Frontiers in Genetics最新文献

{"title":"Comprehensive analysis of mRNA and lncRNA expression for predicting lymph node metastasis in cervical cancer: a novel seven-gene signature approach.","authors":"Jiahui Wei, Ming Wang, Yumei Wu","doi":"10.3389/fgene.2025.1524821","DOIUrl":"https://doi.org/10.3389/fgene.2025.1524821","url":null,"abstract":"<p><strong>Objective: </strong>Lymph node metastasis (LNM) critically determines recurrence and survival in cervical cancer (CC), yet current imaging-based methods lack accuracy. Retroperitoneal lymph node dissection leads to many adverse events. This study aimed to develop a clinically actionable molecular signature to predict LNM, enabling personalized surgical planning and improved patient outcomes.</p><p><strong>Methods: </strong>Transcriptome profiles and clinical data from 193 CC patients, encompassing information on LNM from The Cancer Genome Atlas (TCGA) and an external cohort (GSE26511), were analyzed. The differential expression of mRNAs and lncRNAs was identified using DESeq2. Subsequently, dual machine learning strategies-LASSO regression and the Boruta algorithm-were applied to select robust biomarkers. Finally, the seven-mRNA-lncRNA gene cluster was verified in tumor tissues of CC patients with and without LNM using qRT-PCR.</p><p><strong>Results: </strong>The seven-mRNA-lncRNA gene cluster included four mRNAs (ART3, HRG, MAPT, and SYTL5) and three lncRNAs (AC011239.1, AC125616.1, and RUVBL1.AS1). The expression patterns of the seven DEGs align with their levels in CC tissues. The signature demonstrated high predictive accuracy (AUC: 0.855 in training and 0.807 in testing cohorts). External validation using the GSE26511 dataset confirmed its clinical applicability (AUC: 0.611). Patients with high LNM scores exhibited poorer survival outcomes than those with low LNM scores (<i>p</i> = 0.0034).</p><p><strong>Conclusion: </strong>We constructed a reliable prediction model of LNM in CC patients with a seven-mRNA-lncRNA gene cluster. This model guides lymphadenectomy decisions, reduces overtreatment, and enhances patient survival. Our work bridges molecular insights with clinical practice and provides a foundation for further research into the management of CC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1524821"},"PeriodicalIF":2.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12119550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179834","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":"Integrated transcriptomic analysis of COVID-19 stages and recovery: insights into key gene signatures, immune features, and diagnostic biomarkers through machine learning.","authors":"Zhiyuan Gong, He An","doi":"10.3389/fgene.2025.1599867","DOIUrl":"https://doi.org/10.3389/fgene.2025.1599867","url":null,"abstract":"<p><strong>Background: </strong>COVID-19 progression and recovery involve complex gene expression changes and immune dysregulation, but their dynamic alterations remain poorly understood. Current clinical indicators lack precision in distinguishing severe cases, highlighting the need for molecular biomarkers and diagnostic tools.</p><p><strong>Methods: </strong>Three transcriptomic datasets were analyzed: 1) COVID-19 progression from Healthy, Moderate, Severe, to ICU patients; 2) recovery stages (1, 3, and 6 months) compared to Healthy controls; and 3) COVID-19 ICU versus non-ICU patients. Differential expression analysis, immune cell infiltration estimation, machine learning (LASSO regression and random forest), and functional enrichment were used to identify key genes and molecular mechanisms.</p><p><strong>Results: </strong>Gene expression analysis revealed dynamic changes during COVID-19 progression. Adaptive immune cells (e.g., B cells and T cells) decreased, while innate immune cells (e.g., monocytes and neutrophils) increased, particularly in ICU patients. Recovery analysis showed significantly reduced adaptive immune cells at 1 month, with partial recovery by 3 and 6 months. Machine learning identified CCR5, CYSLTR1, and KLRG1 as diagnostic biomarkers for distinguishing ICU from non-ICU patients, with AUC values of 0.916, 0.885, and 0.899, respectively.</p><p><strong>Conclusion: </strong>This study identified CCR5, CYSLTR1, and KLRG1 as efficient diagnostic biomarkers for severe COVID-19 using machine learning and revealed immune regulatory features across COVID-19 progression and recovery.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1599867"},"PeriodicalIF":2.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12119500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181366","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":"Genome-wide identification and expression analysis of the WRKY transcription factors related to sesquiterpenes biosynthesis in <i>Atractylodes lancea</i>.","authors":"Hua Liang, Weiwei Liu, Zhiqiang Zhao, Yaqian Li, Liangping Zha","doi":"10.3389/fgene.2025.1551991","DOIUrl":"https://doi.org/10.3389/fgene.2025.1551991","url":null,"abstract":"<p><strong>Introduction: </strong><i>Atractylodes lancea</i> (Thunb.) DC., a widely utilized herb in traditional Chinese medicine, contains sesquiterpenoids and polyacetylenes as its primary bioactive components. The WRKY gene family plays a critical role in regulating various biological processes in plants. However, the molecular mechanism underlying AlWRKY regulation of terpenoid synthesis unclear.</p><p><strong>Methods: </strong>The <i>AlWRKY</i> gene family members were identified through bioinformatics approaches. Gene structures, motifs, and phylogenetic relationships were analyzed. Subsequently, their expression profiles across different geographical origins were investigated using transcriptome data. Furthermore, preliminary validation was performed via methyl jasmonate treatment and molecular docking, with a focus on the <i>AlWRKY20</i> and <i>AlWRKY37</i> genes.</p><p><strong>Results: </strong>In this study, 65 <i>AlWRKY</i> genes with conserved domains were identified in <i>A. lancea</i> and classified into three groups: Group I (17 members), Group II (33 members), and Group III (15 members). Tissue-specific expression profiling revealed five rhizome-enriched <i>AlWRKY</i> genes (<i>AlWRKY13</i>, <i>AlWRKY20</i>, <i>AlWRKY21</i>, <i>AlWRKY37</i>, and <i>AlWRKY49</i>) were highly expressed in Hubei accessions compared to Jiangsu accessions, and co-expression analysis demonstrated their strong correlation with 16 <i>AlTPS</i> genes. Quantitative PCR (qPCR) validation confirmed the specific upregulation of <i>AlWRKY20</i>, <i>AlWRKY21</i>, <i>AlWRKY37</i>, and <i>AlWRKY49</i> in Hubei rhizomes, consistent with the accumulation patterns of sesquiterpenes (hinesol, γ-eudesmol, and elemol). Methyl jasmonate (MeJA) induction experiments (12 h) revealed coordinated upregulation of <i>AlWRKY20</i>, <i>AlWRKY37</i>, <i>AlTPS70</i>, <i>AlTPS71</i>, concomitant with significantly increased cis-β-farnesene and α-curcumene content. Molecular docking analysis revealed strong binding affinities of AlWRKY20 to the AlTPS70/AlTPS71 promoter and of AlWRKY37 to the AlTPS70 promoter. Subcellular localization analysis demonstrated that both AlWRKY20 and AlWRKY37 are localized in the nucleus. These results suggest that AlWRKY20 and AlWRKY37 likely function as regulators of sesquiterpene biosynthesis, positively regulating cis-β-farnesene and α-curcumene production through <i>AlTPS</i> gene modulation.</p><p><strong>Discussion: </strong>This study lays the groundwork for further exploration of the molecular mechanisms and functional validation of WRKY transcription factors in <i>A. lancea</i>.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1551991"},"PeriodicalIF":2.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12119531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181528","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":"Reference genome of the leopard seal (<i>Hydrurga leptonyx</i>), a Southern Ocean apex predator.","authors":"J Canitz, S S Kienle, K van der Linde, R Borras-Chavez, E S Sperou, A Leahy, S Rivera, M Autenrieth, J I Hoffman, C A Bonin","doi":"10.3389/fgene.2025.1561273","DOIUrl":"https://doi.org/10.3389/fgene.2025.1561273","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1561273"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12118156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173726","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":"EGFR polymorphisms drive lung cancer risk and survival disparities: a genotype-expression-outcome cohort study.","authors":"Chao Zuo, Ziqiang Wang, Yi Liu, Jing Cheng, Dongli Yang, Yu Wang, Yongchao Qiao","doi":"10.3389/fgene.2025.1591539","DOIUrl":"https://doi.org/10.3389/fgene.2025.1591539","url":null,"abstract":"<p><strong>Purpose: </strong>To investigate the correlation between single-nucleotide polymorphisms (SNPs) of the Epidermal growth factor receptor (EGFR) gene and its protein expression with susceptibility and survival prognosis of lung cancer (LC) patients.</p><p><strong>Methods: </strong>Using SNP-scan high-throughput technology, the EGFR gene's rs2227983, rs2293347, and rs884225 locations were analyzed in 300 LC patients and 150 healthy individuals. And small cell lung cancer (SCLC), lung adenocarcinoma (LUAD), and lung squamous carcinoma (LUSC) were subdivided into groups for lung cancer patients. Chi-square test and logistic regression analysis were used to assess the susceptibility of LC. The correlation between SNP haplotypes and LC risk was analyzed using the SHEsis website. KM curves and Cox regression were used to analyse the association between polymorphisms and survival prognosis of LC patients. Expression differences in protein levels were analyzed using immunohistochemistry.</p><p><strong>Results: </strong>EGFR rs2293347 was associated with LUAD, LUSC, and SCLC susceptibility, and rs884225 was associated with LUAD susceptibility. Haplotype ATT was associated with LC and histological type LUAD and SCLC susceptibility. Meanwhile, rs2293347-TT and rs884225-TT were associated with worse prognosis, and rs2293347-TT was an independent risk factor for prognosis in patients with LC. Furthermore, tumor tissue EGFR protein levels were elevated in patients with both genotypes.</p><p><strong>Conclusion: </strong>EGFR rs2293347 (pan-subtype) and rs884225 (LUAD-specific) polymorphisms increase LC risk through elevated protein expression, with rs2293347-TT conferring worse survival. These genotype-protein correlations highlight their dual role as susceptibility markers and prognostic predictors in precision oncology.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1591539"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173721","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":"Complete assembly of the organellar genome of <i>Rubroshorea johorensis</i> utilizing advanced long-read sequencing technologies.","authors":"Aditya Nugroho, Evayusvita Rustam, Nurin Widyani, Fitri Indriani, Dede J Sudrajat, Mohammad Agus Salim, Muhammad Majiidu, Fifi Gus Dwiyanti, Rahadian Pratama, Iskandar Z Siregar","doi":"10.3389/fgene.2025.1574266","DOIUrl":"https://doi.org/10.3389/fgene.2025.1574266","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1574266"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173716","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":"Prognosis of cholangiocarcinoma patients based on multiple patterns of programmed cell death, integrated analysis of the immune microenvironment and drug sensitivity.","authors":"Yupeng Xu, Jian Sun, Xin Yan, Zhenliao Mao, Yiming Chen","doi":"10.3389/fgene.2025.1457204","DOIUrl":"https://doi.org/10.3389/fgene.2025.1457204","url":null,"abstract":"<p><strong>Background: </strong>Cholangiocarcinoma (CHOL) is a highly malignant bile duct cancer with a poor prognosis and rising incidence. Programmed cell death (PCD) plays a crucial role in cancer biology, influencing tumor immunity and treatment response. This study analyzes the impact of multiple PCD patterns on CHOL prognosis, tumor microenvironment (TME) and drug sensitivity.</p><p><strong>Methods: </strong>RNA sequencing data from TCGA-CHOL and GSE107943 were analyzed to identify PCD-related genes. A PCD-associated Risk Score was constructed using Cox and Lasso regression analyses. The score's prognostic value was assessed through survival analysis, ROC curves, and functional annotation.</p><p><strong>Results: </strong>We identified 111 differentially expressed PCD-related genes, including <i>NCK2</i>, <i>BNIP3</i> and <i>BIK</i>, that constituted PCD-associated Risk Score and correlated with prognosis of CHOL. Functional analyses indicated enrichment in immune-related processes. High-risk patients showed increased immune cell infiltration and higher immune checkpoint expression, suggesting a benefit from immunotherapy. They also demonstrated greater sensitivity to several chemotherapeutic and targeted agents.</p><p><strong>Conclusion: </strong>PCD-associated Risk Score is a robust prognostic tool for CHOL, influencing TME modulation and therapeutic response, and may guide personalized treatment strategies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1457204"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173725","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":"Scaffolded and annotated nuclear and organelle genomes of the North American brown alga <i>Saccharina latissima</i>.","authors":"Kelly DeWeese, Gary Molano, Sara Calhoun, Anna Lipzen, Jerry Jenkins, Melissa Williams, Christopher Plott, Jayson Talag, Jane Grimwood, Jean-Luc Jannink, Igor V Grigoriev, Jeremy Schmutz, Charles Yarish, Sergey Nuzhdin, Scott Lindell","doi":"10.3389/fgene.2025.1494480","DOIUrl":"https://doi.org/10.3389/fgene.2025.1494480","url":null,"abstract":"<p><p>Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga <i>Saccharina latissima</i> (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of <i>Saccharina latissima</i> for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, <i>Saccharina japonica</i>. While <i>Saccharina latissima</i> has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated <i>Saccharina latissima</i> nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This <i>Saccharina latissima</i> genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this <i>Saccharina latissima</i> genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This <i>Saccharina latissima</i> genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1494480"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173728","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: Enhancing livestock breeding through advanced genetic tools and phenotyping systems.","authors":"Yulin Bai","doi":"10.3389/fgene.2025.1617113","DOIUrl":"https://doi.org/10.3389/fgene.2025.1617113","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1617113"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173719","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":"An ethical framework for human genomic enhancement in China.","authors":"Fanhong Chen, Hongjiao Zhang","doi":"10.3389/fgene.2025.1600829","DOIUrl":"https://doi.org/10.3389/fgene.2025.1600829","url":null,"abstract":"<p><p>Human genomic enhancement, or HGE, which improves human traits by introducing genetic and epigenetic changes, has garnered a lot of attention in light of the astounding advancement in genome editing techniques, such as CRISPR-Cas9, in recent years. This study combines doctrinal and empirical analysis methods to examine bioethical issues of HGE in China. The literature currently in publication on these issues indicates that the majority of Chinese academics and the general public are enthusiastic about the present and potential future applications of genome editing techniques within the parameters of appropriate ethical guidelines; regrettably, no workable ethical governance framework has been put forth so far. Considering this, this study offers a more comprehensive discussion of ethical policy on HGE and develops a robust ethical framework that addresses three related issues about HGE: (1) approaching the precautionary principle as an overarching benchmark; (2) producing a multi-stakeholder collaborative governance model to promote stakeholder engagement and dialogue; and (3) establishing regional ethics review centers to have an independent review process. This is done in an effort to address ethical concerns and further inform policymaking on HGE in China.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1600829"},"PeriodicalIF":2.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173714","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}