Epigenomics最新文献_第2页

Development and validation of a novel cell type estimation method for targeted bisulfite sequencing data. 开发和验证一种新的细胞类型估计方法的目标亚硫酸盐测序数据。

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

Epigenetics in evolution and adaptation to environmental challenges: pathways for disease prevention and treatment. 进化和适应环境挑战的表观遗传学：疾病预防和治疗的途径。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-02-13 DOI: 10.1080/17501911.2025.2464529

Hamid Mostafavi Abdolmaleky, Shabnam Nohesara, Jin-Rong Zhou, Sam Thiagalingam

{"title":"Epigenetics in evolution and adaptation to environmental challenges: pathways for disease prevention and treatment.","authors":"Hamid Mostafavi Abdolmaleky, Shabnam Nohesara, Jin-Rong Zhou, Sam Thiagalingam","doi":"10.1080/17501911.2025.2464529","DOIUrl":"10.1080/17501911.2025.2464529","url":null,"abstract":"Adaptation to challenging environmental conditions is crucial for the survival/fitness of all organisms. Alongside genetic mutations that provide adaptive potential during environmental challenges, epigenetic modifications offer dynamic, reversible, and rapid mechanisms for regulating gene expression in response to environmental changes in both evolution and daily life, without altering DNA sequences or relying on accidental favorable mutations. The widespread conservation of diverse epigenetic mechanisms - like DNA methylation, histone modifications, and RNA interference across diverse species, including plants - underscores their significance in evolutionary biology. Remarkably, environmentally induced epigenetic alterations are passed to daughter cells and inherited transgenerationally through germline cells, shaping offspring phenotypes while preserving adaptive epigenetic memory. Throughout anthropoid evolution, epigenetic modifications have played crucial roles in: i) suppressing transposable elements and viral genomes intruding into the host genome; ii) inactivating one of the X chromosomes in female cells to balance gene dosage; iii) genetic imprinting to ensure expression from one parental allele; iv) regulating functional alleles to compensate for dysfunctional ones; and v) modulating the epigenome and transcriptome in response to influence from the gut microbiome among other functions. Understanding the interplay between environmental factors and epigenetic processes may provide valuable insights into developmental plasticity, evolutionary dynamics, and disease susceptibility.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"317-333"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413801","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

N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development. 外转录组中n4 -乙酰胞苷和其他RNA修饰：洞察DNA修复和癌症发展。

IF 3 4区医学

Epigenomics Pub Date : 2025-04-01 Epub Date: 2025-03-05 DOI: 10.1080/17501911.2025.2473308

Eva Bártová, Lenka Stixová, Alena Svobodová Kovaříková

{"title":"N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development.","authors":"Eva Bártová, Lenka Stixová, Alena Svobodová Kovaříková","doi":"10.1080/17501911.2025.2473308","DOIUrl":"10.1080/17501911.2025.2473308","url":null,"abstract":"N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification that plays a crucial role in the epitranscriptome, influencing gene expression and cellular function. This modification occurs at the cytosine base, where an acetyl group is installed to the nitrogen at the 4th position (N4). This co-transcription modification affects RNA stability, RNA structure, and translation efficiency. Recent studies have uncovered a potential link between RNA modifications and DNA repair mechanisms, suggesting that ac4C-modified or methylated RNAs may interact with factors involved in DNA repair pathways; thus, influencing the cellular response to DNA damage. Dysregulation of modified RNAs, including ac4C RNA, has been implicated in cancer development, where aberrant levels of these RNAs may contribute to oncogenic transformation by altering genome stability and the expression of key genes regulating cell proliferation, cell cycle progression, and apoptosis. Understanding the dynamics of modified RNAs offers promising insights into the role of epitranscriptome in DNA repair processes and cancer treatment.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"411-422"},"PeriodicalIF":3.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556265","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

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 : 2025-03-28 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 : 2025-03-18 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

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 : 2025-03-14 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":"https://doi.org/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":"1-14"},"PeriodicalIF":3.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A narrative review of epigenetic marker in H3K27ac and its emerging potential as a therapeutic target in cancer. H3K27ac的表观遗传标记及其作为癌症治疗靶点的潜力的叙述性综述。

IF 3 4区医学

Epigenomics Pub Date : 2025-03-01 Epub Date: 2025-02-21 DOI: 10.1080/17501911.2025.2460900

Meizi Zhu, Xuejin Lu, Danhong Wang, Jinhu Ma, Yi Wang, Rui Wang, Hongye Wang, Wenhui Cheng, Yaling Zhu

{"title":"A narrative review of epigenetic marker in H3K27ac and its emerging potential as a therapeutic target in cancer.","authors":"Meizi Zhu, Xuejin Lu, Danhong Wang, Jinhu Ma, Yi Wang, Rui Wang, Hongye Wang, Wenhui Cheng, Yaling Zhu","doi":"10.1080/17501911.2025.2460900","DOIUrl":"10.1080/17501911.2025.2460900","url":null,"abstract":"Histone acetylation, particularly H3 K27 acetylation (H3K27ac), is a critical post-translational modification that regulates chromatin structure and gene expression, which plays a significant role in various cancers, including breast, colon, lung, hepatocellular, and prostate cancer. However, the mechanisms of H3K27ac in tumorigenesis are not yet comprehensive, especially its epigenetic mechanisms. This review endeavors to discuss findings on the involvement of H3K27ac in carcinogenesis within the past 5 years through a literature search using academic databases such as Web of Science. Firstly, we provide an overview of the diverse landscape of histone modifications, emphasizing the distinctive characteristics and critical significance of H3K27ac. Secondly, we summarize and compare advanced high-throughput sequencing technologies that have been utilized in the construction of the H3K27ac epigenetic map. Thirdly, we elucidate the role of H3K27ac in mediating gene transcription. Fourthly, we venture into the potential molecular mechanism of H3K27ac in cancer development. Finally, we engage in discussing future therapeutic approaches in oncology, with a spotlight on strategies that harness the potential of H3K27 modifications. In conclusion, this review comprehensively summarizes the characteristics of H3K27ac and underscores its pivotal role in cancer, providing valuable insights into its potential as a therapeutic target for cancer intervention.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"263-279"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467430","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

DNA methylation at birth and IgE trajectories from birth to adolescence, different patterns between White and Asian. 出生时的DNA甲基化和从出生到青春期的IgE轨迹，白人和亚洲人之间的模式不同。

IF 3 4区医学

Epigenomics Pub Date : 2025-03-01 Epub Date: 2025-01-18 DOI: 10.1080/17501911.2025.2453412

Hongmei Zhang, Jiasong Duan, Luhang Han, Naznin Alam, Meredith Ray, Fen Yang, Yu Jiang, Susan Ewart, John W Holloway, Wilfried Karmaus, Shu-Li Wang, S Hasan Arshad

{"title":"DNA methylation at birth and IgE trajectories from birth to adolescence, different patterns between White and Asian.","authors":"Hongmei Zhang, Jiasong Duan, Luhang Han, Naznin Alam, Meredith Ray, Fen Yang, Yu Jiang, Susan Ewart, John W Holloway, Wilfried Karmaus, Shu-Li Wang, S Hasan Arshad","doi":"10.1080/17501911.2025.2453412","DOIUrl":"10.1080/17501911.2025.2453412","url":null,"abstract":"Aim: We aim to assess association of DNA methylation (DNAm) at birth with total immunoglobulin E (IgE) trajectories from birth to late adolescence and whether such association is ethnicity-specific.Methods: We examined the association of total IgE trajectories from birth to late adolescence with DNAm at birth in two independent birth cohorts, the Isle of wight birth cohort (IOWBC) in UK (n = 796; White) and the maternal and infant cohort study (MICS) in Taiwan (n = 60; Asian). Biological pathways and methylation quantitative trait loci (methQTL) for associated Cytosine-phosphate-Guanine sites were studied.Results: Two total IgE trajectories, high vs. low, were inferred from each of the two cohorts. Associations of DNAm at 103 CpGs with IgE trajectories in IOWBC and at 476 CpGs in MICS were identified. Between the two cohorts, of the identified CpGs, one was in common, methQTL site cg16711274 (mapped to gene MINAR1), and 17 pathways were common with at least four linked to airway diseases.Conclusion: The findings suggest at-birth epigenetics may explain ethnicity differences in total IgE trajectories later in life.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"213-222"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002520","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

Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis. 新生儿坏死性小肠结肠炎血液样本中肠细胞DNA甲基化特征的检测。

IF 3 4区医学

Epigenomics Pub Date : 2025-03-01 Epub Date: 2025-02-02 DOI: 10.1080/17501911.2025.2459552

Lauren Frazer, Tianjiao Chu, Patricia Shaw, Camille Boufford, Lucas Tavares Naief, Michaela Ednie, Laken Ritzert, Caitlin P Green, Misty Good, David Peters

{"title":"Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis.","authors":"Lauren Frazer, Tianjiao Chu, Patricia Shaw, Camille Boufford, Lucas Tavares Naief, Michaela Ednie, Laken Ritzert, Caitlin P Green, Misty Good, David Peters","doi":"10.1080/17501911.2025.2459552","DOIUrl":"10.1080/17501911.2025.2459552","url":null,"abstract":"Background: Necrotizing enterocolitis (NEC) is an often fatal intestinal injury that primarily affects preterm infants for which screening tools are lacking. We performed a pilot analysis of DNA methylation in peripheral blood samples from preterm infants with and without NEC to identify potential NEC biomarkers.Methods: Peripheral blood samples were collected from infants at NEC diagnosis (n = 15) or from preterm controls (n = 13). Targeted genome-wide analysis was performed to identify DNA methylation differences between cases and controls.Results: Broad differences between NEC cases and controls were identified in distinct genomic elements. Differences between surgical NEC cases and controls were frequently associated with inflammation. Deconvolution analysis to identify cell type-specific DNA signatures revealed increases in ileal, vascular endothelial, and cardiomyocyte cell type proportions and decreases in colonic and neuronal cell type proportions in blood from NEC cases relative to controls.Conclusions: We identified marked differences in DNA methylation of peripheral blood samples from preterm infants with and without NEC. Increased ileal cell-specific methylation signatures in the blood of infants with NEC relative to controls, with a marked increase seen in surgical cases, provides rationale for further analysis of intestinal DNA methylation signatures as biomarkers of NEC.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"235-245"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143079135","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

The eighth annual US DOHAD meeting: promising approaches in epigenetics research of early life exposures. 第八届美国DOHAD年度会议：早期生活暴露的表观遗传学研究的有前途的方法。

IF 3 4区医学

Epigenomics Pub Date : 2025-03-01 Epub Date: 2025-01-28 DOI: 10.1080/17501911.2025.2459550

Amy L Non

{"title":"The eighth annual US DOHAD meeting: promising approaches in epigenetics research of early life exposures.","authors":"Amy L Non","doi":"10.1080/17501911.2025.2459550","DOIUrl":"10.1080/17501911.2025.2459550","url":null,"abstract":"The U.S. Developmental Origins of Health and Disease (DOHaD) meeting is an annual conference of primarily U.S. scientists who study early life programming of health and disease. The eighth annual symposium, entitled \"Exploring Translational DOHaD Science: From Cells to Communities\" was held at the Rizzo Conference Center in Chapel Hill, North Carolina, from October 14 to 16, 2024. The meeting was organized by US-DOHaD President Danielle Christifano and Vice President Kaela Varberg, and other Society Council Members. This year's meeting had record attendance, with 158 attendees from diverse disciplines, and featured 10 keynote speakers, 11 platform talks, and 84 poster presentations. Four major topics were covered: 1) Early nutrition and developmental outcomes, 2) Prenatal origins of child health, 3) Developmental impacts of toxicant exposures, and 4) Metabolic origins of health. Overall, the presented research highlighted the value of studying epigenetic effects of dietary and toxic exposures early in life. Various strategies emerged to address challenges facing the field, such as harnessing the power of nationwide longitudinal birth cohorts, new methods to integrate epigenetic and environmental data across various levels, and the emerging potential of organoids to identify the causal impact of early life exposures.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"209-211"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11853541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051972","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