Frontiers in Genetics最新文献

{"title":"Data report: transcriptome profiling of 13 tissues of Junmu No. 1 boars.","authors":"Chunyan Bai, Jiayi Ning, Junwen Fei, Zhenbo Wang, Yu He, Jing Li, Xiaoran Zhang, Shuang Liang, Dali Wang, Hao Sun, Boxing Sun","doi":"10.3389/fgene.2025.1641395","DOIUrl":"10.3389/fgene.2025.1641395","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1641395"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12433873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074908","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":"Editorial: Mitochondria in metabolic reprogramming and immune activation: the key gene and therapeutic target.","authors":"Yongzheng Guo","doi":"10.3389/fgene.2025.1686852","DOIUrl":"10.3389/fgene.2025.1686852","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1686852"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12434750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074948","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":"A <i>de novo</i> mutation in <i>RAB11A</i> is associated with neurodevelopmental disorder accompanied by variable multisystem abnormalities.","authors":"Huiting Zhang, Jingtao Zhang, Xue Ma, Zhehui Chen, Ying Jin, Mengqiu Li, Hui Dong, Feng Gu, Yao Zhang, Yanling Yang","doi":"10.3389/fgene.2025.1636206","DOIUrl":"10.3389/fgene.2025.1636206","url":null,"abstract":"<p><strong>Introduction: </strong>RAB11A, a Rab GTPase, is crucial for intracellular transport and recycling. Recently, <i>RAB11A</i> mutations have been found to be associated with neurodevelopmental disorders in cohorts. At present, there are still no effective treatment methods for NDDs caused by <i>RAB11A</i> deficiency, thus, identifying pathogenic mutations and generating disease models is crucial for advancing our understanding of these conditions.</p><p><strong>Methods: </strong>We analyzed the clinical presentation of a 4-year and 4-month-old boy with a <i>de novo RAB11A</i> mutation c.370A>G. To examine the consequences of RAB11A mutation during early embryonic development, we disrupted the homologous rab11a gene using CRISPR/Cas9 in zebrafish.</p><p><strong>Results: </strong>The affected boy who exhibited intellectual disability showed phenotypic features including cerebral atrophy, obesity, motor disability and abnormal muscle tone. Protein structure predictions indicated that <i>RAB11A</i> mutation affected protein stability and enzymatic activity. CRISPR/Cas9-mediated <i>rab11a</i> deficiency in zebrafish larvae significantly reduced brain, forebrain, and midbrain size.</p><p><strong>Conclusion: </strong>Our study collectively demonstrated that the <i>RAB11A</i> mutation c.370A>G is associated with neurodevelopmental disorders, characterized by motor deficits and brain anomalies. Additionally, we have successfully developed a zebrafish model to recapitulate these neurodevelopmental disorders associated with <i>RAB11A</i> deficiency, offering a valuable genetic resource for further investigation into this disease.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1636206"},"PeriodicalIF":2.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12434753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074888","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":"Codon usage bias analysis of the <i>WRKY</i> gene family in <i>Musa acuminata</i>.","authors":"Jiaman Sun, Ji Zhang, Jinzhong Zhang, Brett J Ferguson, Andrew Chen","doi":"10.3389/fgene.2025.1647037","DOIUrl":"10.3389/fgene.2025.1647037","url":null,"abstract":"<p><p>Codon usage bias (CUB), a universal evolutionary phenomenon, reflects selective pressures shaping genome adaptation. The <i>WRKY</i> transcription factor family plays a pivotal role in regulating plant responses to physiological and biochemical stresses. This study investigates CUB patterns in 151 <i>WRKY</i> transcription factors of <i>Musa acuminata</i> 'Guijiao 9', a banana cultivar exhibiting resistance to Fusarium wilt Tropical Race 4 (TR4), to elucidate evolutionary drivers of stress adaptation. The codons of these transcription factors were selected based on their expression from RNA-Seq data. The average GC content of <i>MaWRKY</i> genes was 56.55%, with a GC3 content of 62.23%, indicating a preference for G/C-ending codons. Among the codons, 26 were identified as high frequency, with 22 ending in G or C. The high effective number of codons (ENC) values (35.03-60.14) suggested weak CUB. ENC-plot, PR2 bias plot, and neutrality analysis revealed that both natural selection and mutation pressure contributed to the observed CUB, with natural selection being the dominant factor influencing the codon usage of <i>MaWRKY</i> genes in <i>M</i>. <i>acuminata</i> 'Guijiao 9'. Fifteen optimal codons, all ending in G or C, were identified. This analysis provides a theoretical foundation for further understanding the evolutionary mechanisms of <i>WRKY</i> genes in <i>Musa</i>.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1647037"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064353","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":"Identification of oncofetal PIWI-interacting RNAs as potential prognostic biomarkers in non-small cell lung cancer.","authors":"Michelle E Pewarchuk, Vanessa G P Souza, David E Cohn, Nikita Telkar, Greg L Stewart, Katya H Bénard, Patricia P Reis, Victor D Martinez, Wendy P Robinson, Wan L Lam","doi":"10.3389/fgene.2025.1611805","DOIUrl":"10.3389/fgene.2025.1611805","url":null,"abstract":"<p><p>Lung cancer is the leading cause of cancer-related deaths worldwide, with non-small cell lung cancer (NSCLC) accounting for the majority of these cases. Despite advancements in targeted therapies, early detection remains a significant challenge, highlighting the need for novel biomarkers. This study investigates the role of PIWI-interacting RNAs (piRNAs) in lung cancer, specifically focusing on their potential as oncofetal biomarkers in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), the two most common histological subtypes of NSCLC. We hypothesize that piRNAs exhibit oncofetal expression patterns and may contribute to lung cancer development. Through bioinformatics analysis, we identified distinct piRNA profiles in non-neoplastic, malignant, and fetal lung tissues. Among these, 37 piRNAs in LUAD and 46 piRNAs in LUSC displayed oncofetal expression, meaning they were present in tumor tissues but absent in adjacent normal lung tissue. These oncofetal piRNAs showed significant prognostic value in both LUAD and LUSC cohorts, with a specific signature of eight oncofetal piRNAs predicting high-risk patients in LUAD. We validated the robustness of this signature in a separate in-house cohort, which underscores its potential as a prognostic biomarker. Our findings suggest that oncofetal piRNAs could offer new diagnostic and therapeutic opportunities, particularly for early detection.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1611805"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064271","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 blood whole transcriptome profiles in Yili horses pre- and post-5000-meter racing.","authors":"Yi Su, Wanlu Ren, Shikun Ma, Jun Meng, Xinkui Yao, Yaqi Zeng, Zexu Li, Luling Li, Ran Wang, Jianwen Wang","doi":"10.3389/fgene.2025.1651628","DOIUrl":"10.3389/fgene.2025.1651628","url":null,"abstract":"<p><p>This study employed Yili horses participating in a 5000-meter race as a model to investigate exercise-induced gene expression alterations in peripheral blood using whole transcriptome sequencing. Jugular vein blood samples from the three leading horses were collected pre- and immediately post-race, yielding 2,171 differentially expressed mRNAs (2,080 upregulated, 91 downregulated), 4,375 differentially expressed LncRNAs (4,354 upregulated), and 68 differentially expressed circRNAs (64 upregulated). GO/KEGG analyses demonstrated significant enrichment of differential mRNAs in transmembrane transport function and pivotal signaling pathways (cAMP, MAPK, PI3K-Akt). Differential lncRNAs targeted neuro-signaling pathways (e.g., Neuroactive ligand-receptor interaction, Calcium signaling) and developmental regulators (stem cell pluripotency). Source genes of circRNAs were enriched in axon guidance and immune-related T cell receptor signaling. Molecular functions converged on transporter/receptor activity (mRNA/lncRNA) and nucleic acid/GTP binding (circRNA source genes). The protein-protein interaction analysis identified ten central genes within the heat shock protein family, such as <i>HSP90AA1</i> and <i>HSPA4</i>. Notably, significant upregulation of <i>HCN4, IGF1, PTHR1,</i> and <i>FGF23</i> indicated their potential roles in modulating cardiac rhythm, promoting tissue repair, and maintaining calcium-phosphorus homeostasis during exercise adaptation. This study provides comprehensive overview of transcriptomic regulatory mechanisms in the blood of Yili horses, offering a molecular framework for advancing understanding of physiological adaptation to exercise and optimizing equine exercise protocols.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1651628"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064356","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":"The first complete mitochondrial genome of <i>Biotodoma cupido</i> (Cichiliformes: Cichlidae) and its phylogeny.","authors":"Xiaoli Zhang, Shuang-Xi Jia, Cheng-He Sun","doi":"10.3389/fgene.2025.1623517","DOIUrl":"10.3389/fgene.2025.1623517","url":null,"abstract":"<p><p>Traditional classifications of New World cichlids have been subject to persistent controversy. Within the genus <i>Biotodoma</i>, only two species are currently recognized; however, complete mitochondrial sequences for these taxa have remained unavailable. In the present study, we sequenced and characterized the complete mitochondrial genome of <i>Biotodoma cupido.</i> This mitogenome has a total length of 16,621 bp and encodes the standard 37 genes found in vertebrate mitochondria: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region (D-loop). Among the PCGs, only Cox1 gene utilizes GTG as its start codon, while the remaining 12 PCGs start with ATG. Observed termination codons included TAA, AGA, TAG, and the incomplete codons TA and T. The overall base composition of the <i>B. cupido</i> mitochondrial sequence exhibits an A + T bias, with a combined A + T content of 54.1%. In this study, the high mitogenome similarity observed among several species in this study resulted from interspecific hybridization rather than synonymy or taxonomic misidentification. Maximum likelihood and Bayesian inference evolutionary trees were constructed using mitochondrial genome sequences from 44 Cichlidae species. Phylogenetic analyses consistently recovered the tribes Geophaginae, Cichlasomatinae, and Cichlinae as monophyletic groups. In contrast, the tribe Astronotinae was recovered as polyphyletic. These results clarify the evolutionary position of <i>B. cupido</i> within New World cichlids and will contribute to elucidating the complex phylogenetic relationships among cichlid species.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1623517"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064292","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":"Targeted exome sequencing for molecular diagnosis of pediatric Alport syndrome in Southwest China.","authors":"Cong Zhou, Yuanyuan Xiao, Xing Wei, Jing Wang, Shanling Liu","doi":"10.3389/fgene.2025.1580864","DOIUrl":"10.3389/fgene.2025.1580864","url":null,"abstract":"<p><strong>Background: </strong>Alport syndrome (AS) is an inherited disorder affecting basement membrane collagen IV. AS is characterized by hematuria and progressive renal failure, accompanied by high-frequency sensorineural deafness and ocular changes. AS is caused by collagen type IV α3 chain (<i>COL4A3</i>), α4 chain (<i>COL4A4</i>), and α5 chain (<i>COL4A5</i>) variants. We aimed to identify the genetic variants in a cohort of 20 children with clinically suspected AS in Southwest China.</p><p><strong>Results: </strong>We detected 21 <i>COL4A3</i>, <i>COL4A4</i>, and <i>COL4A5</i> variants in 20 probands. Of these variants, 16 (16/21, 76.2%) were classified as pathogenic/likely pathogenic and 5 (5/21, 23.8%) of uncertain significance according to the American College of Medical Genetics and Genomics criteria. A total of 11 (11/21, 52.4%) and 10 (10/21, 47.6%) variants were known and novel, respectively.</p><p><strong>Conclusion: </strong>We performed molecular diagnosis on 15 patients using targeted exome sequencing. Our findings indicate additional <i>COL4A3</i>, <i>COL4A4</i>, and <i>COL4A5</i> variants as involved in AS, having implications for genetic diagnosis, therapy, and counseling of affected families.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1580864"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064364","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":"Affective phenotypes in heterozygous <i>LRRK2</i> R1441G knock-in mice.","authors":"Marcus H F Ng, Jimmy W Y Lam, Zoe Y K Choi, Hui-Fang Liu, Philip W L Ho, Benson W M Lau, Benjamin K Yee","doi":"10.3389/fgene.2025.1629897","DOIUrl":"10.3389/fgene.2025.1629897","url":null,"abstract":"<p><p>Several missense mutations in the <i>LRRK2</i> gene are linked to familial Parkinson's disease (PD). Although <i>LRRK2</i> mutant mouse models typically lack gross motor impairments, their contribution to non-motor PD symptoms remains largely underexplored. In this study, we showed that the R1441G missense mutation promoted behavioural despair in the forced swim test (FST) and led to anhedonia, reflected in reduced sucrose preference, while the typical expression of helplessness in avoidance learning, induced by undermining locus of control, was unaffected. Notably, these depressive phenotypes emerged predominantly in heterozygous R1441G knock-in (KI) mice, and a similar dominant negative phenotype was evident in the elevated plus maze, with heterozygous mutants exhibiting lower anxiety than wild-type (WT) mice. Together, these results suggest that the R1441G mutation may impact select dimensions of affective function in prodromal adult mice, irrespective of sex. In contrast, no overt behavioural phenotypes were detected in cognitive, social, or motor domains, including associative learning, hippocampus-dependent spatial learning, sensorimotor gating, social interaction, motor coordination, grip strength, or spontaneous locomotor activity. Further investigation is warranted to dissect the mechanisms underlying the domain-specific and seemingly dominant-negative behavioural effects of the R1441G mutation, especially in comparison to the behavioural phenotypes associated with other models of <i>LRRK2</i> mutations.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1629897"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12426193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064306","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":"Identification and experimental validation of circular RNA-associated ceRNA networks in intrauterine adhesion.","authors":"Yajie Chang, Rui Xiang, Qi Guo, Jing Li, Xiaolan Li, Zhi Zeng, Jintao Peng, Xiaoyan Liang","doi":"10.3389/fgene.2025.1619698","DOIUrl":"10.3389/fgene.2025.1619698","url":null,"abstract":"<p><p>Intrauterine adhesion (IUA) is characterized by endometrial fibrosis, posing significant risks to women's reproductive health and fertility. This study aimed to uncover a circRNA-associated ceRNA regulatory network relevant to intrauterine adhesion (IUA), thereby contributing to the understanding of its molecular pathogenesis. The expression data of circRNAs and mRNAs in endometrial tissues of IUA and normal controls were analyzed by RNA sequencing, and microRNAs (miRNAs) expression data was downloaded from GSE165321. Our analysis identified 44 differentially expressed (DE) circRNAs, 41 DEmiRNAs, and 640 DEmRNAs. A comprehensive circRNA-miRNA-mRNA network was constructed using Cytoscape. DEmRNAs were mainly enriched in extracellular matrix structural components, collagen fiber complexes. KEGG pathway analysis further implicated the NF-κB signaling pathway, apoptosis, and Notch signaling in IUA development. A protein-protein interaction network for ceRNA-associated mRNAs was developed through the STRING database, highlighting potential hub genes. To validate these transcriptomic findings, RT-qPCR confirmed significant upregulation of the two leading hub circRNAs, hsa_circ_0000439 and hsa_circ_0000994, in IUA samples compared to normal controls, with results showing consistency with RNA sequencing data (p < 0.05). Functional experiments demonstrated that silencing hsa_circ_0000994 with siRNA <i>in vitro</i> significantly decreased the expression levels of fibrosis markers α-SMA and COL1A1 in human endometrial stromal cells treated with TGF-β1. In conclusion, this study presents an in-depth transcriptomic analysis of the aberrantly expressed circRNAs, miRNAs, and mRNAs in endometrial tissues from patients with IUA, culminating in the establishment of a novel circRNA-miRNA-mRNA regulatory network. Hsa_circ_0000994 is likely to play a pivotal role in modulating fibrosis associated with IUA, and represents a promising candidate for targeted therapeutic approaches.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1619698"},"PeriodicalIF":2.8,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12426003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064339","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}