Epigenomics最新文献

Dynamic modifications of circular RNAs drive oncogenesis. 环状rna的动态修饰驱动肿瘤发生。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-15 DOI: 10.1080/17501911.2025.2518918

Jiaojiao Dai, Zhe Wang, Xiaoxun Cheng, Zhengze Hu, Jinghan Hua

{"title":"Dynamic modifications of circular RNAs drive oncogenesis.","authors":"Jiaojiao Dai, Zhe Wang, Xiaoxun Cheng, Zhengze Hu, Jinghan Hua","doi":"10.1080/17501911.2025.2518918","DOIUrl":"https://doi.org/10.1080/17501911.2025.2518918","url":null,"abstract":"Circular RNAs (circRNAs) are a class of covalently closed non-coding RNAs that regulate the progression of multiple cancers. Recent studies have revealed the presence of several post-transcriptional modifications such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytidine (ac4C), and N7-methylguanosine (m7G) on circRNAs. This review synthesizes the results of articles retrieved through systematic searches of PubMed and Web of science databases, mainly focusing on circRNA modifications in cancers. These modifications affect the biogenesis, metabolism, stability, and function of circRNAs in cancers, highlighting the critical roles of circRNAs modifications in cancers. Moreover, circRNAs crosstalk with epigenetic modifications of mRNA across various cancers, offering new perspectives for cancer therapy. Innovations in detection techniques, such as anti-modifying antibodies and mass spectrometry, have improved the identification and sensitivity of epigenetically modified circRNAs. Emerging technologies including artificial intelligence (AI)-based bioinformatics algorithms will accelerate the development of RNA epigenetic modifications-based precision therapies. Herein, we summarize a range of epigenetically modified circRNAs and their future research directions. We hope to develop clinical protocols that targeting circRNAs modification for the treatment of refractory malignancies.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-10"},"PeriodicalIF":3.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144636595","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

Bifaceted functions of histone methyltransferases. 组蛋白甲基转移酶的双面功能。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-13 DOI: 10.1080/17501911.2025.2530925

Jawad Akhtar, Vassiliki Saloura

引用次数: 0

Targeting Tudor domains in leukemia: epigenetic insights for drug development. 靶向Tudor结构域在白血病：药物开发的表观遗传学见解。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-07 DOI: 10.1080/17501911.2025.2525746

Aditi Pedgaonkar, Neha Niranjan, Aniruddha J Deshpande

{"title":"Targeting Tudor domains in leukemia: epigenetic insights for drug development.","authors":"Aditi Pedgaonkar, Neha Niranjan, Aniruddha J Deshpande","doi":"10.1080/17501911.2025.2525746","DOIUrl":"https://doi.org/10.1080/17501911.2025.2525746","url":null,"abstract":"Leukemia is a heterogeneous group of hematological malignancies characterized by uncontrolled proliferation and impaired differentiation of hematopoietic stem and progenitor cells. Epigenetic dysregulation is one of the critical drivers of leukemogenesis, often involving aberrant activity of chromatin-interacting proteins, such as readers, writers, and erasers. Tudor domain-containing proteins, such as SGF29, JMJD2A, 53BP1, Spindlin1, and UHRF1, play pivotal roles in leukemia progression by controlling key processes such as DNA damage response, transcriptional regulation, and RNA metabolism. Several recent efforts have aimed at pharmacologic targeting of the Tudor domain, opening a novel avenue for targeting epigenetic dysregulation. The review explores the structural characteristics of various Tudor domains, their binding preferences for specific histone modifications, and the consequences of these interactions for leukemia. By providing a comprehensive overview of current research, this review underscores the therapeutic potential of Tudor domain-targeting strategies in leukemia and emphasizes the need for further development of epigenetics-based treatment strategies to address resistance and relapse in these malignancies.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583442","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

Methylation levels in keratinocyte basal cells reflect donor age and associate with altered cellular proliferation pathways. 角化细胞基底细胞的甲基化水平反映供体年龄，并与细胞增殖途径的改变有关。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-06 DOI: 10.1080/17501911.2025.2526320

Vasiliki Salameti, Ines M Tomas, David A Gunn

{"title":"Methylation levels in keratinocyte basal cells reflect donor age and associate with altered cellular proliferation pathways.","authors":"Vasiliki Salameti, Ines M Tomas, David A Gunn","doi":"10.1080/17501911.2025.2526320","DOIUrl":"https://doi.org/10.1080/17501911.2025.2526320","url":null,"abstract":"Aims: To determine if epigenomic and mRNA associations with donor age are present in basal keratinocytes in vitro.Methods: Whole-genome methylation (EPIC array), RNAseq analysis, and in vitro cell growth assessments were performed on cultured keratinocytes (n = 9, 22-68 years), enriched for cells expressing the stem cell protein markers ITGB1 and EpCAM.Results: Donor age associated with 1,244 differentially methylated positions (DMPs) (p < 0.01, >20% delta beta) and correlated with estimated ages from the Skin and Blood epigenetic clock (r = 0.83, p = 0.0018). The DMPs correlated with those in an in vivo epidermal dataset (r = 0.71, p < 0.0001). Donor age associated (p < 0.05) with 523 differentially expressed genes (DEGs), but the DEGs only weakly correlated with their changes in an in vivo epidermal dataset (r = 0.24, p < 0.0001). The \"cell growth and proliferation\" ontology term was significantly enriched in the methylation and expression datasets despite only 13 overlapping annotated genes. Decreased keratinocyte proliferation, increased differentiation and a reduced re-epithelialization ability were observed for an older versus a younger cell strain.Conclusion: Basal keratinocytes maintain in vivo age-associated epigenomic changes in vitro making them a good model for studying the impact of age-associated epigenomic changes on cellular function and behavior in vitro.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.0,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575111","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

DNA methylation studies in mouse models of depression: a systematic review. 抑郁症小鼠模型中的DNA甲基化研究：一项系统综述。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-03 DOI: 10.1080/17501911.2025.2525750

Mohammad Mustakim Billah, Chu Guo, Kazunari Mizuno, Yutaka Nakachi, Miki Bundo, Kazuya Iwamoto

{"title":"DNA methylation studies in mouse models of depression: a systematic review.","authors":"Mohammad Mustakim Billah, Chu Guo, Kazunari Mizuno, Yutaka Nakachi, Miki Bundo, Kazuya Iwamoto","doi":"10.1080/17501911.2025.2525750","DOIUrl":"https://doi.org/10.1080/17501911.2025.2525750","url":null,"abstract":"Background: Major depression (MD) is caused by both genetic and environmental factors. Epigenetic mechanisms, particularly DNA methylation (5mC) and hydroxymethylation (5hmC), are thought to mediate gene - environment interactions. However, findings in mouse models remain dispersed.Objective: This review evaluates the studies on 5mC and 5hmC in mouse models of depression.Methods: We systematically searched PubMed, Scopus, and Web of Science using terms related to 5mC/5hmC, depression, and mouse, until December 2024. We grouped the articles as candidate, global, cellular, and comprehensive studies and summarized the findings accordingly.Results: Sixty-eight studies met inclusion criteria. The main findings were environmental models, especially chronic stress paradigms, which were most frequently used to induce depression models. Candidate gene studies focused on Bdnf and Nr3c1, while global and cellular assays revealed both regional and widespread 5mC/5hmC changes. Genome-wide approaches revealed that epigenetic changes are not limited to isolated loci rather affect broad genomic regions involved in neural development and plasticity.Conclusion: This review provides a comprehensive summary of existing research on epigenetic changes in terms of DNA methylation in mouse models of depression. Broader application of standardized, integrative, and cell-type-specific approaches is needed to fully elucidate the role of epigenetic regulation in the pathology of MD.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-13"},"PeriodicalIF":3.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552732","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

Mediators of maternal intergenerational epigenetic inheritance in mammals. 哺乳动物母系代际表观遗传的调节因子。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-03 DOI: 10.1080/17501911.2025.2525749

Christian Belton, Gavin Kelsey

{"title":"Mediators of maternal intergenerational epigenetic inheritance in mammals.","authors":"Christian Belton, Gavin Kelsey","doi":"10.1080/17501911.2025.2525749","DOIUrl":"https://doi.org/10.1080/17501911.2025.2525749","url":null,"abstract":"Experimental models and epidemiological data suggest that environmental factors, for example, adverse nutrition prior to conception, can lead to phenotypes in offspring of exposed parents in the absence of continued exposure. As a result these phenotypes have been described as epigentically inherited. The mechanistic basis for such phenomena has not been established in most cases. In this review, we consider possible contributing mechanisms for environmentaly induced epigenetic inheritance, with a focus on maternally transmitted effects and by comparing to paradigms of epigenetic inheritance with a clear mechanistic understanding. Genomic imprinting has provided an important conceptual framework for how the epigenetic states of parental germlines can determine allelic expression in offspring, yet, generally speaking, imprinted genes appear resilient to epigenetic disruption from altered parental environments. Metastable epialleles are environmentally sensitive and variably expressed loci that can impact organism phenotype, but the nature of any epigenetic marker at these loci transferred to offspring is unclear. Studies of examples across these forms of epigenetic inheritance show predominant effects are mediated by oocyte factors involved inreprogramming of the genome post-fertilization, rather than direct effects on gametic DNA methylation, with the exception of genomic imprinting. The potential contribution of additional oocyte chromatin features to the specific liability of phenotypic effector genes and their potential to persist through this reprogramming, however, remains to be investigated.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552733","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

Methylation aberrations and genomic instability synergistically drive the evolution of intrahepatic cholangiocarcinoma. 甲基化畸变和基因组不稳定性协同驱动肝内胆管癌的进化。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-01 Epub Date: 2025-06-17 DOI: 10.1080/17501911.2025.2518919

Guanghao Li, Youhuang Bai, Feng Tao, Tingting Hu, Ting Wang, Yong Zeng, Deqiang Sun

{"title":"Methylation aberrations and genomic instability synergistically drive the evolution of intrahepatic cholangiocarcinoma.","authors":"Guanghao Li, Youhuang Bai, Feng Tao, Tingting Hu, Ting Wang, Yong Zeng, Deqiang Sun","doi":"10.1080/17501911.2025.2518919","DOIUrl":"10.1080/17501911.2025.2518919","url":null,"abstract":"Aims & methods: DNA methylation and genomic instability are critical drivers of cancer initiation and malignant progression. However, the roles of methylation aberrations and genomic instability in malignant progression have not been thoroughly investigated in intrahepatic cholangiocarcinoma (ICC). To address this, we identified differentially methylated regions (DMRs) and somatic copy number alterations (SCNAs) from 341 ICC samples across various stages.Results: Our findings revealed that stages IAIB, II, IIIA, and IIIB exhibited comparable methylation changes, whereas stage IV ICC showed a pronounced accumulation of stage-specific methylation alterations. Leveraging these findings, we developed a classification model that effectively distinguished stage IV ICC from earlier stages with high accuracy using 15 DMRs. Furthermore, stage IV ICC exhibited slightly higher genomic instability, including an elevated aneuploidy score and a greater proportion of focal amplifications. We also observed a positive correlation between SCNA burden and DNA methylation entropy in the promoter, gene body, and CpG island regions, with the gene body of MDM2 serving as a notable example.Conclusions: These findings highlight the potential of DNA methylation as a biomarker for metastasis diagnosis and the interplay between local genomic instability and aberrant methylation, emphasizing their synergistic roles in driving the evolutionary trajectory of ICC.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"661-674"},"PeriodicalIF":3.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316250","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

Epigenetic age acceleration and psychosocial stressors in early childhood. 儿童早期的表观遗传年龄加速和社会心理压力。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-01 Epub Date: 2025-06-02 DOI: 10.1080/17501911.2025.2508684

Connie J Mulligan

引用次数: 0

Correction. 修正。

IF 3 4区医学

Epigenomics Pub Date : 2025-07-01 Epub Date: 2025-06-26 DOI: 10.1080/17501911.2025.2523710

引用次数: 0

Personalized medicine for cardiovascular diseases: how next generation epigenetic technologies can contribute? 心血管疾病的个体化治疗：下一代表观遗传技术如何发挥作用？

IF 3 4区医学