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Volume 14
Issue 9
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Genes, Volume 14, Issue 9 (September 2023) – 169 articles

Cover Story (view full-size image): The epigenetic clock uses DNA methylation to calculate the metric of “epigenetic age”. Epigenetic age acceleration (epigenetic > chronological age) has been repeatedly linked to pediatric asthma and allergic disease, demonstrating its potential as a diagnostic biomarker. However, questions remain about the accuracy and utility of epigenetic clocks in children. This review examines the most used current epigenetic clocks and details the associations between epigenetic age acceleration and asthma/allergic disease. We explore the potential of the epigenetic clock as a biomarker for asthma and discuss the need for a pediatric epigenetic clock that is accurate in blood samples in order to maximize the utility of this powerful tool. View this paper
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14 pages, 1412 KiB  
Article
Homoplasy of Retrotransposon Insertions in Toothed Whales
by Liliya Doronina, Lynn Ogoniak and Jürgen Schmitz
Genes 2023, 14(9), 1830; https://doi.org/10.3390/genes14091830 - 21 Sep 2023
Cited by 2 | Viewed by 1911
Abstract
Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, [...] Read more.
Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18–0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal. Full article
(This article belongs to the Special Issue Mobile-Element-Related Genetic Variation)
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15 pages, 2284 KiB  
Article
The Chloroplast Genome of Endive (Cichorium endivia L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events
by Giulio Testone, Michele Lamprillo, Maria Gonnella, Giuseppe Arnesi, Anatoly Petrovich Sobolev, Riccardo Aiese Cigliano and Donato Giannino
Genes 2023, 14(9), 1829; https://doi.org/10.3390/genes14091829 - 21 Sep 2023
Cited by 1 | Viewed by 1329
Abstract
The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of [...] Read more.
The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar ‘Confiance’), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within Asteraceae with the well-separated C. endivia and intybus species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the ndhD, ndhA, and psbF genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress. Full article
(This article belongs to the Special Issue Plant Plastid Genome)
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9 pages, 235 KiB  
Article
Aromatic L-Amino-Acid Decarboxylase Deficiency Screening by Analysis of 3-O-Methyldopa in Dried Blood Spots: Results of a Multicentric Study in Neurodevelopmental Disorders
by Susanna Rizzi, Carlotta Spagnoli, Melissa Bellini, Carlo Alberto Cesaroni, Elisabetta Spezia, Patrizia Bergonzini, Elisa Caramaschi, Luca Soliani, Emanuela Claudia Turco, Benedetta Piccolo, Laura Demuth, Duccio Maria Cordelli, Giacomo Biasucci, Daniele Frattini and Carlo Fusco
Genes 2023, 14(9), 1828; https://doi.org/10.3390/genes14091828 - 21 Sep 2023
Cited by 1 | Viewed by 1280
Abstract
Aromatic L-amino acid decarboxylase deficiency (AADCd) is a rare recessive metabolic disorder caused by pathogenic homozygous or compound heterozygous variants in the dopa decarboxylase (DDC) gene. Adeno-associated viral vector-mediated gene transfer of the human DDC gene injected into the putamen is available. The [...] Read more.
Aromatic L-amino acid decarboxylase deficiency (AADCd) is a rare recessive metabolic disorder caused by pathogenic homozygous or compound heterozygous variants in the dopa decarboxylase (DDC) gene. Adeno-associated viral vector-mediated gene transfer of the human DDC gene injected into the putamen is available. The typical presentation is characterized by early-onset hypotonia, severe developmental delay, movement disorders, and dysautonomia. Recently, mild and even atypical phenotypes have been reported, increasing the diagnostic challenge. The aim of this multicentric study is to identify the prevalence of AADCd in a population of patients with phenotypic clusters characterized by neurodevelopmental disorders (developmental delay/intellectual disability, and/or autism) by 3-O-methyldopa (3-OMD) detection in dried blood spots (DBS). It is essential to identify AADCd promptly, especially within non-typical phenotypic clusters, because better results are obtained when therapy is quickly started in mild-moderate phenotypes. Between 2021 and 2023, 390 patients with non-specific phenotypes possibly associated with AADCd were tested; none resulted in a positive result. This result highlights that the population to be investigated for AADCd should have more defined clinical characteristics: association with common signs (hypotonia) and/or pathognomonic symptoms (oculogyric crisis and dysautonomia). It is necessary to continue to screen selected clusters for reaching diagnosis and improving long-term outcomes through treatment initiation. This underscores the role of newborn screening in identifying AADCd. Full article
(This article belongs to the Section Neurogenomics)
13 pages, 2200 KiB  
Article
Identification and Characterization of ABCG15—A Gene Required for Exocarp Color Differentiation in Pear
by Simeng Zhang, Jiayu Xu, Ying Zhang and Yufen Cao
Genes 2023, 14(9), 1827; https://doi.org/10.3390/genes14091827 - 21 Sep 2023
Cited by 1 | Viewed by 1105
Abstract
Exocarp color is a commercially essential quality for pear which can be divided into two types: green and russet. The occurrence of russet color is associated with deficiencies and defects in the cuticular and epidermal layers, which affect the structure of the cell [...] Read more.
Exocarp color is a commercially essential quality for pear which can be divided into two types: green and russet. The occurrence of russet color is associated with deficiencies and defects in the cuticular and epidermal layers, which affect the structure of the cell wall and the deposition of suberin. Until now, the genetic basics triggering this trait have not been well understood, and limited genes have been identified for the trait. To figure out the gene controlling the trait of exocarp color, we perform a comprehensive genome-wide association study, and we describe the candidate genes. One gene encoding the ABCG protein has been verified to be associated with the trait, using an integrative analysis of the metabolomic and transcriptomic data. This review covers a variety of omics resources, which provide a valuable resource for identifying gene-controlled traits of interest. The findings in this study help to elucidate the genetic components responsible for the trait of exocarp color in pear, and the implications of these findings for future pear breeding are evaluated. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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13 pages, 501 KiB  
Article
Functional Variation in the FAAH Gene Is Directly Associated with Subjective Well-Being and Indirectly Associated with Problematic Alcohol Use
by Lisa Bornscheuer, Andreas Lundin, Yvonne Forsell, Catharina Lavebratt and Philippe A. Melas
Genes 2023, 14(9), 1826; https://doi.org/10.3390/genes14091826 - 21 Sep 2023
Cited by 2 | Viewed by 1450
Abstract
Fatty acid amide hydrolase (FAAH) is an enzyme that degrades anandamide, an endocannabinoid that modulates mesolimbic dopamine release and, consequently, influences states of well-being. Despite these known interactions, the specific role of FAAH in subjective well-being remains underexplored. Since well-being is a dynamic [...] Read more.
Fatty acid amide hydrolase (FAAH) is an enzyme that degrades anandamide, an endocannabinoid that modulates mesolimbic dopamine release and, consequently, influences states of well-being. Despite these known interactions, the specific role of FAAH in subjective well-being remains underexplored. Since well-being is a dynamic trait that can fluctuate over time, we hypothesized that we could provide deeper insights into the link between FAAH and well-being using longitudinal data. To this end, we analyzed well-being data collected three years apart using the WHO (Ten) Well-Being Index and genotyped a functional polymorphism in the FAAH gene (rs324420, Pro129Thr) in a sample of 2822 individuals. We found that the A-allele of rs324420, which results in reduced FAAH activity and elevated anandamide levels, was associated with lower well-being scores at both time points (Wave I, B: −0.52, p = 0.007; Wave II, B: −0.41, p = 0.03, adjusted for age and sex). A subsequent phenome-wide association study (PheWAS) affirmed our well-being findings in the UK Biobank (N = 126,132, alternative C-allele associated with elevated happiness, p = 0.008) and revealed an additional association with alcohol dependence. In our cohort, using lagged longitudinal mediation analyses, we uncovered evidence of an indirect association between rs324420 and problematic alcohol use (AUDIT-P) through the pathway of lower well-being (indirect effect Boot: 0.015, 95% CI [0.003, 0.030], adjusted for AUDIT in Wave I). We propose that chronically elevated anandamide levels might influence disruptions in the endocannabinoid system—a biological contributor to well-being—which could, in turn, contribute to increased alcohol intake, though multiple factors may be at play. Further genetic studies and mediation analyses are needed to validate and extend these findings. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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23 pages, 4619 KiB  
Article
Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings
by Wei Ren and Li Chen
Genes 2023, 14(9), 1825; https://doi.org/10.3390/genes14091825 - 20 Sep 2023
Cited by 2 | Viewed by 1417
Abstract
Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland [...] Read more.
Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement)
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25 pages, 2318 KiB  
Review
Genomics of Treatable Traits in Asthma
by Antonio Espuela-Ortiz, Elena Martin-Gonzalez, Paloma Poza-Guedes, Ruperto González-Pérez and Esther Herrera-Luis
Genes 2023, 14(9), 1824; https://doi.org/10.3390/genes14091824 - 20 Sep 2023
Cited by 3 | Viewed by 2099
Abstract
The astounding number of genetic variants revealed in the 15 years of genome-wide association studies of asthma has not kept pace with the goals of translational genomics. Moving asthma diagnosis from a nonspecific umbrella term to specific phenotypes/endotypes and related traits may provide [...] Read more.
The astounding number of genetic variants revealed in the 15 years of genome-wide association studies of asthma has not kept pace with the goals of translational genomics. Moving asthma diagnosis from a nonspecific umbrella term to specific phenotypes/endotypes and related traits may provide insights into features that may be prevented or alleviated by therapeutical intervention. This review provides an overview of the different asthma endotypes and phenotypes and the genomic findings from asthma studies using patient stratification strategies and asthma-related traits. Asthma genomic research for treatable traits has uncovered novel and previously reported asthma loci, primarily through studies in Europeans. Novel genomic findings for asthma phenotypes and related traits may arise from multi-trait and specific phenotyping strategies in diverse populations. Full article
(This article belongs to the Special Issue Genetics of Complex Human Disease 2024)
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10 pages, 1779 KiB  
Case Report
New SLC22A12 (URAT1) Variant Associated with Renal Hypouricemia Identified by Whole-Exome Sequencing Analysis and Bioinformatics Predictions
by Ana Perdomo-Ramírez, Elena Ramos-Trujillo and Félix Claverie-Martín
Genes 2023, 14(9), 1823; https://doi.org/10.3390/genes14091823 - 20 Sep 2023
Cited by 2 | Viewed by 1420
Abstract
Renal hypouricemia (RHUC) is a rare hereditary disorder caused by loss-of-function mutations in the SLC22A12 (RHUC type 1) or SLC2A9 (RHUC type 2) genes, encoding urate transporters URAT1 and GLUT9, respectively, that reabsorb urate in the renal proximal tubule. The characteristics of this [...] Read more.
Renal hypouricemia (RHUC) is a rare hereditary disorder caused by loss-of-function mutations in the SLC22A12 (RHUC type 1) or SLC2A9 (RHUC type 2) genes, encoding urate transporters URAT1 and GLUT9, respectively, that reabsorb urate in the renal proximal tubule. The characteristics of this disorder are low serum urate levels, high renal fractional excretion of urate, and occasional severe complications such as nephrolithiasis and exercise-induced acute renal failure. In this study, we report two Spanish (Caucasian) siblings and a Pakistani boy with clinical characteristics compatible with RHUC. Whole-exome sequencing (WES) analysis identified two homozygous variants: a novel pathogenic SLC22A12 variant, c.1523G>A; p.(S508N), in the two Caucasian siblings and a previously reported SLC2A9 variant, c.646G>A; p.(G216R), in the Pakistani boy. Our findings suggest that these two mutations cause RHUC through loss of urate reabsorption and extend the SLC22A12 mutation spectrum. In addition, this work further emphasizes the importance of WES analysis in clinical settings. Full article
(This article belongs to the Collection Genetics and Genomics of Rare Disorders)
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12 pages, 3545 KiB  
Article
Epigenetic Findings in Twins with Esophageal Atresia
by Michal Błoch, Piotr Gasperowicz, Sylwester Gerus, Katarzyna Rasiewicz, Arleta Lebioda, Pawel Skiba, Rafal Płoski, Dariusz Patkowski, Pawel Karpiński and Robert Śmigiel
Genes 2023, 14(9), 1822; https://doi.org/10.3390/genes14091822 - 20 Sep 2023
Viewed by 1381
Abstract
Esophageal atresia (EA) is the most common malformation of the upper gastrointestinal tract. The estimated incidence of EA is 1 in 3500 births. EA is more frequently observed in boys and in twins. The exact cause of isolated EA remains unknown; a multifactorial [...] Read more.
Esophageal atresia (EA) is the most common malformation of the upper gastrointestinal tract. The estimated incidence of EA is 1 in 3500 births. EA is more frequently observed in boys and in twins. The exact cause of isolated EA remains unknown; a multifactorial etiology, including epigenetic gene expression modifications, is considered. The study included six pairs of twins (three pairs of monozygotic twins and three pairs of dizygotic twins) in which one child was born with EA as an isolated defect, while the other twin was healthy. DNA samples were obtained from the blood and esophageal tissue of the child with EA as well as from the blood of the healthy twin. The reduced representation bisulfite sequencing (RRBS) technique was employed for a whole-genome methylation analysis. The analyses focused on comparing the CpG island methylation profiles between patients with EA and their healthy siblings. Hypermethylation in the promoters of 219 genes and hypomethylation in the promoters of 78 genes were observed. A pathway enrichment analysis revealed the statistically significant differences in methylation profile of 10 hypermethylated genes in the Rho GTPase pathway, previously undescribed in the field of EA (ARHGAP36, ARHGAP4, ARHGAP6, ARHGEF6, ARHGEF9, FGD1, GDI1, MCF2, OCRL, and STARD8). Full article
(This article belongs to the Special Issue Genetics and Genomics of Heritable Pediatric Disorders)
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4 pages, 194 KiB  
Editorial
Editorial for the Special Issue “Genetics and Genomics of Gastrointestinal Cancers: From Prevention to Treatment”
by Monica Marabelli, Lucio Bertario and Davide Serrano
Genes 2023, 14(9), 1821; https://doi.org/10.3390/genes14091821 - 20 Sep 2023
Viewed by 1026
Abstract
According to the latest estimate from GLOBOCAN 2020, approximately 18 [...] Full article
(This article belongs to the Special Issue Genetics and Genomics of Gastrointestinal Cancers: From Prevention to Treatment)
11 pages, 5137 KiB  
Article
Identification of Breast Cancer Metastasis Markers from Gene Expression Profiles Using Machine Learning Approaches
by Jinmyung Jung and Sunyong Yoo
Genes 2023, 14(9), 1820; https://doi.org/10.3390/genes14091820 - 20 Sep 2023
Cited by 4 | Viewed by 2084
Abstract
Cancer metastasis accounts for approximately 90% of cancer deaths, and elucidating markers in metastasis is the first step in its prevention. To characterize metastasis marker genes (MGs) of breast cancer, XGBoost models that classify metastasis status were trained with gene expression profiles from [...] Read more.
Cancer metastasis accounts for approximately 90% of cancer deaths, and elucidating markers in metastasis is the first step in its prevention. To characterize metastasis marker genes (MGs) of breast cancer, XGBoost models that classify metastasis status were trained with gene expression profiles from TCGA. Then, a metastasis score (MS) was assigned to each gene by calculating the inner product between the feature importance and the AUC performance of the models. As a result, 54, 202, and 357 genes with the highest MS were characterized as MGs by empirical p-value cutoffs of 0.001, 0.005, and 0.01, respectively. The three sets of MGs were compared with those from existing metastasis marker databases, which provided significant results in most comparisons (p-value < 0.05). They were also significantly enriched in biological processes associated with breast cancer metastasis. The three MGs, SPPL2C, KRT23, and RGS7, showed highly significant results (p-value < 0.01) in the survival analysis. The MGs that could not be identified by statistical analysis (e.g., GOLM1, ELAVL1, UBP1, and AZGP1), as well as the MGs with the highest MS (e.g., ZNF676, FAM163B, LDOC2, IRF1, and STK40), were verified via the literature. Additionally, we checked how close the MGs were to each other in the protein–protein interaction networks. We expect that the characterized markers will help understand and prevent breast cancer metastasis. Full article
(This article belongs to the Special Issue Advances in Computational Cancer Omics)
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21 pages, 2377 KiB  
Article
Lung and Heart Biology of the Dp16 Mouse Model of down Syndrome: Implications for Studying Cardiopulmonary Disease
by Kelley L. Colvin, Kathleen Nguyen, Katie L. Boncella, Desiree M. Goodman, Robert J. Elliott, Julie W. Harral, Jill Bilodeaux, Bradford J. Smith and Michael E. Yeager
Genes 2023, 14(9), 1819; https://doi.org/10.3390/genes14091819 - 19 Sep 2023
Cited by 1 | Viewed by 1862
Abstract
(1) Background: We sought to investigate the baseline lung and heart biology of the Dp16 mouse model of Down syndrome (DS) as a prelude to the investigation of recurrent respiratory tract infection. (2) Methods: In controls vs. Dp16 mice, we compared peripheral blood [...] Read more.
(1) Background: We sought to investigate the baseline lung and heart biology of the Dp16 mouse model of Down syndrome (DS) as a prelude to the investigation of recurrent respiratory tract infection. (2) Methods: In controls vs. Dp16 mice, we compared peripheral blood cell and plasma analytes. We examined baseline gene expression in lungs and hearts for key parameters related to susceptibility of lung infection. We investigated lung and heart protein expression and performed lung morphometry. Finally, and for the first time each in a model of DS, we performed pulmonary function testing and a hemodynamic assessment of cardiac function. (3) Results: Dp16 mice circulate unique blood plasma cytokines and chemokines. Dp16 mouse lungs over-express the mRNA of triplicated genes, but not necessarily corresponding proteins. We found a sex-specific decrease in the protein expression of interferon α receptors, yet an increased signal transducer and activator of transcription (STAT)-3 and phospho-STAT3. Platelet-activating factor receptor protein was not elevated in Dp16 mice. The lungs of Dp16 mice showed increased stiffness and mean linear intercept and contained bronchus-associated lymphoid tissue. The heart ventricles of Dp16 mice displayed hypotonicity. Finally, Dp16 mice required more ketamine to achieve an anesthetized state. (4) Conclusions: The Dp16 mouse model of DS displays key aspects of lung heart biology akin to people with DS. As such, it has the potential to be an extremely valuable model of recurrent severe respiratory tract infection in DS. Full article
(This article belongs to the Topic Animal Models of Human Disease)
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15 pages, 2756 KiB  
Article
Alpha-Ketoglutarate Regulates Tnfrsf12a/Fn14 Expression via Histone Modification and Prevents Cancer-Induced Cachexia
by Bryan I. Ruiz, Xazmin H. Lowman, Ying Yang, Qi Fan, Tianhong Wang, Hongmei Wu, Eric A. Hanse and Mei Kong
Genes 2023, 14(9), 1818; https://doi.org/10.3390/genes14091818 - 19 Sep 2023
Cited by 1 | Viewed by 2525
Abstract
Previous studies have shown that inhibition of TNF family member FN14 (gene: TNFRSF12A) in colon tumors decreases inflammatory cytokine expression and mitigates cancer-induced cachexia. However, the molecular mechanisms underlying the regulation of FN14 expression remain unclear. Tumor microenvironments are often devoid of [...] Read more.
Previous studies have shown that inhibition of TNF family member FN14 (gene: TNFRSF12A) in colon tumors decreases inflammatory cytokine expression and mitigates cancer-induced cachexia. However, the molecular mechanisms underlying the regulation of FN14 expression remain unclear. Tumor microenvironments are often devoid of nutrients and oxygen, yet how the cachexic response relates to the tumor microenvironment and, importantly, nutrient stress is unknown. Here, we looked at the connections between metabolic stress and FN14 expression. We found that TNFRSF12A expression was transcriptionally induced during glutamine deprivation in cancer cell lines. We also show that the downstream glutaminolysis metabolite, alpha-ketoglutarate (aKG), is sufficient to rescue glutamine-deprivation-promoted TNFRSF12A induction. As aKG is a co-factor for histone de-methylase, we looked at histone methylation and found that histone H3K4me3 at the Tnfrsf12a promoter is increased under glutamine-deprived conditions and rescued via DM-aKG supplementation. Finally, expression of Tnfrsf12a and cachexia-induced weight loss can be inhibited in vivo by DM-aKG in a mouse cancer cachexia model. These findings highlight a connection between metabolic stress and cancer cachexia development. Full article
(This article belongs to the Special Issue Signaling and Gene Regulation in Metabolism)
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15 pages, 5602 KiB  
Article
Expanding the Natural History of SNORD118-Related Ribosomopathy: Hints from an Early-Diagnosed Patient with Leukoencephalopathy with Calcifications and Cysts and Overview of the Literature
by Davide Politano, Guido Catalano, Elena Pezzotti, Costanza Varesio, Fabio Sirchia, Antonella Casella, Elisa Rognone, Anna Pichiecchio, Renato Borgatti and Simona Orcesi
Genes 2023, 14(9), 1817; https://doi.org/10.3390/genes14091817 - 19 Sep 2023
Cited by 2 | Viewed by 1476
Abstract
Leukoencephalopathy with calcifications and cysts (LCC) is a rare autosomal recessive disorder showing a pediatric or adult onset. First described in 1996 by Labrune and colleagues, it was only in 2016 that bi-allelic variants in a non-protein coding gene, SNORD118, were found [...] Read more.
Leukoencephalopathy with calcifications and cysts (LCC) is a rare autosomal recessive disorder showing a pediatric or adult onset. First described in 1996 by Labrune and colleagues, it was only in 2016 that bi-allelic variants in a non-protein coding gene, SNORD118, were found as the cause for LCC, differentiating this syndrome from coats plus (CP). SNORD118 transcribes for a small nucleolar RNA, which is necessary for correct ribosome biogenesis, hence the classification of LCC among ribosomopathies. The syndrome is characterized by a combination of white matter hyperintensities, calcifications, and cysts on brain MRI with varying neurological signs. Corticosteroids, surgery, and recently bevacizumab, have been tried with unclear results since the natural history of the disease remains elusive. To date, 67 patients with a pediatric onset of disease have been described in the literature, with a clinical-radiological follow-up carried out in only eleven of them. We described the clinical-radiological follow-up from birth to almost five years of age of a late-preterm patient diagnosed with LCC and carried out a thorough overview of pediatric patients described in the literature. It is important to gather serial clinical–radiological data from other patients to depict the natural history of this disease, aiming to deeply depict genotype-phenotype correlations and make the role of new therapeutics clearer. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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11 pages, 514 KiB  
Article
Genome-Wide Association Mapping of Processing Quality Traits in Common Wheat (Triticum aestivum L.)
by Hui Jin, Yuanyuan Tian, Yan Zhang, Rui Zhang, Haibin Zhao, Xue Yang, Xizhang Song, Yordan Dimitrov, Yu-e Wu, Qiang Gao, Jindong Liu, Jumei Zhang and Zhonghu He
Genes 2023, 14(9), 1816; https://doi.org/10.3390/genes14091816 - 18 Sep 2023
Viewed by 1474
Abstract
Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by [...] Read more.
Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2–42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection. Full article
(This article belongs to the Special Issue Genetics and Breeding of Grains)
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15 pages, 2362 KiB  
Article
Association Mapping of Candidate Genes Associated with Iron and Zinc Content in Rice (Oryza sativa L.) Grains
by Chance Bahati Bukomarhe, Paul Kitenge Kimwemwe, Stephen Mwangi Githiri, Edward George Mamati, Wilson Kimani, Collins Mutai, Fredrick Nganga, Paul-Martin Dontsop Nguezet, Jacob Mignouna, René Mushizi Civava and Mamadou Fofana
Genes 2023, 14(9), 1815; https://doi.org/10.3390/genes14091815 - 18 Sep 2023
Cited by 1 | Viewed by 2167
Abstract
Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) [...] Read more.
Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) was conducted using 85 diverse rice accessions from the Democratic Republic of Congo (DRC) to identify genomic regions associated with grain Fe and Zn content. The Fe content ranged from 0.95 to 8.68 mg/100 g on a dry weight basis (dwb) while Zn content ranged from 0.87 to 3.8 mg/100 g (dwb). Using MLM and FarmCPU models, we found 10 significant SNPs out of which one SNP on chromosome 11 was associated with the variation in Fe content and one SNP on chromosome 4 was associated with the Zn content, and both were commonly detected by the two models. Candidate genes belonging to transcription regulator activities, including the bZIP family genes and MYB family genes, as well as transporter activities involved in Fe and Zn homeostasis were identified in the vicinity of the SNP markers and selected. The identified SNP markers hold promise for marker-assisted selection in rice breeding programs aimed at enhancing Fe and Zn content in rice. This study provides valuable insights into the genetic factors controlling Fe and Zn uptake and their transport and accumulation in rice, offering opportunities for developing biofortified rice varieties to combat malnutrition among rice consumers. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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10 pages, 554 KiB  
Article
Association of Cognitive Polygenic Index and Cognitive Performance with Age in Cognitively Healthy Adults
by Angeliki Tsapanou, Margaret Gacheru, Seonjoo Lee, Niki Mourtzi, Yunglin Gazes, Christian Habeck, Daniel W. Belsky and Yaakov Stern
Genes 2023, 14(9), 1814; https://doi.org/10.3390/genes14091814 - 18 Sep 2023
Cited by 1 | Viewed by 1368
Abstract
Genome-wide association studies have discovered common genetic variants associated with cognitive performance. Polygenic scores that summarize these discoveries explain up to 10% of the variance in cognitive test performance in samples of adults. However, the role these genetics play in cognitive aging is [...] Read more.
Genome-wide association studies have discovered common genetic variants associated with cognitive performance. Polygenic scores that summarize these discoveries explain up to 10% of the variance in cognitive test performance in samples of adults. However, the role these genetics play in cognitive aging is not well understood. We analyzed data from 168 cognitively healthy participants aged 23–77 years old, with data on genetics, neuropsychological assessment, and brain-imaging measurements from two large ongoing studies, the Reference Abilities Neural Networks, and the Cognitive Reserve study. We tested whether a polygenic index previously related to cognition (Cog PGI) would moderate the relationship between age and measurements of the cognitive domains extracted from a neuropsychological evaluation: fluid reasoning, memory, vocabulary, and speed of processing. We further explored the relationship of Cog PGI and age on cognition using Johnson–Neyman intervals for two-way interactions. Sex, education, and brain measures of cortical thickness, total gray matter volume, and white matter hyperintensity were considered covariates. The analysis controlled for population structure-ancestry. There was a significant interaction effect of Cog PGI on the association between age and the domains of memory (Standardized coefficient = −0.158, p-value = 0.022), fluid reasoning (Standardized coefficient = −0.146, p-value = 0.020), and vocabulary (Standardized coefficient = −0.191, p-value = 0.001). Higher PGI strengthened the negative relationship between age and the domains of memory and fluid reasoning while PGI weakened the positive relationship between age and vocabulary. Based on the Johnson–Neyman intervals, Cog PGI was significantly associated with domains of memory, reasoning, and vocabulary for younger adults. There is a significant moderation effect of genetic predisposition for cognition for the association between age and cognitive performance. Genetics discovered in genome-wide association studies of cognitive performance show a stronger association in young and midlife older adults. Full article
(This article belongs to the Section Neurogenomics)
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17 pages, 1266 KiB  
Article
Non-Random Enrichment of Single-Nucleotide Polymorphisms Associated with Clopidogrel Resistance within Risk Loci Linked to the Severity of Underlying Cardiovascular Diseases: The Role of Admixture
by Mariangeli Monero-Paredes, Roberto Feliu-Maldonado, Kelvin Carrasquillo-Carrion, Pablo Gonzalez, Igor B. Rogozin, Abiel Roche-Lima and Jorge Duconge
Genes 2023, 14(9), 1813; https://doi.org/10.3390/genes14091813 - 17 Sep 2023
Viewed by 1610
Abstract
Cardiovascular disease (CVD) is one of the leading causes of death in Puerto Rico, where clopidogrel is commonly prescribed to prevent ischemic events. Genetic contributors to both a poor clopidogrel response and the severity of CVD have been identified mainly in Europeans. However, [...] Read more.
Cardiovascular disease (CVD) is one of the leading causes of death in Puerto Rico, where clopidogrel is commonly prescribed to prevent ischemic events. Genetic contributors to both a poor clopidogrel response and the severity of CVD have been identified mainly in Europeans. However, the non-random enrichment of single-nucleotide polymorphisms (SNPs) associated with clopidogrel resistance within risk loci linked to underlying CVDs, and the role of admixture, have yet to be tested. This study aimed to assess the possible interaction between genetic biomarkers linked to CVDs and those associated with clopidogrel resistance among admixed Caribbean Hispanics. We identified 50 SNPs significantly associated with CVDs in previous genome-wide association studies (GWASs). These SNPs were combined with another ten SNPs related to clopidogrel resistance in Caribbean Hispanics. We developed Python scripts to determine whether SNPs related to CVDs are in close proximity to those associated with the clopidogrel response. The average and individual local ancestry (LAI) within each locus were inferred, and 60 random SNPs with their corresponding LAIs were generated for enrichment estimation purposes. Our results showed no CVD-linked SNPs in close proximity to those associated with the clopidogrel response among Caribbean Hispanics. Consequently, no genetic loci with a dual predictive role for the risk of CVD severity and clopidogrel resistance were found in this population. Native American ancestry was the most enriched within the risk loci linked to CVDs in this population. The non-random enrichment of disease susceptibility loci with drug-response SNPs is a new frontier in Precision Medicine that needs further attention. Full article
(This article belongs to the Special Issue Single-Nucleotide Polymorphisms: Association, Molecular Function, Application, and Progress)
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24 pages, 2266 KiB  
Article
Quantitative Trait Locus Analysis of Hessian Fly Resistance in Soft Red Winter Wheat
by John W. Bagwell, Madhav Subedi, Suraj Sapkota, Benjamin Lopez, Bikash Ghimire, Zhenbang Chen, G. David Buntin, Bochra A. Bahri and Mohamed Mergoum
Genes 2023, 14(9), 1812; https://doi.org/10.3390/genes14091812 - 17 Sep 2023
Viewed by 1959
Abstract
The Hessian fly (HF) is an invasive insect that has caused millions of dollars in yield losses to southeastern US wheat farms. Genetic resistance is the most sustainable solution to control HF. However, emerging biotypes are quickly overcoming resistance genes in the southeast; [...] Read more.
The Hessian fly (HF) is an invasive insect that has caused millions of dollars in yield losses to southeastern US wheat farms. Genetic resistance is the most sustainable solution to control HF. However, emerging biotypes are quickly overcoming resistance genes in the southeast; therefore, identifying novel sources of resistance is critical. The resistant line “UGA 111729” and susceptible variety “AGS 2038” were crossbred to generate a population of 225 recombinant inbred lines. This population was phenotyped in the growth chamber (GC) during 2019 and 2021 and in field (F) trials in Georgia during the 2021–2022 growing seasons. Visual scoring was utilized in GC studies. The percentage of infested tillers and number of pupae/larvae per tiller, and infested tiller per sample were measured in studies from 2021 to 2022. Averaging across all traits, a major QTL on chromosome 3D explained 42.27% (GC) and 10.43% (F) phenotypic variance within 9.86 centimorgans (cM). SNP marker IWB65911 was associated with the quantitative trait locus (QTL) peak with logarithm of odds (LOD) values of 14.98 (F) and 62.22 (GC). IWB65911 colocalized with resistance gene H32. KASP marker validation verified that UGA 111729 and KS89WGRC06 express H32. IWB65911 may be used for marker-assisted selection. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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7 pages, 2968 KiB  
Review
Exercise Does Not Independently Improve Histological Outcomes in Biopsy-Proven Non-Alcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis
by George Chen, Bubu A. Banini, Albert Do, Craig Gunderson, Saif Zaman and Joseph K. Lim
Genes 2023, 14(9), 1811; https://doi.org/10.3390/genes14091811 - 17 Sep 2023
Cited by 7 | Viewed by 1556
Abstract
Introduction: The independent effect of exercise on liver histology in non-alcoholic fatty liver disease (NAFLD) remains unclear. As such, we conducted a systematic review and meta-analysis of the effect of exercise alone on histological endpoints in biopsy-proven NAFLD. Materials and Methods: A systematic [...] Read more.
Introduction: The independent effect of exercise on liver histology in non-alcoholic fatty liver disease (NAFLD) remains unclear. As such, we conducted a systematic review and meta-analysis of the effect of exercise alone on histological endpoints in biopsy-proven NAFLD. Materials and Methods: A systematic literature search was conducted to include controlled clinical trials investigating the effect of exercise alone on liver histology in biopsy-proven NAFLD. Meta-analysis was conducted for histological outcomes with available data from a minimum of three studies. Pooled estimates of the effect of exercise on histological endpoints were calculated using random-effects models. Results: We identified three controlled clinical trials that assessed the independent effect of exercise on histological outcomes in patients with biopsy-proven NAFLD. The studies consisted of 72 total participants, including 40 subjects in the exercise intervention and 32 individuals in the comparison group. Meta-analysis showed that exercise did not significantly improve Brunt grade, NAFLD activity score, and fibrosis in NAFLD. Discussion: Exercise alone may not lead to significant histopathological improvement in NAFLD. Future well-powered randomized controlled trials are needed to better characterize the impact of exercise on histological outcomes and clinical endpoints. Full article
(This article belongs to the Special Issue Liver Disease: Genetic Research and Clinical Diagnosis)
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22 pages, 9497 KiB  
Article
Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
by Shuning Cui, Hong Liu, Yong Wu, Lugang Zhang and Shanshan Nie
Genes 2023, 14(9), 1810; https://doi.org/10.3390/genes14091810 - 17 Sep 2023
Cited by 2 | Viewed by 1529
Abstract
Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ [...] Read more.
Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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12 pages, 2898 KiB  
Article
Factors Associated with Large Cup-to-Disc Ratio and Blindness in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study
by Anusha Mamidipaka, Isabel Di Rosa, Roy Lee, Yan Zhu, Yineng Chen, Rebecca Salowe, Victoria Addis, Prithvi Sankar, Ebenezer Daniel, Gui-Shuang Ying and Joan M. O’Brien
Genes 2023, 14(9), 1809; https://doi.org/10.3390/genes14091809 - 16 Sep 2023
Cited by 3 | Viewed by 2900
Abstract
Background/Aims: Primary open-angle glaucoma (POAG) disproportionately affects individuals of African ancestry. In these patients’ eyes, a large cup-to-disc ratio (LCDR > 0.90) suggests greater retinal ganglion cell loss, though these patients often display varied visual ability. This study investigated the prevalence and risk [...] Read more.
Background/Aims: Primary open-angle glaucoma (POAG) disproportionately affects individuals of African ancestry. In these patients’ eyes, a large cup-to-disc ratio (LCDR > 0.90) suggests greater retinal ganglion cell loss, though these patients often display varied visual ability. This study investigated the prevalence and risk factors associated with LCDR in African ancestry individuals with POAG and explored the differences between blind (>20/200) and not blind (≤20/200) LCDR eyes. Methods: A case–control methodology was used to investigate the demographic, optic disc, and genetic risk factors of subjects in the Primary Open-Angle African American Glaucoma Genetics Study. Risk factors were analyzed using univariable and multivariable logistic regression models with inter-eye correlation adjusted using generalized estimating equations. Results: Out of 5605 eyes with POAG, 1440 eyes (25.7%) had LCDR. In the multivariable analysis, LCDR was associated with previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.04), decreased mean deviation (OR = 1.08), increased pattern standard deviation (OR = 1.06), thinner retinal nerve fiber layer (OR = 1.05), nasalization of vessels (OR = 2.67), bayonetting of vessels (OR = 1.98), visible pores in the lamina cribrosa (OR = 1.68), and a bean-shaped cup (OR = 2.11). Of LCDR eyes, 30.1% were classified as blind (≤20/200). In the multivariable analysis, the statistically significant risk factors of blindness in LCDR eyes were previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.05), decreased mean deviation (OR = 1.04), and decreased pattern standard deviation (OR = 0.90). Conclusions: These findings underscore the importance of close monitoring of intraocular pressure and visual function in African ancestry POAG patients, particularly those with LCDR, to preserve visual function. Full article
(This article belongs to the Special Issue Study on Genotypes and Phenotypes of Neurodegenerative Diseases)
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18 pages, 2700 KiB  
Article
Correlation between KRAS Mutation and CTLA-4 mRNA Expression in Circulating Tumour Cells: Clinical Implications in Colorectal Cancer
by Sharmin Aktar, Farhadul Islam, Tracie Cheng, Sujani Madhurika Kodagoda Gamage, Indra Neil Choudhury, Md Sajedul Islam, Cu Tai Lu, Faysal Bin Hamid, Hirotaka Ishida, Ichiro Abe, Nan Xie, Vinod Gopalan and Alfred K. Lam
Genes 2023, 14(9), 1808; https://doi.org/10.3390/genes14091808 - 16 Sep 2023
Viewed by 1810
Abstract
Combination strategies of KRAS inhibition with immunotherapy in treating advanced or recurrent colorectal carcinoma (CRC) may need to be assessed in circulating tumour cells (CTCs) to achieve better clinical outcomes. This study aimed to investigate the genomic variations of KRAS in CTCs and [...] Read more.
Combination strategies of KRAS inhibition with immunotherapy in treating advanced or recurrent colorectal carcinoma (CRC) may need to be assessed in circulating tumour cells (CTCs) to achieve better clinical outcomes. This study aimed to investigate the genomic variations of KRAS in CTCs and matched CRC tissues and compared mRNA expression of KRAS and CTLA-4 between wild-type and KRAS-mutated CTCs and CRC tissues. Clinicopathological correlations were also compared. Six known mutations of KRAS were identified at both codon 12 and codon 13 (c.35G>T/G12V, c.35G>A7/G12D, c.35G>C/G12A, c.34G>A/G12S, c.38G>C/G13A, and c.38G>A/G13D). Three CTC samples harboured the identified mutations (16.7%; 3/18), while fifteen matched primary tumour tissues (65.2%, 15/23) showed the mutations. CTCs harbouring the KRAS variant were different from matched CRC tissue. All the mutations were heterozygous. Though insignificant, CTLA-4 mRNA expression was higher in patients carrying KRAS mutations. Patients harbouring KRAS mutations in CTCs were more likely to have poorly differentiated tumours (p = 0.039) and with lymph node metastasis (p = 0.027) and perineural invasion (p = 0.014). KRAS mutations in CTCs were also significantly correlated with overall pathological stages (p = 0.027). These findings imply the genetic basis of KRAS with immunotherapeutic target molecules based on a real-time platform. This study also suggests the highly heterogeneous nature of cancer cells, which may facilitate the assessment of clonal dynamics across a single patient’s disease. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 2850 KiB  
Article
Aldehyde Dehydrogenase Genes as Prospective Actionable Targets in Acute Myeloid Leukemia
by Garrett M. Dancik, Lokman Varisli, Veysel Tolan and Spiros Vlahopoulos
Genes 2023, 14(9), 1807; https://doi.org/10.3390/genes14091807 - 16 Sep 2023
Cited by 3 | Viewed by 1848
Abstract
It has been previously shown that the aldehyde dehydrogenase (ALDH) family member ALDH1A1 has a significant association with acute myeloid leukemia (AML) patient risk group classification and that AML cells lacking ALDH1A1 expression can be readily killed via chemotherapy. In the [...] Read more.
It has been previously shown that the aldehyde dehydrogenase (ALDH) family member ALDH1A1 has a significant association with acute myeloid leukemia (AML) patient risk group classification and that AML cells lacking ALDH1A1 expression can be readily killed via chemotherapy. In the past, however, a redundancy between the activities of subgroup members of the ALDH family has hampered the search for conclusive evidence to address the role of specific ALDH genes. Here, we describe the bioinformatics evaluation of all nineteen member genes of the ALDH family as prospective actionable targets for the development of methods aimed to improve AML treatment. We implicate ALDH1A1 in the development of recurrent AML, and we show that from the nineteen members of the ALDH family, ALDH1A1 and ALDH2 have the strongest association with AML patient risk group classification. Furthermore, we discover that the sum of the expression values for RNA from the genes, ALDH1A1 and ALDH2, has a stronger association with AML patient risk group classification and survival than either one gene alone does. In conclusion, we identify ALDH1A1 and ALDH2 as prospective actionable targets for the treatment of AML in high-risk patients. Substances that inhibit both enzymatic activities constitute potentially effective pharmaceutics. Full article
(This article belongs to the Special Issue Bioinformatics and Computational Biology for Cancer Prediction and Prognosis)
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16 pages, 334 KiB  
Article
Genes Involved in DNA Damage Cell Pathways and Health of the Oldest-Old (85+)
by Maja Šetinc, Matea Zajc Petranović, Goran Slivšek, Sandra Mijač, Željka Celinščak, Anita Stojanović Marković, Vesna Bišof, Marijana Peričić Salihović and Tatjana Škarić-Jurić
Genes 2023, 14(9), 1806; https://doi.org/10.3390/genes14091806 - 15 Sep 2023
Viewed by 1901
Abstract
Some sources report a connection of cellular senescence with chronic pathological conditions; however, the association between particular cellular processes and general health is rarely examined. This study aims to test the relationship of general health with DNA damage pathways that play a crucial [...] Read more.
Some sources report a connection of cellular senescence with chronic pathological conditions; however, the association between particular cellular processes and general health is rarely examined. This study aims to test the relationship of general health with DNA damage pathways that play a crucial role in senescence. The association of ten selected SNPs with subjective and objective general health and functional ability indicators has been tested in 314 oldest-old people from Croatia. Multivariate logistic regression was employed to simultaneously test the impact of variables potentially influencing targeted health and functional ability variables. The best model, explaining 37.1% of the variance, has six independent significant predictors of functional ability scores: rs16847897 in TERC, rs533984 in MRE11A, and rs4977756 in CDKN2B, chronic disease count, Mini-Mental State Examination scores, and age at surveying. In conclusion, the examined ten loci involved in DNA damage repair pathways showed a more significant association with self-rated health and functional ability than with the number of disease or prescribed medicaments. The more frequent, longevity-related homozygote (GG) in rs16847897 was associated with all three aspects of self-assessments—health, mobility, and independence—indicating that this TERC locus might have a true impact on the overall vitality of the oldest-old persons. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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18 pages, 2404 KiB  
Article
Glucocorticoid Receptor Gene (NR3C1) Polymorphisms and Metabolic Syndrome: Insights from the Mennonite Population
by Kathleen Liedtke Kolb, Ana Luiza Sprotte Mira, Eduardo Delabio Auer, Isabela Dall’Oglio Bucco, Carla Eduarda de Lima e Silva, Priscila Ianzen dos Santos, Valéria Bumiller-Bini Hoch, Luana Caroline Oliveira, Aline Borsato Hauser, Jennifer Elisabeth Hundt, Alan R. Shuldiner, Fabiana Leão Lopes, Teide-Jens Boysen, Andre Franke, Luis Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima, Gabriela Canalli Kretzschmar and Angelica Beate Winter Boldt
Genes 2023, 14(9), 1805; https://doi.org/10.3390/genes14091805 - 15 Sep 2023
Cited by 4 | Viewed by 2225
Abstract
The regulation of the hypothalamic-pituitary-adrenal (HPA) axis is associated with polymorphisms and the methylation degree of the glucocorticoid receptor gene (NR3C1) and is potentially involved in the development of metabolic syndrome (MetS). In order to evaluate the association between MetS with [...] Read more.
The regulation of the hypothalamic-pituitary-adrenal (HPA) axis is associated with polymorphisms and the methylation degree of the glucocorticoid receptor gene (NR3C1) and is potentially involved in the development of metabolic syndrome (MetS). In order to evaluate the association between MetS with the polymorphisms, methylation, and gene expression of the NR3C1 in the genetically isolated Brazilian Mennonite population, we genotyped 20 NR3C1 polymorphisms in 74 affected (MetS) and 138 unaffected individuals without affected first-degree relatives (Co), using exome sequencing, as well as five variants from non-exonic regions, in 70 MetS and 166 Co, using mass spectrometry. The methylation levels of 11 1F CpG sites were quantified using pyrosequencing (66 MetS and 141 Co), and the NR3C1 expression was evaluated via RT-qPCR (14 MetS and 25 Co). Age, physical activity, and family environment during childhood were associated with MetS. Susceptibility to MetS, independent of these factors, was associated with homozygosity for rs10482605*C (OR = 4.74, pcorr = 0.024) and the haplotype containing TTCGTTGATT (rs3806855*T_ rs3806854*T_rs10482605*C_rs10482614*G_rs6188*T_rs258813*T_rs33944801*G_rs34176759*A_rs17209258*T_rs6196*T, OR = 4.74, pcorr = 0.048), as well as for the CCT haplotype (rs41423247*C_ rs6877893*C_rs258763*T), OR = 6.02, pcorr = 0.030), but not to the differences in methylation or gene expression. Thus, NR3C1 polymorphisms seem to modulate the susceptibility to MetS in Mennonites, independently of lifestyle and early childhood events, and their role seems to be unrelated to DNA methylation and gene expression. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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27 pages, 3063 KiB  
Article
Sex Differences in Anderson–Fabry Cardiomyopathy: Clinical, Genetic, and Imaging Analysis in Women
by Denise Cristiana Faro, Valentina Losi, Margherita Stefania Rodolico, Elvira Mariateresa Torrisi, Paolo Colomba, Giovanni Duro and Ines Paola Monte
Genes 2023, 14(9), 1804; https://doi.org/10.3390/genes14091804 - 15 Sep 2023
Cited by 5 | Viewed by 1944
Abstract
Anderson–Fabry Disease (AFD) is a rare, systemic lysosomal storage disease triggered by mutations in the GLA gene, leading to α-galactosidase A (α-Gal A) deficiency. The disease’s X-linked inheritance leads to more severe, early-onset presentations in males, while females exhibit variable, often insidious, manifestations, [...] Read more.
Anderson–Fabry Disease (AFD) is a rare, systemic lysosomal storage disease triggered by mutations in the GLA gene, leading to α-galactosidase A (α-Gal A) deficiency. The disease’s X-linked inheritance leads to more severe, early-onset presentations in males, while females exhibit variable, often insidious, manifestations, notably impacting cardiac health. This study aims to examine gender-based AFD cardiac manifestations in correlation with the variant type: classical (CL), late-onset (LO), or variants of uncertain significance (VUS). We analyzed data from 72 AFD patients (53 females, 19 males) referred to the “G. Rodolico” University Hospital, employing enzyme activity measurements, genetic analysis, periodic lyso-Gb3 monitoring, comprehensive medical histories, and advanced cardiac imaging techniques. Statistical analysis was performed using SPSS version 26. Our AFD cohort, with an average age of 45 ± 16.1 years, comprised 12 individuals with hypertrophy (AFD-LVH) and 60 without (AFD-N). Women, representing about 75% of the subjects, were generally older than men (47.2 ± 16.2 vs. 38.8 ± 14.6, p = 0.046). In the female group, 17% had CL variants, 43.3% LO, and 39.6% had VUS, compared to 21.1%, 36.8%, and 31.6% in the male group, respectively. Females exhibited significantly higher α-Gal A values (median 7.9 vs. 1.8 nmol/mL/h, p < 0.001) and lower lyso-Gb3 levels (1.5 [IQR 1.1–1.7] vs. 1.9 [1.5–17.3] nmol/L, p = 0.02). Regarding the NYHA class distribution, 70% of women were in class I and 28% in class II, compared to 84% and 16% of men, respectively. Among women, 7.5% exhibited ventricular arrhythmias (10.5% in men), and 9.4% had atrial fibrillation (10.5% in men). Cardiac MRIs revealed fibrosis in 57% of examined women, compared to 87% of men. Even among patients without LVH, significant differences persisted in α-Gal A and lyso-Gb3 levels (p = 0.003 and 0.04), as well as LVMi (61.5 vs. 77.5 g/sqm, p = 0.008) and GLS values (−20% vs. −17%, p = 0.01). The analysis underscored older age, decreased lyso-Gb3 deposition, reduced hypertrophy, and lesser GLS compromise in females, suggesting later disease onset. Severe cardiac patterns were associated with classic variants, while more nuanced manifestations were noted in those with VUS. Early GLS impairment in males, irrespective of hypertrophy, emphasized the role of subclinical damage in AFD. Full article
(This article belongs to the Special Issue Diagnosis and Therapies for Genetic Diseases)
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11 pages, 9044 KiB  
Article
Involvement of Nucleotide Excision Repair and Rec-Dependent Pathway Genes for UV Radiation Resistance in Deinococcus irradiatisoli 17bor-2
by Gayathri Subramani and Sathiyaraj Srinivasan
Genes 2023, 14(9), 1803; https://doi.org/10.3390/genes14091803 - 15 Sep 2023
Cited by 3 | Viewed by 1140
Abstract
Strain Deinococcus irradiatisoli 17bor-2 was isolated from a soil sample exposed to γ radiation at Seoul Women’s University, Republic of Korea. The genus Deinococcus is a Gram-negative, coccus-shaped, and extremophilic bacterium, well renowned as being a radiation-resistant bacterium. Therefore, the mechanism behind the [...] Read more.
Strain Deinococcus irradiatisoli 17bor-2 was isolated from a soil sample exposed to γ radiation at Seoul Women’s University, Republic of Korea. The genus Deinococcus is a Gram-negative, coccus-shaped, and extremophilic bacterium, well renowned as being a radiation-resistant bacterium. Therefore, the mechanism behind the resistance to radiation and the gene responsible for the resistance could be helpful for detailed experimental studies with biotechnological applications. To study the involvement of genes in UV radiation resistance in strain 17bor-2, the genomic DNA of the strain was sequenced and constructed using the Pacific Biosciences RS II system. In addition, the complete genome sequence of strain 17bor-2 was annotated and interpreted using the Genomes–Expert Review (IMG-ER) system, along with Prodigal and JGI GenePRIMP analysis. The genome analysis of strain 17bor-2 revealed evidence of excinuclease UvrABC genes, which are key enzymes in the nucleotide excision repair (NER) mechanism, as well as genes from the recA-dependent and recQ pathways. The genome of strain Deinococcus irradiatisoli 17bor-2 was a circular chromosome comprising 3,052,043 bp with a GC content of 67.0%, including 2911 coding sequences (CDs), 49 tRNA genes, and 9 rRNA genes. In addition, their complete genome sequence annotation features provided evidence that radiation resistance genes play a central part in adaptation against extreme environmental conditions. In recent decades, excision repair genes have been indicated in considerable detail for both prokaryote and eukaryote resistance against UV-C radiation. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)
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24 pages, 1236 KiB  
Article
Cancer Classification Utilizing Voting Classifier with Ensemble Feature Selection Method and Transcriptomic Data
by Rabea Khatun, Maksuda Akter, Md. Manowarul Islam, Md. Ashraf Uddin, Md. Alamin Talukder, Joarder Kamruzzaman, AKM Azad, Bikash Kumar Paul, Muhammad Ali Abdulllah Almoyad, Sunil Aryal and Mohammad Ali Moni
Genes 2023, 14(9), 1802; https://doi.org/10.3390/genes14091802 - 14 Sep 2023
Cited by 3 | Viewed by 2165
Abstract
Biomarker-based cancer identification and classification tools are widely used in bioinformatics and machine learning fields. However, the high dimensionality of microarray gene expression data poses a challenge for identifying important genes in cancer diagnosis. Many feature selection algorithms optimize cancer diagnosis by selecting [...] Read more.
Biomarker-based cancer identification and classification tools are widely used in bioinformatics and machine learning fields. However, the high dimensionality of microarray gene expression data poses a challenge for identifying important genes in cancer diagnosis. Many feature selection algorithms optimize cancer diagnosis by selecting optimal features. This article proposes an ensemble rank-based feature selection method (EFSM) and an ensemble weighted average voting classifier (VT) to overcome this challenge. The EFSM uses a ranking method that aggregates features from individual selection methods to efficiently discover the most relevant and useful features. The VT combines support vector machine, k-nearest neighbor, and decision tree algorithms to create an ensemble model. The proposed method was tested on three benchmark datasets and compared to existing built-in ensemble models. The results show that our model achieved higher accuracy, with 100% for leukaemia, 94.74% for colon cancer, and 94.34% for the 11-tumor dataset. This study concludes by identifying a subset of the most important cancer-causing genes and demonstrating their significance compared to the original data. The proposed approach surpasses existing strategies in accuracy and stability, significantly impacting the development of ML-based gene analysis. It detects vital genes with higher precision and stability than other existing methods. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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27 pages, 5421 KiB  
Article
Investigating Neuron Degeneration in Huntington’s Disease Using RNA-Seq Based Transcriptome Study
by Nela Pragathi Sneha, S. Akila Parvathy Dharshini, Y.-h. Taguchi and M. Michael Gromiha
Genes 2023, 14(9), 1801; https://doi.org/10.3390/genes14091801 - 14 Sep 2023
Cited by 2 | Viewed by 2213
Abstract
Huntington’s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is [...] Read more.
Huntington’s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD. Full article
(This article belongs to the Topic Advances in Bioinformatics and Computational Biology of Human Disease)
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