Frontiers in Genetics最新文献

{"title":"Bioinformatics revealed biomarkers for diagnosis in kidney stones.","authors":"Ziqi He, Chao Song, Zhong Wang, Caitao Dong, Qinhong Jiang, Xi Yu, Guang Shan","doi":"10.3389/fgene.2025.1542840","DOIUrl":"10.3389/fgene.2025.1542840","url":null,"abstract":"<p><strong>Background: </strong>One of the most prevalent urinary illnesses is kidney stone formation, often known as nephrolithiasis. The precise processes of kidney stone remain poorly known after substantial investigation. In order to successfully prevent and cure stone formation and recurrence, additional research into the pathophysiology of stone formation is of paramount importance. Ferroptosis is linked to a variety of renal diseases and is a critical factor in the death of cells. However, little is known about how ferroptosis-related genes (FRGs) contribute to the development of kidney stones.</p><p><strong>Methods: </strong>The Ferroptosis Database and the Gene Expression Omnibus (GEO) database provided us with information on kidney stones and FRGs, respectively (FerrDb).</p><p><strong>Results: </strong>Eight DE-FRGs related to kidney stones were found in total, and they were all closely related to immune response and autophagy management. Following this, among the 8 DE-FRGs, LASSO and SVM-RFE algorithms chose FZD7, STK11, SUV39H1, and LCN2 as marker genes with suitable diagnostic capabilities. These marker genes may be involved in the control of the PPAR signaling pathway, mTOR signaling system, and fatty acid production of kidney stones, according to the functional enrichment analysis that followed. Additionally, 24 drugs that target two marker genes have been found. Despite this, the ceRNA networks have gained that the regulatory relationship between marker genes is rather complex. Additionally, the findings of the CIBERSORT investigation indicated that FZD7 and SUV39H1 may be linked to variations in the immune milieu of people who have kidney stones.</p><p><strong>Conclusion: </strong>We developed a diagnostic tool and provided information on the development of kidney stones. In order to confirm its diagnostic applicability for kidney stones, more studies are needed before it may be used in clinical practice.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1542840"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763717","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":"Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies.","authors":"Tahira Luqman, Manzoor Hussain, Syed Riaz Ahmed, Iram Ijaz, Zahra Maryum, Sahar Nadeem, Zafran Khan, Sana Muhy Ud Din Khan, Mohammad Aslam, Yongming Liu, Muhammad Kashif Riaz Khan","doi":"10.3389/fgene.2025.1553406","DOIUrl":"10.3389/fgene.2025.1553406","url":null,"abstract":"<p><p>Cotton is a vital fiber crop for the global textile industry, but rising temperatures due to climate change threaten its growth, fiber quality and yields. Heat stress disrupts key physiological and biochemical processes, affecting carbohydrate metabolism, hormone signaling, calcium and gene regulation and expression. This review article explores cotton's defense mechanism against heat stress, including epigenetic regulations and transgenic approaches, with a focus on genome editing tools. Given the limitations of traditional breeding, advanced omics technologies such as GWAS, transcriptomics, proteomics, ionomics, metabolomics, phenomics and CRISPR-Cas9 offer promising solutions for developing heat-resistant cotton varieties. This review highlights the need for innovative strategies to ensure sustainable cotton production under climate change.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1553406"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763736","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":"Structural characteristics of mitochondrial genome of <i>Spirobo-lus walkeri</i> (Spirobolida: Spirobolidae), and phylogenetic analysis of Diplopoda.","authors":"Wenwen Zhang, Shengjun Zhao, Lingna Li, Yingzhu Li, Hongyi Liu, Peng Cui","doi":"10.3389/fgene.2025.1566634","DOIUrl":"10.3389/fgene.2025.1566634","url":null,"abstract":"<p><p>The phylogeny of Diplopoda, a group of ancient arthropod and an important component of modern terrestrial ecosystems, remains unclear. Here, the complete mitogenome of <i>Spirobolus walkeri</i> was determined. The newly sequenced complete mitogenome was circular DNA molecules with sizes of 14,879 bp. The mitogenome was composed of 37 genes and one control region. Negative AT-skews and positive GC-skews were found in whole mitogenome. The gene <i>COX1</i> used CGA as the start codon, while the other PCGs utilized ATN (A, T, G) as the start codons; however, the sequence of the stop codon was variable. The Ser2 exhibited the highest usage bias. All tRNAs have typical cloverleaf structures, except <i>trnS-AGC</i> and <i>trnM</i>. Phylogenetic analysis showed that <i>S. walkeri</i> and <i>Spirobolus bungii</i> shared a close relationship and that they were also closely related with <i>Narceus annularus</i>. This study helps resolve taxonomic ambiguities among morphologically similar species and provides data to support the establishment of evolutionary benchmarks for millipedes, including gene rearrangements and variations in tRNA structure.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1566634"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752297","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":"Exploring the oncogenic role and prognostic value of <i>CKS1B</i> in human lung adenocarcinoma and squamous cell carcinoma.","authors":"Md Solayman Hossain, Tariqul Islam Tusar, Nairita Ahsan Faruqui, Tanjim Ishraq Rahaman, Yasin Arafath Sharker, Shimran Saharia Santo, Abu Tayab Moin, Yusha Araf, Ibrahim Khalil Afif, Shoaib Saikat, Mohammad Jakir Hosen","doi":"10.3389/fgene.2025.1449466","DOIUrl":"10.3389/fgene.2025.1449466","url":null,"abstract":"<p><strong>Introduction: </strong>Lung cancer (LC) is a highly aggressive malignancy and remains a leading cause of cancer-related mortality worldwide. Non-small cell lung cancer (NSCLC), which includes adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), accounts for the majority of these deaths. Due to the lack of early clinical symptoms and late-stage diagnosis, there is an urgent need for precise and targeted therapeutic strategies. Cyclin-dependent kinase regulatory subunit 1B (<i>CKS1B</i>), a key regulator of the cell cycle, has been implicated in various human cancers. Emerging evidence suggests that its upregulation is associated with poor prognosis in NSCLC, highlighting its potential as a biomarker for early detection and targeted therapy.</p><p><strong>Methods: </strong>In this study, we conducted a comprehensive bioinformatics analysis to evaluate the role of <i>CKS1B</i> in LUAD and LUSC. Differential gene expression analysis, survival analysis, immune infiltration correlation, and pathway enrichment analysis were performed using publicly available transcriptomic datasets. Additionally, gene interaction networks were analyzed to assess the functional significance of <i>CKS1B</i> in lung cancer progression.</p><p><strong>Results: </strong>Our findings indicate a significant overexpression of <i>CKS1B</i> in LUAD and LUSC compared to normal lung tissues. Survival analysis demonstrated that higher <i>CKS1B</i> expression correlates with poor prognosis in NSCLC patients. Immune infiltration analysis revealed a potential role of <i>CKS1B</i> in modulating the tumor microenvironment, further supporting its relevance in lung cancer progression. Functional enrichment analysis highlighted its involvement in critical oncogenic pathways, including cell cycle regulation and immune modulation.</p><p><strong>Discussion: </strong>The results suggest that <i>CKS1B</i> serves as a potential biomarker for early detection and prognosis in NSCLC. Its association with immune response pathways underscores its possible role in immunotherapy. However, despite these promising findings, further in vivo and in vitro studies are necessary to validate <i>CKS1B</i>'s clinical applicability as a diagnostic and therapeutic target for lung cancer.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1449466"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752292","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":"weIMPUTE: a user-friendly web-based genotype imputation platform.","authors":"Mingliang Li, Zhuo Li, Defu Liu, Qi Li, Xiaodong Hu, Jun Yu, Jian Lin, Chunguang Bi, Guanshi Ye, Helong Yu, You Tang","doi":"10.3389/fgene.2025.1532464","DOIUrl":"10.3389/fgene.2025.1532464","url":null,"abstract":"<p><strong>Background: </strong>Genotype imputation is a critical preprocessing step in genome-wide association studies (GWAS), enhancing statistical power for detecting associated single nucleotide polymorphisms (SNPs) by increasing marker size.</p><p><strong>Results: </strong>In response to the needs of researchers seeking user-friendly graphical tools for imputation without requiring informatics or computer expertise, we have developed weIMPUTE, a web-based imputation graphical user interface (GUI). Unlike existing genotype imputation software, weIMPUTE supports multiple imputation software, including SHAPEIT, Eagle, Minimac4, Beagle, and IMPUTE2, while encompassing the entire workflow, from quality control to data format conversion. This comprehensive platform enables both novices and experienced users to readily perform imputation tasks. For reference genotype data owners, weIMPUTE can be installed on a server or workstation, facilitating web-based imputation services without data sharing.</p><p><strong>Conclusion: </strong>weIMPUTE represents a versatile imputation solution for researchers across various fields, offering the flexibility to create personalized imputation servers on different operating systems.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1532464"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752303","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":"Case report: Novel homozygous <i>ACVRL1</i> missense variant in a family with hereditary hemorrhagic telangiectasia and pulmonary arterial hypertension: findings suggest a hypomorphic allele.","authors":"Akash Mathavan, Akshay Mathavan, Urszula Krekora, Adityanarayan Rao, Marc S Zumberg, Jeb Justice, Pinar Bayrak-Toydemir, Jamie McDonald, Ali Ataya","doi":"10.3389/fgene.2025.1554624","DOIUrl":"10.3389/fgene.2025.1554624","url":null,"abstract":"<p><p>Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder caused by pathogenic variants in genes within the transforming growth factor beta (TGF-β) signaling pathway, such as <i>ACVRL1</i>, leading to haploinsufficiency. Homozygous variants in HHT-related genes are exceptionally rare and have not been reported in <i>ACVRL1</i>-related HHT to date. We report the first known instance of a novel homozygous missense variant in the <i>ACVRL1</i> gene (c.576C>G; p.Phe192Leu) identified in two siblings from a family of seven, in which three heterozygotes were also present. Comprehensive clinical evaluations revealed striking phenotypic differences between the homozygous and heterozygous family members. Both homozygous individuals exhibited early-onset pulmonary arterial hypertension and diffuse pulmonary arteriovenous malformations. One of them also demonstrated childhood-onset gastrointestinal bleeding-a manifestation unprecedented in HHT that typically has a late-adulthood onset. In contrast, the heterozygotes displayed either mild or equivocal features of HHT, supporting the classification of this variant as a hypomorphic allele. The novel missense variant is located within the intracellular glycine-serine (GS) domain of the protein, suggesting potential impacts on receptor regulation and downstream signaling. Although these findings expand the phenotypic spectrum of <i>ACVRL1</i>-related HHT, they remain limited to clinical observations. Experimental studies, including functional and molecular assays, are therefore essential to confirm the pathogenic impacts of this variant, validate its classification as a hypomorphic allele, and elucidate its effects on BMP-TGF-β signaling.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1554624"},"PeriodicalIF":2.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752285","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":"Discovery of therapeutic targets in cardiovascular diseases using high-throughput chromosome conformation capture (Hi-C).","authors":"Quan Zheng, Ying Liu, Minghao Guo, Xin Zhang, Qingbin Zhang, Xi-Yong Yu, Zhongxiao Lin","doi":"10.3389/fgene.2025.1515010","DOIUrl":"10.3389/fgene.2025.1515010","url":null,"abstract":"<p><p>Epigenetic changes have been associated with several cardiovascular diseases. In recent years, epigenetic inheritance based on spatial changes has gradually attracted attention. Alterations in three-dimensional chromatin structures have been shown to regulate gene expression and influence disease onset and progression. High-throughput Chromosome Conformation Capture (Hi-C) is a powerful method to detect spatial chromatin conformation changes. Since its development, Hi-C technology has been widely adopted for discovering novel therapeutic targets in cardiovascular research. In this review, we summarize key targets identified by Hi-C in cardiovascular diseases and discuss their potential implications for epigenetic therapy.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1515010"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779868","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":"Evolutionary history and divergence times of Tettigoniidae (Orthoptera) inferred from mitochondrial phylogenomics.","authors":"Tianyou Zhao, Zhenbin Lin, Hailin Yang, Fan Song, Zhenyuan Xia, Weidong Huang","doi":"10.3389/fgene.2025.1495754","DOIUrl":"10.3389/fgene.2025.1495754","url":null,"abstract":"<p><strong>Background: </strong>Advances in high-throughput sequencing technology have led to a rapid increase in the number of sequenced mitochondrial genomes (mitogenomes), ensuring the emergence of mitochondrial phylogenomics, as a powerful tool for understanding the evolutionary history of various animal groups.</p><p><strong>Methods: </strong>In this study, we utilized high-throughput sequencing technology to assemble and annotate the mitogenomes of <i>Letana rubescens</i> (Stål) and <i>Isopsera denticulata</i> Ebner. We described the characteristics of the mitochondrial genes of these two species. Utilizing 13 PCGs and 2 rRNA genes, we reconstructed the phylogenetic relationships of Tettigoniidae by combining published data with our newly generated data. We used likelihood mapping, signal-to-noise ratio (SNR), and saturation analysis across different datasets to ensure the robustness of our inferred topologies.</p><p><strong>Results and conclusion: </strong>Selective pressure analysis on the 13 protein-coding genes (PCGs) and 2 ribosomal RNA (rRNA) genes revealed that only <i>ND1</i> and <i>COX1</i> contained positively selected sites, while negative selection dominated across all genes, indicating that mitochondrial genes primarily function to maintain genetic integrity. Additionally, we assessed the evolutionary rates of the 13 PCGs and two rRNA genes across five major subfamilies using mean pairwise identity analysis. Phylogenetic results of our study provide more precise insights into the relationships within Tettigoniidae, spanning subfamilies, tribes, genera, and species. We further estimated the divergence times of Tettigoniidae using four fossil calibration nodes in MCMCTree, dating the origin of katydids to the early Paleogene period (approximately 60.86 Mya), and identifying the divergence nodes for five major subfamilies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1495754"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779873","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":"Corrigendum: Case report and literature review: delayed diagnosis of ARCL1B due to a newly reported homozygous mutation c.464A>C p. (Tyr155Ser) in the EFEMP2 gene.","authors":"Lixue Ouyang, Fan Yang, Hongyu Duan, Chuan Wang","doi":"10.3389/fgene.2025.1589037","DOIUrl":"https://doi.org/10.3389/fgene.2025.1589037","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fgene.2024.1453195.].</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1589037"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11947943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729732","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":"CLMT: graph contrastive learning model for microbe-drug associations prediction with transformer.","authors":"Liqi Xiao, Junlong Wu, Liu Fan, Lei Wang, Xianyou Zhu","doi":"10.3389/fgene.2025.1535279","DOIUrl":"10.3389/fgene.2025.1535279","url":null,"abstract":"<p><p>Accurate prediction of microbe-drug associations is essential for drug development and disease diagnosis. However, existing methods often struggle to capture complex nonlinear relationships, effectively model long-range dependencies, and distinguish subtle similarities between microbes and drugs. To address these challenges, this paper introduces a new model for microbe-drug association prediction, CLMT. The proposed model differs from previous approaches in three key ways. Firstly, unlike conventional GCN-based models, CLMT leverages a Graph Transformer network with an attention mechanism to model high-order dependencies in the microbe-drug interaction graph, enhancing its ability to capture long-range associations. Then, we introduce graph contrastive learning, generating multiple augmented views through node perturbation and edge dropout. By optimizing a contrastive loss, CLMT distinguishes subtle structural variations, making the learned embeddings more robust and generalizable. By integrating multi-view contrastive learning and Transformer-based encoding, CLMT effectively mitigates data sparsity issues, significantly outperforming existing methods. Experimental results on three publicly available datasets demonstrate that CLMT achieves state-of-the-art performance, particularly in handling sparse data and nonlinear microbe-drug interactions, confirming its effectiveness for real-world biomedical applications. On the MDAD, aBiofilm, and Drug Virus datasets, CLMT outperforms the previously best model in terms of Accuracy by 4.3%, 3.5%, and 2.8%, respectively.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1535279"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718589","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}