Genes

12 pages, 277 KiB

Open AccessArticle

Associations of MC4R, LEP, and LEPR Polymorphisms with Obesity-Related Parameters in Childhood and Adulthood

by Asta Raskiliene, Alina Smalinskiene, Vilma Kriaucioniene, Vaiva Lesauskaite and Janina Petkeviciene

Genes 2021, 12(6), 949; https://doi.org/10.3390/genes12060949 - 21 Jun 2021

Cited by 14 | Viewed by 3091

Abstract

MC4R, LEP, and LEPR genes are involved in the hypothalamic leptin-melanocortin regulation pathway, which is important for energy homeostasis. Our study aimed to evaluate the associations between the MC4R rs17782313, LEP rs7799039, and LEPR rs1137101 polymorphisms with obesity-related parameters in childhood [...] Read more.

MC4R, LEP, and LEPR genes are involved in the hypothalamic leptin-melanocortin regulation pathway, which is important for energy homeostasis. Our study aimed to evaluate the associations between the MC4R rs17782313, LEP rs7799039, and LEPR rs1137101 polymorphisms with obesity-related parameters in childhood and adulthood. The data were obtained from the Kaunas Cardiovascular Risk Cohort study, which started in 1977 with 1082 participants aged 12–13 years. In 2012–2014, the follow-up survey was carried out. Genotype analysis of all respondents (n = 509) aged 48–49 years was performed for the gene polymorphisms using Real-Time Polymerase Chain Reaction. Anthropometric measurements were performed in childhood and adulthood. In childhood, only skinfold thicknesses were associated with gene variants being the lowest in children with MC4R TT genotype and LEP AG genotype. In adulthood, odds of obesity and metabolic syndrome was higher in MC4R CT/CC genotype than TT genotype carriers (OR 1.8; 95% CI 1.2–2.8 and OR 1.6; 95% CI 1.1–2.4, respectively). In men, physical activity attenuated the effect of the MC4R rs17782313 on obesity. The LEP GG genotype was associated with higher BMI, waist circumference, and visceral fat level only in men. No associations of the LEPR rs1137101 polymorphisms with anthropometric measurements and leptin level were found. In conclusion, the associations of the MC4R and LEP gene polymorphisms with obesity-related parameters strengthened with age. Full article

(This article belongs to the Special Issue Genetic Research in Paediatric Subjects with Body Fat Excess)

16 pages, 3926 KiB

Open AccessArticle

Administration of AAV-Alpha Synuclein NAC Antibody Improves Locomotor Behavior in Rats Overexpressing Alpha Synuclein

by Yun-Hsiang Chen, Kuo-Jen Wu, Wei Hsieh, Brandon K. Harvey, Barry J. Hoffer, Yun Wang and Seong-Jin Yu

Genes 2021, 12(6), 948; https://doi.org/10.3390/genes12060948 - 21 Jun 2021

Cited by 12 | Viewed by 4265

Abstract

Accumulation of α-Synuclein (αSyn) in nigral dopaminergic neurons is commonly seen in patients with Parkinson′s disease (PD). We recently reported that transduction of intracellular single-chain intrabody targeting the 53–87 amino acid residues of human αSyn by recombinant adeno associated viral vector (AAV-NAC32) downregulated [...] Read more.

Accumulation of α-Synuclein (αSyn) in nigral dopaminergic neurons is commonly seen in patients with Parkinson′s disease (PD). We recently reported that transduction of intracellular single-chain intrabody targeting the 53–87 amino acid residues of human αSyn by recombinant adeno associated viral vector (AAV-NAC32) downregulated αSyn protein in SH-SY5Y cells and rat brain. This study characterizes the behavioral phenotype and dopaminergic protection in animals receiving AAV-NAC32. Our results show that adult DAT-Cre rats selectively overexpress αSyn in nigra dopaminergic neurons after local administration of AAV-DIO-αSyn. These animals develop PD-like phenotype, including bradykinesia and loss of tyrosine hydroxylase (TH) immunoreactivity in substantia nigra pars compacta dorsal tier (SNcd). An injection of AAV-NAC32 to nigra produces a selective antibody against αSyn and normalizes the behavior. AAV-NAC32 significantly increases TH, while reduces αSyn immunoreactivity in SNcd. Altogether, our data suggest that an AAV-mediated gene transfer of NAC32 antibody effectively antagonizes αSyn-mediated dopaminergic degeneration in nigra, which may be a promising therapeutic candidate for synucleinopathy or PD. Full article

(This article belongs to the Special Issue Preclinical and Clinical Genetics in Parkinson’s Disease)

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15 pages, 1391 KiB

Open AccessArticle

QTL Analysis of Stem Elongation and Flowering Time in Lettuce Using Genotyping-by-Sequencing

by O New Lee, Keita Fukushima, Han Yong Park and Saneyuki Kawabata

Genes 2021, 12(6), 947; https://doi.org/10.3390/genes12060947 - 21 Jun 2021

Cited by 5 | Viewed by 3096

Abstract

Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis [...] Read more.

Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis of F5 recombinant inbred lines (RILs) and to map QTLs involved in stem growth and flowering time in lettuce. A set of 127 intra-specific RIL mapping populations derived from a cross between two varieties, green and red leaf lettuce, were used to identify QTLs related to the number of days from sowing to bolting (DTB), to flowering of the first flower (DTF), to seed-setting of the first flower (DTS), and the total number of leaves (LN), plant height (PH), and total number of branches of main inflorescence (BN) for two consecutive years. Of the 15 QTLs detected, one that controls DTB, DTF, DTS, LN, and PH detected on LG 7, and another QTL that controls DTF, DTS, and PH detected on LG 1. Analysis of the genomic sequence corresponding to the QTL detected on LG 7 led to the identification of 22 putative candidate genes. A consistent QTL related to bolting and flowering time, and corresponding candidate genes has been reported. This study will be valuable in revealing the genetic basis of stem growth and flowering time in lettuce. Full article

(This article belongs to the Special Issue Genetic Improvement for Horticultural Plants)

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9 pages, 412 KiB

Open AccessReview

Telomere Length and Pediatric Obesity: A Review

by María Cristina Azcona-Sanjulian

Genes 2021, 12(6), 946; https://doi.org/10.3390/genes12060946 - 21 Jun 2021

Cited by 11 | Viewed by 2568

Abstract

Obesity is a chronic disease, which needs to be early detected early and treated in order prevent its complications. Changes in telomere length (TL) have been associated with obesity and its complications, such as diabetes mellitus and metabolic syndrome. Therefore, we conducted a [...] Read more.

Obesity is a chronic disease, which needs to be early detected early and treated in order prevent its complications. Changes in telomere length (TL) have been associated with obesity and its complications, such as diabetes mellitus and metabolic syndrome. Therefore, we conducted a systematic review to summarize results of studies that have measured TL in children and adolescents with obesity. Fourteen studies aiming to assess TL in pediatric patients with either obesity or who were overweight were included in this review. In conclusion, obesity and adiposity parameters are negatively associated with TL. Shorter telomeres are observed in children with obesity compared with their lean counterparts. Factors involved in obesity etiology, such as diet and physical activity, may contribute to maintenance of TL integrity. In the long term, TL change could be used as a biomarker to predict response to obesity treatment. Full article

(This article belongs to the Special Issue Genetic Research in Paediatric Subjects with Body Fat Excess)

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8 pages, 1692 KiB

Open AccessArticle

A Homozygous Synonymous Variant Likely Cause of Severe Ciliopathy Phenotype

by Gulten Tuncel, Bahar Kaymakamzade, Yeliz Engindereli, Sehime G. Temel and Mahmut Cerkez Ergoren

Genes 2021, 12(6), 945; https://doi.org/10.3390/genes12060945 - 21 Jun 2021

Cited by 6 | Viewed by 3015

Abstract

Joubert syndrome (OMIM #213300) is a rare neurodevelopmental disease characterized by abnormal breathing patterns, intellectual impairment, ocular findings, renal cysts, and hepatic fibrosis. It is classified as a ciliopathy disease, where cilia function or structure in various organs are affected. Here, we report [...] Read more.

Joubert syndrome (OMIM #213300) is a rare neurodevelopmental disease characterized by abnormal breathing patterns, intellectual impairment, ocular findings, renal cysts, and hepatic fibrosis. It is classified as a ciliopathy disease, where cilia function or structure in various organs are affected. Here, we report a 17-year-old male whose main clinical findings are oculomotor apraxia and truncal ataxia. Magnetic resonance imaging revealed the characteristic molar tooth sign of Joubert syndrome. He also has obsessive–compulsive disorder concomitantly, which is not a known feature of Joubert syndrome. Molecular genetic analysis revealed a homozygous c.2106G>A (p.(Thr702=)) variation in the Abelson helper integration 1 (AHI1) gene and another homozygous c.1739C>T (p.Thr580Ile) variation in the coiled-coil and C2 domain-containing protein 1A (CC2D1A) gene. Even though certain AHI1 variations were previously associated with Joubert syndrome (JS), c.2106G>A (p.(Thr702=)) was only reported in one patient in trans with another known pathogenic JS variant. The CC2D1A c.1739C>T (p.Thr580Ile) variation, on the other hand, has been reported to cause autosomal recessive nonsyndromic mental retardation, but there are conflicting interpretations about its pathogenicity. Overall, to our knowledge, this is the first patient representing a severe ciliopathy phenotype caused by a homozygous synonymous AHI1 variation. Further investigations should be performed to determine any involvement of the CC2D1A gene in ciliopathy phenotypes such as Joubert syndrome. Full article

(This article belongs to the Special Issue Genetic Disease in Mediterranean Region)

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20 pages, 6228 KiB

Open AccessArticle

Expression of Wnt and TGF-Beta Pathway Components during Whole-Body Regeneration from Cell Aggregates in Demosponge Halisarca dujardinii

by Ilya Borisenko, Fyodor V. Bolshakov, Alexander Ereskovsky and Andrey I. Lavrov

Genes 2021, 12(6), 944; https://doi.org/10.3390/genes12060944 - 20 Jun 2021

Cited by 6 | Viewed by 2638

Abstract

The phenomenon of whole-body regeneration means rebuilding of the whole body of an animal from a small fragment or even a group of cells. In this process, the old axial relationships are often lost, and new ones are established. An amazing model for [...] Read more.

The phenomenon of whole-body regeneration means rebuilding of the whole body of an animal from a small fragment or even a group of cells. In this process, the old axial relationships are often lost, and new ones are established. An amazing model for studying this process is sponges, some of which are able to regenerate into a definitive organism after dissociation into cells. We hypothesized that during the development of cell aggregates, primmorphs, new axes are established due to the activation of the Wnt and TGF-beta signaling pathways. Using in silico analysis, RNA-seq, and whole-mount in situ hybridization, we identified the participants in these signaling pathways and determined the spatiotemporal changes in their expression in demosponge Halisarca dujardinii. It was shown that Wnt and TGF-beta ligands are differentially expressed during primmorph development, and transcripts of several genes are localized at the poles of primmorphs, in the form of a gradient. We suppose that the Wnt and TGF-beta signaling cascades are involved in the initial axial patterning of the sponge body, which develops from cells after dissociation. Full article

(This article belongs to the Special Issue The Molecular Genetics and Major Concepts Underlying Whole Body Regeneration in the Animal World)

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14 pages, 1243 KiB

Open AccessReview

Models of Distal Arthrogryposis and Lethal Congenital Contracture Syndrome

by Julia Whittle, Aaron Johnson, Matthew B. Dobbs and Christina A. Gurnett

Genes 2021, 12(6), 943; https://doi.org/10.3390/genes12060943 - 20 Jun 2021

Cited by 10 | Viewed by 3185

Abstract

Distal arthrogryposis and lethal congenital contracture syndromes describe a broad group of disorders that share congenital limb contractures in common. While skeletal muscle sarcomeric genes comprise many of the first genes identified for Distal Arthrogyposis, other mechanisms of disease have been demonstrated, including [...] Read more.

Distal arthrogryposis and lethal congenital contracture syndromes describe a broad group of disorders that share congenital limb contractures in common. While skeletal muscle sarcomeric genes comprise many of the first genes identified for Distal Arthrogyposis, other mechanisms of disease have been demonstrated, including key effects on peripheral nerve function. While Distal Arthrogryposis and Lethal Congenital Contracture Syndromes display superficial similarities in phenotype, the underlying mechanisms for these conditions are diverse but overlapping. In this review, we discuss the important insights gained into these human genetic diseases resulting from in vitro molecular studies and in vivo models in fruit fly, zebrafish, and mice. Full article

(This article belongs to the Special Issue Genetic Conditions Affecting the Skeleton: Congenital, Idiopathic Scoliosis and Arthrogryposis)

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18 pages, 5056 KiB

Open AccessArticle

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

by Yongliang Fan, Ziyin Han, Xubin Lu, Abdelaziz Adam Idriss Arbab, Mudasir Nazar, Yi Yang and Zhangping Yang

Genes 2021, 12(6), 942; https://doi.org/10.3390/genes12060942 - 20 Jun 2021

Cited by 9 | Viewed by 3095

Abstract

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) [...] Read more.

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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Histological sections stained with HE. (a) Dairy cow mammary tissue collected at 90 d of lactation. (b) Dairy cow mammary tissue collected at 180 d of lactation. (c) Dairy cow mammary tissue collected at 270 d of lactation. Full article ">Figure 2
Volcano plot of differentially expressed genes (DEGs). (a) Volcano plot of DEGs identified for mid-lactation compared to peak lactation. (b) Volcano plot of DEGs identified for late lactation compared to peak lactation. Full article ">Figure 3
Venn diagram depicting the overlap between the two sets of differentially expressed genes. Full article ">Figure 4
Gene ontology (GO) functional enrichment analysis of differentially expressed genes (DEGs). (a,c) Figures, respectively, show the top 10 significant GO terms for each category from (a) the 90 vs. 180 d group and (c) the 90 d vs. 270 d group. (b,d) Circos plots showing overlapping and specific responses of DEGs enriched in the nine most significant GO terms. Full article ">Figure 4 Cont.
Gene ontology (GO) functional enrichment analysis of differentially expressed genes (DEGs). (a,c) Figures, respectively, show the top 10 significant GO terms for each category from (a) the 90 vs. 180 d group and (c) the 90 d vs. 270 d group. (b,d) Circos plots showing overlapping and specific responses of DEGs enriched in the nine most significant GO terms. Full article ">Figure 5
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs). (a,c) Figures, respectively, show the top 10 significant KEGG pathways of each category from (a) the 90 vs. 180 d group and (c) the 90 vs. 270 d group. (b,d) Circos plots showing overlapping and specific responses of DEGs enriched in the top nine KEGG pathways. Full article ">Figure 5 Cont.
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs). (a,c) Figures, respectively, show the top 10 significant KEGG pathways of each category from (a) the 90 vs. 180 d group and (c) the 90 vs. 270 d group. (b,d) Circos plots showing overlapping and specific responses of DEGs enriched in the top nine KEGG pathways. Full article ">Figure 6
Patterns of gene expression across the three time points inferred by STEM analysis. (a) Sixteen candidate profiles were obtained via STEM analysis. The five colored profiles are significant profiles (FDR ≤ 0.05). (b–f) The green nodes in the PPI networks represent genes in the significant profiles. The yellow nodes in the PPI networks represent key genes in the significant profiles. Full article ">Figure 6 Cont.
Patterns of gene expression across the three time points inferred by STEM analysis. (a) Sixteen candidate profiles were obtained via STEM analysis. The five colored profiles are significant profiles (FDR ≤ 0.05). (b–f) The green nodes in the PPI networks represent genes in the significant profiles. The yellow nodes in the PPI networks represent key genes in the significant profiles. Full article ">Figure 7
Expression levels of 10 differentially expressed genes detected by qRT-PCR and transcriptome sequencing. Full article ">

13 pages, 626 KiB

Open AccessArticle

Framing Effects on Decision-Making for Diagnostic Genetic Testing: Results from a Randomized Trial

by Andrew A. Dwyer, Hongjie Shen, Ziwei Zeng, Matt Gregas and Min Zhao

Genes 2021, 12(6), 941; https://doi.org/10.3390/genes12060941 - 20 Jun 2021

Cited by 4 | Viewed by 3957

Abstract

Genetic testing is increasingly part of routine clinical care. However, testing decisions may be characterized by regret as findings also implicate blood relatives. It is not known if genetic testing decisions are affected by the way information is presented (i.e., framing effects). We [...] Read more.

Genetic testing is increasingly part of routine clinical care. However, testing decisions may be characterized by regret as findings also implicate blood relatives. It is not known if genetic testing decisions are affected by the way information is presented (i.e., framing effects). We employed a randomized factorial design to examine framing effects on hypothetical genetic testing scenarios (common, life-threatening disease and rare, life-altering disease). Participants (n = 1012) received one of six decision frames: choice, default (n = 2; opt-in, opt-out), or enhanced choice (n = 3, based on the Theory of Planned Behavior). We compared testing decision, satisfaction, regret, and decision cognitions across decision frames and between scenarios. Participants randomized to ‘choice’ were least likely to opt for genetic testing compared with default and enhanced choice frames (78% vs. 83–91%, p < 0.05). Neither satisfaction nor regret differed across frames. Perceived autonomy (behavioral control) predicted satisfaction (B = 0.085, p < 0.001) while lack of control predicted regret (B = 0.346, p < 0.001). Opting for genetic testing did not differ between disease scenarios (p = 0.23). Results suggest framing can nudge individuals towards opting for genetic testing. These findings have important implications for individual self-determination in the genomic era. Similarities between scenarios with disparate disease trajectories point to possible modular approaches for web-based decisional support. Full article

(This article belongs to the Special Issue Genetic Tests)

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Full article ">Figure 1
Study schematic. (A) Participants were randomized to one of two scenarios then reviewed information about the respective condition. (B) Participants were then randomized to one of six frames and made a genetic testing decision. Full article ">Figure 2
Framing effects on hypothetical genetic testing decision-making (n = 1012). Participants randomized to the choice frame (white) were significantly less likely to opt for testing (135/171 [78.9%], p < 0.05) compared with default (opt-in: 139/167 [83.2%], opt out: 148/170 [87.1%]), or enhanced choice frames (context/consequences: 144/167 [86.2%], affect/commitment: 151/169 [89.9%], norms: 154/169 [91.1%]). The gray dotted line depicts ‘choice’ as a reference point for default (gray bars) and enhanced choice frames (black bars). * p < 0.05. Full article ">Figure 3
Satisfaction with decision and decision regret according to framing (n = 1012). Satisfaction with decision (SWD) and decision regret (DRS). (a) SWD scores did not differ across frames (F = 1.353, p = 0.24). (b) DRS scores did not differ across decision frames (F = 0.875, p = 0.49). Boxes show mean scores ± one standard deviation (error bars). White = choice, gray = default frames (opt-in, opt-out), and black = enhanced choice (context/consequence, affect/commitments, norms). Full article ">

10 pages, 1221 KiB

Open AccessArticle

Genetic History of the Remnant Population of the Rare Orchid Cypripedium calceolus Based on Plastid and Nuclear rDNA

by Marcin Górniak, Anna Jakubska-Busse and Marek S. Ziętara

Genes 2021, 12(6), 940; https://doi.org/10.3390/genes12060940 - 19 Jun 2021

Viewed by 2858

Abstract

The lady’s slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic [...] Read more.

The lady’s slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic variability, and processes in small populations are therefore crucial for the species’ protection. Nowadays, in south-west Poland, it is only distributed in seven small remnant and isolated populations, which we examined. One nuclear (ITS rDNA) and two plastid (accD-psa1, trnL-F) markers were analyzed and compared globally in this study. Based on the nuclear marker, the most common ancestor of C. calceolus and Cypripedium shanxiense existed about 2 million years ago (95% HPD: 5.33–0.44) in Asia. The division of the C. calceolus population into the European and Asian lineages indicated by C/T polymorphism started about 0.5 million years ago (95% HPD: 1.8–0.01). The observed variation of plastid DNA, which arose during the Pleistocene glacial–interglacial cycles, is still diffuse in Poland. Its distribution is explained by the result of fragmentation or habitat loss due to human impact on the environment. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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20 pages, 3650 KiB

Open AccessArticle

Two RECK Splice Variants (Long and Short) Are Differentially Expressed in Patients with Stable and Unstable Coronary Artery Disease: A Pilot Study

by Chiara Vancheri, Elena Morini, Francesca Romana Prandi, Elie Alkhoury, Roberto Celotto, Francesco Romeo, Giuseppe Novelli and Francesca Amati

Genes 2021, 12(6), 939; https://doi.org/10.3390/genes12060939 - 19 Jun 2021

Cited by 3 | Viewed by 2926

Abstract

Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study [...] Read more.

Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study on PBMCs from CAD patients and control subjects (CTR) and observed 113 differentially regulated AS events (24 up and 89 downregulated) in 86 genes. The RECK (Reversion-inducing-cysteine-rich protein with Kazal motifs) gene was further analyzed in a larger case study (24 CTR subjects, 72 CAD and 32 AMI patients) for its Splicing-Index FC (FC = −2.64; p = 0.0217), the AS event involving an exon (exon 18), and its role in vascular inflammation and remodeling. We observed a significant downregulation of Long RECK splice variant (containing exon 18) in PBMCs of AMI compared to CTR subjects (FC = −3.3; p < 0.005). Interestingly, the Short RECK splice variant (lacking exon 18) was under-expressed in AMI compared to both CTR (FC = −4.5; p < 0.0001) and CAD patients (FC = −4.2; p < 0.0001). A ROC curve, constructed combining Long and Short RECK expression data, shows an AUC = 0.81 (p < 0.001) to distinguish AMI from stable CAD patients. A significant negative correlation between Long RECK and triglycerides in CTR group and a positive correlation in the AMI group was found. The combined evaluation of Long and Short RECK expression levels is a potential genomic biomarker for the discrimination of AMI from CAD patients. Our results underline the relevance of deeper studies on the expression of these two splice variants to elucidate their functional role in CAD development and progression. Full article

(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)

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Heat Map resulting from RNA sequencing in the comparison coronary artery disease (CAD) vs. control subjects (CTR). The Heat Map showed a clear similar mRNA expression pattern between patients of the same group of study and a profile considerably different between each category of patients. In green are represented the downregulated mRNAs compared to the group set as control; in red are represented the upregulated mRNAs compared to the group set as control. Full article ">Figure 2
Alternative splicing events. Percentage of 113 differentially regulated alternative splicing events from 86 distinct genes: 4.4% Alternative Acceptor Splice Site; 12.4% Exon cassette; 5.3% Intron retention; 5.3% Alternative Donor Splice Site; 8.8% Alternative Terminal Exon; 12.4% Alternative First Exon; 51.4% unknown. Full article ">Figure 3
(A) Expression level of Long and Short RECK splice variants in CTR, CAD, and AMI group. Wilcoxon test, **** p < 0.0001. (B) Expression level of Long RECK in CTR, CAD, and AMI groups. Kruskal–Wallis test, ** p < 0.001. (C) Expression level of Short RECK in CTR, CAD, and AMI groups. Kruskal–Wallis test, **** p <0.0001. Expression data are represented as mean ± SD. Full article ">Figure 4
Ratio Long/Short RECK splice variants expression level in CTR, CAD, and AMI groups. Kruskal–Wallis test; * p < 0.05. Expression data are represented as mean ± SD. Full article ">Figure 5
Receiver operator characteristic (ROC) analysis by combining Long and Short RECK expression levels. Area under the ROC curve (AUC) = 0.81, 95% confidence interval 0.73 to 0.90, p < 0.001. Full article ">Figure 6
Correlation analysis of Long and Short RECK splice variants in all case study. Scatter plots depict the relationship between the two RECK splice variants in (A) CTR (R2 = 0.355, p < 0.005, Pearson r = 0.601); (B) CAD (R2 = 0.793, p < 0.0001, Pearson r = 0.890); (C) AMI (R2 = 0.279, p < 0.005, Pearson r = 0.528). Full article ">Figure 7
Correlation analysis of Long RECK splice variant in CTR group (n = 19). Scatter plots depict the relationship among Long RECK and (A) HDL value (R2 = 0.297, p < 0.05, Pearson r = 0.545); (B) Triglycerides levels (R2 = 0.206, p < 0.05, Pearson r = −0.460). Full article ">Figure 8
Correlation analysis of Long splice variant in the AMI group (n = 28). Scatter plot depicts the relationship among Long RECK splice variant and triglycerides levels (R2 = 0.213, p < 0.05, Pearson r = 0.461). Full article ">

20 pages, 3410 KiB

Open AccessArticle

Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight

by Vidya Manian, Jairo Orozco-Sandoval and Victor Diaz-Martinez

Genes 2021, 12(6), 938; https://doi.org/10.3390/genes12060938 - 19 Jun 2021

Cited by 7 | Viewed by 3666

Abstract

Ionizing radiation present in extraterrestrial environment is an important factor that affects plants grown in spaceflight. Pearson correlation-based gene regulatory network inferencing from transcriptional responses of the plant Arabidopsis thaliana L. grown in real and simulated spaceflight conditions acquired by GeneLab, followed by [...] Read more.

Ionizing radiation present in extraterrestrial environment is an important factor that affects plants grown in spaceflight. Pearson correlation-based gene regulatory network inferencing from transcriptional responses of the plant Arabidopsis thaliana L. grown in real and simulated spaceflight conditions acquired by GeneLab, followed by topological and spectral analysis of the networks is performed. Gene regulatory subnetworks are extracted for DNA damage response processes. Analysis of radiation-induced ATR/ATM protein–protein interactions in Arabidopsis reveals interaction profile similarities under low radiation doses suggesting novel mechanisms of DNA damage response involving non-radiation-induced genes regulating other stress responses in spaceflight. The Jaccard similarity index shows that the genes AT2G31320, AT4G21070, AT2G46610, and AT3G27060 perform similar functions under low doses of radiation. The incremental association Markov blanket method reveals non-radiation-induced genes linking DNA damage response to root growth and plant development. Eighteen radiation-induced genes and sixteen non-radiation-induced gene players have been identified from the ATR/ATM protein interaction complexes involved in heat, salt, water, osmotic stress responses, and plant organogenesis. Network analysis and logistic regression ranking detected AT3G27060, AT1G07500, AT5G66140, and AT3G21280 as key gene players involved in DNA repair processes. High atomic weight, high energy, and gamma photon radiation result in higher intensity of DNA damage response in the plant resulting in elevated values for several network measures such as spectral gap and girth. Nineteen flavonoid and carotenoid pigment activations involved in pigment biosynthesis processes are identified in low radiation dose total light spaceflight environment but are not found to have significant regulations under very high radiation dose environment. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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Flow diagram showing the sequence of steps followed for extraction of radiation response subnetworks from the gene expression values in the GLDS datasets and network analysis. Full article ">Figure 2
Subnetwork for cellular response to stress process in Arabidopsis under low radiation dose (LRD3) dataset. Red circles are hub genes. There are 7 significant hub genes in this subnetwork. Larger the circles, higher the value of in-degree distribution. Full article ">Figure 3
Subnetwork for DNA metabolic process under low radiation dose (LRD4) dataset. Red circles are hub genes. The hub genes AT3G27060 (TS02) and AT2G21790 (RNR1) are being activated by the genes at the non-arrow end of the edge. Both of these genes have a high in-degree distribution. Full article ">Figure 4
(A) Subnetwork for flavonoids biosynthesis process under light environment in space <a href="#genes-12-00938-f004" class="html-fig">Figure 4</a>. (GLDS-120) dataset. (B) Subnetwork showing carotenoid AT3G14440 interactions. This is a key enzyme in the biosynthesis of abscisic acid. It is regulated in response to drought and salinity and expressed in roots, flowers and seeds. (C) Markov blanket subnetwork showing causal relations of flavonoids (green) and carotenoids (yellow). Full article ">Figure 5
Subnetwork for DNA metabolic process in Arabidopsis under very high HZE radiation dose. Hub genes are indicated by red circles. There are seven significant hub genes in this subnetwork. Larger the circles, higher the activation of the hub genes. Full article ">Figure 6
Subnetwork for the nucleic acid response process in Arabidopsis under very high γR radiation. Red circles are hub genes. There are nine significant hub genes in this subnetwork. Larger the circles, higher the activation of the hub genes. Full article ">Figure 7
Markov blanket subnetworks for low radiation dose dataset (LRD1). Full article ">Figure 8
Markov blanket subnetworks for low radiation dose dataset (LRD3—left and LRD4—right). Full article ">

9 pages, 986 KiB

Open AccessArticle

Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome

by Ashley Vasko, Theodore G. Drivas and Samantha A. Schrier Vergano

Genes 2021, 12(6), 937; https://doi.org/10.3390/genes12060937 - 19 Jun 2021

Cited by 47 | Viewed by 7197

Abstract

Coffin-Siris syndrome (CSS, MIM 135900) is a multi-system intellectual disability syndrome characterized by classic dysmorphic features, developmental delays, and organ system anomalies. Genes in the BRG1(BRM)-associated factors (BAF, Brahma associated factor) complex have been shown to be causative, including ARID1A, ARID1B, [...] Read more.

Coffin-Siris syndrome (CSS, MIM 135900) is a multi-system intellectual disability syndrome characterized by classic dysmorphic features, developmental delays, and organ system anomalies. Genes in the BRG1(BRM)-associated factors (BAF, Brahma associated factor) complex have been shown to be causative, including ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, and SOX4. In order to describe more robust genotype-phenotype correlations, we collected data from 208 individuals from the CSS/BAF complex registry with pathogenic variants in seven of these genes. Data were organized into cohorts by affected gene, comparing genotype groups across a number of binary and quantitative phenotypes. We determined that, while numerous phenotypes are seen in individuals with variants in the BAF complex, hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features. It has been previously proposed that individuals with ARID-related variants are thought to have more learning and developmental struggles, and individuals with SMARC-related variants, while they also have developmental delay, tend to have more severe organ-related complications. SOX-related variants also have developmental differences and organ-related complications but are most associated with neurodevelopmental differences. While these generalizations still overall hold true, we have found that all individuals with BAF-related conditions are at risk of many aspects of the phenotype, and management and surveillance should be broad. Full article

(This article belongs to the Collection Study on Genotypes and Phenotypes of Pediatric Clinical Rare Diseases)

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20 pages, 1499 KiB

Open AccessReview

Specialized Metabolites and Valuable Molecules in Crop and Medicinal Plants: The Evolution of Their Use and Strategies for Their Production

by Vincenzo D’Amelia, Teresa Docimo, Christoph Crocoll and Maria Manuela Rigano

Genes 2021, 12(6), 936; https://doi.org/10.3390/genes12060936 - 18 Jun 2021

Cited by 25 | Viewed by 4636

Abstract

Plants naturally produce a terrific diversity of molecules, which we exploit for promoting our overall well-being. Plants are also green factories. Indeed, they may be exploited to biosynthesize bioactive molecules, proteins, carbohydrates and biopolymers for sustainable and large-scale production. These molecules are easily [...] Read more.

Plants naturally produce a terrific diversity of molecules, which we exploit for promoting our overall well-being. Plants are also green factories. Indeed, they may be exploited to biosynthesize bioactive molecules, proteins, carbohydrates and biopolymers for sustainable and large-scale production. These molecules are easily converted into commodities such as pharmaceuticals, antioxidants, food, feed and biofuels for multiple industrial processes. Novel plant biotechnological, genetics and metabolic insights ensure and increase the applicability of plant-derived compounds in several industrial sectors. In particular, synergy between disciplines, including apparently distant ones such as plant physiology, pharmacology, ‘omics sciences, bioinformatics and nanotechnology paves the path to novel applications of the so-called molecular farming. We present an overview of the novel studies recently published regarding these issues in the hope to have brought out all the interesting aspects of these published studies. Full article

(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Plant-Derived Compounds for Industrial Purposes)

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Figure 1
(A) Plants produce several bioactive molecules that have a protective or interacting role in the surrounding environment. (B) The biosynthesis of these metabolites is boosted during environmental cues, as well as biotic and abiotic stresses. (C) The environmental constraints or the plant endogenous signalling molecules, which induce the compound accumulation, can be used as an “elicitor” to boost the production of molecules with industrial interest, including in in vitro culture systems (e.g., undifferentiated cell cultures). Full article ">Figure 2
Advantages and disadvantages of plant molecular farming. Full article ">Figure 3
General workflow of antigen production: (A) Peptides tested to boost immunity response can be isolated from human and animal pathogens. In (B), the corresponding encoding sequences of the antigen can be amplified from the pathogen genome and cloned in an appropriate binary vector; (C) The binary vector carrying the antigen encoding sequence is transformed into A. tumefaciens; (D) The recombinant A. tumefaciens is then used to infect plants and then introduce the recombinant sequence encoding the antigen into plant cells. Finally, obtained transgenic plants become platforms for the antigen production. The use of transgenic crops (such as, tomato, banana or potato) may allow us to exploit the edible part as direct oral antigen delivery for vaccination. Full article ">

11 pages, 1309 KiB

Open AccessArticle

Comprehensive Analysis of RNA Expression Correlations between Biofluids and Human Tissues

by Ruya Sun, Chunmei Cui, Yuan Zhou and Qinghua Cui

Genes 2021, 12(6), 935; https://doi.org/10.3390/genes12060935 - 18 Jun 2021

Cited by 1 | Viewed by 1957

Abstract

In recent years, biofluid has been considered a promising source of non-invasive biomarkers for health monitoring and disease diagnosis. However, the expression consistency between biofluid and human tissue, which is fundamental to RNA biomarker development, has not been fully evaluated. In this study, [...] Read more.

In recent years, biofluid has been considered a promising source of non-invasive biomarkers for health monitoring and disease diagnosis. However, the expression consistency between biofluid and human tissue, which is fundamental to RNA biomarker development, has not been fully evaluated. In this study, we collected expression profiles across 53 human tissues and five main biofluid types. Utilizing the above dataset, we uncovered a globally positive correlation pattern between various biofluids (including blood, urine, bile, saliva and stool) and human tissues. However, significantly varied biofluid–tissue similarity levels and tendencies were observed between mRNA and lncRNA. Moreover, a higher correlation was found between biofluid types and their functionally related and anatomically closer tissues. In particular, a highly specific correlation was discovered between urine and the prostate. The biological sex of the donor was also proved to be an important influencing factor in biofluid–tissue correlation. Moreover, genes enriched in basic biological processes were found to display low variability across biofluid types, while genes enriched in catabolism-associated pathways were identified as highly variable. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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Figure 1

Figure 1
Overview of biofluid–tissue expression correlations. (A) Data source of collected biofluid genome profiles. The number of samples collected from each data source and the proportion of samples in the whole sample pool (n = 444) are labeled in the inner and outer pies separately. (B) Frequency of mRNA and lncRNA in transcriptome profile collected from different data sources and final intersection matrix used for analysis. The color of the bars corresponds to different gene biotypes. (C) The bar plot shows the tissues of the top 10 highest BTSI value for each biofluid type from whole transcriptome view. Only tissues significantly correlated with biofluid (Spearman’s correlation, p-value < 0.05) and presented higher correlation with biofluid samples than randomized GTEx samples (n = 1000; t-test, 10 times repeat, p-value < 0.05) are labeled using ‘*’. The color of each bar represents the rank of the tissue BTSI value for the corresponding biofluid. Full article ">Figure 2
Estimated mixture components of biofluids. (A) Heatmap describing the dtangle estimated tissue composition of each biofluid type. (B) Heatmap describing the 67 cell-type-specific enrichment scores of each biofluid type. Full article ">Figure 3
Biofluid–tissue correlation in mRNA and lncRNA view. (A) The bar plot at the top and heatmap at the bottom separately describe the BTSI levels between biofluids and all human tissues, as well as each human tissue in mRNA (left) and lncRNA (right). (B) The half violin plots show the comparison results of the BTSI levels between BF-mRNAs, T-mRNAs, BF-lncRNAs and T-lncRNAs before (left) and after correction (right); the dot represents the corresponding average BTSI value. ****, ** and * are used to label the p-values of the t-test results (p-value < 0.0001, p-value < 0.01, p-value < 0.05). (C) The scatter plot demonstrates the correlation between BTSI and the non-zero gene number of the biofluid samples in the whole transcriptome (left), mRNA (middle) and lncRNA (right). The R2 and p-values of the linear regression results are labeled. Full article ">Figure 4
Potential influencing factor of biofluid–tissue correlation. Boxplot depicting the comparison results of the BTSI levels between biofluids and tissues taken from female donors and male donors from the whole transcriptome (A), mRNA (B) and lncRNA (C); the middle line of each box represents the corresponding median BTSI value. The colors of each boxplot indicate biological sexes of biofluid and tissue donors, including both female (F~F), both male (M~M) and different sexes (female biofluid~male tissue or male biofluid~female tissue, F~M). Relevant comparisons were performed with t-test, and the resulting p-values are provided at the top of each boxplot. Full article ">Figure 5
Functional enrichment analysis of highly variable genes (HVGs) and lowly variable genes (LVGs) across biofluid transcriptomes. The bar plots depict functional enrichment results of the top 500 HVGs (A) and LVGs (B) across the merged biofluid gene expression profiles. The colors of each bar represent different GO items, including the biological process (BP) and cellular component (CC). Full article ">

14 pages, 925 KiB T Stop Codon (p.R391*) in SERPINC1 Gene and c.1691G>A Transition (p.R506Q) in F5 Gene and Selected GWAS Multilocus Approach in Inherited Thrombophilia" data-journal="genes">

Open AccessArticle

Cis-Segregation of c.1171C>T Stop Codon (p.R391*) in SERPINC1 Gene and c.1691G>A Transition (p.R506Q) in F5 Gene and Selected GWAS Multilocus Approach in Inherited Thrombophilia

by Donato Gemmati, Giovanna Longo, Eugenia Franchini, Juliana Araujo Silva, Ines Gallo, Barbara Lunghi, Stefano Moratelli, Iva Maestri, Maria Luisa Serino and Veronica Tisato

Genes 2021, 12(6), 934; https://doi.org/10.3390/genes12060934 - 18 Jun 2021

Cited by 10 | Viewed by 3383

Abstract

Inherited thrombophilia (e.g., venous thromboembolism, VTE) is due to rare loss-of-function mutations in anticoagulant factors genes (i.e., SERPINC1, PROC, PROS1), common gain-of-function mutations in procoagulant factors genes (i.e., F5, F2), and acquired risk conditions. Genome Wide Association Studies [...] Read more.

Inherited thrombophilia (e.g., venous thromboembolism, VTE) is due to rare loss-of-function mutations in anticoagulant factors genes (i.e., SERPINC1, PROC, PROS1), common gain-of-function mutations in procoagulant factors genes (i.e., F5, F2), and acquired risk conditions. Genome Wide Association Studies (GWAS) recently recognized several genes associated with VTE though gene defects may unpredictably remain asymptomatic, so calculating the individual genetic predisposition is a challenging task. We investigated a large family with severe, recurrent, early-onset VTE in which two sisters experienced VTE during pregnancies characterized by a perinatal in-utero thrombosis in the newborn and a life-saving pregnancy-interruption because of massive VTE, respectively. A nonsense mutation (CGA > TGA) generating a premature stop-codon (c.1171C>T; p.R391*) in the exon 6 of SERPINC1 gene (1q25.1) causing Antithrombin (AT) deficiency and the common missense mutation (c.1691G>A; p.R506Q) in the exon 10 of F5 gene (1q24.2) (i.e., FV Leiden; rs6025) were coinherited in all the symptomatic members investigated suspecting a cis-segregation further confirmed by STR-linkage-analyses [i.e., SERPINC1 IVS5 (ATT)_5–18, F5 IVS2 (AT)_6–33 and F5 IVS11 (GT)_12–16] and SERPINC1 intragenic variants (i.e., rs5878 and rs677). A multilocus investigation of blood-coagulation balance genes detected the coexistence of FV Leiden (rs6025) in trans with FV HR2-haplotype (p.H1299R; rs1800595) in the aborted fetus, and F11 rs2289252, F12 rs1801020, F13A1 rs5985, and KNG1 rs710446 in the newborn and other members. Common selected gene variants may strongly synergize with less common mutations tuning potential life-threatening conditions when combined with rare severest mutations. Merging classic and newly GWAS-identified gene markers in at risk families is mandatory for VTE risk estimation in the clinical practice, avoiding partial risk score evaluation in unrecognized at risk patients. Full article

(This article belongs to the Special Issue Genetics and Genomics of Vascular, Glomerular Disorders and Thrombosis)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
(a) Full pedigree of the original family. Black symbols refer to thrombotic subjects carrying the combined AT-FV Leiden defect (i.e., SERPINC1-F5 mutations). Grey symbols refer to thrombotic subjects in the absence of any identified defect. The asterisk indicates an asymptomatic carrier of a single F5 p.R506Q defect. The triangle symbol indicates aborted fetus. Dashed frame indicates subfamily described in <a href="#genes-12-00934-f001" class="html-fig">Figure 1</a>b. (b). Extended pedigree of the previous investigated family [<a href="#B2-genes-12-00934" class="html-bibr">2</a>]. This is part of the full pedigree shown in <a href="#genes-12-00934-f001" class="html-fig">Figure 1</a>a (dashed frame). The different symbols are specified in figure legend (bottom left of the figure). The triangle symbol indicates aborted fetus. Strike-through symbols indicate dead individuals. Full article ">Figure 1 Cont.
(a) Full pedigree of the original family. Black symbols refer to thrombotic subjects carrying the combined AT-FV Leiden defect (i.e., SERPINC1-F5 mutations). Grey symbols refer to thrombotic subjects in the absence of any identified defect. The asterisk indicates an asymptomatic carrier of a single F5 p.R506Q defect. The triangle symbol indicates aborted fetus. Dashed frame indicates subfamily described in <a href="#genes-12-00934-f001" class="html-fig">Figure 1</a>b. (b). Extended pedigree of the previous investigated family [<a href="#B2-genes-12-00934" class="html-bibr">2</a>]. This is part of the full pedigree shown in <a href="#genes-12-00934-f001" class="html-fig">Figure 1</a>a (dashed frame). The different symbols are specified in figure legend (bottom left of the figure). The triangle symbol indicates aborted fetus. Strike-through symbols indicate dead individuals. Full article ">Figure 2
Sequence analysis of SERPINC1 gene showing: p.R391* STOP-codon (upper panel); p.Q337Q synonymous variant (middle panel); intronic (IVS 6–7) C > G variant (rs677) (lower panel). Full article ">

15 pages, 2676 KiB

Open AccessArticle

A Methodological Framework to Discover Pharmacogenomic Interactions Based on Random Forests

by Salvatore Fasola, Giovanna Cilluffo, Laura Montalbano, Velia Malizia, Giuliana Ferrante and Stefania La Grutta

Genes 2021, 12(6), 933; https://doi.org/10.3390/genes12060933 - 18 Jun 2021

Cited by 2 | Viewed by 2170

Abstract

The identification of genomic alterations in tumor tissues, including somatic mutations, deletions, and gene amplifications, produces large amounts of data, which can be correlated with a diversity of therapeutic responses. We aimed to provide a methodological framework to discover pharmacogenomic interactions based on [...] Read more.

The identification of genomic alterations in tumor tissues, including somatic mutations, deletions, and gene amplifications, produces large amounts of data, which can be correlated with a diversity of therapeutic responses. We aimed to provide a methodological framework to discover pharmacogenomic interactions based on Random Forests. We matched two databases from the Cancer Cell Line Encyclopaedia (CCLE) project, and the Genomics of Drug Sensitivity in Cancer (GDSC) project. For a total of 648 shared cell lines, we considered 48,270 gene alterations from CCLE as input features and the area under the dose-response curve (AUC) for 265 drugs from GDSC as the outcomes. A three-step reduction to 501 alterations was performed, selecting known driver genes and excluding very frequent/infrequent alterations and redundant ones. For each model, we used the concordance correlation coefficient (CCC) for assessing the predictive performance, and permutation importance for assessing the contribution of each alteration. In a reasonable computational time (56 min), we identified 12 compounds whose response was at least fairly sensitive (CCC > 20) to the alteration profiles. Some diversities were found in the sets of influential alterations, providing clues to discover significant drug-gene interactions. The proposed methodological framework can be helpful for mining pharmacogenomic interactions. Full article

(This article belongs to the Special Issue Pharmacogenomics: Challenges and Future)

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Figure 1
(A) Alteration dataset with the 48,270 rows (alteration types, reported on the x-axis) and the 648 columns (cell lines, reported on the y-axis) in increasing order of alteration frequency. Black dots indicate altered cells. Frequency (percentages) above the plot indicate row positions at which those alteration frequencies are reached for the first time; (B) Response dataset with the 265 rows (compounds, reported on the x-axis) in increasing order of sample size, and the 648 columns (cell lines, reported on the y-axis) in increasing order of alteration frequency. Grey dots indicate missing AUCs. The two frequencies (percentages) above the plot indicate the largest and smallest number of missing AUCs, respectively. Full article ">Figure 2
(A) Concordance correlation coefficient (CCC) between alteration variances/squared correlations before and after missing data removal, as a function of sample size; (B) Frequency of variances/correlations violating the thresholds set, as a function of sample size. Full article ">Figure 3
(A) Computational times elapsed as a function of sample size. The p-value is from linear regression (red line); (B) Distribution of the stability indicator through the 265 models. Full article ">Figure 4
(A) Concordance correlation coefficient (CCC) distribution through the 265 Random Forests; (B) CCC as a function of sample size; (C) CCC as a function of average compound AUC. The p-values are from linear regressions (red lines). Dashed lines correspond to the thresholds of no concordance (CCC = 0) and fair concordance (CCC = 20). Full article ">Figure 5
Graphical inspection of a drug-gene interaction involving the two compounds PLX4720 and Nutlin-3a, and the two alterations BRAF.V600E_MUT and TP53_MUT. Boxplots represent the median (central line), the mean (square), 25th–75th percentiles (box), and min-max non-outlier values (whiskers); p-values are from the t-test. Full article ">Figure 6
Graphical inspection of a drug-gene interaction involving the two compounds Dabrafenib and Afatinib (rescreen), and the two alterations BRAF.V600E_MUT and IKZF3_AMP. Boxplots represent the median (central line), the mean (square), 25th–75th percentiles (box), and min-max non-outlier values (whiskers); p-values are from the t-test. Full article ">

11 pages, 35971 KiB

Open AccessArticle

Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport

by Fabien Lombardo, Pietro Gramazio and Hiroshi Ezura

Genes 2021, 12(6), 932; https://doi.org/10.3390/genes12060932 - 18 Jun 2021

Cited by 6 | Viewed by 2672

Abstract

The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of [...] Read more.

The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species. Full article

(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)

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Figure 1

Figure 1
The larger fruits of hws-1 are associated with wider pedicels. (a) Pedicels carrying fruits aged from 7 to 16 DAA (○: 7~9; □: 11~12; ⋄: 13~14; Δ: 15~16) were cut halfway between the fruit and the abscission zone. (b) Pedicels of hws-1 are markedly wider than their WT counterparts, and the differences are statistically significant with <math display="inline"><semantics> <mrow> <mi>p</mi> <mo><</mo> <mn>0.001</mn> </mrow> </semantics></math> in an unpaired t-test. In both (a,b), section areas were measured using the ImageJ software [<a href="#B17-genes-12-00932" class="html-bibr">17</a>,<a href="#B18-genes-12-00932" class="html-bibr">18</a>]; <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>60</mn> </mrow> </semantics></math>. Full article ">Figure 2
Transverse sections of representative pedicels showing wider phloem and narrower xylem rings in hws-1. All sections were stained with toluidine blue prior to light microscopy observation. (a) Sections of WT pedicels. Each section is reconstructed from four segments of different pedicels. Segments are shown in a increasing diameter arrangement, clockwise from the bottom left segment. pp, pith parenchyma; Pi, internal phloem; X, xylem; Pe, external phloem; Co, collenchyma; s, sclerenchyma (blue-green stained); E, epidermis. Scale bar represents 250 <math display="inline"><semantics> <mi mathvariant="sans-serif">μ</mi> </semantics></math><math display="inline"><semantics> <mi mathvariant="normal">m</mi> </semantics></math>. (b) Sections of hws-1 pedicels, similarly to (a). (c) Details of selected WT and hws-1 pedicels with comparable diameters, showing vascular elements of strikingly different sizes. Scale bar represents 100 <math display="inline"><semantics> <mi mathvariant="sans-serif">μ</mi> </semantics></math><math display="inline"><semantics> <mi mathvariant="normal">m</mi> </semantics></math>. (d) Lower magnification of pedicels in c, shown for reference. Scale bar represents 300 <math display="inline"><semantics> <mi mathvariant="sans-serif">μ</mi> </semantics></math><math display="inline"><semantics> <mi mathvariant="normal">m</mi> </semantics></math>. Full article ">Figure 3
Phloem exudates from hws-1 contain more sugar than WT ones. Pedicels carrying 8 DAA to 20 DAA-old fruits were cut and phloem exudates were collected for seven of the dark hours in EDTA-HEPES. (a) Average glucose concentration in phloem sap exudates (b) Similarly to (a) for fructose (c) Similarly to (a) for sucrose. Bars represent mean values with standard deviation. Unpaired t-tests indicate significant differences (annotated with * on the graphs) for all three sugars at the <math display="inline"><semantics> <mrow> <mi>p</mi> <mo><</mo> <mn>0.05</mn> </mrow> </semantics></math> level (<math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>26</mn> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>15</mn> </mrow> </semantics></math> for WT and hws-1, resp.). Full article ">Figure 4
Light-response curves show comparable photosynthetic assimilation between WT and mutant lines. Photosynthetic assimilation was measured on the fourth leaves of 1-month-old plants. Error bars represent standard deviation. Unpaired t-tests indicate that difference are not significant at the <math display="inline"><semantics> <mrow> <mi>p</mi> <mo><</mo> <mn>0.05</mn> </mrow> </semantics></math> level (<math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>8</mn> </mrow> </semantics></math>). Full article ">Figure 5
HWS orthologs and putative orthologs in crops of interest. The alignement was performed using Clustal Omega [<a href="#B20-genes-12-00932" class="html-bibr">20</a>]. Note that there is some uncertainty about the translational start of the OsEP3 gene [<a href="#B9-genes-12-00932" class="html-bibr">9</a>]; the sequence displayed here is a truncated version of the originally published one [<a href="#B12-genes-12-00932" class="html-bibr">12</a>]. Full article ">

11 pages, 14373 KiB

Open AccessArticle

Altered Expression of TSPAN32 during B Cell Activation and Systemic Lupus Erythematosus

by Paolo Fagone, Katia Mangano, Roberto Di Marco, Zyanya Reyes-Castillo, José Francisco Muñoz-Valle and Ferdinando Nicoletti

Genes 2021, 12(6), 931; https://doi.org/10.3390/genes12060931 - 18 Jun 2021

Cited by 5 | Viewed by 2335

Abstract

Systemic lupus erythematosus (SLE) is a chronic inflammatory disease with various clinical features. Autoreactive B cells play a role in disease pathogenesis, through the production of multiple autoantibodies, which form immune complexes and induce the inflammatory response and tissue damage associated with SLE. [...] Read more.

Systemic lupus erythematosus (SLE) is a chronic inflammatory disease with various clinical features. Autoreactive B cells play a role in disease pathogenesis, through the production of multiple autoantibodies, which form immune complexes and induce the inflammatory response and tissue damage associated with SLE. Recently, tetraspanins, and in particular, TSPAN32, have been recognized to play a central role in immunity, as they are involved in various biological processes, such as the antigen presentation and the activation of lymphocytes. Evidence suggests that tetraspanins could represent in the future a target for therapeutic purposes in patients suffering from autoimmune/immunoinflammatory disorders. In the present study, by performing in silico analyses of high-throughput data, we evaluated the expression levels of TSPAN32 in B cell activation and investigated its modulation in circulating B cells from SLE patients. Our data show that B cell activation is associated with a significant downregulation of TSPAN32. Additionally, significantly lower levels of TSPAN32 were observed in circulating plasmablasts from SLE patients as compared to healthy donor plasmablasts. In addition, type I interferons (IFNs)-related genes were enriched among the genes negatively correlated to TSPAN32, in SLE plasmablasts. Accordingly, IFN-α is able to induce a dose-dependent downregulation of TSPAN32 in B cells. Overall, the data here presented suggest the potential use of TSPAN32 as a diagnostic marker and therapeutic target for the evaluation and management of humoral immune responses in chronic diseases, such as SLE. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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Figure 1
Modulation of TSPAN32 expression in B cells following activation. The transcription levels of TSPAN32 during the activation of B cells were evaluated using the publicly available GSE15606, GSE20477, GSE35998, GSE84948, and GSE147497 datasets. (A) TSPAN32 expression levels in murine primary B-lymphocytes purified from spleens and stimulated with IL-4 (5 ng/mL) and CD40L (200 ng/mL) and anti-mouse IgM (2.5 μg/mL) for 3 h were obtained from the GSE15606 dataset. (B) TSPAN32 expression data in primary B lymphocytes stimulated with 10 μg/mL anti-IgM for 30 min, then incubated for 0.5, 1, 3, and 6 h were retrieved from the GSE20477 dataset. (C) TSPAN32 gene expression profiles of naïve B cells, B cells activated with LPS, and B cells activated with LPS + anti-CD40 for 24 and 72 h were obtained from the GSE35998 dataset. (D) TSPAN32 levels in B cells cultured in the presence of either Th1 or Th2 polarized CD4+ T cells for 1–4 days were retrieved from the GSE84948 dataset. (E) TSPAN32 expression data in B cells activated with LPS and collected at 3 and 10 h post-stimulation, as well as data from expanded activated B cells and plasmablasts collected at day 4 post-stimulation were retrieved from the GSE147497 dataset. Full article ">Figure 2
Transcriptional levels of TSPAN32 in B cell subpopulations from SLE patients. The expression levels of TSPAN32 and of the related family of tetraspanins in B cell subpopulations from 4 SLE patients and 4 healthy donors were obtained from the GSE156751 dataset. (A) TSPAN32 levels in naive B cells, memory B cells, and plasmablasts from SLE patients and healthy donors. (B) Heatmap showing the expression levels of TSPAN32 and related tetraspanins in naïve B cells, memory B cells, and plasmablasts from SLE patients and healthy donors. (C) Gene similarity matrix for all the analyzed tetraspanins calculated using the spearman rank correlation, as similarity metrics, on the samples included in the GSE156751 dataset. Full article ">Figure 3
Gene Ontology and MCODE analysis for the genes that correlated most with TSPAN32 in SLE plasmablasts. Genes significantly correlated to TSPAN32 in SLE plasmablasts were identified by calculating the cosine similarity and the statistical significance was computed using a permutation test, with 1000 random permutations. (A) Hierarchical clustering showing the most enriched biological processes and gene ontologies among the genes significantly correlated to TSPAN32, as determined using the web-based utility, Metascape. (B) MCODE (Molecular Complex Detection) clusters enriched among the genes significantly correlated to TSPAN32. (C) MCODE clusters showing the genes based on their correlation to TSPAN32. Full article ">Figure 4
IFN-α downregulates TSPAN32 expression. (A) Expression levels of TSPAN32 in CD19+ B cells isolated from splenocytes of 6-week-old male C57BL/6mice, treated with 5 10-scalar concentrations of IFN-α (range 0.1–1000 U/mL) for 2 h, as determined from the GSE75194 dataset. (B) The levels of TSPAN32 were evaluated in splenocytes from IFN-α transgenic mice, as obtained from the analysis of the publicly available GSE123549 dataset. Full article ">

12 pages, 547 KiB

Open AccessArticle

Association of TGF-β1 and IL-10 Gene Polymorphisms with Osteoporosis in a Study of Taiwanese Osteoporotic Patients

by Min-Yu Tu, Kuei-Yang Han, Ying-Wei Lan, Ku-Yi Chang, Cheng-Wei Lai, Theresa Staniczek, Chung-Yu Lai, Kowit-Yu Chong and Chuan-Mu Chen

Genes 2021, 12(6), 930; https://doi.org/10.3390/genes12060930 - 18 Jun 2021

Cited by 11 | Viewed by 2644

Abstract

Osteoporosis is a rising health threat in the increasingly aging world population. It is a common skeletal disease strongly linked to genetic predisposition. We aim to identify the effects of the anti-inflammatory TGF-β1- and IL-10-specific single-nucleotide polymorphism (SNP) combination on the [...] Read more.

Osteoporosis is a rising health threat in the increasingly aging world population. It is a common skeletal disease strongly linked to genetic predisposition. We aim to identify the effects of the anti-inflammatory TGF-β1- and IL-10-specific single-nucleotide polymorphism (SNP) combination on the risk for osteoporosis. We investigated and analyzed the relationships between three TGF-β1 SNPs (−509C/T, +869 T/C and +29T/C), one IL-10 SNP (+1927A/C) and the level of bone mineral density (BMD), as well as the risk of osteoporosis in Taiwanese osteoporotic patients. A total of 217 subjects were recruited, including 88 osteoporotic patients and 129 healthy controls, for SNPs, BMD and clinical characteristics statistical analyses. Females with TGF-β1 SNP (−509 C/C) and IL-10 SNP (+1927 C/C) genotypes showed a great benefit for femoral neck T-scores. However, the combination of TGF-β1 SNP (−509 T/T) and IL-10 SNP (+1927 A/A) genotypes in all subjects showed a significant decrease in total hip BMD T-scores. The TGF-β1 SNP (−509 C/T) genotype in all subjects and TGF-β1 SNP (−509 T/T) and IL-10 SNP (+1927 A/C) genotypes in males showed positive effects on body height. The combination of the many SNPs in the anti-inflammatory TGF-β1 and IL-10 genes may be cooperatively involved in the development of osteoporosis. Our data suggested that the specific SNP combination of TGF-β1 (−509) and IL-10 (+1927) may act as a predictive factor for postmenopausal osteoporosis in Taiwanese women. Full article

(This article belongs to the Special Issue Key Genetic Determinants of Osteoporosis: From Bench to Bedside)

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9 pages, 530 KiB

Open AccessArticle

Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria

by Christen Grettenberger, Dawn Y. Sumner, Jonathan A. Eisen, Anne D. Jungblut and Tyler J. Mackey

Genes 2021, 12(6), 929; https://doi.org/10.3390/genes12060929 - 18 Jun 2021

Cited by 1 | Viewed by 2960

Abstract

The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of [...] Read more.

The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of aerobic respiration likely evolved after the evolution of oxygenic photosynthesis. However, complex I of the respiratory complex chain can be involved in anaerobic processes and, therefore, may have pre-dated the evolution of oxygenic photosynthesis. If so, aerobic respiration may have built upon respiratory chains that pre-date the rise of oxygen in Earth’s atmosphere. The Melainabacteria provide a unique opportunity to examine this hypothesis because they contain genes for aerobic respiration but likely diverged from the Cyanobacteria before the evolution of oxygenic photosynthesis. Here, we examine the phylogenies of translated complex I sequences from 44 recently published Melainabacteria metagenome assembled genomes and genomes from other Melainabacteria, Cyanobacteria, and other bacterial groups to examine the evolutionary history of complex I. We find that complex I appears to have been present in the common ancestor of Melainabacteria and Cyanobacteria, supporting the idea that aerobic respiration built upon respiratory chains that pre-date the evolution of oxygenic photosynthesis and the rise of oxygen. Full article

(This article belongs to the Special Issue Genomics, Metagenomics and Phylogenomics of Cyanobacteria and Related Lineages)

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13 pages, 2522 KiB

Open AccessReview

The Crazy Ovary

by Philippe Monget, Ken McNatty and Danielle Monniaux

Genes 2021, 12(6), 928; https://doi.org/10.3390/genes12060928 - 18 Jun 2021

Cited by 15 | Viewed by 4864

Abstract

From fetal life until senescence, the ovary is an extremely active tissue undergoing continuous structural and functional changes. These ever-changing events are best summarized by a quotation attributed to Plato when describing motion in space and time—‘nothing ever is but is always becoming…’. [...] Read more.

From fetal life until senescence, the ovary is an extremely active tissue undergoing continuous structural and functional changes. These ever-changing events are best summarized by a quotation attributed to Plato when describing motion in space and time—‘nothing ever is but is always becoming…’. With respect to the ovary, these changes include, at the beginning, the processes of follicular formation and thereafter those of follicular growth and atresia, steroidogenesis, oocyte maturation, and decisions relating to the number of mature oocytes that are ovulated for fertilization and the role of the corpus luteum. The aims of this review are to offer some examples of these complex and hitherto unknown processes. The ones herein have been elucidated from studies undertaken in vitro or from normal in vivo events, natural genetic mutations or after experimental inactivation of gene function. Specifically, this review offers insights concerning the initiation of follicular growth, pathologies relating to poly-ovular follicles, the consequences of premature loss of germ cells or oocytes loss, the roles of AMH (anti-Müllerian hormone) and BMP (bone morphogenetic protein) genes in regulating follicular growth and ovulation rate together with species differences in maintaining luteal function during pregnancy. Collectively, the evidence suggests that the oocyte is a key organizer of normal ovarian function. It has been shown to influence the phenotype of the adjacent somatic cells, the growth and maturation of the follicle, and to determine the ovulation rate. When germ cells or oocytes are lost prematurely, the ovary becomes disorganized and a wide range of pathologies may arise. Full article

(This article belongs to the Special Issue Genetic and Genomic Regulation of Ovarian and Testicular Functions in Animals)

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Ovarian fragmentation, in vitro Akt stimulation and auto-grafting promoted follicle growth in POI (premature ovarian insufficiency) patients and generated mature oocytes are able to be fertilized in vitro leading to a pregnancy and a baby after embryo transfer. Ovaries removed under laparoscopic were cut into strips, the latter being vitrified. After thawing, strips were fragmented into small cubes (1–2 mm3) that disrupted the Hippo signaling pathway, and treated with Akt stimulators (bpV (hopic) and 740YP). Forty-eight hours later, cubes were autografted under laparoscopic surgery beneath serosa of Fallopian tubes. After detection of antral follicles via transvaginal ultrasound, patients were treated with gonadotrophins, and mature oocytes were subjected to IVF (in vitro fertilization) before cryopreservation of four-cell stage embryos. Patients then received hormonal treatments to prepare the endometrium for implantation followed by transferring of thawed embryos. Several babies have been born using this technique around the world ([<a href="#B3-genes-12-00928" class="html-bibr">3</a>], with permission). Full article ">Figure 2
Summary of the ovarian and reproductive features of Omcg1ocKo females. Oocyte death and arrest of folliculogenesis at the primary follicle stage, leading to a kind of premature ovarian insufficiency (POI), were observed in Omcg1ocKo females. The ovarian somatic compartment was remodeled, allowing the production of oestradiol (E2), which might occur along a two-cell compartment scheme similar to what is found between theca cells and granulosa cells in preovulatory follicles. Surprisingly, despite the absence of cyclic follicular growth and then of preovulatory follicles, Omcg1ocKo females displayed features of sexual cyclicity as wild-type mice (adapted from [<a href="#B4-genes-12-00928" class="html-bibr">4</a>]). Full article ">Figure 3
Representative micrographs of ovary sections from Fancd2-WT (A) and Fancd2-KO (B–J) mice at 2.5 (A–C), 5–9 (D–I) and 12 (J) months of age after birth. Note the appearance of primordial (arrow) (B), preantral (arrowhead) (B) and antral (C) follicles in ovaries of Fancd2-KO mice similar to that in WT mice (A). Common abnormal ovarian phenotypes in Fancd2-KO mince include: the formation of numerous sex cords (arrows) (D); tubules (high magnification inset, arrow) (E); invagination of ovarian surface epithelium (high magnification inset, arrow) (F); cystic papillary hyperplasia (high magnification inset, (G); luteomas containing large areas of cells of spongy appearance (high magnification inset, (H); cystadenocarcinoma whereby mitotically-active cells are invading extraovarian fat cells High magnification inset, (I) and; large areas containing numerous tumour phenotypes of epithelial origin, including adenocarcinomas (arrows) (J). Reproduced with permission from UPV/EHU Press from [<a href="#B9-genes-12-00928" class="html-bibr">9</a>]. Full article ">Figure 4
Schematic representation of some mechanisms currently known to regulate germ cell cyst breakdown and follicle assembly in the fetal or neonatal ovary. A germ cell cyst is represented (delineated by a dotted line), containing oocytes (blue round cells) and pre-granulosa cells (small pink cells). Some known interactions between germ and somatic cells participating to these processes are zoomed in the right part of the figure (adapted from [<a href="#B32-genes-12-00928" class="html-bibr">32</a>]). Full article ">Figure 5
Differences between the bovine and porcine species in terms of anti-Müllerian hormone (AMH) production that could explain the regulation of ovulation number. We propose this model to explain a potential role of AMH in the regulation of the ovulation rate in porcine compared to bovine ovaries. Porcine AMH promoter and porcine granulosa cells are less sensitive to bone morphogenetic protein (BMP) stimulation, leading to a low production of AMH by porcine compared to bovine growing antral follicles. As AMH is known to be an inhibitor primordial follicle activation, this low level of AMH in the pig would lead to a huge number of growing follicles in the porcine compared to the bovine species. The reduced BMP sensitivity of granulosa cells and the low intra-follicular AMH concentrations of antral follicles could contribute to sensitizing granulosa cells to FSH (follicle stimulating hormone), resulting in a high follicular survival rate in the cohort of terminally developing follicles and a higher ovulation rate in the porcine, compared to the bovine species (from [<a href="#B45-genes-12-00928" class="html-bibr">45</a>], with permission). Full article ">Figure 6
Poly-ovulation in ewes carrying loss of function mutations in the ovarian BMP system. It seems that BMP15 and GDF9 determine the stage at which follicular maturation occurs. In the case of loss of function, one can consider these mutations as having “brake-release” functions, thereby resulting in follicles ready to ovulate at smaller diameters. Additionally, as these mutations have no consequences on the capacity of oestradiol secretion by granulosa cells ([<a href="#B52-genes-12-00928" class="html-bibr">52</a>] for Booroola mutants; [<a href="#B53-genes-12-00928" class="html-bibr">53</a>] for heterozygous BMP15 mutant), we can hypothesize that the increase in the ovulation rate is due to the need to have a sufficient number of granulosa cells to secrete enough oestradiol necessary for the induction of the GnRH surge [<a href="#B54-genes-12-00928" class="html-bibr">54</a>]. Full article ">Figure 7
Evolution and diversity of non-steroidal luteotrophic factors in eutherians. In primates, duplication of the luteinizing hormone (LH) gene generated chorionic gonadotropins (CG), which are expressed by trophoblast and impair corpus luteum lysis in the first months of pregnancy. In rodents, pituitary prolactin (PRL) released in response to coitus inhibits 20-hydroxysteroid dehydrogenase (20α-HSD), this function being subsequently assumed by placental lactogens (PL-1 and PL-2). In ruminants, duplication of the IFNW gene generated interferon-τ (IFNT) secreted by the blastocyst and acting on the endometrium to inhibit the prostaglandin F2α (PGF2α) luteolytic signal. In elephants, the PRL gene expressed in the placenta is responsible for pregnancy maintenance by accessory corpora lutea. In red, proteins born after gene duplication (adapted from [<a href="#B58-genes-12-00928" class="html-bibr">58</a>]). Full article ">

12 pages, 2716 KiB

Open AccessArticle

Ocular Involvement in Hereditary Transthyretin Amyloidosis: A Case Series Describing Novel Potential Biomarkers

by Angelo Maria Minnella, Roberta Rissotto, Martina Maceroni, Angela Romano, Romina Fasciani, Marco Luigetti, Mario Sabatelli, Stanislao Rizzo and Benedetto Falsini

Genes 2021, 12(6), 927; https://doi.org/10.3390/genes12060927 - 18 Jun 2021

Cited by 13 | Viewed by 2475

Abstract

Hereditary transthyretin amyloidosis (hATTR) is a rare disease caused by a point mutation in the transthyretin (TTR) gene and inherited in an autosomal dominant fashion. TTR is a plasma protein that functions as a carrier for thyroxine (T4) and retinol (vitamin A). Ophthalmological [...] Read more.

Hereditary transthyretin amyloidosis (hATTR) is a rare disease caused by a point mutation in the transthyretin (TTR) gene and inherited in an autosomal dominant fashion. TTR is a plasma protein that functions as a carrier for thyroxine (T4) and retinol (vitamin A). Ophthalmological manifestations are due to both the hepatic and ocular production of mutated TTR. In this case series, we report the ocular manifestations of hATTR in eighteen eyes of nine consecutive patients. Corneal nerve abnormalities as well as morphological and functional changes in the retina were investigated. The study was a single-center, retrospective, observational, clinical case series. In all patients, corneal confocal microscopy (CCM), multimodal imaging of the retina, including fundus photography and Optical Coherence Tomography (OCT), as well as rod and cone electroretinography (ERG) were performed. Eight patients had active disease and one was an unaffected carrier. In all study eyes, corneal nerve plexa examined with CCM were poorly represented or absent. Mixed rod-cone and cone ERG b-wave amplitudes were reduced, and photopic b-wave responses were significantly delayed. Photopic Negative Response (PhNR) amplitude was significantly reduced, while PhNR latency was significantly augmented. In 13/18 eyes, vitreous opacities and abnormalities of vitreo-retinal interface were found. The current results highlight the presence of corneal nerve damage. Functional retinal abnormalities, detected by ERG, can be found even in the presence of minimal or absent structural retinal damage. These findings support the use of CCM and ERGs to detect early biomarkers for primary hATTR. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Neuromuscular Disorders)

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21 pages, 1736 KiB

Open AccessReview

How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

by Harmen P. Doekes, Piter Bijma and Jack J. Windig

Genes 2021, 12(6), 926; https://doi.org/10.3390/genes12060926 - 18 Jun 2021

Cited by 58 | Viewed by 7377

Abstract

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as [...] Read more.

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates. Full article

(This article belongs to the Special Issue Inbreeding)

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15 pages, 20440 KiB

Open AccessArticle

Kinase Inhibitors of DNA-PK, ATM and ATR in Combination with Ionizing Radiation Can Increase Tumor Cell Death in HNSCC Cells While Sparing Normal Tissue Cells

by Eva-Maria Faulhaber, Tina Jost, Julia Symank, Julian Scheper, Felix Bürkel, Rainer Fietkau, Markus Hecht and Luitpold V. Distel

Genes 2021, 12(6), 925; https://doi.org/10.3390/genes12060925 - 17 Jun 2021

Cited by 20 | Viewed by 3924

Abstract

(1) Kinase inhibitors (KI) targeting components of the DNA damage repair pathway are a promising new type of drug. Combining them with ionizing radiation therapy (IR), which is commonly used for treatment of head and neck tumors, could improve tumor control, but could [...] Read more.

(1) Kinase inhibitors (KI) targeting components of the DNA damage repair pathway are a promising new type of drug. Combining them with ionizing radiation therapy (IR), which is commonly used for treatment of head and neck tumors, could improve tumor control, but could also increase negative side effects on surrounding normal tissue. (2) The effect of KI of the DDR (ATMi: AZD0156; ATRi: VE-822, dual DNA-PKi/mTORi: CC-115) in combination with IR on HPV-positive and HPV-negative HNSCC and healthy skin cells was analyzed. Cell death and cell cycle arrest were determined using flow cytometry. Additionally, clonogenic survival and migration were analyzed. (3) Studied HNSCC cell lines reacted differently to DDRi. An increase in cell death for all of the malignant cells could be observed when combining IR and KI. Healthy fibroblasts were not affected by simultaneous treatment. Migration was partially impaired. Influence on the cell cycle varied between the cell lines and inhibitors; (4) In conclusion, a combination of DDRi with IR could be feasible for patients with HNSCC. Side effects on healthy cells are expected to be limited to normal radiation-induced response. Formation of metastases could be decreased because cell migration is impaired partially. The treatment outcome for HPV-negative tumors tends to be improved by combined treatment. Full article

(This article belongs to the Special Issue Mechanisms of DNA Damage, Repair and Mutagenesis)

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Graphical abstract
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Gating strategies for cell death and cell cycle data and dose escalation studies. (A) Dot plot of CAL33 cells untreated, treated with AZD0156, irradiated with 2 Gy, and combined IR and KI treatment to demonstrate the gating strategy of cell death data acquired from flow cytometry analysis. (B) Exemplary histograms depicting flow cytometry analysis of cell cycle with focus on G0/G1 and G2/M phases. Histograms show CAL33 cells untreated, treated with AZD0156, irradiated with 2 Gy, and combined IR and KI treatment. (C) Dose escalation study for the induction of apoptosis or necrosis (cell death) by the inhibitors CC 115, AZD0156, and VE 822 conducted on HSC4 and CAL33 cells. Each value represents mean ± SD (n = 3). Full article ">Figure 2
Flow cytometry analysis of cell death. Cells are grouped into normal donor cells (SBLF7, SBLF9), HPV-negative (HSC4, CAL33), and HPV-positive (UM SCC 47, UD SCC 2) HNSCC cell lines. Cell death was determined through flow cytometry by apoptosis (Annexin V) and necrosis (7AAD) detection. Irradiated samples are compared to non-irradiated samples. Effects of increasing concentrations of kinase inhibitors on each cell line are shown. For CC 115 and AZD0156 0.5, 1 and 2 µM, for VE 822 0.1 and 0.5 µM of the inhibitor were used. Each value represents mean ± SD (n ≥ 3). Significance was determined by two-tailed Mann Whitney U test * p ≤ 0.05 and ** p ≤ 0.01. Full article ">Figure 3
Cell cycle analysis. Cells are grouped into normal donor cells (SBLF7, SBLF9) and HPV-negative (HSC4, CAL33), and HPV-positive (UM SCC 47, UD SCC 2) HNSCC cell lines. The graphs show the proportion of cells in the G2/M phase of the cell cycle and the alteration of G2/M phase under treatment. Cells were either untreated or received IR, KI, or a combination of IR and KI. For CC 115 and AZD0156 1 µM was used, for VE 822 0.1 µM was used. Each value represents mean ± SD (n ≥ 3). Significance was determined by two-tailed Mann Whitney U test * p ≤ 0.05 and ** p ≤ 0.01. Full article ">Figure 4
Colony forming assay of HNSCC cell lines and normal controls. Cells are shown grouped into normal cells (SBLF7, SBLF9) and HPV-negative (HSC4, CAL33), and HPV-positive (UM SCC 47, UD SCC 2) HNSCC cells. Graphs show cell survival at 0 Gy and 2 Gy, either with additional treatment of kinase inhibitors (0.5 µM CC 115, 0.5 µM AZD0156, 5 nM VE-822) or without. Additionally, cell survival under KI treatment was normalized to detect synergistic effects. Dashed line represents mean survival fraction normalized to the cytotoxicity induced by KI alone. Each value represents mean ± SD (n ≥ 3). Significance was determined by one-tailed Mann Whitney U test * p ≤ 0.05 and ** p ≤ 0.01. p = 0.004: UM SCC 47 + CC 115, UM SCC 47 + CC 115 norm., UM SCC 47 + AZD0156, and UM SCC 47 + AZD0156 norm.; UM SCC 47 + VE 822 and UM SCC 47 + VE 822 norm.; p = 0.008: CAL33 + AZD0156 and CAL33 + AZD0156 norm.; p = 0.028: CAL33 + VE 822 norm.; p = 0.016: SBLF9 + AZD0156; p = 0.018: UD SCC 2 + AZD0156 and UD SCC 2 + AZD0156 norm.; p = 0.028: UD SCC 2 + VE 822; p = 0.050: HSC4 + VE 822, HSC4 + VE 822 norm., SBLF7 + CC-115; p = 0.050: HSC4 + CC 115, HSC4 + AZD0156 and HSC4 + AZD0156 norm. Full article ">Figure 5
Analysis of cell migration over 24 and 48 h. (A) Change of scratch area over 48 h by the example of normal skin fibroblasts SBLF7 and HPV-positive HNSCC cell line UM SCC 47. Graphs show cells untreated, under IR, under KI (1 µM CC 115, 1 µM AZD0156, 0.1 µM VE 822) and under combination therapy. (B) Area under the curve (AUC) was calculated representing cell migration over 48 h of four HNSCC cell lines and two normal fibroblast cell lines for all three tested KI. Each value represents mean ± SD (n ≥ 3). Significance was determined by one tailed Mann Whitney U test * p ≤ 0.05. Full article ">

32 pages, 1239 KiB

Open AccessReview

Cytogenetics of Pediatric Acute Myeloid Leukemia: A Review of the Current Knowledge

by Julie Quessada, Wendy Cuccuini, Paul Saultier, Marie Loosveld, Christine J. Harrison and Marina Lafage-Pochitaloff

Genes 2021, 12(6), 924; https://doi.org/10.3390/genes12060924 - 17 Jun 2021

Cited by 50 | Viewed by 12803

Abstract

Pediatric acute myeloid leukemia is a rare and heterogeneous disease in relation to morphology, immunophenotyping, germline and somatic cytogenetic and genetic abnormalities. Over recent decades, outcomes have greatly improved, although survival rates remain around 70% and the relapse rate is high, at around [...] Read more.

Pediatric acute myeloid leukemia is a rare and heterogeneous disease in relation to morphology, immunophenotyping, germline and somatic cytogenetic and genetic abnormalities. Over recent decades, outcomes have greatly improved, although survival rates remain around 70% and the relapse rate is high, at around 30%. Cytogenetics is an important factor for diagnosis and indication of prognosis. The main cytogenetic abnormalities are referenced in the current WHO classification of acute myeloid leukemia, where there is an indication for risk-adapted therapy. The aim of this article is to provide an updated review of cytogenetics in pediatric AML, describing well-known WHO entities, as well as new subgroups and germline mutations with therapeutic implications. We describe the main chromosomal abnormalities, their frequency according to age and AML subtypes, and their prognostic relevance within current therapeutic protocols. We focus on de novo AML and on cytogenetic diagnosis, including the practical difficulties encountered, based on the most recent hematological and cytogenetic recommendations. Full article

(This article belongs to the Special Issue Genetics and Epigenetics of Pediatric Leukemia)

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14 pages, 1489 KiB

Open AccessArticle

Characteristics of the Diploid, Triploid, and Tetraploid Versions of a Cannabigerol-Dominant F₁ Hybrid Industrial Hemp Cultivar, Cannabis sativa ‘Stem Cell CBG’

by Seth Crawford, Brendan M. Rojas, Eric Crawford, Matthew Otten, Thecla A. Schoenenberger, Andrea R. Garfinkel and Hsuan Chen

Genes 2021, 12(6), 923; https://doi.org/10.3390/genes12060923 - 17 Jun 2021

Cited by 18 | Viewed by 6650

Abstract

Hemp (Cannabis sativa L.) has recently become an important crop due to the growing market demands for products containing cannabinoids. Unintended cross-pollination of C. sativa crops is one of the most important threats to cannabinoid production and has been shown to reduce [...] Read more.

Hemp (Cannabis sativa L.) has recently become an important crop due to the growing market demands for products containing cannabinoids. Unintended cross-pollination of C. sativa crops is one of the most important threats to cannabinoid production and has been shown to reduce cannabinoid yield. Ploidy manipulation has been used in other crops to improve agronomic traits and reduce fertility; however, little is known about the performance of C. sativa polyploids. In this study, colchicine was applied to two proprietary, inbred diploid C. sativa inbred lines, ‘TS1-3’ and ‘P163’, to produce the tetraploids ‘TS1-3 (4x)’ and ‘P163 (4x)’. The diploid, triploid, and tetraploid F₁ hybrids from ‘TS1-3’ × ‘P163’, ‘TS1-3 (4x)’ × ‘P163’, and ‘TS1-3 (4x)’ × ‘P163 (4x)’ were produced to test their fertilities, crossing compatibilities, and yields. The results indicated a reduction in fertility in the triploids and the tetraploids, relative to their diploid counterparts. When triploids were used as females, seed yields were less than 2% compared to when diploids were used as females; thus, triploids were determined to be female infertile. The triploids resulting from the crosses made herein displayed increases in biomass and inflorescence weight compared to the diploids created from the same parents in a field setting. Statistical increases in cannabinoid concentrations were not observed. Lastly, asymmetric crossing compatibility was observed between the diploids and the tetraploids of the genotypes tested. The results demonstrate the potential benefits of triploid C. sativa cultivars in commercial agriculture. Full article

(This article belongs to the Special Issue Investigations on Nuclear DNA Content and DNA Synthesis in Plants and Fungi Using Flow Cytometry and Fluorescence Microscopy)

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Crossing combinations used to produce diploid, triploid, and tetraploid F1 hybrid C. sativa plants. Colchicine treatments were applied on commercial inbred lines ‘TS1-3’ and ‘P163’ to produce tetraploid versions. The silver thiosulfate (STS) treatment was applied to ‘P163’ and ‘P163 (4x)’ plants to produce viable pollen. The diploid, triploid, and tetraploid F1 hybrids were made from crossing combinations of TS1-3 (2x) × P163 (2x), TS1-3 (4x) × P163 (2x), and TS1-3 (4x) × P163 (4x). Full article ">Figure 2
Ploidy identification by flow cytometry and chromosome squashes. Flow cytometric analysis of (A) a diploid C. sativa ‘Stem Cell CBG’ shown with the internal standard, (B) diploid, triploid, and tetraploid F1 hybrids, and (C) a tetraploid F1 hybrid and internal standard. Chromosome squash of (D) a diploid C. sativa ‘Stem Cell CBG’ (2n = 2x = 20), (E) a triploid ‘Stem Cell CBG Seedless’ (2n = 3x = 30), and (F) a tetraploid F1 hybrid (2n = 4x = 40). Internal standard (standard) = QA reference beads UV bright 3 μm (Quantum Analysis GmbH, Münster, Germany). Bar = 10 µm. Full article ">Figure 3
Results from interploidy crossing compatibility investigations of diploid, triploid, and tetraploid F1 hybrid Cannabis sativa. (A) Average seed count of the three ploidies of F1 hybrids, derived from crosses using diploid pollen donors and (B) tetraploid pollen donors. The star indicates that an average of 232.75 unfilled seeds and 0 filled seeds per plant were observed and the unfilled circle represents an observation outside of the 1.5 × inner quartile range cutoff as represented by the box and whiskers plots. (C) Seeds from several interploidy crossing combinations; one cut seed is displayed in the center of the grid to show seed development. Pericarps that developed as a result of the 2x × 4x crosses did not contain an embryo or endosperm. Bar = 1 cm. Full article ">Figure 4
Whole-plant and inflorescence architectures of diploid and triploid hybrid C. sativa plants in the field. (A) Plants 60 days following transplant growing in the field. Diploid plants are on the left and triploid plants are on the right. Bar = 30 cm. (B) Dried terminal inflorescences of three diploid (left) and three triploid C. sativa plants (right). Bar = 10 cm. Full article ">

15 pages, 1738 KiB

Open AccessArticle

Whole Exome Sequencing of 23 Multigeneration Idiopathic Scoliosis Families Reveals Enrichments in Cytoskeletal Variants, Suggests Highly Polygenic Disease

by Elizabeth A. Terhune, Cambria I. Wethey, Melissa T. Cuevas, Anna M. Monley, Erin E. Baschal, Morgan R. Bland, Robin Baschal, G. Devon Trahan, Matthew R. G. Taylor, Kenneth L. Jones and Nancy Hadley Miller

Genes 2021, 12(6), 922; https://doi.org/10.3390/genes12060922 - 16 Jun 2021

Cited by 9 | Viewed by 3868

Abstract

Adolescent idiopathic scoliosis (AIS) is a lateral spinal curvature >10° with rotation that affects 2–3% of healthy children across populations. AIS is known to have a significant genetic component, and despite a handful of risk loci identified in unrelated individuals by GWAS and [...] Read more.

Adolescent idiopathic scoliosis (AIS) is a lateral spinal curvature >10° with rotation that affects 2–3% of healthy children across populations. AIS is known to have a significant genetic component, and despite a handful of risk loci identified in unrelated individuals by GWAS and next-generation sequencing methods, the underlying etiology of the condition remains largely unknown. In this study, we performed exome sequencing of affected individuals within 23 multigenerational families, with the hypothesis that the occurrence of rare, low frequency, disease-causing variants will co-occur in distantly related, affected individuals. Bioinformatic filtering of uncommon, potentially damaging variants shared by all sequenced family members revealed 1448 variants in 1160 genes across the 23 families, with 132 genes shared by two or more families. Ten genes were shared by >4 families, and no genes were shared by all. Gene enrichment analysis showed an enrichment of variants in cytoskeletal and extracellular matrix related processes. These data support a model that AIS is a highly polygenic disease, with few variant-containing genes shared between affected individuals across different family lineages. This work presents a novel resource for further exploration in familial AIS genetic research. Full article

(This article belongs to the Special Issue Genetic Conditions Affecting the Skeleton: Congenital, Idiopathic Scoliosis and Arthrogryposis)

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13 pages, 642 KiB

Open AccessReview

From Stem Cells to Populations—Using hiPSC, Next-Generation Sequencing, and GWAS to Explore the Genetic and Molecular Mechanisms of Congenital Heart Defects

by Martin Broberg, Johanna Hästbacka and Emmi Helle

Genes 2021, 12(6), 921; https://doi.org/10.3390/genes12060921 - 16 Jun 2021

Cited by 7 | Viewed by 3645

Abstract

Congenital heart defects (CHD) are developmental malformations affecting the heart and the great vessels. Early heart development requires temporally regulated crosstalk between multiple cell types, signaling pathways, and mechanical forces of early blood flow. While both genetic and environmental factors have been recognized [...] Read more.

Congenital heart defects (CHD) are developmental malformations affecting the heart and the great vessels. Early heart development requires temporally regulated crosstalk between multiple cell types, signaling pathways, and mechanical forces of early blood flow. While both genetic and environmental factors have been recognized to be involved, identifying causal genes in non-syndromic CHD has been difficult. While variants following Mendelian inheritance have been identified by linkage analysis in a few families with multiple affected members, the inheritance pattern in most familial cases is complex, with reduced penetrance and variable expressivity. Furthermore, most non-syndromic CHD are sporadic. Improved sequencing technologies and large biobank collections have enabled genome-wide association studies (GWAS) in non-syndromic CHD. The ability to generate human to create human induced pluripotent stem cells (hiPSC) and further differentiate them to organotypic cells enables further exploration of genotype–phenotype correlations in patient-derived cells. Here we review how these technologies can be used in unraveling the genetics and molecular mechanisms of heart development. Full article

(This article belongs to the Special Issue Genetics and Epigenetics of Human Congenital Heart Disease)

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21 pages, 3808 KiB

Open AccessArticle

New RAD51 Inhibitors to Target Homologous Recombination in Human Cells

by Irina S. Shkundina, Alexander A. Gall, Alexej Dick, Simon Cocklin and Alexander V. Mazin

Genes 2021, 12(6), 920; https://doi.org/10.3390/genes12060920 - 16 Jun 2021

Cited by 26 | Viewed by 5169

Abstract

Targeting DNA repair proteins with small-molecule inhibitors became a proven anti-cancer strategy. Previously, we identified an inhibitor of a major protein of homologous recombination (HR) RAD51, named B02. B02 inhibited HR in human cells and sensitized them to chemotherapeutic drugs in vitro and [...] Read more.

Targeting DNA repair proteins with small-molecule inhibitors became a proven anti-cancer strategy. Previously, we identified an inhibitor of a major protein of homologous recombination (HR) RAD51, named B02. B02 inhibited HR in human cells and sensitized them to chemotherapeutic drugs in vitro and in vivo. Here, using a medicinal chemistry approach, we aimed to improve the potency of B02. We identified the B02 analog, B02-isomer, which inhibits HR in human cells with significantly higher efficiency. We also show that B02-iso sensitizes triple-negative breast cancer MDA-MB-231 cells to the PARP inhibitor (PARPi) olaparib. Full article

(This article belongs to the Special Issue The Key of DNA Recombination and Replication—Recombination Mediator Proteins)

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Genes, Volume 12, Issue 6 (June 2021) – 162 articles

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