CHEPO polypeptide antibody to an activated chromatographic resin.
  • Polyclonal immunogiobulins are prepared from immune sera either by precipitation with ammonium sulfate or by purification on immobilized Protein A (Pharmacia LKB Biotechnology, Piscataway, N.J.).
  • monoclonal antibodies are prepared from mouse ascites fluid by ammonium sulfate precipitation or chromatography on immobilized Protein A.
  • Partially purified immunoglobulin is covalently attached to a chromatographic resin such as CnBr-activated SEPHAROSETM (Pharmacia LKB Biotechnology). The antibody is coupled to the resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's instructions.
  • Such an immunoaffinity column is utilized in the purification of CHEPO polypeptide by preparing a fraction from cells containing CHEPO polypeptide in a soluble form. This preparation is derived by solubilization of the whole cell or of a subcellular fraction obtained via differential centrifugation by the addition of detergent or by other methods well known in the art. Alternatively, soluble CHEPO polypeptide containing a signal sequence may be secreted in useful quantity into the medium in which the cells are grown.
  • a soluble CHEPO polypeptide-containing preparation is passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of CHEPO polypeptide (e.g., high ionic strength buffers in the presence of detergent). Then, the column is eluted under conditions that disrupt antibody/CHEPO polypeptide binding
  • CHEPO polypeptide is collected.
  • a low pH buffer such as approximately pH 2-3, or a high concentration of a chaotrope such as urea or thiocya ⁇ ate ion
  • CHEPO polypeptide is collected.
  • Drug Screening This invention is particularly useful for screening compounds by using CHEPO polypeptides or binding fragment thereof in any of a variety of drug screening techniques.
  • the CHEPO polypeptide or fragment employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface, or located intraceliularl ⁇ .
  • One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the CHEPO polypeptide or fragment. Drugs are screened against such transformed ceils in competitive binding assays. Such cells, either in viable or fixed form, can be used for standard binding assays.
  • the present invention provides methods of screening for drugs or any other agents which can affect a CHEPO polypeptide-associated disease or disorder. These methods comprise contacting such an agent with an CHEPO polypeptide or fragment thereof and assaying (I) for the presence of a complex between the agent and the CHEPO polypeptide or fragment, or (ii) for the presence of a complex between the CHEPO polypeptide or fragment and the cell, by methods well known in the art. In such competitive binding assays, the CHEPO polypeptide or fragment is typically labeled.
  • free CHEPO polypeptide or fragment is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of the particular agent to bind to CHEPO polypeptide or to interfere with the CHEPO polypeptide/cell complex.
  • Another technique for drug screening provides high throughput screening for compounds having suitable binding affinity to a polypeptide and is described in detail in WO 84/03564, published on September 13, 1 84. Briefly stated, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. As applied to a CHEPO polypeptide, the peptide test compounds are reacted with CHEPO polypeptide and washed. Bound CHEPO polypeptide is detected by methods well known in the art. Purified CHEPO polypeptide can also be coated directly onto plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing antibodies can be used to capture the peptide and immobilize it on the solid support.
  • This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding CHEPO polypeptide specifically compete with a test compound for binding to CHEPO polypeptide or fragments thereof. In this manner, the antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with CHEPO polypeptide.
  • the goal of rational drug design is to produce structural analogs of biologically active polypeptide of interest (i.e., a CHEPO polypeptide) or of small molecules with which they interact, e.g., agonists, antagonists, or inhibitors. Any of these examples can be used to fashion drugs which are more active or stable forms of the CHEPO polypeptide or which enhance or interfere with the function of the CHEPO polypeptide in vivo (c.f, Hodgson, Bio/Technology, 9: 19-21 (1991)).
  • the three-dimensional structure of the CHEPO polypeptide, or of an CHEPO polypeptide-i ⁇ hibitor complex is determined by x-ray crystallography, by computer modeling or, most typically, by a combination of the two approaches.
  • Both the shape and charges of the CHEPQ polypeptide must be ascertained to elucidate the structure and to determine active site(s) of the molecule.
  • useful information regarding the structure of the CHEPO polypeptide may be gained by modeling based on the structure of homologous proteins. In both cases, relevant structural information is used to design analogous CHEPO polypeptide-like molecules or to identify efficient inhibitors.
  • Useful examples of rational drug design may include molecules which have improved activity or stability as shown by Braxton and Wells, Biochemistry,
  • a target-specific antibody selected by functional assay, as described above, and then to solve its crystal structure.
  • This approach in principle, yields a pharmacore upon which subsequent drug design can be based. It is possible to bypass protein crystallography altogether by generating anti-idiotypic antibodies (anti-ids) to a functional, pharmacologically active antibody. As a mirror image of a mirror image, the binding site of the anti-ids would be expected to be an analog of the original receptor. The anti-id could then be used to identify and isolate peptides from banks of chemically or biologically produced peptides. The isolated peptides would then act as the pharmacore.
  • anti-ids anti-idiotypic antibodies
  • CHEPO polypeptide may be made available to perform such analytical studies as X-ray crystallography.
  • knowledge of the CHEPO polypeptide amino acid sequence provided herein will provide guidance to those employing computer modeling techniques in place of or in addition to x-ray crystallography.

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  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Diabetes (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
  • Peptides Or Proteins (AREA)
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  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
EP00928879A 1999-05-07 2000-05-05 Erythropoietinpolypeptide und dafür kodierende nukleinsäuren von schimpansen Withdrawn EP1177285A1 (de)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US30730799A 1999-05-07 1999-05-07
US28759400P 1999-05-07 1999-05-07
US307307 1999-05-07
US287594P 2000-03-28
US09/552,265 US6555343B1 (en) 1999-05-07 2000-04-19 Chimpanzee erythropoietin (CHEPO) polypeptides and nucleic acids encoding the same
US552265 2000-04-19
PCT/US2000/012370 WO2000068376A1 (en) 1999-05-07 2000-05-05 Novel chimpanzee erythropoietin (chepo) polypeptides and nucleic acids encoding the same

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EP (1) EP1177285A1 (de)
JP (1) JP3660880B2 (de)
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IL (1) IL145785A0 (de)
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WO (1) WO2000068376A1 (de)

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US6831060B2 (en) * 1999-05-07 2004-12-14 Genentech, Inc. Chimpanzee erythropoietin (CHEPO) polypeptides and nucleic acids encoding the same
US7067110B1 (en) 1999-07-21 2006-06-27 Emd Lexigen Research Center Corp. Fc fusion proteins for enhancing the immunogenicity of protein and peptide antigens
ATE316982T1 (de) 1999-08-09 2006-02-15 Lexigen Pharm Corp Mehrere zytokin-antikörper komplexen
JP2003514552A (ja) * 1999-11-12 2003-04-22 メルク パテント ゲゼルシャフト ミット ベシュレンクテル ハフトング 改善された性質を有するエリトロポエチンの形態
ES2269366T3 (es) 2000-02-11 2007-04-01 Merck Patent Gmbh Mejoramiento de la vida media en circulacion de proteinas de fusion basadas en anticuerpos.
RU2272644C2 (ru) 2000-06-29 2006-03-27 Мерк Патент Гмбх Усиление иммунной реакции, медиатором которой является слитый протеин антитело-цитокин, при помощи комбинированного лечения агентами, увеличивающими поглощение иммуноцитокина
KR100900176B1 (ko) 2001-03-07 2009-06-02 메르크 파텐트 게엠베하 하이브리드 이소타입 항체 부분구조를 포함하는 단백질을위한 발현 기술
US6992174B2 (en) 2001-03-30 2006-01-31 Emd Lexigen Research Center Corp. Reducing the immunogenicity of fusion proteins
KR20040032094A (ko) * 2001-04-04 2004-04-14 젠오디세 에리트로포이에틴 유전자의 신규한 폴리뉴클레오티드 및폴리펩티드
HUP0400284A3 (en) 2001-05-03 2012-09-28 Merck Patent Gmbh Recombinant tumor specific antibody and use thereof
DK1454138T3 (da) 2001-12-04 2012-02-13 Merck Patent Gmbh Immunocytokiner med moduleret selektivitet
ES2346205T3 (es) 2002-12-17 2010-10-13 Merck Patent Gmbh Anticuerpo humanizado (h14.18) del anticurpo 14.18 de raton que se enlaza con gd2 y su fusion con la il-2.
EP1608672A4 (de) * 2003-04-02 2007-11-21 Epimmune Inc Peptide, polypeptide und proteine mit reduzierter immunogenität und verfahren zu deren herstellung
EP1699821B1 (de) 2003-12-31 2012-06-20 Merck Patent GmbH Fc-ERYTHROPOIETIN-FUSIONSPROTEIN MIT VERBESSERTER PHARMAKOKINETIK

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JP3660880B2 (ja) 2005-06-15
AU4704700A (en) 2000-11-21
JP2002543784A (ja) 2002-12-24
IL145785A0 (en) 2002-07-25
WO2000068376B1 (en) 2001-02-15
MXPA01011264A (es) 2002-07-02
WO2000068376A1 (en) 2000-11-16
AU766507B2 (en) 2003-10-16

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