Epigenomics最新文献

Epigenetic insights of olanzapine-induced insulin resistance. 奥氮平诱发胰岛素抵抗的表观遗传学启示。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-04 DOI: 10.1080/17501911.2025.2489341

David Frond, Adam Rettig, Kyle Burghardt

引用次数: 0

Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling.

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.

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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Immune cell composition is an important contributor to epigenetic age variation.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-06 DOI: 10.1080/17501911.2025.2476391

Saara Marttila

引用次数: 0

Identification of a chromatin regulator signature and potential candidate drugs for primary open-angle glaucoma.

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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stage-specific DNA methylation dynamics in mammalian heart development.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-02-21 DOI: 10.1080/17501911.2025.2467024

Fangfang Zhang, Todd Evans

引用次数: 0

Epigenetics in persons living with HIV: trauma, coping, and FKBP5 and SLC6A4 methylation.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-11 DOI: 10.1080/17501911.2025.2476389

Cassidy J Tomlinson, Laura Ryniker, Haley M Cook, Rebecca M Schwartz, Amy L Non

{"title":"Epigenetics in persons living with HIV: trauma, coping, and FKBP5 and SLC6A4 methylation.","authors":"Cassidy J Tomlinson, Laura Ryniker, Haley M Cook, Rebecca M Schwartz, Amy L Non","doi":"10.1080/17501911.2025.2476389","DOIUrl":"10.1080/17501911.2025.2476389","url":null,"abstract":"Aim: People living with HIV (PLWH) have an increased risk for lifetime trauma and mental health difficulties. However, no studies have evaluated stress-related genes in relation to early-life adversity, lifetime trauma, or post-traumatic stress disorder (PTSD) in PLWH.Methods: Using bisulfite pyrosequencing, we evaluated DNA methylation (DNAm) in intron 7 of FKBP5, a glucocorticoid feedback regulator, and in the promoter of SLC6A4, the serotonin transporter gene, in whole blood of a random sample of 70 PLWH recruited from an HIV program, and 51 individuals 2 years later (n = 48 at both time points). Exploratory regression analyses were conducted with DNAm in relation to trauma exposure, mental health symptoms, and coping strategies.Results: Higher DNAm at one site of SLC6A4 was associated with lower levels of anxiety (B = -0.62 (SE = 0.23), p = 0.0109), depression (B = -0.06 (SE = 0.03), p = 0.0435), and PTSD symptoms at baseline (B = -0.03 (SE = 0.01), p = 0.0374). DNAm at FKBP5 was negatively associated with measures of anxiety (B = -0.30 (SE = 0.07), p = 0.0001) and depression symptoms (B = -0.2 (SE = 0.10), p = 0.0103). Various coping strategies were also associated with sites in both genes across time points, e.g. self-blame and substance use.Conclusion: Our findings generate intriguing hypotheses linking mental health symptoms and DNA methylation, to be replicated with larger samples.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"297-307"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604552","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

Circulating non-coding RNAs as a tool for liquid biopsy in solid tumors.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-05 DOI: 10.1080/17501911.2025.2467021

Beyza Karaca Dogan, Seda Salman Yilmaz, Gizem Nur Izgi, Mustafa Ozen

{"title":"Circulating non-coding RNAs as a tool for liquid biopsy in solid tumors.","authors":"Beyza Karaca Dogan, Seda Salman Yilmaz, Gizem Nur Izgi, Mustafa Ozen","doi":"10.1080/17501911.2025.2467021","DOIUrl":"10.1080/17501911.2025.2467021","url":null,"abstract":"Solid tumors are significant causes of global mortality and morbidity. Recent research has primarily concentrated on finding pathology-specific molecules that can be acquired non-invasively and that can change as the disease progresses or in response to treatment. The focus of research has moved to RNA molecules that are either freely circulating in body fluids or bundled in microvesicles and exosomes because of their great stability in challenging environments, ease of accessibility, and changes in level in response to therapy. In this context, there are many non-coding RNAs that can be used for this purpose in liquid biopsies. Out of these, microRNAs have been extensively studied. However, there has been an increase of interest in studying long non-coding RNAs, piwi interacting RNAs, circular RNAs, and other small non-coding RNAs. In this article, an overview of the most researched circulating non-coding RNAs in solid tumors will be reviewed, along with a discussion of the significance of these molecules for early diagnosis, prognosis, and therapeutic targets. The publications analyzed were extracted from the PubMed database between 2008 and June 2024.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"335-358"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556263","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

Association between imprinting disorders and assisted reproductive technologies.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-03 DOI: 10.1080/17501911.2025.2471269

Masayo Kagami, Kaori Hara-Isono, Aiko Sasaki, Mitsuyoshi Amita

引用次数: 0

Development and validation of a novel cell type estimation method for targeted bisulfite sequencing data.

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-18 DOI: 10.1080/17501911.2025.2479423

F Berg, E Köper, A S Limberg, K Mattonet, B Budeus, R Kumsta, E M Hummel, D A Moser

{"title":"Development and validation of a novel cell type estimation method for targeted bisulfite sequencing data.","authors":"F Berg, E Köper, A S Limberg, K Mattonet, B Budeus, R Kumsta, E M Hummel, D A Moser","doi":"10.1080/17501911.2025.2479423","DOIUrl":"10.1080/17501911.2025.2479423","url":null,"abstract":"Aims: Epidemiological studies of DNA methylation often use buccal swabs, which contain mixtures of cell types, but no low-cost methods exist for statistical correction in candidate gene studies using targeted bisulfite sequencing. This study aims to address this gap by estimating the proportion of buccal epithelial cells in swab and mouthwash samples.Materials & methods: We applied a recently described and smoothly to implement method for estimating the proportion of buccal epithelial cells in buccal swab and mouthwash samples using targeted bisulfite sequencing. Additionally, we investigated the methylation of actinin alpha 3 (ACTN3), a marker for cell type-specific methylation, following psychosocial and physical stress.Results: The proposed estimation method showed strong correlation with the EpiDISH algorithm and effectively controlled for cellular heterogeneity. Over 90% of the variance in ACTN3 methylation was explained by including the epithelial cell proportion in the model.Conclusion: Our findings provide a solution for controlling cellular heterogeneity in buccal swab and mouthwash DNA methylation studies. This method is particularly relevant for candidate gene studies in clinical settings, but future work should refine it for more detailed analyses of cell type proportions to improve precision.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"389-396"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0