Genes最新文献

{"title":"Methylation of LINE-1 Retroelement in People with Type 1 Diabetes.","authors":"Andromachi Katsanou, Charilaos Kostoulas, Evangelos Liberopoulos, Agathocles Tsatsoulis, Ioannis Georgiou, Stelios Tigas","doi":"10.3390/genes16070759","DOIUrl":"https://doi.org/10.3390/genes16070759","url":null,"abstract":"<p><strong>Introduction: </strong>Emerging research indicates that alterations in the methylation of retrotransposons may contribute to genomic instability and cellular aging in various autoimmune disorders and diabetes mellitus (DM). As relevant information for people with type 1 diabetes mellitus (PwT1D) is limited, we aimed to investigate long interspersed nuclear element-1 (LINE-1) methylation status in this population.</p><p><strong>Methods: </strong>DNA methylation levels and patterns of LINE-1 were examined in the peripheral blood of 35 PwT1D and 28 healthy controls (age- and sex-matched), by using the COmbined Bisulfite Restriction Analysis methodology (COBRA).</p><p><strong>Results: </strong>Total LINE-1 methylation rate (mC) was higher in PwT1D compared to controls [47.3% (46.6-47.8%) vs. 46.5% (44.7-47.3%), <i>p</i> < 0.05]. The partial LINE-1 methylation pattern (uCmC) was less frequently observed in patients vs. controls [28.4% (24.7-33.3%) vs. 33.1% (27.8-37.9%), <i>p</i> < 0.05]. Prevalence of other methylation patterns [partially methylated (mCuC), hypermethylated (mCmC) and hypomethylated (uCuC)] was similar in the two groups. Furthermore, levels of fasting glucose and glycated hemoglobin (HbA1c) were positively associated with total methylation (mC) [Spearman's rho = 0.380, <i>p</i> = 0.002 and rho = 0.342, <i>p</i> = 0.006, respectively], but negatively associated with the partially methylated (uCmC) pattern [Spearman's rho = -0.383, <i>p</i> = 0.002 and rho = -0.270, <i>p</i> = 0.033, respectively]. The LINE-1 (uCmC) methylation pattern was negatively associated with the age at diagnosis of T1D [Spearman's rho = -0.341, <i>p</i> = 0.049], but positively associated with disease duration [Spearman's rho = 0.388, <i>p</i> = 0.021].</p><p><strong>Conclusions: </strong>PwT1D were found to have higher total LINE-1 methylation rate (mC) compared to healthy controls. The partial methylation pattern (uCmC) was less frequently observed in these patients and was negatively associated with the glycemic status and the age at diagnosis of T1D, while demonstrating a positive correlation with disease duration.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RETRACTED: Zhao et al. Analysis of the Molecular Mechanism of Energy Metabolism in the Sex Differentiation of Chickens Based on Transcriptome Sequencing. <i>Genes</i> 2024, <i>15</i>, 1035.","authors":"Ziduo Zhao, Zongyi Zhao, Fufu Cheng, Zhe Wang, Qingqing Geng, Yingjie Wang, Yingjie Niu, Qisheng Zuo, Yani Zhang","doi":"10.3390/genes16070750","DOIUrl":"10.3390/genes16070750","url":null,"abstract":"<p><p>The journal retracts the article \"Analysis of the Molecular Mechanism of Energy Metabolism in the Sex Differentiation of Chickens Based on Transcriptome Sequencing\" [...].</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144505528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Analysis of Codon Usage Bias in Transcriptomes of Eight Species of Formicidae.","authors":"Wenhui Zhu, Jiawei Wang, Jing Wang, Linlin Nie","doi":"10.3390/genes16070749","DOIUrl":"https://doi.org/10.3390/genes16070749","url":null,"abstract":"<p><p><b>Background:</b>Ants are among the most widely distributed eusocial insects, and desert ants, in particular, serve as important model organisms for studying animal navigation. <b>Methods</b>: In this study, we provide high-quality de novo transcriptomes for eight ant species: <i>Cataglyphis aenescens</i> (Nylander, 1849), <i>Formica approximans</i> Wheeler, 1933, <i>Lasius coloratus</i> Santschi, 1937, <i>Proformica mongolica</i> (Emery, 1901), <i>Proformica muusensis</i> Zhu, Wu, Duan & Xu, 2022, <i>Tapinoma geei</i> Wheeler, 1927, <i>Tapinoma rectinotum</i> Wheeler, 1927, and <i>Tetramorium tsushimae</i> Emery, 1925. <b>Results</b>: The GC content of coding sequences (CDSs) ranged from 43.61% to 46.20%, indicating a slightly AT-rich composition. Codon usage analysis identified 27 to 33 optimal codons per species, the majority of which ended with A or U. <b>Conclusions</b>: These transcriptomic resources provide critical insights into codon usage bias and establish a foundation for future research on molecular evolution, gene regulation, and environmental adaptation in ants inhabiting fragile desert ecosystems.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selecting Tolerant Maize Hybrids Using Factor Analytic Models and Environmental Covariates as Drought Stress Indicators.","authors":"Domagoj Stepinac, Ivan Pejić, Krešo Pandžić, Tanja Likso, Hrvoje Šarčević, Domagoj Šimić, Miroslav Bukan, Ivica Buhiniček, Antun Jambrović, Bojan Marković, Mirko Jukić, Jerko Gunjača","doi":"10.3390/genes16070754","DOIUrl":"https://doi.org/10.3390/genes16070754","url":null,"abstract":"<p><p><b>Background/Objectives</b>: A critical part of the maize life cycle takes place during the summer, and due to climate change, its growth and development are increasingly exposed to the irregular and unpredictable effects of drought stress. Developing and using new cultivars with increased drought tolerance for farmers is the easiest and cheapest solution. One of the concepts to screen for drought tolerance is to expose germplasm to various growth scenarios (environments), expecting that random drought will occur in some of them. <b>Methods</b>: In the present study, thirty-two maize hybrids belonging to four FAO maturity groups were tested for grain yield at six locations over two consecutive years. In parallel, data of the basic meteorological elements such as air temperature, relative humidity and precipitation were collected and used to compute two indices, scPDSI (Self-calibrating Palmer Drought Severity Index) and VPD (Vapor Pressure Deficit), that were assessed as indicators of drought (water deficit) severity during the vegetation period. Practical implementation of these indices was carried out indirectly by first analyzing yield data using a factor analytic model to detect latent environmental variables affecting yield and then correlating those latent variables with drought indices. <b>Results</b>: The first latent variable, which explained 47.97% of the total variability, was correlated with VPD (r = -0.58); the second latent variable explained 9.57% of the total variability and was correlated with scPDSI (r = -0.74). Furthermore, latent regression coefficients (i.e., genotypic sensitivities to latent environmental variables) were correlated with genotypic drought tolerance. <b>Conclusions</b>: This could be considered an indication that there were two different acting mechanisms in which drought affected yield.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial for the \"Genetic Studies of Fish\" Special Issue.","authors":"Yang Liu","doi":"10.3390/genes16070752","DOIUrl":"https://doi.org/10.3390/genes16070752","url":null,"abstract":"<p><p>Fish represent the most diverse vertebrate group, with over 32,000 species [...].</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Key Genes Associated with Overall Survival in Glioblastoma Multiforme Using TCGA RNA-Seq Expression Data.","authors":"Lilies Handayani, Denis Chegodaev, Ray Steven, Kenji Satou","doi":"10.3390/genes16070755","DOIUrl":"https://doi.org/10.3390/genes16070755","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Glioblastoma multiforme (GBM) is an aggressive and heterogeneous brain tumor with poor prognosis, emphasizing the need for reliable molecular biomarkers to improve patient stratification and treatment planning. This study aimed to identify key genes associated with overall survival in GBM by employing and comparing machine learning (ML) and deep learning (DL) approaches using RNA-Seq gene expression data. <b>Methods:</b> RNA-Seq expression and clinical data for primary GBM tumors were obtained from The Cancer Genome Atlas (TCGA). A univariate Cox proportional hazards regression was used to identify survival-associated genes. For survival prediction, ML-based feature selection techniques-RF, GB, SVM-RFE, RF-RFE, and PCA-were used to construct multivariate Cox models. Separately, DeepSurv, a DL-based survival model, was trained using the significant genes from the univariate analysis. Gradient-based importance scoring was applied to determine key genes from the DeepSurv model. <b>Results:</b> Univariate analysis yielded 694 survival-associated genes. The best ML-based Cox model (RF-RFE with 90% training data) achieved a c-index of 0.725. In comparison, DeepSurv demonstrated superior performance with a c-index of 0.822. The top 10 genes were identified from the DeepSurv analysis, including <i>CMTR1</i>, <i>GMPR</i>, and <i>PPY</i>. Kaplan-Meier survival curves confirmed their prognostic significance, and network analysis highlighted their roles in processes such as purine metabolism, RNA processing, and neuroendocrine signaling. <b>Conclusions:</b> This study demonstrates the effectiveness of combining ML and DL models to identify prognostic gene expression biomarkers in GBM, with DeepSurv providing higher predictive accuracy. The findings offer valuable insights into GBM biology and highlight candidate biomarkers for further validation and therapeutic development.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding Non-Coding RNA Regulators in DITRA: From Genomic Insights to Potential Biomarkers and Therapeutic Targets.","authors":"Sofia Spanou, Athena Andreou, Katerina Gioti, Dimitrios Chaniotis, Apostolos Beloukas, Louis Papageorgiou, Trias Thireou","doi":"10.3390/genes16070753","DOIUrl":"https://doi.org/10.3390/genes16070753","url":null,"abstract":"<p><strong>Background: </strong>Deficiency of <i>IL-36</i> Receptor Antagonist (DITRA) is a rare monogenic autoinflammatory disease, characterized by dysregulation of <i>IL-36</i> signaling and phenotypically classified as a subtype of generalized pustular psoriasis.</p><p><strong>Objectives: </strong>This study aimed to explore the role of potentially coding and non-coding RNAs (ncRNAs) in the <i>IL36RN</i> interactome to identify putative pathogenic mechanisms, biomarkers, and therapeutic targets for DITRA.</p><p><strong>Methods: </strong>A systems biology approach was applied using the STRING database to construct the IL36RN protein-protein interaction network. Key ncRNA interactions were identified using RNAInter. The networks were visualized and analyzed with Cytoscape v3 and the CytoHubba plugin to identify central nodes and interaction hubs. Pathway enrichment analysis was then performed to determine the biological relevance of candidate ncRNAs and genes.</p><p><strong>Results: </strong>Analysis identified thirty-eight ncRNAs interacting with the IL36RN network, including six lncRNAs and thirty-two miRNAs. Of these, thirty-three were associated with key DITRA-related signaling pathways, while five remain to be validated. Additionally, seven protein-coding genes were highlighted, with three (<i>TINCR</i>, <i>PLEKHA1</i>, and <i>HNF4A</i>) directly implicated in biological pathways related to DITRA. Many of the identified ncRNAs have prior associations with immune-mediated diseases, including psoriasis, supporting their potential relevance in DITRA pathogenesis.</p><p><strong>Conclusions: </strong>This study provides novel insights into the ncRNA-mediated regulation of <i>IL36RN</i> and its network in the context of DITRA. The findings support the potential utility of specific ncRNAs and genes, such as <i>TINCR</i>, <i>PLEKHA1</i>, and <i>HNF4A</i>, as key genomic elements warrant further functional characterization to confirm their mechanistic roles and may inform biomarker discovery and targeted therapeutic development in DITRA.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aluminum Stress Response Is Regulated Through a miR156/SPL13 Module in <i>Medicago sativa</i>.","authors":"Gamalat Allam, Solihu K Sakariyahu, Binghui Shan, Banyar Aung, Tim McDowell, Yousef Papadopoulos, Mark A Bernards, Abdelali Hannoufa","doi":"10.3390/genes16070751","DOIUrl":"https://doi.org/10.3390/genes16070751","url":null,"abstract":"<p><strong>Background: </strong>Aluminum (Al) toxicity severely limits <i>Medicago sativa</i> (alfalfa) production on acidic soils, resulting in major yield losses worldwide. The highly conserved miRNA156 (miR156) functions by downregulating at least 11 SQUAMOSA promoter-binding protein-like (SPL) transcription factors in alfalfa, including SPL13, but its role in Al stress remains unclear. This study aimed to investigate the miR156/SPL regulatory network's function in alfalfa under Al stress.</p><p><strong>Methods: </strong>Gene expression analyses, histochemical staining, nutrient profiling, phenotypic assays, transcriptome profiling, and ChIP-seq were conducted on alfalfa plants with altered miR156 and SPL13 expression to assess their roles in the Al stress response.</p><p><strong>Results: </strong>Al stress induced SPL13 expression while repressing miR156 in the roots. Elevated miR156 intensified Al accumulation, lipid peroxidation, and plasma membrane damage, accompanied by reduced leaf nitrogen, magnesium, sulfur, and phosphorus content. Phenotypically, increased SPL13 enhanced the root length and Al tolerance, whereas SPL13 silencing reduced tolerance. Transcriptome profiling of SPL13-silenced plants identified differentially expressed genes involved in the Al response, including aluminum-activated malate transporters and various transcription factors (GRAS, Myb-related, bHLH041, NAC, WRKY53, bZIP, and MADS-box). ChIP-seq revealed that SPL13 directly regulates genes encoding a protein kinase, cytochrome P450, and fasciclin-like arabinogalactan proteins.</p><p><strong>Conclusions: </strong>The MsmiR156/MsSPL13 network plays a crucial regulatory role in alfalfa's response to Al toxicity. These findings provide novel genetic targets and foundational knowledge to advance molecular breeding for enhanced Al tolerance in alfalfa.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021.","authors":"Felipe Avila, Elizabeth Esdaile, Rebecca R Bellone","doi":"10.3390/genes16070748","DOIUrl":"https://doi.org/10.3390/genes16070748","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Standardbreds, a breed of horses used in harness racing at either the trot or the pace, established a closed studbook in 1973. Concerns about genetic diversity within the breed led the United States Trotting Association (USTA) to establish a limit of mares bred per stallion (i.e., a studbook cap) in 2009. Here, we aimed to evaluate the impact of the breeding restrictions on genetic diversity between and among subpopulations. <b>Methods</b>: Sixteen short tandem repeats (STRs) were analyzed across a dataset of 176,424 Standardbreds foaled in the United States between 1998 and 2021. We examined allelic richness (<i>Na</i>), number of effective alleles (<i>Ne</i>), expected heterozygosity (<i>H_E</i>), observed heterozygosity (<i>H_O</i>), inbreeding coefficient (<i>F_IS</i>), and fixation index (<i>F_ST</i>) across 24 years, differentiating by gate type, and comparing pre-(1998-2009) and post-(2010-2021) studbook cap periods using regression analysis. <b>Results</b>: Our results support decreased genetic diversity for both trotters and pacers over time. However, pacing Standardbreds exhibited significantly slower rates of decrease in genetic diversity after the 2009 studbook cap, as evidenced by <i>Ne</i>, <i>H_E</i>, and <i>F_IS</i> (<i>P_Bonferroni</i> < 0.01). Additionally, moderate levels of genetic differentiation were found between trotters and pacers (0.05 < <i>F_ST</i> < 0.09), which increased over time. <b>Conclusions</b>: Given that the rate of loss of diversity does not appear to differ pre and post studbook cap in trotters and that there is an increase in genetic differentiation between the groups over time, developing additional breeding tools and strategies is necessary to help the subpopulation mitigate further decline.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential Expression of Epstein-Barr Virus Sequences in Various Breast Cancer Subtypes.","authors":"Alexander Blanchard, Namarig Elmalih, Perpetua Muganda","doi":"10.3390/genes16070756","DOIUrl":"https://doi.org/10.3390/genes16070756","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Breast cancer (BC) is the most common source of new cancer diagnoses among women and the second leading cause of cancer-related deaths in this group. The role of viral factors in the etiology, heterogeneity, and pathogenesis of this disease and its subtypes has not been incontrovertibly determined. Thus, in this study we began to address this problem by testing the hypothesis that the oncogenic Epstein-Barr virus (EBV) plays a role in this process. The approach involved determining the differential expression and predicted role of EBV gene sequences present in various subtypes of breast tumors as compared to those in control normal tissues. <b>Methods</b>: We utilized existing deep sequencing RNA-seq datasets derived from seventeen breast tumors and three control normal breast tissue samples to investigate the differential expression of EBV gene sequences. <b>Results</b>: We report three-fold higher levels of normalized total EBV-expressed sequences in tumors as compared to in control breast tissue. We also demonstrate differential expression of EBV gene transcript sequences in four categories of 26 known genes in breast cancer tumors as compared to that in normal breast tissue controls. Tumor-specific expression of EBV gene transcript sequences localized to seventeen genes; of these, tumor-specific EBV gene transcript-expressed sequences localizing to nine genes were strongly differentially expressed in a breast cancer subtype-specific manner. Furthermore, in a proof-of-concept investigation, we report, for the first time, that functional analysis of the differentially expressed integrated EBV transcript sequences demonstrate the capacity of these sequences to generate novel EBV miRNAs. We conclude that these integrated EBV sequences could potentially play a role in the pathogenesis of BC and its most aggressive subtypes. The functional role of these findings is currently under study.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 7","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}