Epigenetics communications最新文献

{"title":"From parental responsibility towards mutual understanding: reimagining the employment of epigenetic knowledge","authors":"Emma Moormann","doi":"10.1186/s43682-024-00026-8","DOIUrl":"https://doi.org/10.1186/s43682-024-00026-8","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141381185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the effect of childbearing on blood DNA methylation through comparison of parous and nulliparous females","authors":"Su Chen, Miranda Johs, Wilfried Karmaus, John W. Holloway, Parnian Kheirkhah Rahimabad, J. Goodrich, Karen E. Peterson, D. Dolinoy, S. Arshad, S. Ewart","doi":"10.1186/s43682-024-00025-9","DOIUrl":"https://doi.org/10.1186/s43682-024-00025-9","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140717837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in histone lysine acetylation, but not DNA methylation during facultative hibernation in Syrian hamster liver","authors":"Marloes M. Oosterhof, Louis Coussement, Alienke van Pijkeren, Marcel Kwiatkowski, M. R. Zwinderman, Frank J. Dekker, Tim de Meyer, Vera A. Reitsema, Rainer Bischoff, Victor Guryev, H. Bouma, Rob H. Henning, Marianne G. Rots","doi":"10.1186/s43682-023-00024-2","DOIUrl":"https://doi.org/10.1186/s43682-023-00024-2","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"11 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139444150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells.","authors":"Jagadeesh Puvvula, Joseph M Braun, Emily A DeFranco, Shuk-Mei Ho, Yuet-Kin Leung, Shouxiong Huang, Xiang Zhang, Ann M Vuong, Stephani S Kim, Zana Percy, Antonia M Calafat, Julianne C Botelho, Aimin Chen","doi":"10.1186/s43682-024-00027-7","DOIUrl":"10.1186/s43682-024-00027-7","url":null,"abstract":"<p><strong>Background: </strong>Exposure to environmental chemicals such as phthalates, phenols, and polycyclic aromatic hydrocarbons (PAHs) during pregnancy can increase the risk of adverse newborn outcomes. We explored the associations between maternal exposure to select environmental chemicals and DNA methylation in cord blood mononuclear cells (CBMC) and placental tissue (maternal and fetal sides) to identify potential mechanisms underlying these associations.</p><p><strong>Method: </strong>This study included 75 pregnant individuals who planned to give birth at the University of Cincinnati Hospital between 2014 and 2017. Maternal urine samples during the delivery visit were collected and analyzed for 37 biomarkers of phenols (12), phthalates (13), phthalate replacements (4), and PAHs (8). Cord blood and placenta tissue (maternal and fetal sides) were also collected to measure the DNA methylation intensities using the Infinium HumanMethylation450K BeadChip. We used linear regression, adjusting for potential confounders, to assess CpG-specific methylation changes in CBMC (<i>n</i> = 54) and placenta [fetal (<i>n</i> = 67) and maternal (<i>n</i> = 68) sides] associated with gestational chemical exposures (29 of 37 biomarkers measured in this study). To account for multiple testing, we used a false discovery rate q-values < 0.05 and presented results by limiting results with a genomic inflation factor of 1±0.5. Additionally, gene set enrichment analysis was conducted using the Kyoto Encyclopedia of Genes and Genomics pathways.</p><p><strong>Results: </strong>Among the 29 chemical biomarkers assessed for differential methylation, maternal concentrations of PAH metabolites (1-hydroxynaphthalene, 2-hydroxyfluorene, 4-hydroxyphenanthrene, 1-hydroxypyrene), monocarboxyisononyl phthalate, mono-3-carboxypropyl phthalate, and bisphenol A were associated with altered methylation in placenta (maternal or fetal side). Among exposure biomarkers associated with epigenetic changes, 1-hydroxynaphthalene, and mono-3-carboxypropyl phthalate were consistently associated with differential CpG methylation in the placenta. Gene enrichment analysis indicated that maternal 1-hydroxynaphthalene was associated with lipid metabolism and cellular processes of the placenta. Additionally, mono-3-carboxypropyl phthalate was associated with organismal systems and genetic information processing of the placenta.</p><p><strong>Conclusion: </strong>Among the 29 chemical biomarkers assessed during delivery, 1-hydroxynaphthalene and mono-3-carboxypropyl phthalate were associated with DNA methylation in the placenta.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1186/s43682-024-00027-7.</p>","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"4 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11217138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Navigating epigenetic epidemiology publications","authors":"Weisen Yu, E. Drzymalla, Matheus Fernandes Gyorfy, M. Khoury, Yan V. Sun, M. Gwinn","doi":"10.1186/s43682-023-00023-3","DOIUrl":"https://doi.org/10.1186/s43682-023-00023-3","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139248187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Connections between cross-tissue and intra-tissue biomarkers of aging biology in older adults","authors":"R. Waziry, Y. Gu, O. Williams, S. Hägg","doi":"10.1186/s43682-023-00022-4","DOIUrl":"https://doi.org/10.1186/s43682-023-00022-4","url":null,"abstract":"Abstract Background Saliva measures are generally more accessible than blood, especially in vulnerable populations. However, connections between aging biology biomarkers in different body tissues remain unknown. Methods The present study included individuals ( N = 2406) who consented for saliva and blood draw in the Health and Retirement Telomere length study in 2008 and the Venous blood study in 2016 who had complete data for both tissues. We assessed biological aging based on telomere length in saliva and DNA methylation and physiology measures in blood. DNA methylation clocks combine information from CpGs to produce the aging measures representative of epigenetic aging in humans. We analyzed DNA methylation clocks proposed by Horvath (353 CpG sites), Hannum (71 CpG sites), Levine or PhenoAge, (513 CpG sites), GrimAge, (epigenetic surrogate markers for select plasma proteins), Horvath skin and blood (391 CpG sites), Lin (99 CpG sites), Weidner (3 CpG sites), and VidalBralo (8 CpG sites). Physiology measures (referred to as phenotypic age) included albumin, creatinine, glucose, [log] C-reactive protein, lymphocyte percent, mean cell volume, red blood cell distribution width, alkaline phosphatase, and white blood cell count. The phenotypic age algorithm is based on parametrization of Gompertz proportional hazard models. Average telomere length was assayed using quantitative PCR (qPCR) by comparing the telomere sequence copy number in each patient’s sample (T) to a single-copy gene copy number (S). The resulting T/S ratio was proportional to telomere length, mean. Within individual, relationships between aging biology measures in blood and saliva and variations according to sex were assessed. Results Saliva-based telomere length showed inverse associations with both physiology-based and DNA methylation-based aging biology biomarkers in blood. Longer saliva-based telomere length was associated with 1 to 4 years slower biological aging based on blood-based biomarkers with the highest magnitude being Weidner ( β = − 3.97, P = 0.005), GrimAge ( β = − 3.33, P < 0.001), and Lin ( β = − 3.45, P = 0.008) biomarkers of DNA methylation. Conclusions There are strong connections between aging biology biomarkers in saliva and blood in older adults. Changes in telomere length vary with changes in DNA methylation and physiology biomarkers of aging biology. We observed variations in the relationship between each body system represented by physiology biomarkers and biological aging, particularly at the DNA methylation level. These observations provide novel opportunities for integration of both blood-based and saliva-based biomarkers in clinical care of vulnerable and clinically difficult to reach populations where either or both tissues would be accessible for clinical monitoring purposes.","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136013129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip","authors":"Diljeet Kaur, Sol Moe Lee, David Goldberg, Nathan J. Spix, Toshinori Hinoue, Hong-Tao Li, Varun B. Dwaraka, Ryan Smith, Hui Shen, Gangning Liang, Nicole Renke, Peter W. Laird, Wanding Zhou","doi":"10.1186/s43682-023-00021-5","DOIUrl":"https://doi.org/10.1186/s43682-023-00021-5","url":null,"abstract":"Abstract Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease.","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135538584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Being against reductionism regarding epigenetics","authors":"C. Dupras","doi":"10.1186/s43682-023-00020-6","DOIUrl":"https://doi.org/10.1186/s43682-023-00020-6","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49534068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Will epigenetics ever be a biosocial science? A reply to Chiapperino and Paneni","authors":"S. Zaina","doi":"10.1186/s43682-023-00018-0","DOIUrl":"https://doi.org/10.1186/s43682-023-00018-0","url":null,"abstract":"","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42597392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A longitudinal epigenome-wide association study of preeclamptic and normotensive pregnancy.","authors":"Shuwei Liu, Haoyi Fu, Mitali Ray, Lacey W Heinsberg, Yvette P Conley, Cindy M Anderson, Carl A Hubel, James M Roberts, Arun Jeyabalan, Daniel E Weeks, Mandy J Schmella","doi":"10.1186/s43682-022-00014-w","DOIUrl":"10.1186/s43682-022-00014-w","url":null,"abstract":"<p><strong>Background: </strong>While preeclampsia (PE) is a leading cause of pregnancy-related morbidity/mortality, its underlying mechanisms are not fully understood. DNA methylation (DNAm) is a dynamic regulator of gene expression that may offer insight into PE pathophysiology and/or serve as a biomarker (e.g., risk, subtype, a therapeutic response). This study's purpose was to evaluate for differences in blood-based DNAm across all trimesters between individuals eventually diagnosed with PE (cases) and individuals who remained normotensive throughout pregnancy, did not develop proteinuria, and birthed a normally grown infant (controls).</p><p><strong>Results: </strong>In the discovery phase, longitudinal, genome-wide DNAm data were generated across three trimesters of pregnancy in 56 participants (<i>n</i>=28 cases, <i>n</i>=28 controls) individually matched on self-identified race, pre-pregnancy body mass index, smoking, and gestational age at sample collection. An epigenome-wide association study (EWAS) was conducted, using surrogate variable analysis to account for unwanted sources of variation. No CpGs met the genome-wide significance <i>p</i> value threshold of 9×10^-8, but 16 CpGs (trimester 1: 5; trimester 2: 1; trimester 3: 10) met the suggestive significance threshold of 1×10^-5. DNAm data were also evaluated for differentially methylated regions (DMRs) by PE status. Three DMRs in each trimester were significant after Bonferonni-adjustment. Since only third-trimester samples were available from an independent replication sample (<i>n</i>=64 cases, <i>n</i>=50 controls), the top suggestive hits from trimester 3 (cg16155413 and cg21882990 associated with <i>TRAF3IP2-AS1/TRAF3IP2</i> genes, which also made up the top DMR) were carried forward for replication. During replication, DNAm data were also generated for validation purposes from discovery phase third trimester samples. While significant associations between DNAm and PE status were observed at both sites in the validation sample, no associations between DNAm and PE status were observed in the independent replication sample.</p><p><strong>Conclusions: </strong>The discovery phase findings for cg16155413/cg21882990 (<i>TRAF3IP2-AS1/TRAF3IP2</i>) were validated with a new platform but were not replicated in an independent sample. Given the differences in participant characteristics between the discovery and replication samples, we cannot rule out important signals for these CpGs. Additional research is warranted for cg16155413/cg21882990, as well as top hits in trimesters 1-2 and significant DMRs that were not examined in the replication phase.</p>","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10101051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9693603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}