EpigenomicsPub Date : 2024-11-14DOI: 10.1080/17501911.2024.2426441
Anne K Bozack, Leonardo Trasande
{"title":"Prenatal chemical exposures and the methylome: current evidence and opportunities for environmental epigenetics.","authors":"Anne K Bozack, Leonardo Trasande","doi":"10.1080/17501911.2024.2426441","DOIUrl":"https://doi.org/10.1080/17501911.2024.2426441","url":null,"abstract":"<p><p>Exposure to pollutants and chemicals during critical developmental periods in early life can impact health and disease risk across the life course. Research in environmental epigenetics has provided increasing evidence that prenatal exposures affect epigenetic markers, particularly DNA methylation. In this article, we discuss the role of DNA methylation in early life programming and review evidence linking the intrauterine environment to epigenetic modifications, with a focus on exposure to tobacco smoke, metals, and endocrine-disrupting chemicals. We also discuss challenges and novel approaches in environmental epigenetic research and explore the potential of epigenetic biomarkers in studies of pediatric populations as indicators of exposure and disease risk. Overall, we aim to highlight how advancements in environmental epigenetics may transform our understanding of early-life exposures and inform new approaches for supporting long-term health.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617519","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}
EpigenomicsPub Date : 2024-11-12DOI: 10.1080/17501911.2024.2408217
Stephanie W Waldrop, Wei Perng, Iain R Konigsberg, Sarah J Borengasser
{"title":"The potential utility of cord blood DNA methylation in pediatric clinical practice.","authors":"Stephanie W Waldrop, Wei Perng, Iain R Konigsberg, Sarah J Borengasser","doi":"10.1080/17501911.2024.2408217","DOIUrl":"https://doi.org/10.1080/17501911.2024.2408217","url":null,"abstract":"<p><p>Our understanding of the origins of noncommunicable diseases has evolved over the years with greater consideration given to the lasting influence exposures and experiences during the preconceptional and prenatal periods can have. Research highlights the associations of parental exposures (e.g., diet, obesity, gestational diabetes, lipid profile, toxic exposures and microbiome) with the infant/fetal methylome and suggest associations with infant, child and/or adolescent chronic health outcomes. Thus, epigenetics and specifically cord blood DNA methylation may have utility as biomarkers for disease risk identification and stratification in pediatrics. However, for cord blood DNA methylation analyses to be leveraged as biomarkers of disease risk in pediatric clinical practice, the results must be replicable, validated and clinically meaningful. Challenges and opportunities to this prospect are herein discussed.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-8"},"PeriodicalIF":3.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617523","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}
EpigenomicsPub Date : 2024-11-08DOI: 10.1080/17501911.2024.2419357
Cal Rosete, Annie Vogel Ciernia
{"title":"The Two Faces of HDAC3: Neuroinflammation in Disease and Neuroprotection in Recovery.","authors":"Cal Rosete, Annie Vogel Ciernia","doi":"10.1080/17501911.2024.2419357","DOIUrl":"https://doi.org/10.1080/17501911.2024.2419357","url":null,"abstract":"<p><p>Histone deacetylase 3 (HDAC3) is a critical regulator of gene expression, influencing a variety of cellular processes in the central nervous system. As such, dysfunction of this enzyme may serve as a key driver in the pathophysiology of various neuropsychiatric disorders and neurodegenerative diseases. HDAC3 plays a crucial role in regulating neuroinflammation, and is now widely recognized as a major contributor to neurological conditions, as well as in promoting neuroprotective recovery following brain injury, hemorrhage and stroke. Emerging evidence suggests that pharmacological inhibition of HDAC3 can mitigate behavioral and neuroimmune deficits in various brain diseases and disorders, offering a promising therapeutic strategy. Understanding HDAC3 in the healthy brain lays the necessary foundation to define and resolve its dysfunction in a disease state. This review explores the mechanisms of HDAC3 in various cell types and its involvement in disease pathology, emphasizing the potential of HDAC3 inhibition to address neuroimmune, gene expression and behavioral deficits in a range of neurodegenerative and neuropsychiatric conditions.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-16"},"PeriodicalIF":3.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603219","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}
EpigenomicsPub Date : 2024-11-08DOI: 10.1080/17501911.2024.2419362
Vanessa Nicolì, Marianna Giangreco, Eleonora Pardini, Iacopo Petrini, Diana Bacchin, Vittorio Aprile, Franca Melfi, Marco Lucchi, Melania Guida, Roberta Ricciardi, Michelangelo Maestri, Martina Lari, Lucia Migliore, Andrea Stoccoro, Fabio Coppedè
{"title":"DNA methylation analysis of multiple genes in thymic epithelial tumors.","authors":"Vanessa Nicolì, Marianna Giangreco, Eleonora Pardini, Iacopo Petrini, Diana Bacchin, Vittorio Aprile, Franca Melfi, Marco Lucchi, Melania Guida, Roberta Ricciardi, Michelangelo Maestri, Martina Lari, Lucia Migliore, Andrea Stoccoro, Fabio Coppedè","doi":"10.1080/17501911.2024.2419362","DOIUrl":"https://doi.org/10.1080/17501911.2024.2419362","url":null,"abstract":"<p><p><b>Aim:</b> To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs).<b>Materials & methods:</b> We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples.<b>Results:</b> thymic carcinomas (TCs) showed hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with thymomas (TMs) and healthy thymic tissues. <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes.<b>Conclusion:</b> The present study confirms <i>GHSR, ELF3, IL1RN</i> and <i>RAG1</i> as TET epigenetic biomarkers.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-14"},"PeriodicalIF":3.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603177","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}
{"title":"Gastric microbiome composition accompanied with the <i>Helicobacter pylori</i> related DNA methylation anomaly.","authors":"Takuya Shijimaya, Tomomitsu Tahara, Tsubasa Shimogama, Jumpei Yamazaki, Sanshiro Kobayashi, Naohiro Nakamura, Yu Takahashi, Takashi Tomiyama, Toshiro Fukui, Makoto Naganuma","doi":"10.1080/17501911.2024.2418803","DOIUrl":"https://doi.org/10.1080/17501911.2024.2418803","url":null,"abstract":"<p><p><b>Aim:</b> DNA methylation is associated with gastric cancer and <i>Helicobacter pylori</i> (<i>H. pylori</i>) infection, while increasing evidence indicated involvement of other microbes reside in gastric mucosa during gastric tumorigenesis. We investigated bacterial communities in the gastric mucosa accompanied with <i>H. pylori</i> related methylation anomaly.<b>Materials & methods:</b> Gastric mucosa samples from antrum were obtained from 182 cancer-free patients. Bacterial communities were evaluated using 16S rRNA sequencing. The result was correlated with <i>H. pylori</i> related promoter CpG island (CGI) methylation of five genes (<i>IGF2, SLC16A12, SOX11, P2RX7 and MYOD1</i>), LINE1 hypomethylation and telomere length.<b>Results & conclusion:</b> We showed correlation between lower bacterial alpha diversity and higher CGI methylation. Multivariate analysis demonstrated older age (t = 3.46, <i>p</i> = 0.0007), <i>H. pylori</i> infection (t = 9.99, <i>p</i> < 0.0001) and lower bacterial alfa diversity (Shannon index: t = -2.34, <i>p</i> = 0.02) were significantly associated with CGI hypermethylation. In genus or family levels, increased abundance of <i>Helicobacter</i> was associated with hyper CGI methylation with strongest correlation, while decreased abundance of four bacteria (<i>Intrasporangiaceae family, Macellibacteroides</i>, <i>Peptostreptococcus</i> and <i>Dietziaceae family</i>) was also associated with hyper CGI methylation. Our findings suggest the potential correlation between CGI methylation induction and lower bacterial alpha diversity in the gastric mucosa accompanied by <i>H. pylori</i> infection.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-8"},"PeriodicalIF":3.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567844","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}
EpigenomicsPub Date : 2024-10-28DOI: 10.1080/17501911.2024.2415278
Yeon-Su Lee, Yong Sun Lee
{"title":"The mystique of epigenetic regulation: the remarkable case of a human noncoding RNA, nc886.","authors":"Yeon-Su Lee, Yong Sun Lee","doi":"10.1080/17501911.2024.2415278","DOIUrl":"https://doi.org/10.1080/17501911.2024.2415278","url":null,"abstract":"<p><p>nc886 is a regulatory noncoding RNA that is transcribed by RNA polymerase III (Pol III), is variably expressed in different biological contexts, and plays roles in inflammation and cancer. Epigenetic mechanisms play an intriguing role in regulating nc886 expression. As a maternally imprinted gene and metastable epiallele, nc866 exhibits polymorphic imprinting, with a methylation status that is influenced by environmental and biological factors. Consequently, the promoter DNA methylation status and the different resulting RNA expression levels of nc886 are associated with physiological and pathological conditions. In this review, we summarize the literature and explore the significance in relation to diverse roles of nc886.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-17"},"PeriodicalIF":3.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142497486","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}
{"title":"Differential methylation patterns from clusters associated with glucose metabolism: evidence from a Shanghai twin study.","authors":"Jingyuan Feng, Zhenni Zhu, Rongfei Zhou, Hongwei Liu, Zihan Hu, Fei Wu, Huiting Wang, Junhong Yue, Tong Zhou, Li Yang, Fan Wu","doi":"10.2217/epi-2023-0449","DOIUrl":"10.2217/epi-2023-0449","url":null,"abstract":"<p><p><b>Aim:</b> To assess the associations between genome-wide DNA methylation (DNAm) and glucose metabolism among a Chinese population, in particular the multisite correlation. <b>Materials & methods:</b> Epigenome-wide associations with fasting plasma glucose (FPG) and hemoglobin A1c (HbA1c) were analyzed among 100 Shanghai monozygotic (MZ) twin pairs using the Infinium HumanMethylationEPIC v2.0 BeadChip. We conducted a Pearson's correlation test, hierarchical cluster and pairwise analysis to examine the differential methylation patterns from clusters. <b>Results:</b> Cg01358804 (<i>TXNIP</i>) was identified as the most significant site associated with FPG and HbA1c. Two clusters with hypermethylated and hypomethylated patterns were observed for both FPG and HbA1c. <b>Conclusion:</b> Differential methylation patterns from clusters may provide new clues for epigenetic changes and biological mechanisms in glucose metabolism.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"445-459"},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971498","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}
{"title":"<i>hsa_circ_0087100/hsa-miR-6743-5p</i> affects Th1 cell differentiation by regulating <i>STAT1</i> in diabetic retinopathy.","authors":"Shuai He, Dongwei Lai, Chenggong Ma, Chunren Meng, Chunyang Cai, Qian Chen, Chufeng Gu, Qinghua Qiu","doi":"10.2217/epi-2023-0359","DOIUrl":"10.2217/epi-2023-0359","url":null,"abstract":"<p><p><b>Objective:</b> To elucidate the role of the competitive endogenous RNA (ceRNA) network in immune infiltration of diabetic retinopathy (DR). <b>Methods:</b> We obtained differentially expressed (DE) circRNAs, miRNAs and mRNAs from the Gene Expression Omnibus database. Then, we identified immune infiltration by CIBERSORT and single-sample gene set enrichment analysis and discovered co-expression genes by weighted gene co-expression network analysis. Furthermore, <i>STAT1</i>-mediated Th1 differentiation was determined in DR cell models, DR patients and DR mouse models. <b>Results:</b> <i>hsa_circ_0087100/hsa-miR-6743-5p/STAT1</i> was involved in immune infiltration of Th1 cells. Aberrant expression of the ceRNA network and <i>STAT1</i>-mediated Th1 differentiation was thus verified <i>in vitro</i> and <i>in vivo</i>. <b>Conclusion:</b> <i>hsa_circ_0087100/hsa-miR-6743-5p/STAT1</i> may affect Th1 cell differentiation in DR.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"427-444"},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971497","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}
EpigenomicsPub Date : 2024-04-01Epub Date: 2024-03-14DOI: 10.2217/epi-2023-0343
Meiqi Yang, Mei Wang, Xiaoyu Zhao, Feifei Xu, Shuang Liang, Yifan Wang, Nanxi Wang, Muhammed Lamin Sambou, Yue Jiang, Juncheng Dai
{"title":"DNA methylation marker identification and poly-methylation risk score in prediction of healthspan termination.","authors":"Meiqi Yang, Mei Wang, Xiaoyu Zhao, Feifei Xu, Shuang Liang, Yifan Wang, Nanxi Wang, Muhammed Lamin Sambou, Yue Jiang, Juncheng Dai","doi":"10.2217/epi-2023-0343","DOIUrl":"10.2217/epi-2023-0343","url":null,"abstract":"<p><p><b>Aim:</b> To elucidate the epigenetic consequences of DNA methylation in healthspan termination (HST), considering the current limited understanding. <b>Materials & methods:</b> Genetically predicted DNA methylation models were established (n = 2478). These models were applied to genome-wide association study data on HST. Then, a poly-methylation risk score (PMRS) was established in 241,008 individuals from the UK Biobank. <b>Results:</b> Of the 63,046 CpGs from the prediction models, 13 novel CpGs were associated with HST. Furthermore, people with high PMRSs showed higher HST risk (hazard ratio: 1.18; 95% CI: 1.13-1.25). <b>Conclusion:</b> The study indicates that DNA methylation may influence HST by regulating the expression of genes (e.g., <i>PRMT6</i>, <i>CTSK</i>). PMRSs have a promising application in discriminating subpopulations to facilitate early prevention.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"461-472"},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119138","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}
EpigenomicsPub Date : 2024-04-01Epub Date: 2024-03-21DOI: 10.2217/epi-2023-0244
Srinath Sriharikrishnaa, Femi E John, Medha Bairy, Sachin Shetty, Padmanaban S Suresh, Shama P Kabekkodu
{"title":"A comprehensive review on the functional role of miRNA clusters in cervical cancer.","authors":"Srinath Sriharikrishnaa, Femi E John, Medha Bairy, Sachin Shetty, Padmanaban S Suresh, Shama P Kabekkodu","doi":"10.2217/epi-2023-0244","DOIUrl":"10.2217/epi-2023-0244","url":null,"abstract":"<p><p>Cervical cancer (CC) poses a significant health threat in women globally. MicroRNA clusters (MCs), comprising multiple miRNA-encoding genes, are pivotal in gene regulation. Various factors, including circular RNA and DNA methylation, govern MC expression. Dysregulated MC expression correlates strongly with CC development via promoting the acquisition of cancer hallmarks. Certain MCs show promise for diagnosis, prognosis and therapy selection due to their distinct expression patterns in normal, premalignant and tumor tissues. This review explains the regulation and biological functions of MCs and highlights the clinical relevance of abnormal MC expression in CC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"493-511"},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179499","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}