Epigenomics最新文献

{"title":"Impact of 14 weeks combined exercise on serum cadmium levels, DNA methylation, and epigenetic aging in older women.","authors":"Guilherme da Silva Rodrigues, Natalia Yumi Noronha, João Gabriel Ribeiro de Lima, Chanachai Sae-Lee, Pitaksin Chitta, Andressa Crystine da Silva Sobrinho, Isabella Harumi Yonehara Noma, Luísa Maria Diani, Fernando Barbosa Júnior, Carla Barbosa Nonino, Lígia Moriguchi Watanabe, Carlos Roberto Bueno Júnior","doi":"10.1080/17501911.2026.2672104","DOIUrl":"10.1080/17501911.2026.2672104","url":null,"abstract":"<p><strong>Introduction: </strong>Cadmium is a toxic heavy metal linked to impaired cardiorespiratory fitness and altered DNA methylation patterns. This study investigated the effects of 14 weeks of combined exercise training on epigenetic modifications and blood cadmium levels in women with varying aerobic fitness.</p><p><strong>Methods: </strong>Participants underwent three weekly training sessions totaling 180 minutes. Pre- and post-intervention evaluations included anthropometry, blood pressure, physical performance, and heavy metal analysis. DNA methylation was assessed using the Illumina EPIC BeadChip.</p><p><strong>Results: </strong>Based on baseline 6-minute walk test and age, participants were divided into lower (LAF, <i>n</i> = 32) and higher (HAF, <i>n</i> = 17) aerobic fitness groups. Pre-intervention, LAF had significantly higher cadmium levels than HAF (<i>p</i> = 0.003). After the intervention, LAF showed a significant reduction of 0.056 µg/L (63%), while HAF decreased by 0.019 µg/L (28%) (<i>p</i> = 0.046). A total of 513 differentially methylated regions (DMRs) related to cadmium were identified, with enrichment in pathways associated with neurodegeneration-related processes. Intrinsic epigenetic age acceleration (IEAA) also differed significantly between groups at baseline.</p><p><strong>Conclusion: </strong>Combined exercise training significantly reduced cadmium levels in women aged 50-70 years with low aerobic fitness and induced locus-specific epigenetic changes associated with cadmium-related pathways, which may be relevant to pathways implicated in age-related neurological conditions.</p><p><strong>Clinical trial: </strong>The study was registered in the Brazilian Clinical Trials Registry (ReBEC; identifier RBR-3g38dx).</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"575-589"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147927570","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}

{"title":"Epigenetic mechanisms and therapeutic targeting across diverse malignancies.","authors":"Akshara Harihar, Rithika Venkataramanan, Marina Alice Mathew, Anuraag Dasgupta, Koustav Sarkar","doi":"10.1080/17501911.2026.2667351","DOIUrl":"10.1080/17501911.2026.2667351","url":null,"abstract":"<p><p>Genetic abnormalities cause cancer, a heterogeneous disease. These abnormalities comprise unregulated proliferation, invasion, and metastasis. Transcriptional factors are altered by dysregulation, like DNA methylation, histone modifications, and chromatin remodeling, during tumor formation, progression, and resistance to therapy. These can be reversed and transmitted to subsequent generations. Consequently, tumor suppressor genes can be deactivated without altering DNA sequences. Epigenetic markers have been detected in carcinomas, sarcomas, hematological malignancies, and organ-specific tumors, influencing diagnostic accuracy, prognosis assessment, and treatment strategies. Several epigenetic drugs have been developed due to recent advances in epigenetic research. These include DNA methyltransferase inhibitors, histone deacetylase inhibitors and novel modulators focusing on RNA methylation and chromatin regulation. These pharmaceuticals may facilitate normal gene expression restoration, enhance the sensitivity of treatment-resistant malignancies and improve the efficacy of conventional and immunotherapeutic interventions. Significant challenges, such as tumor heterogeneity, limited target specificity, and off-target toxicity, continue to impede widespread clinical application; others are less challenging. The integration of comprehensive epigenetic profiling with precision oncology frameworks presents transformative opportunities to tailor treatment programs, initiate therapy sooner and enhance long-term patient outcomes. Increasing cancer's epigenome knowledge has led to increased interest in developing personalized, mechanism-based treatments addressing cancer's dynamic and adaptive nature.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"611-629"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835250","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}

{"title":"hsa_circ_0005963 downregulation suppresses NSCLC malignant progression by miR-506-3p/SOX9-mediated stemness regulation.","authors":"Xuechao Zhou, Yu Yao, Huaiyin Ding","doi":"10.1080/17501911.2026.2654577","DOIUrl":"10.1080/17501911.2026.2654577","url":null,"abstract":"<p><strong>Purpose: </strong>This study investigated the role and regulatory mechanisms underlying hsa_circ_0005963 in NSCLC.</p><p><strong>Methods: </strong>FISH and RT-qPCR were used to assess hsa_circ_0005963 expression in NSCLC cells and tissues. Dual-luciferase reporter assay was employed to characterize hsa_circ_0005963 downstream targets. Transwell migration and EdU incorporation were performed to detect NSCLC cell proliferation and migration. A mouse tumor xenograft model was constructed to assess hsa_circ_0005963 functions in NSCLC metastasis and progressions.</p><p><strong>Results: </strong>hsa_circ_0005963 expression was upregulated in NSCLC tissues and cells. High hsa_circ_0005963 expression indicates poor prognosis, including overall survival. hsa_circ_0005963 silencing inhibited NSCLC proliferation and migration. Experiments confirmed that hsa_circ_0005963 downregulation suppresses A549 tumor invasions. A dual-luciferase reporter assay identified SOX9 and microRNA as hsa_circ_0005963 downstream targets, which was validated by RT-qPCR. SOX9 overexpression or miR-506-3p downregulation reversed the hsa_circ_0005963 silencing inhibitory effects upon proliferation and migrations. SOX9 overexpression reversed miR-506-3p effects to inhibit proliferation and migration in both cell lines.</p><p><strong>Conclusion: </strong>hsa_circ_0005963 promotes NSCLC development by sponging miR-506-3p to enhance SOX9 expression.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"565-573"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147986992","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}

{"title":"DNA methylation microarray analysis of human DNA samples contaminated with mouse DNA.","authors":"Takahiro Ebata, Qichun Wang, Hideyuki Takeshima, Yumi Furuichi, Satoshi Yamashita, Kouya Shiraishi, Shigehiro Yagishita, Akinobu Hamada, Toshikazu Ushijima","doi":"10.1080/17501911.2026.2667134","DOIUrl":"10.1080/17501911.2026.2667134","url":null,"abstract":"<p><strong>Aim: </strong>To establish an analytical method for human DNA contamination with mouse DNA using a DNA methylation microarray.</p><p><strong>Materials and methods: </strong>A pure human DNA sample was generated by mixing fully methylated and unmethylated DNA originating from the human cell line HCT116 and fully methylated mouse DNA. The pure human DNA sample, human DNA samples mixed with 30% and 60% mouse DNA, and the pure mouse DNA samples were analyzed using the Infinium MethylationEPIC v2.0 kit. Cell line xenografts (CDX) were prepared from RKO and Pa-Tu-8902 cell lines.</p><p><strong>Results: </strong>We identified 7,446 low-reproducibility probes using pure human DNA samples and 133,377 mouse cross-reacting probes using pure mouse DNA. After excluding these probes, functional probes improved the correlation in methylation levels between pure human DNA samples and those mixed with mouse DNA. Functional probes improved the correlation between DNA methylation levels in human CDX samples and their parental cancer cell lines.</p><p><strong>Conclusion: </strong>Our established method can minimize the effect of mouse DNA contamination in human DNA samples, thereby enabling the analysis of human CDX and patient-derived xenograft (PDX) models.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"543-550"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766328","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}

{"title":"Early-life air pollution exposure: epigenetics and child allergy.","authors":"Guangfei Li, Yuan Xiao, ZhiSheng Wu, Xianhai Zeng, Jiangqi Liu","doi":"10.1080/17501911.2026.2671164","DOIUrl":"10.1080/17501911.2026.2671164","url":null,"abstract":"<p><p>Globally, the incidence of allergic diseases in children has shown a significant upward trend, closely linked to environmental exposure in early life through epigenetic regulation mechanisms. Epigenetics enables dynamic regulation of genetic information via DNA methylation, histone modification, and non coding RNA without altering DNA sequence. The critical window from pregnancy to the first 1000 days of life is extremely sensitive to environmental factors exerting epigenetic effects, potentially influencing lifelong allergy susceptibility through fetal programming. This narrative review synthesizes current evidence on how early life air pollution exposure contributes to childhood allergic diseases via epigenetic mechanisms. A literature search was conducted using PubMed, Web of Science, Scopus, and Embase databases (up to December 2025). Studies were selected that provided mechanistic insights, epidemiological evidence from birth cohorts, or experimental findings relevant to epigenetic regulation. This review aims to provide a comprehensive overview of common air pollutant sources, their epigenetic effects at different developmental stages, and potential interventions during key windows to inform prevention and treatment strategies for childhood allergic diseases.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"631-646"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147873810","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}

{"title":"Emerging roles of m⁶A modification in endodontic diseases: a systematic review.","authors":"Suping Liao, Jihua Guo, Rong Jia","doi":"10.1080/17501911.2026.2667348","DOIUrl":"10.1080/17501911.2026.2667348","url":null,"abstract":"<p><strong>Aim: </strong>This review aims to synthesize and evaluate the evidence on the role of N⁶-methyladenosine (m⁶A) modification in pathogenesis, progression, and tissue repair of endodontic diseases, focusing on its regulatory functions in dental stem cells.</p><p><strong>Methods: </strong>Two reviewers independently searched four databases for studies published by May 2025. The protocol was registered with PROSPERO (CRD420251233698). The certainty of findings was assessed using the CERQual approach.</p><p><strong>Results: </strong>Of 680 initial records, 27 studies were included. Findings demonstrated that m⁶A modification dynamically regulates enamel/root development, osteogenic/odontogenic differentiation of dental stem cells, and inflammatory responses in endodontic diseases. Five key themes were identified: pulpitis pathogenesis and repair, apical periodontitis pathogenesis and repair, and tooth development/pulp regeneration. Mechanistically, in pulpitis, METTL3 exacerbates inflammation <i>via</i> NF-κB/MAPK pathways, whereas FTO aggravates bone destruction in apical periodontitis. M⁶A regulates stem cell differentiation by modulating osteogenic/odontogenic gene expression and lncRNA/miRNA networks. METTL3 promotes tissue repair by stabilizing target mRNAs, while FTO enhances RUNX2 splicing. M⁶A regulates tooth morphogenesis through WTAP-SHH and METTL3-NFIC pathways.</p><p><strong>Conclusions: </strong>This review establishes m⁶A modification as an important epitranscriptomic regulator that modulates inflammation and repair in endodontic diseases. Further clinical studies are needed to validate these mechanisms and their therapeutic potential.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"647-660"},"PeriodicalIF":2.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147812729","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}

{"title":"Reduction in <i>ELOVL2</i> methylation following curative surgery in lung cancer patients: an observational study.","authors":"Peixian Li, Zhuxing Chen, Xiaowen Zhang, Cheng Zeng, Yihao Chen, Shengli Yang, Yaming Xiong","doi":"10.1080/17501911.2026.2665461","DOIUrl":"10.1080/17501911.2026.2665461","url":null,"abstract":"<p><strong>Background: </strong>While tumors are known to accelerate epigenetic aging, it remains unclear whether curative surgery can reverse this effect in early-stage lung cancer patients. <i>ELOVL2</i> methylation is a well-established biomarker of epigenetic age, yet its dynamics following lung cancer resection have not been characterized.</p><p><strong>Results: </strong>We prospectively analyzed <i>ELOVL2</i> methylation in peripheral blood from 242 patients with stage I lung cancer before and three months after curative surgery using droplet digital PCR. Postoperative methylation levels were significantly reduced compared to preoperative values (<i>p</i> < 0.0001). The reduction in methylation was more pronounced in female patients, whereas classification accuracy was lower in older individuals.</p><p><strong>Significance: </strong>Our findings show that curative surgery is associated with a decrease in <i>ELOVL2</i> methylation-a marker of epigenetic aging-in early-stage lung cancer patients. This observation warrants further investigation.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"535-541"},"PeriodicalIF":2.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766352","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}

{"title":"The signaling upstream of DOT1L-mediated H3K79 methylation.","authors":"Chu Chen, Di Wu, Canran Lv, Peng Zhu, Zihao Chen, Qi Li, Junming Li, Jian Yang, Jing Zhang","doi":"10.1080/17501911.2026.2665450","DOIUrl":"10.1080/17501911.2026.2665450","url":null,"abstract":"<p><p>Histone lysine methylation is a post-translational modification system that has a profound impact on gene expression. The methylation of H3K79 plays an important role in gene transcription, repair of DNA damage, and cell cycle. In recent years, it has been discovered that Disruptor of telomeric silencing 1-like (DOT1L) can methylate H3K79 and is the only known H3K79 methyltransferase. DOT1L activity in leukemia cells interacts with ubiquitinated H2B to promote nucleosome binding. AF family proteins bind DNA to ENL to recruit DOT1L to the promoters of KMT2A (formerly MLL1)-rearranged leukemia target genes, promoting HOXA9 overexpression, a key event in leukemia. Moreover, DOT1L O-GlcNAcylation promotes its protein stability and proliferation of MLL fusion leukemia cells. This review summarizes the structure, biological functions and upstream regulatory mechanisms of DOT1L-mediated H3K79 methylation. Relevant literature was searched in PubMed and Web of Science for studies published from 2000 to 2024 using keywords including \"DOT1L,\" \"H3K79 methylation\" and \"KMT2A leukemia.\"</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"603-610"},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147812773","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}

{"title":"Combining epigenetic therapy and immunotherapeutic avenues for chronic HBV infection.","authors":"Yin-Han Chou, Markus Cornberg","doi":"10.1080/17501911.2026.2664392","DOIUrl":"10.1080/17501911.2026.2664392","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"531-533"},"PeriodicalIF":2.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766292","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}

{"title":"miRNA profiling of a mutation-negative PKD cohort reveals PKD1/PKD2 ADPKD shared signatures and differences.","authors":"Bruna De Felice, Ersilia Nigro, Maria Amicone, Antonio Pisani, Aurora Daniele, Federica Farinella","doi":"10.1080/17501911.2026.2652277","DOIUrl":"10.1080/17501911.2026.2652277","url":null,"abstract":"<p><strong>Background: </strong>Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by mutations in PKD1 or PKD2 genes, but a subgroup of patients has no detectable mutation and remains understudied. We profiled microRNAs (miRNAs) in this mutation-negative group and compared them with PKD1, PKD2, and healthy controls.</p><p><strong>Methods: </strong>Targeted miRNA profiling was used to measure miRNAs expression. We tested five prespecified contrasts using Welch's two-sided t-test (<i>p</i> < 0.05). For interpretation, experimentally supported miRNA-mRNA interactions were assembled and visualized into networks.</p><p><strong>Results: </strong>miR-92a was found upregulated across all patient-control groups. Interestingly, the mutation-negative cohort showed the broadest deregulation, pointing toward higher expression together with enhanced extracellular-matrix remodeling. PKD1 vs controls displayed a more restricted number of deregulated miRNAs; when PKD1 was compared directly with the mutation-negative group, we observed selective reductions, most notably miR-134-5p. PKD2 vs controls showed fewer changes overall but overlapped with the core signature observed in other groups and no miRNAs met the threshold in PKD2 vs mutation-negative.</p><p><strong>Discussion: </strong>The results indicate that miRNA dysregulation is present in the absence of identifiable PKD1/PKD2 mutations, supporting the idea of common pathways and highlighting the translational potential of miRNAs as biomarkers or therapeutic targets.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"371-383"},"PeriodicalIF":3.1,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13166239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147608319","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}