EpigenomicsPub Date : 2024-01-01Epub Date: 2024-07-17DOI: 10.1080/17501911.2024.2366157
Florence Z Martin, Kayleigh E Easey, Laura D Howe, Abigail Fraser, Deborah A Lawlor, Caroline L Relton, Gemma C Sharp
{"title":"A novel hypothesis-generating approach for detecting phenotypic associations using epigenetic data.","authors":"Florence Z Martin, Kayleigh E Easey, Laura D Howe, Abigail Fraser, Deborah A Lawlor, Caroline L Relton, Gemma C Sharp","doi":"10.1080/17501911.2024.2366157","DOIUrl":"10.1080/17501911.2024.2366157","url":null,"abstract":"<p><p><b>Aim:</b> Hypotheses about what phenotypes to include in causal analyses, that in turn can have clinical and policy implications, can be guided by hypothesis-free approaches leveraging the epigenome, for example.<b>Materials & methods:</b> Minimally adjusted epigenome-wide association studies (EWAS) using ALSPAC data were performed for example conditions, dysmenorrhea and heavy menstrual bleeding (HMB). Differentially methylated CpGs were searched in the EWAS Catalog and associated traits identified. Traits were compared between those with and without the example conditions in ALSPAC.<b>Results:</b> Seven CpG sites were associated with dysmenorrhea and two with HMB. Smoking and adverse childhood experience score were associated with both conditions in the hypothesis-testing phase.<b>Conclusion:</b> Hypothesis-generating EWAS can help identify associations for future analyses.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"851-864"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141626340","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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-09-11DOI: 10.1080/17501911.2024.2394380
Fabio Coppedè
{"title":"DNA methylation in amyotrophic lateral sclerosis: where do we stand and what is next?","authors":"Fabio Coppedè","doi":"10.1080/17501911.2024.2394380","DOIUrl":"10.1080/17501911.2024.2394380","url":null,"abstract":"<p><p>Genes involved in immune response, inflammation and metabolism are among those most likely affected by changes in DNA methylation (DNAm) and expression levels in amyotrophic lateral sclerosis (ALS) tissues. Unfortunately, it is still largely unclear whether any of these changes precede the onset of disease symptoms or whether most of them are the result of the muscular and metabolic changes that follow symptoms onset. In this article the author discusses the strengths and limitations of the available studies of DNAm in ALS and provides some suggestions on what, in his opinion, could be done in the near future for a better understanding of the DNAm changes occurring in ALS, their link with environmental exposures and their potential clinical utility.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1185-1196"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282449","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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-01-03DOI: 10.2217/epi-2023-0326
Valerio Gristina, Umberto Malapelle
{"title":"Dissecting the nuances of cancer epigenomics in liquid biopsy.","authors":"Valerio Gristina, Umberto Malapelle","doi":"10.2217/epi-2023-0326","DOIUrl":"10.2217/epi-2023-0326","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"79-83"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139080448","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 : 2024-01-01Epub Date: 2024-01-15DOI: 10.2217/epi-2023-0336
Luqiao Luo, Fei Qiao, Ke Zhou, Qiang Tu, Jiao He, Haoqi Huang, Chao Liu, Huihua Cai
{"title":"Constructed competitive endogenous RNA network and patterns of immune infiltration revealing the prognostic signature for cervical cancer.","authors":"Luqiao Luo, Fei Qiao, Ke Zhou, Qiang Tu, Jiao He, Haoqi Huang, Chao Liu, Huihua Cai","doi":"10.2217/epi-2023-0336","DOIUrl":"10.2217/epi-2023-0336","url":null,"abstract":"<p><p><b>Aim:</b> To investigate the relationship between potential abnormal epigenetic modification and immune cell infiltration in patients with cervical carcinoma. <b>Materials & methods:</b> RNA expression profiles from The Cancer Genome Atlas database were used to explore the relationship between key biomarkers and tumor-infiltrating immune cells and for clinical specimen validation. <b>Results:</b> Two nomogram models were developed, one with specific ceRNA and the other based on biological markers of related tumor-infiltrating immune cells. Moreover, a key biomarker (RIPOR2), which was significantly relevant to CD8 T cells. <b>Conclusion:</b> RIPOR2 and CD8 T cells play a crucial role in the development and progression of cervical carcinoma, suggesting their potential as markers for guiding future therapeutic strategies.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"23-39"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466494","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 : 2024-01-01Epub Date: 2024-09-03DOI: 10.1080/17501911.2024.2375187
Jared Schuetter, Angela Minard-Smith, Brandon Hill, Jennifer L Beare, Alexandria Vornholt, Thomas W Burke, Vel Murugan, Anthony K Smith, Thiruppavai Chandrasekaran, Hiba J Shamma, Sarah C Kahaian, Keegan L Fillinger, Mary Anne S Amper, Wan-Sze Cheng, Yongchao Ge, Mary Catherine George, Kristy Guevara, Nora Lovette-Okwara, Avinash Mahajan, Nada Marjanovic, Natalia Mendelev, Vance G Fowler, Micah T McClain, Clare M Miller, Sagie Mofsowitz, Venugopalan D Nair, German Nudelman, Thomas G Evans, Flora Castellino, Irene Ramos, Stas Rirak, Frederique Ruf-Zamojski, Nitish Seenarine, Alessandra Soares-Shanoski, Sindhu Vangeti, Mital Vasoya, Xuechen Yu, Elena Zaslavsky, Lishomwa C Ndhlovu, Michael J Corley, Scott Bowler, Steven G Deeks, Andrew G Letizia, Stuart C Sealfon, Christopher W Woods, Rachel R Spurbeck
{"title":"Integrated epigenomic exposure signature discovery.","authors":"Jared Schuetter, Angela Minard-Smith, Brandon Hill, Jennifer L Beare, Alexandria Vornholt, Thomas W Burke, Vel Murugan, Anthony K Smith, Thiruppavai Chandrasekaran, Hiba J Shamma, Sarah C Kahaian, Keegan L Fillinger, Mary Anne S Amper, Wan-Sze Cheng, Yongchao Ge, Mary Catherine George, Kristy Guevara, Nora Lovette-Okwara, Avinash Mahajan, Nada Marjanovic, Natalia Mendelev, Vance G Fowler, Micah T McClain, Clare M Miller, Sagie Mofsowitz, Venugopalan D Nair, German Nudelman, Thomas G Evans, Flora Castellino, Irene Ramos, Stas Rirak, Frederique Ruf-Zamojski, Nitish Seenarine, Alessandra Soares-Shanoski, Sindhu Vangeti, Mital Vasoya, Xuechen Yu, Elena Zaslavsky, Lishomwa C Ndhlovu, Michael J Corley, Scott Bowler, Steven G Deeks, Andrew G Letizia, Stuart C Sealfon, Christopher W Woods, Rachel R Spurbeck","doi":"10.1080/17501911.2024.2375187","DOIUrl":"10.1080/17501911.2024.2375187","url":null,"abstract":"<p><p><b>Aim:</b> The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis.<b>Materials & methods:</b> Here we developed and implemented a machine learning algorithm, the exposure signature discovery algorithm (ESDA), to identify the most important features present in multiple epigenomic and transcriptomic datasets to produce an integrated exposure signature (ES).<b>Results:</b> Signatures were developed for seven exposures including <i>Staphylococcus aureus</i>, human immunodeficiency virus, SARS-CoV-2, influenza A (H3N2) virus and <i>Bacillus anthracis</i> vaccinations. ESs differed in the assays and features selected and predictive value.<b>Conclusion:</b> Integrated ESs can potentially be utilized for diagnosis or forensic attribution. The ESDA identifies the most distinguishing features enabling diagnostic panel development for future precision health deployment.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1013-1029"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142119318","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":"<i>LncRNA SSTR5-AS1</i> promotes esophageal carcinoma through regulating <i>ITGB6/JAK1/STAT3</i> signaling.","authors":"Zhaohui Tang, Yongjun Jiang, Yuyu Zong, Sijuan Ding, Chen Wu, Zhangwen Tang, Lin Liao, Shaohui Jiang, Ruoting Tang, Fang Li, Pengfei Luo","doi":"10.1080/17501911.2024.2388018","DOIUrl":"10.1080/17501911.2024.2388018","url":null,"abstract":"<p><p><b>Aim:</b> To investigate function of somatostatin receptor 5 antisense RNA 1 (SSTR5-AS1) in esophageal carcinoma (ESCA).<b>Materials & methods:</b> The cellular function was assessed using EdU staining and Transwell assay. The localization of SSTR5-AS1 was measured using fluorescence <i>in situ</i> hybridization staining.<b>Results:</b> <i>SSTR5-AS1</i> shRNA repressed invasion and migration and induced apoptosis in ESCA cells. SSTR5-AS1 was distributed in cytoplasm, and it regulated its subunit integrin beta 6 (ITGB6) via eukaryotic translation initiation factor 4A3 (EIF4A3). SSTR5-AS1 shRNA inactivated ITGB6 and JAK1/STAT3 signaling. SSTR5-AS1 silencing attenuated the malignant behavior of ESCA cells through the ITGB6-mediated JAK1/STAT3 axis.<b>Conclusion:</b> SSTR5-AS1 promotes tumorigenesis of ESCA by interacting with EIF4A3 to regulate ITGB6/JAK1/STAT3 axis, which serves a basis for discovering strategies against ESCA.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1133-1148"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132197","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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-06-17DOI: 10.1080/17501911.2024.2351792
Elisangela da Silva Rodrigues Marçal, Jéssica Bassani Borges, Gisele Medeiros Bastos, Thiago Dominguez Crespo Hirata, Victor Fernandes de Oliveira, Rodrigo Marques Gonçalves, Andre Arpad Faludi, João Italo Dias França, Daiana Vitor de Oliveira Silva, Vanessa Barbosa Malaquias, Andre Ducati Luchessi, Vivian Nogueira Silbiger, Marcelo Arruda Nakazone, Tayanne Silva Carmo, Dorotéia Rossi Silva Souza, Marcelo Ferraz Sampaio, Rosario Dominguez Crespo Hirata, Mario Hiroyuki Hirata
{"title":"Methylation status of <i>LDLR</i>, <i>PCSK9</i> and <i>LDLRAP1</i> is associated with cardiovascular events in familial hypercholesterolemia.","authors":"Elisangela da Silva Rodrigues Marçal, Jéssica Bassani Borges, Gisele Medeiros Bastos, Thiago Dominguez Crespo Hirata, Victor Fernandes de Oliveira, Rodrigo Marques Gonçalves, Andre Arpad Faludi, João Italo Dias França, Daiana Vitor de Oliveira Silva, Vanessa Barbosa Malaquias, Andre Ducati Luchessi, Vivian Nogueira Silbiger, Marcelo Arruda Nakazone, Tayanne Silva Carmo, Dorotéia Rossi Silva Souza, Marcelo Ferraz Sampaio, Rosario Dominguez Crespo Hirata, Mario Hiroyuki Hirata","doi":"10.1080/17501911.2024.2351792","DOIUrl":"10.1080/17501911.2024.2351792","url":null,"abstract":"<p><p><b>Aim:</b> Methylation of <i>LDLR</i>, <i>PCSK9</i> and <i>LDLRAP1</i> CpG sites was assessed in patients with familial hypercholesterolemia (FH). <b>Methods:</b> DNA methylation of was analyzed by pyrosequencing in 131 FH patients and 23 normolipidemic (NL) subjects.<b>Results: </b> <i>LDLR</i>, <i>PCSK9</i> and <i>LDLRP1</i> methylation was similar between FH patients positive (MD) and negative (non-MD) for pathogenic variants in FH-related genes. <i>LDLR</i> and <i>PCSK9</i> methylation was higher in MD and non-MD groups than NL subjects (<i>p</i> < 0.05). <i>LDLR</i>, <i>PCSK9</i> and <i>LDLRAP1</i> methylation profiles were associated with clinical manifestations and cardiovascular events in FH patients (<i>p</i> < 0.05).<b>Conclusion:</b> Differential methylation of <i>LDLR</i>, <i>PCSK9</i> and <i>LDLRAP1</i> is associated with hypercholesterolemia and cardiovascular events. This methylation profile maybe useful as a biomarker and contribute to the management of FH.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"809-820"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330598","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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-07-18DOI: 10.1080/17501911.2024.2373682
Eileen M Crimmins, Eric T Klopack, Jung Ki Kim
{"title":"Generations of epigenetic clocks and their links to socioeconomic status in the Health and Retirement Study.","authors":"Eileen M Crimmins, Eric T Klopack, Jung Ki Kim","doi":"10.1080/17501911.2024.2373682","DOIUrl":"10.1080/17501911.2024.2373682","url":null,"abstract":"<p><p><b>Aim:</b> This is a brief description of links between nine epigenetic clocks related to human aging and socioeconomic and behavioral characteristics as well as health outcomes.<b>Materials & methods:</b> We estimate frequently used and novel clocks from one data source, the Health and Retirement Study.<b>Results:</b> While all of these clocks are thought to reflect \"aging,\" they use different CpG sites and do not strongly relate to each other. First and fourth generation clocks are not as linked to socioeconomic status or health outcomes as second and third generation clocks.<b>Conclusion:</b> Epigenetic clocks reflect exciting new tools and their continued evolution is likely to improve our understanding of how exposures get under the skin to accelerate aging.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1031-1042"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632984","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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-07-29DOI: 10.1080/17501911.2024.2374702
Firoz Ahmed, Nitish Kumar Mishra, Othman A Alghamdi, Mohammad Imran Khan, Aamir Ahmad, Nargis Khan, Mohammad Rehan
{"title":"Deciphering <i>KDM8</i> dysregulation and CpG methylation in hepatocellular carcinoma using multi-omics and machine learning.","authors":"Firoz Ahmed, Nitish Kumar Mishra, Othman A Alghamdi, Mohammad Imran Khan, Aamir Ahmad, Nargis Khan, Mohammad Rehan","doi":"10.1080/17501911.2024.2374702","DOIUrl":"10.1080/17501911.2024.2374702","url":null,"abstract":"<p><p><b>Aim:</b> This study investigates the altered expression and CpG methylation patterns of histone demethylase <i>KDM8</i> in hepatocellular carcinoma (HCC), aiming to uncover insights and promising diagnostics biomarkers.<b>Materials & methods:</b> Leveraging TCGA-LIHC multi-omics data, we employed R/Bioconductor libraries and Cytoscape to analyze and construct a gene correlation network, and LASSO regression to develop an HCC-predictive model.<b>Results:</b> In HCC, <i>KDM8</i> downregulation is correlated with CpGs hypermethylation. Differential gene correlation analysis unveiled a liver carcinoma-associated network marked by increased cell division and compromised liver-specific functions. The LASSO regression identified a highly accurate HCC prediction signature, prominently featuring CpG methylation at cg02871891.<b>Conclusion:</b> Our study uncovers CpG hypermethylation at cg02871891, possibly influencing <i>KDM8</i> downregulation in HCC, suggesting these as promising biomarkers and targets.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"961-983"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787658","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}
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