Sarah Holmes Watkins, Christian Testa, Jarvis T Chen, Immaculata De Vivo, Andrew J Simpkin, Kate Tilling, Ana V Diez Roux, George Davey Smith, Pamela D Waterman, Matthew Suderman, Caroline Relton, Nancy Krieger
{"title":"Epigenetic clocks and research implications of the lack of data on whom they have been developed: a review of reported and missing sociodemographic characteristics.","authors":"Sarah Holmes Watkins, Christian Testa, Jarvis T Chen, Immaculata De Vivo, Andrew J Simpkin, Kate Tilling, Ana V Diez Roux, George Davey Smith, Pamela D Waterman, Matthew Suderman, Caroline Relton, Nancy Krieger","doi":"10.1093/eep/dvad005","DOIUrl":"10.1093/eep/dvad005","url":null,"abstract":"<p><p>Epigenetic clocks are increasingly being used as a tool to assess the impact of a wide variety of phenotypes and exposures on healthy ageing, with a recent focus on social determinants of health. However, little attention has been paid to the sociodemographic characteristics of participants on whom these clocks have been based. Participant characteristics are important because sociodemographic and socioeconomic factors are known to be associated with both DNA methylation variation and healthy ageing. It is also well known that machine learning algorithms have the potential to exacerbate health inequities through the use of unrepresentative samples - prediction models may underperform in social groups that were poorly represented in the training data used to construct the model. To address this gap in the literature, we conducted a review of the sociodemographic characteristics of the participants whose data were used to construct 13 commonly used epigenetic clocks. We found that although some of the epigenetic clocks were created utilizing data provided by individuals from different ages, sexes/genders, and racialized groups, sociodemographic characteristics are generally poorly reported. Reported information is limited by inadequate conceptualization of the social dimensions and exposure implications of gender and racialized inequality, and socioeconomic data are infrequently reported. It is important for future work to ensure clear reporting of tangible data on the sociodemographic and socioeconomic characteristics of all the participants in the study to ensure that other researchers can make informed judgements about the appropriateness of the model for their study population.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvad005"},"PeriodicalIF":4.8,"publicationDate":"2023-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10547124","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}
Millissia Ben Maamar, Yue Wang, Eric E Nilsson, Daniel Beck, Wei Yan, Michael K Skinner
{"title":"Transgenerational sperm DMRs escape DNA methylation erasure during embryonic development and epigenetic inheritance.","authors":"Millissia Ben Maamar, Yue Wang, Eric E Nilsson, Daniel Beck, Wei Yan, Michael K Skinner","doi":"10.1093/eep/dvad003","DOIUrl":"10.1093/eep/dvad003","url":null,"abstract":"<p><p>Germline transmission of epigenetic information is a critical component of epigenetic inheritance. Previous studies have suggested that an erasure of DNA methylation is required to develop stem cells in the morula embryo. An exception involves imprinted genes that escape this DNA methylation erasure. Transgenerational differential DNA methylation regions (DMRs) have been speculated to be imprinted-like and escape this erasure. The current study was designed to assess if morula embryos escape the erasure of dichlorodiphenyltrichloroethane-induced transgenerational sperm DMR methylation. Observations demonstrate that the majority (98%) of transgenerational sperm DMR sites retain DNA methylation and are not erased, so appearing similar to imprinted-like sites. Interestingly, observations also demonstrate that the majority of low-density CpG genomic sites had a significant increase in DNA methylation in the morula embryo compared to sperm. This is in contrast to the previously observed DNA methylation erasure of higher-density CpG sites. The general erasure of DNA methylation during embryogenesis appears applicable to high-density DNA methylation sites (e.g. CpG islands) but neither to transgenerational DMR methylation sites nor to low-density CpG deserts, which constitute the vast majority of the genome's DNA methylation sites. The role of epigenetics during embryogenesis appears more dynamic than the simple erasure of DNA methylation.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvad003"},"PeriodicalIF":3.8,"publicationDate":"2023-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/78/1a/dvad003.PMC10281242.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9702598","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}
Geetha Venkatesh, Sina Tönges, Katharina Hanna, Yi Long Ng, Rose Whelan, Ranja Andriantsoa, Annika Lingenberg, Suki Roy, Sanjanaa Nagarajan, Steven Fong, Günter Raddatz, Florian Böhl, Frank Lyko
{"title":"Context-dependent DNA methylation signatures in animal livestock.","authors":"Geetha Venkatesh, Sina Tönges, Katharina Hanna, Yi Long Ng, Rose Whelan, Ranja Andriantsoa, Annika Lingenberg, Suki Roy, Sanjanaa Nagarajan, Steven Fong, Günter Raddatz, Florian Böhl, Frank Lyko","doi":"10.1093/eep/dvad001","DOIUrl":"10.1093/eep/dvad001","url":null,"abstract":"<p><p>DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvad001"},"PeriodicalIF":3.8,"publicationDate":"2023-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f3/1f/dvad001.PMC10019019.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145699","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}
Andy Madrid, Reid S Alisch, Elias Rizk, Ligia A Papale, Kirk J Hogan, Bermans J Iskandar
{"title":"Transgenerational epigenetic inheritance of axonal regeneration after spinal cord injury.","authors":"Andy Madrid, Reid S Alisch, Elias Rizk, Ligia A Papale, Kirk J Hogan, Bermans J Iskandar","doi":"10.1093/eep/dvad002","DOIUrl":"10.1093/eep/dvad002","url":null,"abstract":"<p><p>Human epidemiological studies reveal that dietary and environmental alterations influence the health of the offspring and that the effect is not limited to the F1 or F2 generations. Non-Mendelian transgenerational inheritance of traits in response to environmental stimuli has been confirmed in non-mammalian organisms including plants and worms and are shown to be epigenetically mediated. However, transgenerational inheritance beyond the F2 generation remains controversial in mammals. Our lab previously discovered that the treatment of rodents (rats and mice) with folic acid significantly enhances the regeneration of injured axons following spinal cord injury <i>in vivo</i> and <i>in vitro</i>, and the effect is mediated by DNA methylation. The potential heritability of DNA methylation prompted us to investigate the following question: Is the enhanced axonal regeneration phenotype inherited transgenerationally without exposure to folic acid supplementation in the intervening generations? In the present review, we condense our findings showing that a beneficial trait (i.e., enhanced axonal regeneration after spinal cord injury) and accompanying molecular alterations (i.e., DNA methylation), triggered by an environmental exposure (i.e., folic acid supplementation) to F0 animals only, are inherited transgenerationally and beyond the F3 generation.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvad002"},"PeriodicalIF":3.8,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9949995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9464541","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":"Hexavalent chromium-induced epigenetic instability and transposon activation lead to phenotypic variations and tumors in <i>Drosophila</i>.","authors":"Rasesh Y Parikh, Vamsi K Gangaraju","doi":"10.1093/eep/dvac030","DOIUrl":"10.1093/eep/dvac030","url":null,"abstract":"<p><p>Developmental robustness represents the ability of an organism to resist phenotypic variations despite environmental insults and inherent genetic variations. Derailment of developmental robustness leads to phenotypic variations that can get fixed in a population for many generations. Environmental pollution is a significant worldwide problem with detrimental consequences of human development. Understanding the genetic basis for how pollutants affect human development is critical for developing interventional therapies. Here, we report that environmental stress induced by hexavalent chromium, Cr(VI), a potent industrial pollutant, compromises developmental robustness, leading to phenotypic variations in the progeny. These phenotypic variations arise due to epigenetic instability and transposon activation in the somatic tissues of the progeny rather than novel genetic mutations and can be reduced by increasing the dosage of Piwi - a Piwi-interacting RNA-binding protein, in the ovary of the exposed mother. Significantly, the derailment of developmental robustness by Cr(VI) exposure leads to tumors in the progeny, and the predisposition to develop tumors is fixed in the population for at least three generations. Thus, we show for the first time that environmental pollution can derail developmental robustness and predispose the progeny of the exposed population to develop phenotypic variations and tumors.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvac030"},"PeriodicalIF":4.8,"publicationDate":"2022-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9892686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9281336","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}
Jessica Townsend, Camila U Braz, Todd Taylor, Hasan Khatib
{"title":"Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep.","authors":"Jessica Townsend, Camila U Braz, Todd Taylor, Hasan Khatib","doi":"10.1093/eep/dvac029","DOIUrl":"10.1093/eep/dvac029","url":null,"abstract":"<p><p>Environmental effects on gene expression and offspring development can be mediated by epigenetic modifications. It is well established that maternal diet influences DNA methylation patterns and phenotypes in the offspring; however, the epigenetic effects of paternal diet on developing offspring warrants further investigation. Here, we examined how a prepubertal methionine-enriched paternal diet affected sperm DNA methylation and its subsequent effects on embryo gene expression. Three treatment and three control rams were bred to seven ewes, and blastocysts were flushed for RNA extraction. Semen was collected from all rams and submitted for reduced representation bisulfite sequencing analysis. In total, 166 differentially methylated cytosines were identified in the sperm from treatment versus control rams. Nine genes were found to be differentially expressed in embryos produced from treatment versus control rams, and seven differentially methylated cytosines in the sperm were found to be highly correlated with gene expression in the embryos. Our results demonstrate that sperm methylation differences induced by diet may influence fetal programming.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvac029"},"PeriodicalIF":3.8,"publicationDate":"2022-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9885981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10642166","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}
Meghna Rajaprakash, Lorraine T Dean, Meredith Palmore, Sara B Johnson, Joan Kaufman, Daniele M Fallin, Christine Ladd-Acosta
{"title":"DNA methylation signatures as biomarkers of socioeconomic position.","authors":"Meghna Rajaprakash, Lorraine T Dean, Meredith Palmore, Sara B Johnson, Joan Kaufman, Daniele M Fallin, Christine Ladd-Acosta","doi":"10.1093/eep/dvac027","DOIUrl":"10.1093/eep/dvac027","url":null,"abstract":"<p><p>This review article provides a framework for the use of deoxyribonucleic acid (DNA) methylation (DNAm) biomarkers to study the biological embedding of socioeconomic position (SEP) and summarizes the latest developments in the area. It presents the emerging literature showing associations between individual- and neighborhood-level SEP exposures and DNAm across the life course. In contrast to questionnaire-based methods of assessing SEP, we suggest that DNAm biomarkers may offer an accessible metric to study questions about SEP and health outcomes, acting as a personal dosimeter of exposure. However, further work remains in standardizing SEP measures across studies and evaluating consistency across domains, tissue types, and time periods. Meta-analyses of epigenetic associations with SEP are offered as one approach to confirm the replication of DNAm loci across studies. The development of DNAm biomarkers of SEP would provide a method for examining its impact on health outcomes in a more robust way, increasing the rigor of epidemiological studies.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvac027"},"PeriodicalIF":3.8,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9869656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378028","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":"Environmental epigenetics and climate change.","authors":"Michael K Skinner","doi":"10.1093/eep/dvac028","DOIUrl":"10.1093/eep/dvac028","url":null,"abstract":"","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvac028"},"PeriodicalIF":3.8,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9869649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10618752","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}
Yaxu Wang, Jung-Ying Tzeng, Yueyang Huang, Rachel Maguire, Cathrine Hoyo, Terrence K Allen
{"title":"Duration of exposure to epidural anesthesia at delivery, DNA methylation in umbilical cord blood and their association with offspring asthma in Non-Hispanic Black women.","authors":"Yaxu Wang, Jung-Ying Tzeng, Yueyang Huang, Rachel Maguire, Cathrine Hoyo, Terrence K Allen","doi":"10.1093/eep/dvac026","DOIUrl":"10.1093/eep/dvac026","url":null,"abstract":"<p><p>Epidural anesthesia is an effective pain relief modality, widely used for labor analgesia. Childhood asthma is one of the commonest chronic medical illnesses in the USA which places a significant burden on the health-care system. We recently demonstrated a negative association between the duration of epidural anesthesia and the development of childhood asthma; however, the underlying molecular mechanisms still remain unclear. In this study of 127 mother-child pairs comprised of 75 Non-Hispanic Black (NHB) and 52 Non-Hispanic White (NHW) from the Newborn Epigenetic Study, we tested the hypothesis that umbilical cord blood DNA methylation mediates the association between the duration of exposure to epidural anesthesia at delivery and the development of childhood asthma and whether this differed by race/ethnicity. In the mother-child pairs of NHB ancestry, the duration of exposure to epidural anesthesia was associated with a marginally lower risk of asthma (odds ratio = 0.88, 95% confidence interval = 0.76-1.01) for each 1-h increase in exposure to epidural anesthesia. Of the 20 CpGs in the NHB population showing the strongest mediation effect, 50% demonstrated an average mediation proportion of 52%, with directional consistency of direct and indirect effects. These top 20 CpGs mapped to 21 genes enriched for pathways engaged in antigen processing, antigen presentation, protein ubiquitination and regulatory networks related to the Major Histocompatibility Complex (MHC) class I complex and Nuclear Factor Kappa-B (<i>NFkB</i>) complex. Our findings suggest that DNA methylation in immune-related pathways contributes to the effects of the duration of exposure to epidural anesthesia on childhood asthma risk in NHB offspring.</p>","PeriodicalId":11774,"journal":{"name":"Environmental Epigenetics","volume":"9 1","pages":"dvac026"},"PeriodicalIF":3.8,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/56/4b/dvac026.PMC9854336.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10618749","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}