Epigenetics communications最新文献

{"title":"Visions, expectations, and reservations in epigenetic editing: towards responsible innovation.","authors":"Sophie van Baalen, Thomas Verra, Phil Macnaghten, Eline Bunnik, Michelle Gjl Habets","doi":"10.1186/s43682-026-00047-5","DOIUrl":"10.1186/s43682-026-00047-5","url":null,"abstract":"<p><p>In Science and Technology Studies (STS), scholars highlight the guiding role of expectations, promises, visions, and assumptions of scientists, shaping the development of research fields and technologies. Making these expectations and visions explicit, opens them to reflection and adjustment by diverse stakeholders, fostering more responsible and inclusive technological innovation. In this paper, we study the visions and expectations of scientists in academia and in industry (<i>n</i> = 19) in the field of epigenetics and epigenetic editing. Epigenetic editing is a technique that is used to modify the epigenome to gain regulatory control of gene expression. In the future, this could lead to the development of new biomedicines and biotechnologies to improve crops. We found that respondents broadly endorsed a vision of epigenetic editing as being milder and safer than genetic editing, and therefore more acceptable to the public, making it easier to embed epigenetic applications in society. However, respondents simultaneously questioned some of the underlying assumptions of this dominantly held vision and consequently expressed reservations. Although a limited number of studies have shown that epigenetic edits can be reversible and stable, uncertainty exists whether this is generalizable. Reservations are also linked to the possibility of heritability of edits, and to the level of complexity of (epi)genetic networks. In general, respondents were uncertain about the readiness of the technology to be currently implemented in the medical or agricultural sector. This contrasts with the current move of some companies to initiate clinical trials. To allow for more inclusive decision-making and co-shaping the research field and future applications, it is important to improve reflexivity among researchers and to enable public engagement. Having made these visions explicit, they become a topic for scientists, policymakers, and the public to reflect on and adapt or adjust, allowing for the co-creation of technological innovation.</p>","PeriodicalId":72947,"journal":{"name":"Epigenetics communications","volume":"6 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13099719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790947","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":"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}