{"title":"Correction: Analysis and validation of novel biomarkers related to palmitoylation in adenomyosis.","authors":"Hongyu Zhang, Yufeng Li, Huijuan Cao, Yiling Zhao, Hongwen Zhu, Tiansheng Qin","doi":"10.3389/fgene.2025.1683914","DOIUrl":"10.3389/fgene.2025.1683914","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fgene.2025.1614573.].</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1683914"},"PeriodicalIF":2.8,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015089","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":"Small nucleolar RNA SNORD13H suppresses tumor progression via FBL-dependent 2'-O-methylation in hepatocellular carcinoma.","authors":"Minglu Zhang, Jianbo He, Rao Fu, Guojian Bao, Yijun Lu, Zechuan Zhang, Jiawu Yan, Jialu Ding, Fei Yang, Beicheng Sun","doi":"10.3389/fgene.2025.1620552","DOIUrl":"10.3389/fgene.2025.1620552","url":null,"abstract":"<p><strong>Introduction: </strong>Small nucleolar RNA (snoRNA) mediates RNA modifications, including 2'-O-methylation (Nm) and pseudouridine (Ψ), which has been proven to impact tumor progression. However, the role of snoRNA in the epigenetics of tumors remains poorly understood due to the lack of sufficiently effective experimental methods to identify snoRNA targets. Here, we identified SNORD13H, a C/D box snoRNA, as being downregulated in hepatocellular carcinoma (HCC), and its low expression was associated with HCC development.</p><p><strong>Methods: </strong>To elucidate specific roles of SNORD13H in HCC, we used a comprehensive array of methodologies, including flow cytometry, xenograft mouse model, reverse transcription at low dNTP concentration followed by PCR (RTL-P) assay, and surface sensing of translation (SUnSET) assay.</p><p><strong>Results: </strong>In this study, we first demonstrated that reduced SNORD13H serves as a biomarker for HCC, facilitating cellular proliferation. SNORD13H mediates 2'-O-methylations of 18S rRNA and RAS mRNA, thereby enhancing translation efficiency and regulating RAS protein levels in HCC. The diminution of SNORD13H activates the RAS pathway, contributing to the progression of HCC.</p><p><strong>Discussion: </strong>Our study establishes SNORD13H as a dual-function regulator in HCC progression. Furthermore, our findings indicate that SNORD13H is detectable in plasma, highlighting its potential utility in tumor screening.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1620552"},"PeriodicalIF":2.8,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12408296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015061","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":"Unraveling the pathogenicity role of the novel compound heterozygous mutations of MED25 gene in a Chinese patient with BVSYS.","authors":"Linbing Zou, Ruikang Qiu, Zhijun Dai, Yulei Li, Yunjiao Liao, Yan Zhou","doi":"10.3389/fgene.2025.1654336","DOIUrl":"10.3389/fgene.2025.1654336","url":null,"abstract":"<p><strong>Introduction: </strong>Mediator of RNA polymerase II transcription subunit 25 (<i>MED25</i>), a crucial component of the transcriptional coactivator complex, plays a significant role in the transcription of most RNA polymerase II-dependent genes. Mutations in <i>MED25</i> have been linked to various genetic syndromes, including Basel-Vanagaite-Smirin-Yosef Syndrome (BVSYS) and Intellectual Disability (ID). This study elucidated the molecular mechanism through which compound heterozygous mutations in the <i>MED25</i> gene impaired pre-mRNA splicing, ultimately causing BVSYS.</p><p><strong>Methods: </strong>Whole exome sequencing (WES) was performed to identify genetic variants, followed by Sanger sequencing for validation. Clinical data were correlated with established <i>MED25</i>-related syndrome phenotypes. Bioinformatics tools were utilized to predict splicing effects and protein structural alterations. Functional characterization involved in vitro minigene splicing assays for the c.1965+1dup mutation and RT-PCR analysis of patient-derived transcripts, while the impact of p.R224G was assessed through protein structure modeling.</p><p><strong>Results: </strong>The proband presented with clinical manifestations such as cognitive impairment, language difficulties, intellectual disability, and microcephaly. The study identified a compound heterozygous mutation in the <i>MED25</i> gene (NM_030973.4), consisting of c.670C>G (p.R224G) and c.1965+1dup, which was associated with the observed clinical phenotype. Bioinformatics analysis and in vivo/in vitro splicing assays demonstrated that the c.1965+1dup mutation disrupts <i>MED25</i> pre-mRNA splicing, whereas the c.670C>G (p.R224G) variant does not exhibit this effect. However, bioinformatics analysis suggested that the mutation c.670C>G (p.R224G) may affect gene function by altering the structure of the <i>MED25</i> protein.</p><p><strong>Conculsion: </strong>These findings demonstrated that two mutation sites identified in the <i>MED25</i> gene in this case are pathogenic or likely pathogenic and may be associated with the clinical phenotype of the proband in this study.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1654336"},"PeriodicalIF":2.8,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000450","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}
Frontiers in GeneticsPub Date : 2025-08-20eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1675361
Claudia Gonzaga-Jauregui, Ferran Casals, Vajira H W Dissanayake
{"title":"Editorial: Rare diseases research and diagnosis in low- and middle-income countries.","authors":"Claudia Gonzaga-Jauregui, Ferran Casals, Vajira H W Dissanayake","doi":"10.3389/fgene.2025.1675361","DOIUrl":"10.3389/fgene.2025.1675361","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1675361"},"PeriodicalIF":2.8,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000478","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}
Frontiers in GeneticsPub Date : 2025-08-20eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1619911
Meirong Feng, Yan Chai, Jinna Li, Qi Wang, Dekui Zhang
{"title":"A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.","authors":"Meirong Feng, Yan Chai, Jinna Li, Qi Wang, Dekui Zhang","doi":"10.3389/fgene.2025.1619911","DOIUrl":"10.3389/fgene.2025.1619911","url":null,"abstract":"<p><strong>Background and purpose: </strong>In recent years, research on the relationship between hepatitis B virus-related cirrhosis (HBV-LC) and gut microbiota has grown, but studies focusing on the Northwest Chinese population are scarce. This study characterized the gut microbiota composition and function in HBV-LC patients vs. healthy individuals in Northwest China, aiming to provide a scientific basis for region-specific precision therapies.</p><p><strong>Materials and methods: </strong>A cross-sectional study enrolled 43 HBV-LC patients and 43 age-/sex-matched healthy controls (HC) from Gansu Province. Clinical parameters including liver function, blood routine, coagulation function, blood biochemistry were measured. Shotgun metagenomic sequencing was conducted to analyze gut microbiota taxonomic composition and function.</p><p><strong>Results: </strong>HBV-LC patients showed significantly elevated alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), γ-glutamyl transferase (γ-GGT), prothrombin time, international normalized ratio (INR), and thrombin time, but reduced triglycerides (TG), total cholesterol (TC), erythrocytes, thrombocytes, total protein, albumin, and prothrombin time activity (PT-ratio). Alpha-diversity based on Shannon and Simpson indices was lower in HBV-LC. At the genus level, <i>Bacteroides</i>, <i>Prevotella</i>, <i>Escherichia</i>, <i>Parabacteroides</i>, <i>Veillonella</i>, and <i>Klebsiella</i> were enriched in HBV-LC, while <i>Bifidobacterium</i>, <i>Faecalibacterium, Roseburia</i>, <i>Ruminococcus</i>, <i>Anaerostipes</i>, <i>Blautia</i>, <i>Eubacterium</i>, and <i>Fusicatenibacter</i> were reduced. Species-level analysis identified distinct enrichment of <i>Prevotella copri, Bacteroides vulgatus, Escherichia coli, Fusobacterium nucleatum, and Veillonella</i> spp. in HBV-LC. Functional analysis revealed 482 metabolic pathways. HBV-LC showed enhanced lipid, amino acid, and nucleotide metabolism, menaquinol biosynthesis, and anaerobic energy metabolism, but reduced acetate/lactate production, lactose/galactose degradation, and peptidoglycan biosynthesis. Metagenome-wide association study revealed HBV-LC-enriched opportunistic species (e.g., <i>E. coli, Veillonella</i> spp.) correlated positively with hepatic enzymes and coagulation parameters, and negatively with TC, TG, and erythrocyte counts.</p><p><strong>Conclusion: </strong>HBV-LC patients in Northwest China exhibit altered clinical indicators, gut microbial composition (reduced diversity, increased opportunistic pathogens, decreased beneficial species), and metabolic function. These findings highlight the potential of gut microbiome-targeted interventions for regional precision medicine of HBV-LC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1619911"},"PeriodicalIF":2.8,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12404923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000391","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}
Frontiers in GeneticsPub Date : 2025-08-19eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1627482
Rajni Parmar, Sapna Thakur, Ram Kumar Sharma
{"title":"Editorial: Genome-wide identification of functional markers to enhance molecular breeding efforts in agriculturally important, underutilized, and less explored plant species.","authors":"Rajni Parmar, Sapna Thakur, Ram Kumar Sharma","doi":"10.3389/fgene.2025.1627482","DOIUrl":"10.3389/fgene.2025.1627482","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1627482"},"PeriodicalIF":2.8,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12401692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992273","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}
Frontiers in GeneticsPub Date : 2025-08-18eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1550205
Zhiming Hu, Qiong Wang, Yuqi Wang, Yao Gao, Jianhua Hao, Rui Li, Hua Zhao, Shuping Guo, Hongzhou Cui
{"title":"Bioinformatics analysis combined with untargeted metabolomics reveals lipid metabolism-related genes and their biological markers in chronic spontaneous urticaria.","authors":"Zhiming Hu, Qiong Wang, Yuqi Wang, Yao Gao, Jianhua Hao, Rui Li, Hua Zhao, Shuping Guo, Hongzhou Cui","doi":"10.3389/fgene.2025.1550205","DOIUrl":"10.3389/fgene.2025.1550205","url":null,"abstract":"<p><strong>Background: </strong>Chronic spontaneous urticaria (CSU) is an immune-driven skin condition with a multifaceted and not yet fully understood pathogenesis. Although substantial research has been conducted, viable therapeutic targets are still scarce. Studies indicate that disruptions in lipid metabolism significantly influence the development of immune-related disorders. Nevertheless, the precise relationship between lipid metabolism and CSU remains underexplored, warranting further investigation.</p><p><strong>Methods: </strong>We obtained the GSE72540 and GSE57178 datasets from the Gene Expression Omnibus (GEO) repository. For the GSE72540 dataset, we identified differentially expressed genes (DEGs) and performed weighted gene co-expression network analysis (WGCNA) on them. The identified DEGs were cross-referenced with lipid metabolism-related genes (LMRGs). To identify hub genes, we constructed a protein-protein interaction (PPI) network. These hub genes were validated using the GSE57178 dataset to identify potential diagnostic markers. Additionally, gene set enrichment analysis (GSEA) and receiver operating characteristic (ROC) curve analysis were employed to evaluate their diagnostic potential. In the CSU mouse model, we further validated the expression levels of these hub genes. Finally, untargeted metabolomics was conducted to detect lipid metabolism-related metabolites in the serum of CSU patients.</p><p><strong>Result: </strong>Using bioinformatics analysis, three hub genes were identified: <i>SLC2A4</i>, <i>PTGS2</i>, and <i>PLA2G2A</i>. In skin tissues from CSU-like mouse models, the mRNA levels of <i>PTGS2</i> and <i>PLA2G2A</i> were significantly upregulated compared to the control group. Additionally, untargeted metabolomics revealed 60 distinct lipid metabolites, with a marked increase in arachidonic acid levels observed in the CSU group.</p><p><strong>Conclusion: </strong><i>PTGS2</i> and <i>PLA2G2A</i> are key hub genes for CSU, and arachidonic acid can serve as a potential serum biomarker.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1550205"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12399643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992197","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}
Frontiers in GeneticsPub Date : 2025-08-18eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1644874
Xuanpeng Wang, Dandan Gao, Gaowei Zhang, Yongchun Ge, Xinhai Wang
{"title":"High-density SNP-based linkage map construction and QTL analysis for growth-related traits in <i>Luciobarbus brachycephalus</i> using whole-genome resequencing data.","authors":"Xuanpeng Wang, Dandan Gao, Gaowei Zhang, Yongchun Ge, Xinhai Wang","doi":"10.3389/fgene.2025.1644874","DOIUrl":"10.3389/fgene.2025.1644874","url":null,"abstract":"<p><strong>Introduction: </strong><i>Luciobarbus brachycephalus</i> (commonly known as the Aral barbel) represents a commercially valuable fish species in China, contributing significantly to regional aquaculture economies. High-density genetic linkage mapping coupled with quantitative trait locus (QTL) analysis has emerged as a powerful approach for elucidating the genetic mechanism of complex traits in aquatic species.</p><p><strong>Method: </strong>The present study aimed to construct a SNP-based high-density linkage map using male parent, female parent, and 165 F<sub>1</sub> full-sib progenies through whole-genome resequencing strategy, and subsequently perform comprehensive QTL mapping of six economically important growth-related traits, in order to identify candidate genes underlying growth regulation in <i>L. brachycephalus</i>.</p><p><strong>Results: </strong>Pearson correlation analysis demonstrated strong associations among all six growth-related traits (<i>r</i> > 0.8, <i>P</i> < 0.001), indicating likely pleiotropic regulation through shared genetic factors. The high-density linkage map for <i>L. brachycephalus</i> incorporated 164,435 high-quality SNPs distributed across 50 linkage groups, achieving complete genome coverage of 6,425.95 cM. The exceptional marker density (average inter-marker distance = 0.10 cM) establishes this as the most precise genetic map reported for this species to date, enabling the accurate candidate gene localization and enhanced marker-assisted selection. Through QTL mapping analysis, several genomic regions significantly associated with growth-related traits were identified based on genome-wide peak logarithm of odds scores. Specifically, one major QTL for body height was located on linkage group (LG27), and two distinct QTL for body weight were positioned on LG20 and LG26. Notably, four longitudinal growth traits (total length, body length, fork length, and preanal body length) were found to co-localize within the same significant QTL interval on LG27. These QTL intervals identified 6.27-39.36% of the phenotypic variance explained for the respective traits. Furthermore, putative candidate genes potentially regulating each target trait were identified through comprehensive analysis of these significant QTL intervals.</p><p><strong>Discussion: </strong>This integrated approach provides a foundation for marker-assisted selection and enhances the understanding of growth-related genetic mechanisms in this important species.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1644874"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12399722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992259","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":"Four novel genetic mutations are associated with patent foramen ovale in Tibetan population using whole exome sequencing.","authors":"Hongwei Li, Yongjun He, Yong Wu, Lanxin Liu, Wei Du, Duika Wang, Zeng He, Liming Zhao","doi":"10.3389/fgene.2025.1592306","DOIUrl":"10.3389/fgene.2025.1592306","url":null,"abstract":"<p><strong>Objective: </strong>Patent foramen ovale (PFO), a prevalent congenital cardiac defect, is linked to clinical conditions such as cryptogenic stroke and migraine. The genetic underpinnings of PFO remain poorly elucidated, particularly in Tibet. This study aimed to identify potential pathogenic mutations in Tibetan PFO patients via whole exome sequencing (WES) to clarify its genetic basis.</p><p><strong>Methods: </strong>Eighteen Tibetan PFO patients diagnosed by echocardiography were enrolled. Peripheral blood samples underwent WES using Illumina HiSeq platform, followed by bioinformatics analysis to filter rare variants. Pathogenicity was assessed using predictive tools (SIFT, PolyPhen V2, and MutationTaster) and cardiac development-related gene databases (OMIM, HPO, HGMD, and MGI).</p><p><strong>Results: </strong>In this study, we identified four novel pathogenetic mutations in Tibetan PFO patients, including <i>GABRP</i> rs201584759 (c.421C>T: p. R141C), <i>GJB4</i> rs200602523 (c.292C>T: p. R98C), <i>RTTN</i> rs199568901 (c.5410G>A: E1804K), and <i>USH2A</i> rs144768593 (c.5608C>T: p. R1870W). Further analysis indicated that <i>GABRP</i>, <i>GJB4</i>, and <i>RTTN</i> were significantly associated with the occurrence of congenital heart disease.</p><p><strong>Conclusion: </strong>This study first reveals genetic characteristics of Tibetan PFO patients, implicating <i>GABRP</i>, <i>GJB4</i>, <i>RTTN</i>, and <i>USH2A</i> mutations in disrupting cardiac developmental pathways, potentially contributing to the occurrence of PFO. Findings underscore genetic factors regarding PFO prevalence in populations living in high-altitude and provide insights for molecular research and precision medicine.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1592306"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12399560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992210","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}
Frontiers in GeneticsPub Date : 2025-08-18eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1604541
Bing Zhao, Xuegui Tang
{"title":"Identification of anoikis-related genes to develop a risk model and predict the prognosis and tumor microenvironment in rectal adenocarcinoma.","authors":"Bing Zhao, Xuegui Tang","doi":"10.3389/fgene.2025.1604541","DOIUrl":"10.3389/fgene.2025.1604541","url":null,"abstract":"<p><strong>Background: </strong>Rectal adenocarcinoma (READ) is a common malignant tumor. This study aims to establish a risk model based on anoikis-related genes (ARGs) to predict prognosis and the tumor microenvironment in READ.</p><p><strong>Methods: </strong>Transcriptomic data and clinical data downloaded from the TCGA and GEO databases were used for differential analysis and Cox regression analysis. An ARGs-based prognostic risk model was constructed for READ. The survival curves and ROC curves were plotted to determine the predictive ability of the model for READ patients. The model was externally validated in the GSE87211 dataset. A nomogram, immune analysis, drug sensitivity analysis, and functional enrichment analysis were also performed to comprehensively validate the model.</p><p><strong>Results: </strong>The risk model included 6 prognostic genes (ALDH1A1, BRCA1, GSN, KRT17, SCD, and SNCG). Kaplan-Meier curves for the TCGA training cohort (P < 0.0001), testing cohort (P = 0.018), and GSE87211 dataset (P = 0.036) showed better prognoses in the low-risk group. The AUC for 1-year, 3-year, and 5-year overall survival in the TCGA training cohort, testing cohort, and GSE87211 dataset were (0.962, 0.923, 0.956), (0.887, 0.838, 0.833), and (0.73, 0.817, 0.743), respectively. The nomogram showed that the risk score served as an independent predictor of overall survival. Drug sensitivity analysis revealed differences in the IC50 values of OSI-027, PLX-4720, UMI-77, and Sapitinib between the high-risk and low-risk groups. Immune microenvironment analysis suggested distinct differences in immune cells between the two risk groups. Enrichment analysis revealed that these prognostic ARGs were primarily enriched in pathways and biological processes related to tumorigenesis.</p><p><strong>Conclusion: </strong>The risk model of ARGs can effectively predict READ prognosis and provide potential therapeutic targets.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1604541"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12399626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992264","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}