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A comprehensive review on the functional role of miRNA clusters in cervical cancer. 全面回顾 miRNA 簇在宫颈癌中的功能作用。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-04-01 Epub Date: 2024-03-21 DOI: 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}
引用次数: 0
Epigenetics and the neurodegenerative process. 表观遗传学和神经退行性病变过程。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-04-01 Epub Date: 2024-03-21 DOI: 10.2217/epi-2023-0416
Bartosz Słowikowski, Wojciech Owecki, Jan Jeske, Michał Jezierski, Michał Draguła, Ulyana Goutor, Paweł P Jagodziński, Wojciech Kozubski, Jolanta Dorszewska
{"title":"Epigenetics and the neurodegenerative process.","authors":"Bartosz Słowikowski, Wojciech Owecki, Jan Jeske, Michał Jezierski, Michał Draguła, Ulyana Goutor, Paweł P Jagodziński, Wojciech Kozubski, Jolanta Dorszewska","doi":"10.2217/epi-2023-0416","DOIUrl":"10.2217/epi-2023-0416","url":null,"abstract":"<p><p>Neurological diseases are multifactorial, genetic and environmental. Environmental factors such as diet, physical activity and emotional state are epigenetic factors. Environmental markers are responsible for epigenetic modifications. The effect of epigenetic changes is increased inflammation of the nervous system and neuronal damage. In recent years, it has been shown that epigenetic changes may cause an increased risk of neurological disorders but, currently, the relationship between epigenetic modifications and neurodegeneration remains unclear. This review summarizes current knowledge about neurological disorders caused by epigenetic changes in diseases such as Alzheimer's disease, Parkinson's disease, stroke and epilepsy. Advances in epigenetic techniques may be key to understanding the epigenetics of central changes in neurological diseases.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"473-491"},"PeriodicalIF":3.8,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179501","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
Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. 缩小差距：R 环介导的基因组不稳定性及其对神经系统疾病的影响。
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-26 DOI: 10.2217/epi-2023-0379
Katherine R Westover, Peng Jin, Bing Yao
{"title":"Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases.","authors":"Katherine R Westover, Peng Jin, Bing Yao","doi":"10.2217/epi-2023-0379","DOIUrl":"10.2217/epi-2023-0379","url":null,"abstract":"<p><p>R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287243","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
Combined therapy targeting AR and EZH2 curbs castration-resistant prostate cancer enhancing anti-tumor T-cell response. 针对 AR 和 EZH2 的联合疗法可抑制阉割耐药前列腺癌，增强抗肿瘤 T 细胞反应。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-26 DOI: 10.2217/epi-2023-0374
Irene Fischetti, Laura Botti, Roberta Sulsenti, Valeria Cancila, Claudia Enriquez, Renata Ferri, Marco Bregni, Filippo Crivelli, Claudio Tripodo, Mario P Colombo, Elena Jachetti
{"title":"Combined therapy targeting AR and EZH2 curbs castration-resistant prostate cancer enhancing anti-tumor T-cell response.","authors":"Irene Fischetti, Laura Botti, Roberta Sulsenti, Valeria Cancila, Claudia Enriquez, Renata Ferri, Marco Bregni, Filippo Crivelli, Claudio Tripodo, Mario P Colombo, Elena Jachetti","doi":"10.2217/epi-2023-0374","DOIUrl":"10.2217/epi-2023-0374","url":null,"abstract":"<p><p><b>Aim:</b> Castration-resistant prostate cancer (CRPC) eventually becomes resistant to androgen receptor pathway inhibitors like enzalutamide. Immunotherapy also fails in CRPC. We propose a new approach to simultaneously revert enzalutamide resistance and rewire anti-tumor immunity. <b>Methods:</b> We investigated <i>in vitro</i> and in subcutaneous and spontaneous mouse models the effects of combining enzalutamide and GSK-126, a drug inhibiting the epigenetic modulator EZH2. <b>Results:</b> Enzalutamide and GSK-126 synergized to reduce CRPC growth, also restraining tumor neuroendocrine differentiation. The anti-tumor activity was lost in immunodeficient mice. Indeed, the combination treatment awoke cytotoxic activity and IFN-γ production of tumor-specific CD8<sup>+</sup> T lymphocytes. <b>Conclusion:</b> These results promote the combination of enzalutamide and GSK-126 in CRPC, also offering new avenues for immunotherapy in prostate cancer.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287244","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
Coregulatory effects of multiple histone modifications in key ferroptosis-related genes for lung adenocarcinoma. 多种组蛋白修饰对肺腺癌关键铁变态相关基因的核心调节作用
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-21 DOI: 10.2217/epi-2023-0403
Ye-Chen Qi, Hui Bai, Si-Le Hu, Shu-Juan Li, Qian-Zhong Li
{"title":"Coregulatory effects of multiple histone modifications in key ferroptosis-related genes for lung adenocarcinoma.","authors":"Ye-Chen Qi, Hui Bai, Si-Le Hu, Shu-Juan Li, Qian-Zhong Li","doi":"10.2217/epi-2023-0403","DOIUrl":"10.2217/epi-2023-0403","url":null,"abstract":"<p><p><b>Aim:</b> The present study was designed to investigate the coregulatory effects of multiple histone modifications (HMs) on gene expression in lung adenocarcinoma (LUAD). <b>Materials & methods:</b> Ten histones for LUAD were analyzed using ChIP-seq and RNA-seq data. An innovative computational method is proposed to quantify the coregulatory effects of multiple HMs on gene expression to identify strong coregulatory genes and regions. This method was applied to explore the coregulatory mechanisms of key ferroptosis-related genes in LUAD. <b>Results:</b> Nine strong coregulatory regions were identified for six ferroptosis-related genes with diverse coregulatory patterns (<i>CA9</i>, <i>PGD</i>, <i>CDKN2A</i>, <i>PML</i>, <i>OTUB1</i> and <i>NFE2L2</i>). <b>Conclusion:</b> This quantitative method could be used to identify important HM coregulatory genes and regions that may be epigenetic regulatory targets in cancers.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179500","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
Toward a more holistic approach to the study of exposures and child outcomes. 以更全面的方法研究暴露与儿童结果。
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-14 DOI: 10.2217/epi-2023-0424
Barry M Lester, Marie Camerota, Todd M Everson, Coral L Shuster, Carmen J Marsit
{"title":"Toward a more holistic approach to the study of exposures and child outcomes.","authors":"Barry M Lester, Marie Camerota, Todd M Everson, Coral L Shuster, Carmen J Marsit","doi":"10.2217/epi-2023-0424","DOIUrl":"10.2217/epi-2023-0424","url":null,"abstract":"<p><p><b>Aim:</b> The current work was designed to demonstrate the application of the exposome framework in examining associations between exposures and children's long-term neurodevelopmental and behavioral outcomes. <b>Methods:</b> Longitudinal data were collected from birth through age 6 from 402 preterm infants. Three statistical methods were utilized to demonstrate the exposome framework: exposome-wide association study, cumulative exposure and machine learning models, with and without epigenetic data. <b>Results:</b> Each statistical approach answered a distinct research question regarding the impact of exposures on longitudinal child outcomes. Findings highlight associations between exposures, epigenetics and executive function. <b>Conclusion:</b> Findings demonstrate how an exposome-based approach can be utilized to understand relationships between internal (e.g., DNA methylation) and external (e.g., prenatal risk) exposures and long-term developmental outcomes in preterm children.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11157992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119139","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
Predicting locus-specific DNA methylation levels in cancer and paracancer tissues. 预测癌症和癌旁组织中基因座特异性 DNA 甲基化水平
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-13 DOI: 10.2217/epi-2023-0114
Shuzheng Zhang, Baoshan Ma, Yu Liu, Yiwen Shen, Di Li, Shuxin Liu, Fengju Song
{"title":"Predicting locus-specific DNA methylation levels in cancer and paracancer tissues.","authors":"Shuzheng Zhang, Baoshan Ma, Yu Liu, Yiwen Shen, Di Li, Shuxin Liu, Fengju Song","doi":"10.2217/epi-2023-0114","DOIUrl":"10.2217/epi-2023-0114","url":null,"abstract":"<p><p><b>Aim:</b> To predict base-resolution DNA methylation in cancerous and paracancerous tissues. <b>Material & methods:</b> We collected six cancer DNA methylation datasets from The Cancer Genome Atlas and five cancer datasets from Gene Expression Omnibus and established machine learning models using paired cancerous and paracancerous tissues. Tenfold cross-validation and independent validation were performed to demonstrate the effectiveness of the proposed method. <b>Results:</b> The developed cross-tissue prediction models can substantially increase the accuracy at more than 68% of CpG sites and contribute to enhancing the statistical power of differential methylation analyses. An XGBoost model leveraging multiple correlating CpGs may elevate the prediction accuracy. <b>Conclusion:</b> This study provides a powerful tool for DNA methylation analysis and has the potential to gain new insights into cancer research from epigenetics.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11158003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109702","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
Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma. 基于 miRNA 的全基因组甲基化分析构建肝细胞癌的预后模型。
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-13 DOI: 10.2217/epi-2023-0365
Zhaoqi Shi, Xiaolong Liu, Duguang Li, Xiaoxiao Fan, Lifeng He, Daizhan Zhou, Hui Lin
{"title":"Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma.","authors":"Zhaoqi Shi, Xiaolong Liu, Duguang Li, Xiaoxiao Fan, Lifeng He, Daizhan Zhou, Hui Lin","doi":"10.2217/epi-2023-0365","DOIUrl":"10.2217/epi-2023-0365","url":null,"abstract":"<p><p><b>Aim:</b> Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). <b>Materials & methods:</b> least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. <b>Results:</b> A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. <b>Conclusion:</b> The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109701","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
Methylation changes of liver DNA during the formation of gallstones. 胆结石形成过程中肝脏 DNA 的甲基化变化
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-06 DOI: 10.2217/epi-2023-0391
Junbin Peng, Haojie Li, Fang Tong, Jinlong Hu, Min Li, Gan Chen, Dongquan Liu, Jinshan Liu, Rui Wang, Hongyu Xu, Xuanxuan Li, Xinguo Zhong, Jiaming Yao, Baoqiang Cao
{"title":"Methylation changes of liver DNA during the formation of gallstones.","authors":"Junbin Peng, Haojie Li, Fang Tong, Jinlong Hu, Min Li, Gan Chen, Dongquan Liu, Jinshan Liu, Rui Wang, Hongyu Xu, Xuanxuan Li, Xinguo Zhong, Jiaming Yao, Baoqiang Cao","doi":"10.2217/epi-2023-0391","DOIUrl":"10.2217/epi-2023-0391","url":null,"abstract":"<p><p><b>Aim:</b> To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. <b>Methods:</b> Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. <b>Results:</b> A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. <b>Conclusion:</b> We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039008","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
Neural tube defects and epigenetics: role of histone post-translational histone modifications. 神经管缺陷与表观遗传学：组蛋白翻译后修饰的作用。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.2217/epi-2023-0357
Rosa Pardo V, Richard H Finnell, M Elizabeth Ross, Pablo Alarcón, José Suazo
{"title":"Neural tube defects and epigenetics: role of histone post-translational histone modifications.","authors":"Rosa Pardo V, Richard H Finnell, M Elizabeth Ross, Pablo Alarcón, José Suazo","doi":"10.2217/epi-2023-0357","DOIUrl":"10.2217/epi-2023-0357","url":null,"abstract":"<p><p>Neural tube defects (NTDs) are the most common congenital anomalies of the CNS. It is widely appreciated that both genetic and environmental factors contribute to their etiology. The inability to ascribe clear genetic patterns of inheritance to various NTD phenotypes suggests it is possible that epigenetic mechanisms are involved in the etiology of NTDs. In this context, the contribution of DNA methylation as an underlying contributing factor to the etiology of NTDs has been extensively reviewed. Here, an updated accounting of the evidence linking post-translational histone modifications to these birth defects, relying heavily upon studies in humans, and the possible molecular implications inferred from reports based on cellular and animal models, are presented.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"419-426"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971500","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
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