Epigenomics最新文献_第8页

Understanding epigenetic regulation in the endometrium - lessons from mouse models with implantation defects. 了解子宫内膜的表观遗传调控——来自植入缺陷小鼠模型的经验教训。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-04-14 DOI: 10.1080/17501911.2025.2491298

Ryosuke Kobayashi, Izuho Hatada

{"title":"Understanding epigenetic regulation in the endometrium - lessons from mouse models with implantation defects.","authors":"Ryosuke Kobayashi, Izuho Hatada","doi":"10.1080/17501911.2025.2491298","DOIUrl":"10.1080/17501911.2025.2491298","url":null,"abstract":"Endometrial function, crucial for successful embryo implantation, is significantly influenced by epigenetic regulation. This review investigates the crucial roles of DNA methylation, histone modifications, chromatin remodeling, and RNA methylation in endometrial receptivity and implantation, based on a survey of recent literature on knockout mouse models with implantation defects. These models illuminate how epigenetic disruptions contribute to implantation failure, a significant human reproductive health concern. DNA methylation and histone modifications modulate endometrial receptivity by affecting gene silencing and chromatin structure, respectively. Chromatin remodeling factors also play a critical role in endometrial dynamics, influencing gene expression. Furthermore, RNA methylation emerges as critical in implantation through transcriptional and translational control. While human studies provide limited epigenetic snapshots, mouse models with suppressed epigenetic regulators reveal direct causal links between epigenetic alterations and implantation failure. Understanding these epigenetic interactions offers potential for novel therapies addressing reproductive disorders.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"541-554"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers. DNA甲基化在胃肠道癌症预后和治疗反应预测中的作用。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-03-14 DOI: 10.1080/17501911.2025.2476380

Abudurousuli Reyila, Xianchun Gao, Jun Yu, Yongzhan Nie

{"title":"Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers.","authors":"Abudurousuli Reyila, Xianchun Gao, Jun Yu, Yongzhan Nie","doi":"10.1080/17501911.2025.2476380","DOIUrl":"10.1080/17501911.2025.2476380","url":null,"abstract":"Gastrointestinal (GI) cancers impose a significant disease burden, underscoring the critical importance of accurate prognosis prediction and treatment response evaluation. DNA methylation, one of the most extensively studied epigenetic modifications, has gained prominence due to its reliable measurement across various sample types. Numerous studies have reported that DNA methylation was linked to the diagnosis, prognosis and treatment response in malignancies, including GI cancers. While its diagnostic role in GI cancers has been comprehensively reviewed. Recent research has increasingly highlighted its potential in prognosis prediction and treatment response evaluation. However, no existing reviews have exclusively focused on these two aspects. In this review, we retrieved relevant studies and included 230 of them in our discussion, thereby providing an overview of the clinical applicability of aberrant DNA methylation in these two fields among patients with esophageal, gastric, colorectal, pancreatic cancers, and hepatocellular carcinomas. Additionally, we discuss the limitations of the current literature and propose directions for future research. Specifically, we emphasize the need for standardized DNA methylation methodologies and advocate for the integration of gene panels, rather than single genes, to address tumor heterogeneity more effectively.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"475-488"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Three generations of epigenetic clocks in mediating the adverse effect of smoking on metabolic health. 三代表观遗传时钟介导吸烟对代谢健康的不利影响。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-04-18 DOI: 10.1080/17501911.2025.2494497

Chen-Yu Yeh, Wan-Yu Lin

{"title":"Three generations of epigenetic clocks in mediating the adverse effect of smoking on metabolic health.","authors":"Chen-Yu Yeh, Wan-Yu Lin","doi":"10.1080/17501911.2025.2494497","DOIUrl":"https://doi.org/10.1080/17501911.2025.2494497","url":null,"abstract":"Aims: Metabolic syndrome (MetS) is a composite disorder that includes abdominal obesity, impaired glucose levels, high blood pressure, and dyslipidemia. Smoking can alter epigenetic profiles and is a critical modifiable risk factor for MetS. We aim to explore the epigenetic age acceleration (EAA) that can mainly deliver smoking influences on metabolic health.Methods: We conducted a mediation analysis of 2,474 individuals with data in the Taiwan Biobank. Current and former smoking and the respective pack-years were included as four exposure factors. Seven markers of DNA methylation (DNAm) covering three generations of epigenetic clocks were included as mediators. Seven metabolic outcomes included MetS status (yes vs. no) and six related traits.Results: GrimEAA and DunedinPACE mediated the associations of the four smoking factors with MetS, fasting glucose, triglyceride, and high-density lipoprotein cholesterol levels (false discovery rate < 0.05). GrimEAA and DunedinPACE respectively mediated 48.2% and 24.2% of current smoking's effect on MetS and 60.9% and 26.1% of current smoking pack-year's effect on MetS risk. The DNAm plasminogen activator inhibitor 1 level mediated the adverse effects of current smoking status and pack-years on all seven metabolic outcomes.Conclusion: The GrimEAA-mediated proportions were approximately two times greater than the DunedinPACE-mediated proportions.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":"17 7","pages":"453-461"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

tRF5-22-SerGCT-1 protects the heart against myocardial injury by targeting MSK1. tRF5-22-SerGCT-1通过靶向MSK1保护心脏免受心肌损伤。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-04-23 DOI: 10.1080/17501911.2025.2495544

Fanji Meng, Hemanyun Bai, Kangling Ke, Lingyan Fang, Haitao Huang, Xiao Liang, Weiyan Li, Xiongwen Chen, Can Chen

{"title":"tRF5-22-SerGCT-1 protects the heart against myocardial injury by targeting MSK1.","authors":"Fanji Meng, Hemanyun Bai, Kangling Ke, Lingyan Fang, Haitao Huang, Xiao Liang, Weiyan Li, Xiongwen Chen, Can Chen","doi":"10.1080/17501911.2025.2495544","DOIUrl":"10.1080/17501911.2025.2495544","url":null,"abstract":"Aim: This study aims to explore the expression profiles and potential functions of tsRNAs in MI.Methods: Using a mouse model of MI induced by coronary artery ligation, we used smallRNA array to obtain tsRNAs expression profiles. Reverse transcription quantitative polymerase chain reaction(RT-qPCR), Western Blot, tRF5-22-SerGCT-1 mimics and inhibitors, cell proliferation and apoptosis detection, luciferase reporter assay, and bioinformatics analysis were employed to screen differentially expressed tsRNAs and identify the functions of tsRNAs after MI.Results: A total of 175 significantly different tsRNAs (FC > 1.5, p < 0.05) were identified in MI mice, including 98 upregulated and 77 downregulated tsRNAs. Bioinformatics and target gene prediction revealed that two differentially expressed tsRNAs (5'tiRNA-34-GlnCTG-4, tRF5-22-SerGCT-1) may be involved in processes like autophagy and apoptosis, as well as in key signaling pathways such as MAPK and autophagy. Further investigation of tRF5-22-SerGCT-1 revealed that its overexpression or inhibition in vitro affected MSK1 levels and cardiomyocytes apoptosis following oxygen-glucose deprivation, providing a protective effect. Dual-luciferase assays confirmed that tRF5-22-SerGCT-1 targets MSK1.Conclusion: We found differentially expressed tsRNAs in MI. In addition, our research showed first that tRF5-22-SerGCT-1 might be involved in the MAPK pathways by targeting the MSK1, modulating apoptosis.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":"17 7","pages":"439-451"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Menin: from molecular insights to clinical impact. Menin：从分子洞察到临床影响。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-03-28 DOI: 10.1080/17501911.2025.2485019

Margaret R Brown, Yadira M Soto-Feliciano

引用次数: 0

Edge of RNA m6A modification on LINE-1 retrotransposons in central nervous system: merely a transcriptional control? 中枢神经系统LINE-1逆转录转座子上RNA m6A修饰的边缘：仅仅是转录控制？

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-03-18 DOI: 10.1080/17501911.2025.2479424

Amit Sharma, Tikam Chand Dakal, Ingo G H Schmidt-Wolf, Jarek Maciaczyk, Giedrius Steponaitis

引用次数: 0

Cardiometabolic disease management: influences from epigenetics. 心脏代谢疾病管理：来自表观遗传学的影响。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-01 Epub Date: 2025-04-21 DOI: 10.1080/17501911.2025.2489921

Natalia Atzemian, Shafeeq Mohammed, Ludovica Di Venanzio, Era Gorica, Sarah Costantino, Frank Ruschitzka, Francesco Paneni

引用次数: 0

Identification of a chromatin regulator signature and potential candidate drugs for primary open-angle glaucoma. 原发性开角型青光眼的染色质调节因子特征和潜在候选药物的鉴定。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-17 DOI: 10.1080/17501911.2025.2479420

Xinyue Zhang, Lulu Xiao, Xiaoyu Zhou, Jiahao Xu, Li Liao, Ping Wu, Zhimin Liao, Xuanchu Duan

{"title":"Identification of a chromatin regulator signature and potential candidate drugs for primary open-angle glaucoma.","authors":"Xinyue Zhang, Lulu Xiao, Xiaoyu Zhou, Jiahao Xu, Li Liao, Ping Wu, Zhimin Liao, Xuanchu Duan","doi":"10.1080/17501911.2025.2479420","DOIUrl":"10.1080/17501911.2025.2479420","url":null,"abstract":"Aims: This research aims to establish a chromatin regulator (CR) signature to provide new epigenetic insights into the pathogenesis of primary open-angle glaucoma (POAG).Materials & methods: The expression profile of CRs in trabecular meshwork (TM) tissues was analyzed by bioinformatics analysis; The selected hub CRs were further verified by cell experiments.Results: We found the immune microenvironment of the TMwas changed in POAG patients and identified 3 differentially expressed CRs that were relevant to immunity. Then, we successfully constructed and proved a predicted signature based on these 3 CRs, which could effectively predict the risk of POAG. The genes co-expressed with these 3 CRs and miRNAs with are gulatory relationship were identified, and a miRNA-hub CR network was successfully constructed. The results of the Gene Set Enrichment analysis indicated that these 3 hub CRs were all associated with neurodegenerative diseases. Moreover, the human trabecular meshwork cell (HTMC) oxidative stress model was constructed, and KDM5B was significantly down-regulated in this cell model. Finally, we found 10 agents that might be helpful for patients with POAG.Conclusions: Dysregulation of CR expression in TM tissues may be involved in the occurrence and progression of POAG through multiple mechanisms.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"377-387"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling. 通过表观基因组分析鉴定IL-34和Slc7al作为MASLD进展的潜在关键调节因子。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-02-16 DOI: 10.1080/17501911.2025.2467028

Chuanfei Zeng, Mingliang Wei, Huan Li, Linxin Yu, Chuang Wang, Ziqi Mu, Ziyin Huang, Yujia Ke, Lian-Yun Li, Yong Xiao, Min Wu, Ming-Kai Chen

{"title":"Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling.","authors":"Chuanfei Zeng, Mingliang Wei, Huan Li, Linxin Yu, Chuang Wang, Ziqi Mu, Ziyin Huang, Yujia Ke, Lian-Yun Li, Yong Xiao, Min Wu, Ming-Kai Chen","doi":"10.1080/17501911.2025.2467028","DOIUrl":"10.1080/17501911.2025.2467028","url":null,"abstract":"Objective: Epigenetic alterations are critical regulators in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the dynamic epigenomic landscapes are not well defined. Our previous study found that H3K27ac and H3K9me3 play important roles in regulating lipid metabolic pathways in the early stages of MASLD. However, the epigenomic status in the inflammation stages still needs to be determined.Method: C57BL/6 male mice were fed with the methionine- and choline-deficient (MCD) or normal diet, and their serum and liver samples were collected after 6 weeks. Serum alanine aminotransferase (ALT), aspartate amino transferase (AST), total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were measured. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac and H3K9me3 was performed together with RNA sequencing (RNA-seq) and key regulators were analyzed.Results: The target genes of enhancers with increased H3K27ac and decreased H3K9me3 signals are enriched in lipid metabolism and immuno-inflammatory pathways. Il-34 and Slc7al are identified as potential regulators in MASLD.Conclusion: Our study reveals that active enhancers and heterochromatin associated with metabolic and inflammatory genes are extensively reprogrammed in MCD-diet mice, and Il-34 and Slc7al are potentially key genes regulating the progression of MASLD.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"281-295"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenomic mechanisms of dietary prescriptions for obesity therapy. 肥胖治疗饮食处方的表观基因组机制。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-02 DOI: 10.1080/17501911.2025.2473309

Omar Ramos-Lopez

{"title":"Epigenomic mechanisms of dietary prescriptions for obesity therapy.","authors":"Omar Ramos-Lopez","doi":"10.1080/17501911.2025.2473309","DOIUrl":"10.1080/17501911.2025.2473309","url":null,"abstract":"Dietary modification is a cornerstone and a primary goal for weight loss, whose effects may be related to epigenetic phenomena. In this literature review, a comprehensive search without time restriction was performed in PubMed/Medline, Cochrane, SciELO, and Scopus databases to identify epigenetic signatures related to obesity outcomes upon dietary advice. In this context, experimental studies and clinical trials have identified certain DNA methylation marks, miRNA expression profiles and histone modifications putatively associated with adiposity outcomes after different nutritional interventions. These include traditional dietary patterns, diets with different macronutrient compositions, and supplementation with fatty acids, amino acids and derivatives, methyl donors, vitamins and minerals, probiotics and prebiotics, and bioactive food compounds. Some of these epigenetic signatures have been mapped to genes involved in food intake control, adipogenesis, lipolysis, fatty acid oxidation, body fat deposition, and gut microbiota modulation. However, additional studies are still required to address dosage and follow-up variability, validation of epigenetic marks, genome-wide approaches, and appropriate statistical settings. Although more investigation is required, these insights may contribute to the characterization of epigenetic biomarkers of body weight regulation toward the prescription of tailored dietary strategies targeting the epigenome for a more precise obesity management and control.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"423-434"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0