Epigenomics最新文献_第2页

Resolving sequencing-based HIV-1 epitranscriptomics. 解决基于测序的HIV-1表转录组学。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-16 DOI: 10.1080/17501911.2025.2504333

Michael S Bosmeny, Joao I Mamede, Keith T Gagnon

引用次数: 0

The predictive power of profiling the DNA methylome in human health and disease. 分析DNA甲基组在人类健康和疾病中的预测能力。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-10 DOI: 10.1080/17501911.2025.2500907

Paraskevi Christofidou, Christopher G Bell

{"title":"The predictive power of profiling the DNA methylome in human health and disease.","authors":"Paraskevi Christofidou, Christopher G Bell","doi":"10.1080/17501911.2025.2500907","DOIUrl":"10.1080/17501911.2025.2500907","url":null,"abstract":"Early and accurate diagnosis significantly improves the chances of disease survival. DNA methylation (5mC), the major DNA modification in the human genome, is now recognized as a biomarker of immense clinical potential. This is due to its ability to delineate precisely cell-type, quantitate both internal and external exposures, as well as tracking chronological and biological components of the aging process. Here, we survey the current state of DNA methylation as a biomarker and predictor of traits and disease. This includes Epigenome-wide association study (EWAS) findings that inform Methylation Risk Scores (MRS), EpiScore long-term estimators of plasma protein levels, and machine learning (ML) derived DNA methylation clocks. These all highlight the significant benefits of accessible peripheral blood DNA methylation as a surrogate measure. However, detailed DNA methylation biopsy analysis in real-time is also empowering pathological diagnosis. Furthermore, moving forward, in this multi-omic and biobank scale era, novel insights will be enabled by the amplified power of increasing sample sizes and data integration.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"599-610"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993186","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

Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer. 泛素蛋白酶体系统（UPS）：癌症表观遗传景观的关键决定因素。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-08 DOI: 10.1080/17501911.2025.2501524

Srija Roy, Mrinal K Ghosh

引用次数: 0

SNP-associated differential methylation in ARHGEF38: insights into genetic-epigenetic interactions. ARHGEF38中snp相关的差异甲基化：遗传-表观遗传相互作用的见解。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-30 DOI: 10.1080/17501911.2025.2513215

Emese H C Kovács, Lucas G Casten, Niamh Mullins, Jenny Gringer Richards, Aislinn J Williams, John A Wemmie, Vincent A Magnotta, Jess G Fiedorowicz, Jacob Michaelson, Marie E Gaine

{"title":"SNP-associated differential methylation in ARHGEF38: insights into genetic-epigenetic interactions.","authors":"Emese H C Kovács, Lucas G Casten, Niamh Mullins, Jenny Gringer Richards, Aislinn J Williams, John A Wemmie, Vincent A Magnotta, Jess G Fiedorowicz, Jacob Michaelson, Marie E Gaine","doi":"10.1080/17501911.2025.2513215","DOIUrl":"10.1080/17501911.2025.2513215","url":null,"abstract":"Objective: Associations have been seen between suicide and differential DNA methylation, with one study showing significant hypomethylation of ARHGEF38 in individuals with bipolar disorder who died by suicide. Our objective was to explore ARHGEF38 methylation in individuals with bipolar disorder and a history of suicide attempt.Method: With pyrosequencing, we looked at the previously identified region of interest in ARHGEF38. We investigated the methylation levels of three CpG sites in 47 individuals with bipolar disorder and a history of suicide attempt, 47 individuals with bipolar disorder without a history of suicide attempt, and 47 non-bipolar disorder controls.Results: None of the CpG sites measured had an association between groups, although there were distinct clusters of differential methylation in each group. Applying genotypes of SNPs found in the region of interest, rs2121558 and rs1447093, these clusters showed stepwise methylation at each CpG site, regardless of phenotype.Conclusions: In this small sample size study, differential methylation in ARHGEF38 was not associated with history of suicide attempt, failing to replicate findings from a related outcome, suicide death. However, we did provide evidence of SNP and DNA methylation interplay in this region. This highlights the relevance of considering genetics when interrogating epigenetic mechanisms.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"579-588"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186832","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

Transcriptome-wide N6-methyladenosine methylation dynamic profile in type 1 diabetes progression. 1型糖尿病进展中转录组范围内n6 -甲基腺苷甲基化动态特征

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-27 DOI: 10.1080/17501911.2025.2510196

Wu Duan, Ziyi Peng, Kun Yang, Mengyuan Hu, Xuefeng Yu, Benping Zhang, Li Liu

{"title":"Transcriptome-wide N6-methyladenosine methylation dynamic profile in type 1 diabetes progression.","authors":"Wu Duan, Ziyi Peng, Kun Yang, Mengyuan Hu, Xuefeng Yu, Benping Zhang, Li Liu","doi":"10.1080/17501911.2025.2510196","DOIUrl":"10.1080/17501911.2025.2510196","url":null,"abstract":"Aims: To map transcriptome-wide N6-methyladenosine (m6A) profile at different stages of type 1 diabetes (T1D).Materials & methods: RNA extracted from islet tissues of non-obese diabetic mice at different ages (4-week-old control group, 8-week-old pre-diabetes group, and 14-week-old diabetes group) was analyzed by MeRIP-seq and mRNA-seq. Bioinformatics analyses, including m6A motif enrichment, differential methylation, gene ontology and pathway analysis.Results: Bioinformatic analysis revealed a progressive increase in m6A methylation sites and unique peaks throughout diabetes progression. The predominant m6A motif was \"GGACU\" in the control and pre-diabetes stages, shifting to \"GGACU/A\" in the diabetes stage. m6A modifications were primarily enriched at the start codon, coding region, and stop codon. Integrated analysis found pre-diabetes, diabetes groups showed distinct m6A and mRNA changes versus control. Pathway analysis indicated that differentially expressed mRNAs with m6A methylation were predominantly enriched in insulin/IGF-MAPKK/MAPK cascades, apoptosis, T-cell activation, interleukins, CCKR, and inflammation-related pathways in the pre-diabetes stage. As diabetes progressed, additional pathways, including Wnt, EGF receptor, PDGF, GnRH receptor, and angiogenesis, became involved in disease development. In vitro, cytokine stimulation of INS-1 cells increased m6A methylation, upregulated METTL3, downregulated ALKBH5.Conclusions: m6A methyl group dynamics in T1D disease progression, potentially influencing mRNA expression and signal transduction pathways.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"511-522"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149795","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

METTL3-mediated m6A modification in sepsis: current evidence and future perspectives. mettl3介导的脓毒症m6A修饰：当前证据和未来展望

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-04-19 DOI: 10.1080/17501911.2025.2494983

Zijun Wu, Changhong Miao, Hao Zhang

引用次数: 0

Association of placental weight and placental-fetal weight ratio with DNA methylation in placenta. 胎盘重量和胎重比与胎盘DNA甲基化的关系。

IF 3 4区医学

Epigenomics Pub Date : 2025-06-01 Epub Date: 2025-05-25 DOI: 10.1080/17501911.2025.2510190

Suvo Chatterjee, Jing Wu, Marion Ouidir, Katherine L Grantz, Fasil Tekola-Ayele

{"title":"Association of placental weight and placental-fetal weight ratio with DNA methylation in placenta.","authors":"Suvo Chatterjee, Jing Wu, Marion Ouidir, Katherine L Grantz, Fasil Tekola-Ayele","doi":"10.1080/17501911.2025.2510190","DOIUrl":"10.1080/17501911.2025.2510190","url":null,"abstract":"Aim: To investigate the association between placental methylation and placenta weight (PW) and placental-fetal weight ratio (PFR), which are markers of placental function linked to adverse pregnancy outcomes and risk for diseases in later life.Methods: We examined the association between placental epigenome-wide methylation and PW and PFR at birth (n = 301). Further tests assessed whether methylation levels of the cytosine-guanine sites (CpGs) linked to PW and PFR are associated with placental expression of nearby genes.Results: At a 5% false discovery rate (FDR), methylation at 27 CpGs was associated with PW, of which two CpGs were also associated with PFR. Methylation at four of the 27 CpGs was associated with placental expression of nearby genes including LEPR, RPS6KA1, and COX5A which have known roles in early development, cellular growth, and oxidative stress. The identified CpGs overlap with previously reported methylation sites associated with perinatal and adult health outcomes such as preeclampsia, preterm delivery, obesity, and type 2 diabetes.Conclusions: The findings reveal epigenetic underpinnings of placental development and functional efficiency, and suggest their potential roles in mediating fetal development and late-onset diseases.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"589-598"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141831","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

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

Regulatory roles of transposable elements on autism molecular neuropathology. 转座因子在自闭症分子神经病理学中的调控作用。

IF 3 4区医学

Epigenomics Pub Date : 2025-05-06 DOI: 10.1080/17501911.2025.2501520

Peerapa Techaniyom, Chawin Korsirikoon, Pitaksin Chitta, Chanachai Sae-Lee

{"title":"Regulatory roles of transposable elements on autism molecular neuropathology.","authors":"Peerapa Techaniyom, Chawin Korsirikoon, Pitaksin Chitta, Chanachai Sae-Lee","doi":"10.1080/17501911.2025.2501520","DOIUrl":"https://doi.org/10.1080/17501911.2025.2501520","url":null,"abstract":"Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by challenges in social communication and the presence of repetitive behaviors, typically diagnosed in early childhood. In this review, we searched PubMed and Google Scholar databases for relevant articles. ASD displays considerable heterogeneity in symptomatology and is more common in males, though shifting demographics indicate rising rates among minority populations. Transposable elements (TEs), which constitute approximately 50% of the mammalian genome, are increasingly recognized for their contribution to neurodevelopmental disorders, including ASD. These mobile genetic elements can induce genomic instability and modulate gene expression, thereby influencing ASD pathology. Evidence suggests that specific TEs, such as L1 and Alu elements, can disrupt genes critical for neurodevelopment and contribute to the disorder's genetic complexity. Furthermore, prenatal environmental exposures may activate TEs, potentially contributing to neuroinflammation observed in ASD. While the precise regulatory roles of non-coding TEs in ASD are still under investigation and require careful interpretation, integrating epigenetic aging markers like epigenetic clocks holds promise for advancing the field. Future research focused on the intricate relationship between TEs, environmental factors, epigenetic mechanisms, and neurodevelopmental processes is essential for identifying novel biomarkers and therapeutic targets, ultimately improving early diagnosis and interventions for ASD.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980468","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

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