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Schaffner SL, Casazza W, Artaud F, Konwar C, Merrill SM, Domenighetti C, Schulze-Hentrich JM, Lesage S, Brice A, Corvol JC, Mostafavi S, Dennis JK, Elbaz A, Kobor MS. Genetic variation and pesticide exposure influence blood DNA methylation signatures in females with early-stage Parkinson's disease. NPJ Parkinsons Dis 2024; 10:98. [PMID: 38714693 PMCID: PMC11076573 DOI: 10.1038/s41531-024-00704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 04/05/2024] [Indexed: 05/10/2024] Open
Abstract
Although sex, genetics, and exposures can individually influence risk for sporadic Parkinson's disease (PD), the joint contributions of these factors to the epigenetic etiology of PD have not been comprehensively assessed. Here, we profiled sex-stratified genome-wide blood DNAm patterns, SNP genotype, and pesticide exposure in agricultural workers (71 early-stage PD cases, 147 controls) and explored replication in three independent samples of varying demographics (n = 218, 222, and 872). Using a region-based approach, we found more associations of blood DNAm with PD in females (69 regions) than in males (2 regions, Δβadj| ≥0.03, padj ≤ 0.05). For 48 regions in females, models including genotype or genotype and pesticide exposure substantially improved in explaining interindividual variation in DNAm (padj ≤ 0.05), and accounting for these variables decreased the estimated effect of PD on DNAm. The results suggested that genotype, and to a lesser degree, genotype-exposure interactions contributed to variation in PD-associated DNAm. Our findings should be further explored in larger study populations and in experimental systems, preferably with precise measures of exposure.
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Affiliation(s)
- S L Schaffner
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - W Casazza
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - F Artaud
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - C Konwar
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - S M Merrill
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - C Domenighetti
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - J M Schulze-Hentrich
- Department of Genetics/Epigenetics, Faculty NT, Saarland University, 66041, Saarbrücken, Germany
| | - S Lesage
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - A Brice
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - J C Corvol
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
- Sorbonne University, Assistance Publique Hôpitaux de Paris, Paris Brain Insitute - ICM, Inserm, CNRS, Department of Neurology and CIC Neurosciences, Pitié-Salpêtrière Hospital, Paris, France
| | - S Mostafavi
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
- Paul Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - J K Dennis
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - A Elbaz
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - M S Kobor
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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2
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Song B, Yu J, Li X, Li J, Fan J, Liu H, Wei W, Zhang L, Gu K, Liu D, Zhao K, Wu J. Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement. Genome Biol 2024; 25:87. [PMID: 38581061 PMCID: PMC10996114 DOI: 10.1186/s13059-024-03220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. RESULTS Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. CONCLUSIONS Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jinshan Yu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Hainan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weilin Wei
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Lingchao Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dongliang Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China.
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3
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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4
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early-life adversity are exposure-dependent in wild baboons. Proc Natl Acad Sci U S A 2024; 121:e2309469121. [PMID: 38442181 PMCID: PMC10945818 DOI: 10.1073/pnas.2309469121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
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Affiliation(s)
- Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Amanda J. Lea
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | | | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Mercy Y. Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi00502, Kenya
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig04103, Germany
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5
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Fong WJ, Tan HM, Garg R, Teh AL, Pan H, Gupta V, Krishna B, Chen ZH, Purwanto NY, Yap F, Tan KH, Chan KYJ, Chan SY, Goh N, Rane N, Tan ESE, Jiang Y, Han M, Meaney M, Wang D, Keppo J, Tan GCY. Comparing feature selection and machine learning approaches for predicting CYP2D6 methylation from genetic variation. Front Neuroinform 2024; 17:1244336. [PMID: 38449836 PMCID: PMC10915285 DOI: 10.3389/fninf.2023.1244336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/18/2023] [Indexed: 03/08/2024] Open
Abstract
Introduction Pharmacogenetics currently supports clinical decision-making on the basis of a limited number of variants in a few genes and may benefit paediatric prescribing where there is a need for more precise dosing. Integrating genomic information such as methylation into pharmacogenetic models holds the potential to improve their accuracy and consequently prescribing decisions. Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene conventionally associated with the metabolism of commonly used drugs and endogenous substrates. We thus sought to predict epigenetic loci from single nucleotide polymorphisms (SNPs) related to CYP2D6 in children from the GUSTO cohort. Methods Buffy coat DNA methylation was quantified using the Illumina Infinium Methylation EPIC beadchip. CpG sites associated with CYP2D6 were used as outcome variables in Linear Regression, Elastic Net and XGBoost models. We compared feature selection of SNPs from GWAS mQTLs, GTEx eQTLs and SNPs within 2 MB of the CYP2D6 gene and the impact of adding demographic data. The samples were split into training (75%) sets and test (25%) sets for validation. In Elastic Net model and XGBoost models, optimal hyperparameter search was done using 10-fold cross validation. Root Mean Square Error and R-squared values were obtained to investigate each models' performance. When GWAS was performed to determine SNPs associated with CpG sites, a total of 15 SNPs were identified where several SNPs appeared to influence multiple CpG sites. Results Overall, Elastic Net models of genetic features appeared to perform marginally better than heritability estimates and substantially better than Linear Regression and XGBoost models. The addition of nongenetic features appeared to improve performance for some but not all feature sets and probes. The best feature set and Machine Learning (ML) approach differed substantially between CpG sites and a number of top variables were identified for each model. Discussion The development of SNP-based prediction models for CYP2D6 CpG methylation in Singaporean children of varying ethnicities in this study has clinical application. With further validation, they may add to the set of tools available to improve precision medicine and pharmacogenetics-based dosing.
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Affiliation(s)
- Wei Jing Fong
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Hong Ming Tan
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Rishabh Garg
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hong Pan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Varsha Gupta
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Bernadus Krishna
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Zou Hui Chen
- Computational Biology, National University of Singapore, Singapore, Singapore
| | | | - Fabian Yap
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
| | - Kok Yen Jerry Chan
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- National University Hospital, Singapore, Singapore
| | | | - Nikita Rane
- Institute of Mental Health,Singapore, Singapore
| | | | | | - Mei Han
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Michael Meaney
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dennis Wang
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jussi Keppo
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Geoffrey Chern-Yee Tan
- Computational Biology, National University of Singapore, Singapore, Singapore
- Institute of Mental Health,Singapore, Singapore
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6
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Díez-Villanueva A, Martín B, Moratalla-Navarro F, Morón-Duran FD, Galván-Femenía I, Obón-Santacana M, Carreras A, de Cid R, Peinado MA, Moreno V. Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios. Sci Rep 2023; 13:21266. [PMID: 38042866 PMCID: PMC10693549 DOI: 10.1038/s41598-023-48517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Genome-wide association studies have identified thousands of loci associated with common diseases and traits. However, a large fraction of heritability remains unexplained. Epigenetic modifications, such as the observed in DNA methylation have been proposed as a mechanism of intergenerational inheritance. To investigate the potential contribution of DNA methylation to the missing heritability, we analysed the methylomes of four healthy trios (two parents and one offspring) using whole genome bisulphite sequencing. Of the 1.5 million CpGs (19%) with over 20% variability between parents in at least one family and compatible with a Mendelian inheritance pattern, only 3488 CpGs (0.2%) lacked correlation with any SNP in the genome, marking them as potential sites for intergenerational epigenetic inheritance. These markers were distributed genome-wide, with some preference to be located in promoters. They displayed a bimodal distribution, being either fully methylated or unmethylated, and were often found at the boundaries of genomic regions with high/low GC content. This analysis provides a starting point for future investigations into the missing heritability of simple and complex traits.
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Affiliation(s)
- Anna Díez-Villanueva
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Berta Martín
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Ferran Moratalla-Navarro
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Francisco D Morón-Duran
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Iván Galván-Femenía
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Anna Carreras
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Miguel A Peinado
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain.
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain.
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7
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Zhang S, Shi K, Lyu N, Zhang Y, Liang G, Zhang W, Wang X, Wen H, Wen L, Ma H, Wang J, Yu X, Guan L. Genome-wide DNA methylation analysis in families with multiple individuals diagnosed with schizophrenia and intellectual disability. World J Biol Psychiatry 2023; 24:741-753. [PMID: 37017099 DOI: 10.1080/15622975.2023.2198595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
OBJECTIVES Schizophrenia (SZ) and intellectual disability (ID) are both included in the continuum of neurodevelopmental disorders (NDDs). DNA methylation is known to be important in the occurrence of NDDs. The family study is conducive to eliminate the effects of relative epigenetic backgrounds, and to screen for differentially methylated positions (DMPs) and regions (DMRs) that are truly associated with NDDs. METHODS Four monozygotic twin families were recruited, and both twin individuals suffered from NDDs (either SZ, ID, or SZ plus ID). Genome-wide methylation analysis was performed in all samples and each family. DMPs and DMRs between NDD patients and unaffected individuals were identified. Functional and pathway enrichment analyses were performed on the annotated genes. RESULTS Two significant DMPs annotated to CYP2E1 were found in all samples. In Family One, 1476 DMPs mapped to 880 genes, and 162 DMRs overlapping with 153 unique genes were recognised. Our results suggested that the altered methylation levels of FYN, STAT3, RAC1, and NR4A2 were associated with the development of SZ and ID. Neurodevelopment and the immune system may participate in the occurrence of SZ and ID. CONCLUSIONS Our findings suggested that DNA methylation participated in the development of NDDs by affecting neurodevelopment and the immune system.
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Affiliation(s)
- Shengmin Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Kaiyu Shi
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nan Lyu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Beijing Anding Hospital, Beijing Key Laboratory of Mental Disorders, The National Clinical Research Centre for Mental Disorders, The Advanced Innovation Centre for Human Brain Protection, Capital Medical University, Beijing, China
| | - Yunshu Zhang
- The Sixth People's Hospital of Hebei Province, Hebei Mental Health Centre, Baoding, Hebei, China
| | | | - Wufang Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xijin Wang
- The First Psychiatric Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hong Wen
- The Third Hospital of Mianyang, Mianyang, Sichuan, China
| | - Liping Wen
- Zigong Mental Health Centre, Zigong, Sichuan, China
| | - Hong Ma
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jijun Wang
- Shanghai Mental Health Centre, Shanghai Jiaotong University School of Medicine, Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xin Yu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Lili Guan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
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8
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Cheng Y, Justice A, Wang Z, Li B, Hancock DB, Johnson EO, Xu K. Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits. BMC Genomics 2023; 24:556. [PMID: 37730558 PMCID: PMC10510240 DOI: 10.1186/s12864-023-09661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Cocaine use (CU) is associated with psychiatric and medical diseases. Little is known about the mechanisms of CU-related comorbidities. Findings from preclinical and clinical studies have suggested that CU is associated with aberrant DNA methylation (DNAm) that may be influenced by genetic variants [i.e., methylation quantitative trait loci (meQTLs)]. In this study, we mapped cis-meQTLs for CU-associated DNAm sites (CpGs) in an HIV-positive cohort (Ntotal = 811) and extended the meQTLs to multiple traits. RESULTS We conducted cis-meQTL analysis for 224 candidate CpGs selected for their association with CU in blood. We identified 7,101 significant meQTLs [false discovery rate (FDR) < 0.05], which mostly mapped to genes involved in immunological functions and were enriched in immune pathways. We followed up the meQTLs using phenome-wide association study and trait enrichment analyses, which revealed 9 significant traits. We tested for causal effects of CU on these 9 traits using Mendelian Randomization and found evidence that CU plays a causal role in increasing hypertension (p-value = 2.35E-08) and decreasing heel bone mineral density (p-value = 1.92E-19). CONCLUSIONS These findings suggest that genetic variants for CU-associated DNAm have pleiotropic effects on other relevant traits and provide new insights into the causal relationships between cocaine use and these complex traits.
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Affiliation(s)
- Youshu Cheng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Amy Justice
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA.
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
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9
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Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. Commun Biol 2023; 6:780. [PMID: 37587191 PMCID: PMC10432557 DOI: 10.1038/s42003-023-05070-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023] Open
Abstract
Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.
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Affiliation(s)
- Sally Mortlock
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Camran Nezhat
- Stanford University Medical Center, Palo Alto, CA, USA
- University of California San Francisco, San Francisco, CA, USA
- Camran Nezhat Institute, Center for Special Minimally Invasive and Robotic Surgery, Woodside, CA, USA
| | - Allison F Vitonis
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shan V Andrews
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Parker Grosjean
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew W Horne
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Alison Jacoby
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeannette Lager
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Opoku-Anane
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kim Chi Vo
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Evelina Manvelyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sushmita Sen
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhanna Ghukasyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Frances Collins
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Xavier Santamaria
- Carlos Simon Foundation, Health Research Institute, Valencia, Spain
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Philippa Saunders
- Centre for Inflammation Research, Institute for Regeneration and Repair University of Edinburgh, Edinburgh, UK
| | - Kord Kober
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Allan F McRae
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
| | - Júlia Vallvé-Juanico
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Christian Becker
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter A W Rogers
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Melbourne, Australia
| | - Juan C Irwin
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Krina Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Stacey Missmer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Division of Neonatology, University of California San Francisco, San Francisco, CA, USA
| | - Linda Giudice
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA.
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10
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Villicaña S, Castillo-Fernandez J, Hannon E, Christiansen C, Tsai PC, Maddock J, Kuh D, Suderman M, Power C, Relton C, Ploubidis G, Wong A, Hardy R, Goodman A, Ong KK, Bell JT. Genetic impacts on DNA methylation help elucidate regulatory genomic processes. Genome Biol 2023; 24:176. [PMID: 37525248 PMCID: PMC10391992 DOI: 10.1186/s13059-023-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. RESULTS We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). CONCLUSIONS Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk .
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Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | | | | | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jane Maddock
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - George Ploubidis
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Rebecca Hardy
- School of Sport, Exercise & Health Sciences, Loughborough University, Loughborough, UK
- UCL Social Research Institute, University College London, London, UK
| | - Alissa Goodman
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Ken K Ong
- MRC Epidemiology Unit and Department of Paediatrics, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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11
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Gorzkiewicz M, Łoś-Rycharska E, Gawryjołek J, Gołębiewski M, Krogulska A, Grzybowski T. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between Polish infants with the food allergy and/or atopic dermatitis and without the disease. Front Immunol 2023; 14:1209190. [PMID: 37520545 PMCID: PMC10373304 DOI: 10.3389/fimmu.2023.1209190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Objectives Epigenetic dynamics has been indicated to play a role in allergy development. The environmental stimuli have been shown to influence the methylation processes. This study investigated the differences in CpGs methylation rate of immune-attached genes between healthy and allergic infants. The research was aimed at finding evidence for the impact of environmental factors on methylation-based regulation of immunological processes in early childhood. Methods The analysis of methylation level of CpGs in the IL4, IL5, IL10, IFNG and FOXP3 genes was performed using high resolution melt real time PCR technology. DNA was isolated from whole blood of Polish healthy and allergic infants, with food allergy and/or atopic dermatitis, aged under six months. Results The significantly lower methylation level of FOXP3 among allergic infants compared to healthy ones was reported. Additional differences in methylation rates were found, when combining with environmental factors. In different studied groups, negative correlations between age and the IL10 and FOXP3 methylation were detected, and positive - in the case of IL4. Among infants with different allergy symptoms, the decrease in methylation level of IFNG, IL10, IL4 and FOXP3 associated with passive smoke exposure was observed. Complications during pregnancy were linked to different pattern of the IFNG, IL5, IL4 and IL10 methylation depending on allergy status. The IFNG and IL5 methylation rates were higher among exclusively breastfed infants with atopic dermatitis compared to the non-breastfed. A decrease in the IFNG methylation was noted among allergic patients fed exclusively with milk formula. In different study groups, a negative correlation between IFNG, IL5 methylation and maternal BMI or IL5 methylation and weight was noted. Some positive correlations between methylation rate of IL10 and child's weight were found. A higher methylation of IL4 was positively correlated with the number of family members with allergy. Conclusion The FOXP3 methylation in allergic infants was lower than in the healthy ones. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between the studied groups. The results offer insights into epigenetic regulation of immunological response in early childhood.
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Affiliation(s)
- Marta Gorzkiewicz
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Ewa Łoś-Rycharska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Julia Gawryjołek
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Aneta Krogulska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
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12
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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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13
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Chundru VK, Marioni RE, Prendergast JGD, Lin T, Beveridge AJ, Martin NG, Montgomery GW, Hume DA, Deary IJ, Visscher PM, Wray NR, McRae AF. Rare genetic variants underlie outlying levels of DNA methylation and gene-expression. Hum Mol Genet 2023; 32:1912-1921. [PMID: 36790133 PMCID: PMC10196672 DOI: 10.1093/hmg/ddad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on DNA methylation (DNAm) as effect sizes are expected to be larger for molecular traits compared with complex traits. Here, we investigate DNAm in healthy ageing populations-the Lothian Birth Cohorts of 1921 and 1936-and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic single nucleotide polymorphisms (SNPs) within 1 kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels toward the tails of the population distribution. This study demonstrates the role of rare SNPs in the phenotypic variation of DNAm and the effect of extreme levels of DNAm on gene expression.
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Affiliation(s)
- V Kartik Chundru
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan J Beveridge
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, The University of Glasgow, Glasgow G61 1QH, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David A Hume
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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14
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Horsthemke B, Bird A. Loss of CpG island immunity to DNA methylation induced by mutation. Epigenetics Chromatin 2023; 16:17. [PMID: 37170330 PMCID: PMC10173581 DOI: 10.1186/s13072-023-00488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
The inheritance of acquired traits in mammals is a highly controversial topic in biology. Recently, Takahashi et al. (Cell 186:715-731, 2023) have reported that insertion of CpG-free DNA into a CpG island (CGI) can induce DNA methylation of the CGI and that this aberrant methylation pattern can be transmitted across generations, even after removal of the foreign DNA. These results were interpreted as evidence for transgenerational inheritance of acquired DNA methylation patterns. Here, we discuss several interpretational issues raised by this study and consider alternative explanations.
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Affiliation(s)
- Bernhard Horsthemke
- Institut Für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122, Essen, Germany.
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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15
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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16
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Weihs A, Chaker L, Martin TC, Braun KV, Campbell PJ, Cox SR, Fornage M, Gieger C, Grabe HJ, Grallert H, Harris SE, Kühnel B, Marioni RE, Martin NG, McCartney DL, McRae AF, Meisinger C, van Meurs JB, Nano J, Nauck M, Peters A, Prokisch H, Roden M, Selvin E, Beekman M, van Heemst D, Slagboom EP, Swenson BR, Tin A, Tsai PC, Uitterlinden A, Visser WE, Völzke H, Waldenberger M, Walsh JP, Köttgen A, Wilson SG, Peeters RP, Bell JT, Medici M, Teumer A. Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9. Thyroid 2023; 33:301-311. [PMID: 36719767 PMCID: PMC10024591 DOI: 10.1089/thy.2022.0373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.
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Affiliation(s)
- Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Layal Chaker
- Erasmus MC Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus MC Academic Center for Thyroid Diseases, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tiphaine C. Martin
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Twin Research and Genetic Epidemiology, St Thomas' Hospital Campus, King's College London, London, United Kingdom
| | - Kim V.E. Braun
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Purdey J. Campbell
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology; Institute of Genetics and Cancer; University of Edinburgh, Edinburgh, United Kingdom
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, Houston, Texas, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Site Rostock, Greifswald, Germany
| | - Harald Grallert
- Research Unit Molecular Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology; Institute of Genetics and Cancer; University of Edinburgh, Edinburgh, United Kingdom
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer; University of Edinburgh, Edinburgh, United Kingdom
| | | | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer; University of Edinburgh, Edinburgh, United Kingdom
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Joyce B.J. van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Orthopeadics and Sports Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jana Nano
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute for Medical Informatics, Biometrics and Epidemiology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Medical Informatics, Biometrics and Epidemiology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Computational Health Center; Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Medical Faculty; Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty; Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Diana van Heemst
- Section of Gerontology and Geriatrics, Department of Internal Medicine; Leiden University Medical Center, Leiden, Netherlands
| | - Eline P. Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Brenton R. Swenson
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, St Thomas' Hospital Campus, King's College London, London, United Kingdom
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - W. Edward Visser
- Erasmus MC Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henry Völzke
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine; University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Epidemiology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - John P. Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
- Medical School, University of Western Australia, Crawley, Australia
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
| | - Scott G. Wilson
- Department of Twin Research and Genetic Epidemiology, St Thomas' Hospital Campus, King's College London, London, United Kingdom
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Robin P. Peeters
- Erasmus MC Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St Thomas' Hospital Campus, King's College London, London, United Kingdom
| | - Marco Medici
- Erasmus MC Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexander Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine; University Medicine Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
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17
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Ricci F, Leggat W, Page CE, Ainsworth TD. Coral growth anomalies, neoplasms, and tumors in the Anthropocene. Trends Microbiol 2022; 30:1160-1173. [PMID: 35718641 DOI: 10.1016/j.tim.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/13/2023]
Abstract
One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.
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Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia.
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan 2309, NSW, Australia
| | - Charlotte E Page
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
| | - Tracy D Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
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18
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Dapas M, Dunaif A. Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification. Endocr Rev 2022; 43:927-965. [PMID: 35026001 PMCID: PMC9695127 DOI: 10.1210/endrev/bnac001] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/16/2023]
Abstract
Polycystic ovary syndrome (PCOS) is among the most common disorders in women of reproductive age, affecting up to 15% worldwide, depending on the diagnostic criteria. PCOS is characterized by a constellation of interrelated reproductive abnormalities, including disordered gonadotropin secretion, increased androgen production, chronic anovulation, and polycystic ovarian morphology. It is frequently associated with insulin resistance and obesity. These reproductive and metabolic derangements cause major morbidities across the lifespan, including anovulatory infertility and type 2 diabetes (T2D). Despite decades of investigative effort, the etiology of PCOS remains unknown. Familial clustering of PCOS cases has indicated a genetic contribution to PCOS. There are rare Mendelian forms of PCOS associated with extreme phenotypes, but PCOS typically follows a non-Mendelian pattern of inheritance consistent with a complex genetic architecture, analogous to T2D and obesity, that reflects the interaction of susceptibility genes and environmental factors. Genomic studies of PCOS have provided important insights into disease pathways and have indicated that current diagnostic criteria do not capture underlying differences in biology associated with different forms of PCOS. We provide a state-of-the-science review of genetic analyses of PCOS, including an overview of genomic methodologies aimed at a general audience of non-geneticists and clinicians. Applications in PCOS will be discussed, including strengths and limitations of each study. The contributions of environmental factors, including developmental origins, will be reviewed. Insights into the pathogenesis and genetic architecture of PCOS will be summarized. Future directions for PCOS genetic studies will be outlined.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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19
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Verdikt R, Armstrong AA, Allard P. Transgenerational inheritance and its modulation by environmental cues. Curr Top Dev Biol 2022; 152:31-76. [PMID: 36707214 PMCID: PMC9940302 DOI: 10.1016/bs.ctdb.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The epigenome plays an important role in shaping phenotypes. However, whether the environment can alter an organism's phenotype across several generations through epigenetic remodeling in the germline is still a highly debated topic. In this chapter, we briefly review the mechanisms of epigenetic inheritance and their connection with germline development before highlighting specific developmental windows of susceptibility to environmental cues. We further discuss the evidence of transgenerational inheritance to a range of different environmental cues, both epidemiological in humans and experimental in rodent models. Doing so, we pinpoint the current challenges in demonstrating transgenerational inheritance to environmental cues and offer insight in how recent technological advances may help deciphering the epigenetic mechanisms at play. Together, we draw a detailed picture of how our environment can influence our epigenomes, ultimately reshaping our phenotypes, in an extended theory of inheritance.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States.
| | - Abigail A Armstrong
- Department of Obstetrics/Gynecology and Division of Reproductive Endocrinology and Infertility, University of California, Los Angeles, CA, United States
| | - Patrick Allard
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States.
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20
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Xu J, Xia X, Li Q, Dou Y, Suo X, Sun Z, Liu N, Han Y, Sun X, He Y, Qin W, Zhang S, Banaschewski T, Flor H, Grigis A, Gowland P, Heinz A, Brühl R, Martinot JL, Artiges E, Nees F, Paus T, Poustka L, Hohmann S, Walter H, Sham PC, Schumann G, Wu X, Li MJ, Yu C. A causal association of ANKRD37 with human hippocampal volume. Mol Psychiatry 2022; 27:4432-4445. [PMID: 36195640 DOI: 10.1038/s41380-022-01800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022]
Abstract
Human hippocampal volume has been separately associated with single nucleotide polymorphisms (SNPs), DNA methylation and gene expression, but their causal relationships remain largely unknown. Here, we aimed at identifying the causal relationships of SNPs, DNA methylation, and gene expression that are associated with hippocampal volume by integrating cross-omics analyses with genome editing, overexpression and causality inference. Based on structural neuroimaging data and blood-derived genome, transcriptome and methylome data, we prioritized a possibly causal association across multiple molecular phenotypes: rs1053218 mutation leads to cg26741686 hypermethylation, thus leads to overactivation of the associated ANKRD37 gene expression in blood, a gene involving hypoxia, which may result in the reduction of human hippocampal volume. The possibly causal relationships from rs1053218 to cg26741686 methylation to ANKRD37 expression obtained from peripheral blood were replicated in human hippocampal tissue. To confirm causality, we performed CRISPR-based genome and epigenome-editing of rs1053218 homologous alleles and cg26741686 methylation in mouse neural stem cell differentiation models, and overexpressed ANKRD37 in mouse hippocampus. These in-vitro and in-vivo experiments confirmed that rs1053218 mutation caused cg26741686 hypermethylation and ANKRD37 overexpression, and cg26741686 hypermethylation favored ANKRD37 overexpression, and ANKRD37 overexpression reduced hippocampal volume. The pairwise relationships of rs1053218 with hippocampal volume, rs1053218 with cg26741686 methylation, cg26741686 methylation with ANKRD37 expression, and ANKRD37 expression with hippocampal volume could be replicated in an independent healthy young (n = 443) dataset and observed in elderly people (n = 194), and were more significant in patients with late-onset Alzheimer's disease (n = 76). This study revealed a novel causal molecular association mechanism of ANKRD37 with human hippocampal volume, which may facilitate the design of prevention and treatment strategies for hippocampal impairment.
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Affiliation(s)
- Jiayuan Xu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Xianyou Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, PR China
| | - Qiaojun Li
- College of Information Engineering, Tianjin University of Commerce, Tianjin, 300052, PR China
| | - Yan Dou
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Xinjun Suo
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Zuhao Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Nana Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Yating Han
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, PR China
| | - Xiaodi Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Yukun He
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, PR China
| | - Wen Qin
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China
| | - Shijie Zhang
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, PR China
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159, Mannheim, Germany
| | - Herta Flor
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, 68131, Mannheim, Germany
| | - Antoine Grigis
- NeuroSpin, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Penny Gowland
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, UK
| | - Andreas Heinz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charitéplatz 1, Berlin, Germany
| | - Rüdiger Brühl
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2 - 12, Berlin, Germany
| | - Jean-Luc Martinot
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale, INSERM U1299 "Developmental trajectories & psychiatry"; Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
| | - Eric Artiges
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale, INSERM U1299 "Developmental trajectories & psychiatry"; Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli; Gif-sur-Yvette; and Etablissement Public de Santé (EPS) Barthélemy Durand, 91700, Sainte-Geneviève-des-Bois, France
| | - Frauke Nees
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159, Mannheim, Germany
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, Germany
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - Tomáš Paus
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital and Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, M6A 2E1, Canada
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Centre Göttingen, von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - Sarah Hohmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159, Mannheim, Germany
| | - Henrik Walter
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charitéplatz 1, Berlin, Germany
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, 999077, P.R. China
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence 20 (ISTBI), Fudan University, Shanghai, P.R. China
- PONS Centre, Department of Psychiatry and Psychotherapy, CCM, Charite Universitaetsmedizin Berlin, Berlin, Germany
| | - Xudong Wu
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, PR China.
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, PR China.
| | - Mulin Jun Li
- Department of Pharmacology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, PR China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Chunshui Yu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, PR China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, PR China.
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21
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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22
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Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. EPIGENOMES 2022; 6:epigenomes6040031. [PMID: 36278677 PMCID: PMC9589984 DOI: 10.3390/epigenomes6040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.
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23
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Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
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Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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24
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Inaba Y, Iwamoto S, Nakayama K. Genome-wide DNA methylation status of Mongolians exhibits signs of cellular stress response related to their nomadic lifestyle. J Physiol Anthropol 2022; 41:30. [PMID: 35986394 PMCID: PMC9388360 DOI: 10.1186/s40101-022-00305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetics is crucial for connecting environmental stresses with physiological responses in humans. Mongolia, where nomadic livestock pastoralism has been the primal livelihood, has a higher prevalence of various chronic diseases than the surrounding East Asian regions, which are more suitable for crop farming. The genes related to dietary stress and pathogenesis of related disorders may have varying epigenetic statuses among the human populations with diverse dietary cultures. Hence, to understand such epigenetic differences, we conducted a comparative analysis of genome-wide DNA methylation of Mongolians and crop-farming East Asians. Methods Genome-wide DNA methylation status of peripheral blood cells (PBCs) from 23 Mongolian adults and 24 Thai adults was determined using the Infinium Human Methylation 450K arrays and analyzed in combination with previously published 450K data of 20 Japanese and 8 Chinese adults. CpG sites/regions differentially methylated between Mongolians and crop-farming East Asians were detected using a linear model adjusted for sex, age, ethnicity, and immune cell heterogeneity on RnBeads software. Results Of the quality-controlled 389,454 autosomal CpG sites, 223 CpG sites were significantly differentially methylated among Mongolians and the four crop farming East Asian populations (false discovery rate < 0.05). Analyses focused on gene promoter regions revealed that PM20D1 (peptidase M20 domain containing 1), which is involved in mitochondrial uncoupling and various processes, including cellular protection from reactive oxygen species (ROS) and thermogenesis, was the top differentially methylated gene. Moreover, gene ontology enrichment analysis revealed that biological processes related to ROS metabolism were overrepresented among the top 1% differentially methylated genes. The promoter regions of these genes were generally hypermethylated in Mongolians, suggesting that the metabolic pathway detoxifying ROS might be globally suppressed in Mongolians, resulting in the high susceptibility of this population to various chronic diseases. Conclusions This study showed a significantly diverse DNA methylation status among Mongolians and crop-farming East Asians. Further, we found an association between the differentially methylated genes and various metabolic and neurodegenerative diseases. Knowledge of the epigenetic regulators might help in proper understanding, treatment, and control of such disorders, and physiological adaptation in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s40101-022-00305-0.
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25
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Silk T, Dipnall L, Wong YT, Craig JM. Epigenetics and ADHD. Curr Top Behav Neurosci 2022; 57:269-289. [PMID: 35505060 DOI: 10.1007/7854_2022_339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
There is robust evidence of genetic susceptibility to Attention-Deficit Hyperactivity Disorder (ADHD); however, there still remains significant variability that is not attributable to genetic factors. The emerging field of epigenetics is beginning to reveal how genotypic expression can be mediated by an array of variables including external environmental exposure, inter-individual developmental variation, and by the genome itself. Epigenetic modification plays a central role in neurobiological and developmental processes, and disturbances to these processes can have implications for a range of mental health problems. Although the field is still in its early days, this chapter will discuss the current standing of epigenetic research into ADHD. Firstly, key relevant epigenetic processes will be discussed. This will be followed by an overview of the key findings to date investigating the role of epigenetics in ADHD. Human studies have included the theory-driven approach of candidate-gene studies (CGS), as well as the increasingly popular exploratory approach of epigenome-wide association studies (EWAS). Overall, the findings are heterogeneous. However, it is possible that with more longitudinal studies and better characterised cohorts, both predictive and protective links between epigenetic processes and ADHD will be revealed.
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Affiliation(s)
- Timothy Silk
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Lillian Dipnall
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia
| | - Yen Ting Wong
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute, Parkville, VIC, Australia.,Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
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26
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Ribeiro AMF, Sanglard LP, Wijesena HR, Ciobanu DC, Horvath S, Spangler ML. DNA methylation profile in beef cattle is influenced by additive genetics and age. Sci Rep 2022; 12:12016. [PMID: 35835812 PMCID: PMC9283455 DOI: 10.1038/s41598-022-16350-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/08/2022] [Indexed: 11/15/2022] Open
Abstract
DNA methylation (DNAm) has been considered a promising indicator of biological age in mammals and could be useful to increase the accuracy of phenotypic prediction in livestock. The objectives of this study were to estimate the heritability and age effects of site-specific DNAm (DNAm level) and cumulative DNAm across all sites (DNAm load) in beef cattle. Blood samples were collected from cows ranging from 217 to 3,192 days (0.6 to 8.7 years) of age (n = 136). All animals were genotyped, and DNAm was obtained using the Infinium array HorvathMammalMethylChip40. Genetic parameters for DNAm were obtained from an animal model based on the genomic relationship matrix, including the fixed effects of age and breed composition. Heritability estimates of DNAm levels ranged from 0.18 to 0.72, with a similar average across all regions and chromosomes. Heritability estimate of DNAm load was 0.45. The average age effect on DNAm level varied among genomic regions. The DNAm level across the genome increased with age in the promoter and 5′ UTR and decreased in the exonic, intronic, 3′ UTR, and intergenic regions. In addition, DNAm level increased with age in regions enriched in CpG and decreased in regions deficient in CpG. Results suggest DNAm profiles are influenced by both genetics and the environmental effect of age in beef cattle.
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Affiliation(s)
| | - Leticia P Sanglard
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA
| | - Hiruni R Wijesena
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA
| | - Daniel C Ciobanu
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. .,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Matthew L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA.
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27
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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28
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Marzilli E, Cerniglia L, Tambelli R, Cimino S. Children’s ADHD and Dysregulation Problems, DAT1 Genotype and Methylation, and their Interplay with Family Environment. CHILD & YOUTH CARE FORUM 2022. [DOI: 10.1007/s10566-022-09687-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Abstract
Background
International literature has underlined the complex interplay between genetic and environmental variables in shaping children’s emotional-behavioral functioning.
Objective
This study aimed to explore the dynamic relationship between children’s Dopamine Transporter (DAT1) genotype and methylation, and maternal and paternal affective environment, on children’s Attention Deficit Hyperactivity Disorder (ADHD) problems and dysregulation problems.
Method
In a community sample of 76 families with school-aged children, we assessed children’s DAT1 genotype and methylation, their own ADHD problems and dysregulation profile (CBCL 6–18 DP), and maternal and paternal psychopathological risk, parenting stress, and marital adjustment. Hierarchical regressions were carried out to verify the possible moderation of children’s genotype on the relationship between children’s methylation and psychopathological risk, parental environment and children’s methylation, and parental environment and children’s psychopathological risk.
Results
The levels of methylation at M1 CpG significantly predicted ADHD problems among children with 10/10 genotype, whereas high levels of methylation at M6 CpG predicted low ADHD problems for children with 9/x genotype. High levels of methylation at M3 CpG were associated with high scores of CBCL DP. DAT1 genotype moderated the relationship between maternal and paternal variables with children’s methylation and psychopathological risk. The scores of maternal and paternal Dyadic Adjustment Scale showed indirect effects on children’s methylation and psychopathological risk in relation to those exerted by risk factors.
Conclusion
Our study has supported the emerging evidence on the complex nature of children’s emotional-behavioral functioning and the associated risk and protective factors, with important implications for the planning of preventive programs.
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29
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Li S, Ye Z, Mather KA, Nguyen TL, Dite GS, Armstrong NJ, Wong EM, Thalamuthu A, Giles GG, Craig JM, Saffery R, Southey MC, Tan Q, Sachdev PS, Hopper JL. Early life affects late-life health through determining DNA methylation across the lifespan: A twin study. EBioMedicine 2022; 77:103927. [PMID: 35301182 PMCID: PMC8927831 DOI: 10.1016/j.ebiom.2022.103927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/07/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Background Previous findings for the genetic and environmental contributions to DNA methylation variation were for limited age ranges only. We investigated the lifespan contributions and their implications for human health for the first time. Methods 1,720 monozygotic twin (MZ) pairs and 1,107 dizygotic twin (DZ) pairs aged 0-92 years were included. Familial correlations (i.e., correlations between twins) for 353,681 methylation sites were estimated and modelled as a function of twin pair cohabitation history. Findings The methylome average familial correlation was around zero at birth (MZ pair: -0.01; DZ pair: -0.04), increased with the time of twins living together during childhood at rates of 0.16 (95%CI: 0.12-0.20) for MZ pairs and 0.13 (95%CI: 0.07-0.20) for DZ pairs per decade, and decreased with the time of living apart during adulthood at rates of 0.026 (95%CI: 0.019-0.033) for MZ pairs and 0.027 (95%CI: 0.011-0.043) for DZ pairs per decade. Neither the increasing nor decreasing rate differed by zygosity (both P>0.1), consistent with cohabitation environment shared by twins, rather than genetic factors, influencing the methylation familial correlation changes. Familial correlations for 6.6% (23,386/353,681) sites changed with twin pair cohabitation history. These sites were enriched for high heritability, proximal promoters, and epigenetic/genetic associations with various early-life factors and late-life health conditions. Interpretation Early life strongly influences DNA methylation variation across the lifespan, and the effects are stronger for heritable sites and sites biologically relevant to the regulation of gene expression. Early life could affect late-life health through influencing DNA methylation. Funding Victorian Cancer Agency, Cancer Australia, Cure Cancer Foundation.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.
| | - Zhoufeng Ye
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Genetic Technologies Ltd, Fitzroy, Victoria, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Western Australia, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Jeffrey M Craig
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, New South Wales, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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30
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Corbin LJ, White SJ, Taylor AE, Williams CM, Taylor K, van den Bosch MT, Teasdale JE, Jones M, Bond M, Harper MT, Falk L, Groom A, Hazell GG, Paternoster L, Munafò MR, Nordestgaard BG, Tybjærg-Hansen A, Bojesen SE, Relton C, Min JL, Davey Smith G, Mumford AD, Poole AW, Timpson NJ. Epigenetic Regulation of F2RL3 Associates With Myocardial Infarction and Platelet Function. Circ Res 2022; 130:384-400. [PMID: 35012325 PMCID: PMC8812435 DOI: 10.1161/circresaha.121.318836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND DNA hypomethylation at the F2RL3 (F2R like thrombin or trypsin receptor 3) locus has been associated with both smoking and atherosclerotic cardiovascular disease; whether these smoking-related associations form a pathway to disease is unknown. F2RL3 encodes protease-activated receptor 4, a potent thrombin receptor expressed on platelets. Given the role of thrombin in platelet activation and the role of thrombus formation in myocardial infarction, alterations to this biological pathway could be important for ischemic cardiovascular disease. METHODS We conducted multiple independent experiments to assess whether DNA hypomethylation at F2RL3 in response to smoking is associated with risk of myocardial infarction via changes to platelet reactivity. Using cohort data (N=3205), we explored the relationship between smoking, DNA hypomethylation at F2RL3, and myocardial infarction. We compared platelet reactivity in individuals with low versus high DNA methylation at F2RL3 (N=41). We used an in vitro model to explore the biological response of F2RL3 to cigarette smoke extract. Finally, a series of reporter constructs were used to investigate how differential methylation could impact F2RL3 gene expression. RESULTS Observationally, DNA methylation at F2RL3 mediated an estimated 34% of the smoking effect on increased risk of myocardial infarction. An association between methylation group (low/high) and platelet reactivity was observed in response to PAR4 (protease-activated receptor 4) stimulation. In cells, cigarette smoke extract exposure was associated with a 4.9% to 9.3% reduction in DNA methylation at F2RL3 and a corresponding 1.7-(95% CI, 1.2-2.4, P=0.04) fold increase in F2RL3 mRNA. Results from reporter assays suggest the exon 2 region of F2RL3 may help control gene expression. CONCLUSIONS Smoking-induced epigenetic DNA hypomethylation at F2RL3 appears to increase PAR4 expression with potential downstream consequences for platelet reactivity. Combined evidence here not only identifies F2RL3 DNA methylation as a possible contributory pathway from smoking to cardiovascular disease risk but from any feature potentially influencing F2RL3 regulation in a similar manner.
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Affiliation(s)
- Laura J. Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Stephen J. White
- Department of Life Sciences, Manchester Metropolitan University, United Kingdom (S.J.W.)
| | - Amy E. Taylor
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom (A.E.T.)
| | - Christopher M. Williams
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Kurt Taylor
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
- UK Centre for Tobacco and Alcohol Studies and School of Experimental Psychology (M.R.M.), University of Bristol, United Kingdom
- School of Cellular and Molecular Medicine (A.D.M.), University of Bristol, United Kingdom
- Department of Life Sciences, Manchester Metropolitan University, United Kingdom (S.J.W.)
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, United Kingdom (A.E.T.)
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Department of Clinical Biochemistry, Rigshospitalet (A.T.-H.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Marion T. van den Bosch
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Jack E. Teasdale
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Matthew Jones
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Mark Bond
- Translational Health Sciences, Bristol Medical School (J.E.T., M.J., M.B.), University of Bristol, United Kingdom
| | - Matthew T. Harper
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
| | - Louise Falk
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Alix Groom
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Georgina G.J. Hazell
- Department of Pharmacology, University of Cambridge, Tennis Court Road (M.T.H., G.G.J.H.)
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Marcus R. Munafò
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- UK Centre for Tobacco and Alcohol Studies and School of Experimental Psychology (M.R.M.), University of Bristol, United Kingdom
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Anne Tybjærg-Hansen
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Department of Clinical Biochemistry, Rigshospitalet (A.T.-H.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N., S.E.B.), Copenhagen University Hospital, Denmark
- The Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H., S.E.B.), Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H., S.E.B.)
| | - Caroline Relton
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Josine L. Min
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine (A.D.M.), University of Bristol, United Kingdom
| | - Alastair W. Poole
- School of Physiology, Pharmacology and Neuroscience (C.M.W., M.T.v.d.B., A.W.P.), University of Bristol, United Kingdom
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, United Kingdom (L.J.C., L.F., A.G., L.P., M.R.M., C.R., J.L.M., G.D.S., N.J.T.)
- Population Health Sciences, Bristol Medical School (L.J.C., A.E.T., K.T., L.F., A.G., L.P., C.R., J.L.M., G.D.S., N.J.T.), University of Bristol, United Kingdom
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Zhang R, Dang W, Zhang J, He R, Li G, Zhang L, Wang Z, Zong H, Liu N, Jia W. Methylation quantitative locus rs3758653 in the DRD4 gene is associated with duration from first heroin exposure to addiction. Brain Res 2022; 1775:147746. [PMID: 34864042 DOI: 10.1016/j.brainres.2021.147746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/14/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]
Abstract
Opioid addiction is a chronic brain disease with a high heritability. However, the genetic underpinnings remain uncertain. DNA methylation is involved in the adaptive changes in neuroplasticity after prolonged drug use. The dopamine receptor D4 (DRD4) has an essential role in the reward processes associated with addictive drugs. To further elucidate the potential role and mechanism of the DRD4 gene variants in heroin addiction, we detected the methylation level of 46 CpG sites in the promoter region and the genotypes of three SNPs in the DRD4 gene. Correlations between the SNPs and methylation levels of the CpG sites, i.e., the analysis of methylation quantitative trait loci (mQTLs) was conducted. Following the identification of mQTLs that are unique in the heroin addiction group, we performed an association study between the mQTLs and traits of heroin addiction. Our results revealed that there were several correlations of SNPs rs3758653 and rs11246226 with the methylation levels of some CpG sites in the DRD4 gene. Among these SNP-CpG pairs, rs3758653-DRD4_04, rs3758653-DRD4_05, rs3758653-DRD4_13 and rs3758653-DRD4_03 were unique in the heroin addiction group. Moreover, we found that mQTL rs3758653 was associated with duration from first heroin exposure to addiction, and the expression level of the DRD4 gene in human brain regions of the frontal cortex and hippocampus. Our findings suggested that some mQTLs in the genome may be associated with traits of opioid addiction through implicating the processes of DNA methylation and gene expression.
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Affiliation(s)
- Rui Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Wei Dang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China.
| | - Jianbo Zhang
- Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ruifeng He
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Guibin Li
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Luying Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Zhikang Wang
- Psychiatry Department, Xi'an Daxing Hospital, Xi'an, Shaanxi, China
| | - Hua Zong
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Ning Liu
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
| | - Wei Jia
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi, China
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32
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Chen GK, Yan Q, Paul KC, Kusters CD, Folle AD, Furlong M, Keener A, Bronstein J, Horvath S, Ritz B. Stochastic Epigenetic Mutations Influence Parkinson's Disease Risk, Progression, and Mortality. JOURNAL OF PARKINSON'S DISEASE 2022; 12:545-556. [PMID: 34842194 PMCID: PMC9076404 DOI: 10.3233/jpd-212834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Stochastic epigenetic mutations (SEM) reflect a deviation from normal site-specific methylation patterns. Epigenetic mutation load (EML) captures the accumulation of SEMs across an individual's genome and may reflect dysfunction of the epigenetic maintenance system in response to epigenetic challenges. OBJECTIVE We investigate whether EML is associated with PD risk and time to events (i.e., death and motor symptom decline). METHODS We employed logistic regression and Cox proportional hazards regression to assess the association between EML and several outcomes. Our analyses are based on 568 PD patients and 238 controls from the Parkinson's disease, Environment and Genes (PEG) study, for whom blood-based methylation data was available. RESULTS We found an association for PD onset and EML in all genes (OR = 1.90; 95%CI 1.52-2.37) and PD-related genes (OR = 1.87; 95%CI 1.50-2.32). EML was also associated with time to a minimum score of 35 points on the motor UPDRS exam (OR = 1.28; 95%CI 1.06-1.56) and time to death (OR = 1.29, 95%CI 1.11-1.49). An analysis of PD related genes only revealed five intragenic hotspots of high SEM density associated with PD risk. CONCLUSION Our findings suggest an enrichment of methylation dysregulation in PD patients in general and specifically in five PD related genes. EML may also be associated with time to death and motor symptom progression in PD patients.
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Affiliation(s)
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly C. Paul
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Cynthia D.J. Kusters
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Melissa Furlong
- Department of Community, Environment and Policy, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Adrienne Keener
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA,Correspondence to: Beate Ritz, UCLA, Epidemiology, Box 951772, Los Angeles, CA 90095, USA.
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Usman T, Ali N, Wang Y, Yu Y. Association of Aberrant DNA Methylation Level in the CD4 and JAK-STAT-Pathway-Related Genes with Mastitis Indicator Traits in Chinese Holstein Dairy Cattle. Animals (Basel) 2021; 12:ani12010065. [PMID: 35011171 PMCID: PMC8749870 DOI: 10.3390/ani12010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
The present study was designed to evaluate the gene expression and DNA methylation level in the promoter region of the CD4 and the JAK-STAT-pathway-related genes. A total of 24 samples were deployed in the gene expression and 118 samples were used in the DNA methylation study. Student's t-tests were used to analyze the gene expression and DNA methylation. The evaluation of DNA methylation in promoter regions of JAK2 and STAT5A revealed hypo-methylation levels of CpG sites and higher gene expression in cows diagnosed with mastitis as compared to the healthy control, and vice versa in those with CD4. DNA methylation was negatively correlated with gene expression in JAK2, STAT5A, and CD4 genes. Six, two, and four active transcription factors were identified on the CpG sites in the promoter regions of JAK2, STAT5A, and CD4 genes, respectively. Regarding correlation analysis, the DNA methylation levels of CD4 showed significantly higher positive correlations with somatic cell counts (p < 0.05). Findings of the current study inferred that aberrant DNA methylation in the CpG sites at the 1 kb promoter region in JAK2, STAT5A, and CD4 genes due to mastitis in cows can be used as potential epigenetic markers to estimate bovine mastitis susceptibility in dairy cattle.
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Affiliation(s)
- Tahir Usman
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
- College of Veterinary Science and Animal Husbandry, Abdul Wali Khan University, Mardan 23200, Pakistan
- Correspondence: (T.U.); (Y.Y.); Tel.: +92-313-092-0177 (T.U.); +86-10-62-734-611 (Y.Y.); Fax: +86-10-62-732-439 (Y.Y.)
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Pakistan;
| | - Yachun Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Ying Yu
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
- Correspondence: (T.U.); (Y.Y.); Tel.: +92-313-092-0177 (T.U.); +86-10-62-734-611 (Y.Y.); Fax: +86-10-62-732-439 (Y.Y.)
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34
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Affiliation(s)
- Ying Zhang
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF, Université Laval, Québec, Québec, Canada
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Clarke S, Caulton A, McRae K, Brauning R, Couldrey C, Dodds K. Beyond the genome: a perspective on the use of DNA methylation profiles as a tool for the livestock industry. Anim Front 2021; 11:90-94. [PMID: 34934534 PMCID: PMC8683129 DOI: 10.1093/af/vfab060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | - Alex Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Kathryn McRae
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | | | - Ken Dodds
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
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Johnson KM, Sirovy KA, Kelly MW. Differential DNA methylation across environments has no effect on gene expression in the eastern oyster. J Anim Ecol 2021; 91:1135-1147. [PMID: 34882793 DOI: 10.1111/1365-2656.13645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters Crassostrea virginica from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments. An analysis of CpG observed/expected values (CpG O/E) across the C. virginica genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation and higher and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression. Taken together, the differential methylation results suggest that only a small portion of the C. virginica genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.
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Affiliation(s)
- Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA.,California Sea Grant, University of California San Diego, La Jolla, CA, USA
| | - Kyle A Sirovy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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37
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Tin A, Schlosser P, Matias-Garcia PR, Thio CHL, Joehanes R, Liu H, Yu Z, Weihs A, Hoppmann A, Grundner-Culemann F, Min JL, Kuhns VLH, Adeyemo AA, Agyemang C, Ärnlöv J, Aziz NA, Baccarelli A, Bochud M, Brenner H, Bressler J, Breteler MMB, Carmeli C, Chaker L, Coresh J, Corre T, Correa A, Cox SR, Delgado GE, Eckardt KU, Ekici AB, Endlich K, Floyd JS, Fraszczyk E, Gao X, Gào X, Gelber AC, Ghanbari M, Ghasemi S, Gieger C, Greenland P, Grove ML, Harris SE, Hemani G, Henneman P, Herder C, Horvath S, Hou L, Hurme MA, Hwang SJ, Kardia SLR, Kasela S, Kleber ME, Koenig W, Kooner JS, Kronenberg F, Kühnel B, Ladd-Acosta C, Lehtimäki T, Lind L, Liu D, Lloyd-Jones DM, Lorkowski S, Lu AT, Marioni RE, März W, McCartney DL, Meeks KAC, Milani L, Mishra PP, Nauck M, Nowak C, Peters A, Prokisch H, Psaty BM, Raitakari OT, Ratliff SM, Reiner AP, Schöttker B, Schwartz J, Sedaghat S, Smith JA, Sotoodehnia N, Stocker HR, Stringhini S, Sundström J, Swenson BR, van Meurs JBJ, van Vliet-Ostaptchouk JV, Venema A, Völker U, Winkelmann J, Wolffenbuttel BHR, Zhao W, Zheng Y, Loh M, Snieder H, Waldenberger M, Levy D, Akilesh S, Woodward OM, Susztak K, Teumer A, Köttgen A. Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. Nat Commun 2021; 12:7173. [PMID: 34887389 PMCID: PMC8660809 DOI: 10.1038/s41467-021-27198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E-7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits.
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Affiliation(s)
- Adrienne Tin
- Department of Medicine, University of Mississippi Medical Center, Jackson, 39216, MS, USA.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Roby Joehanes
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hongbo Liu
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Zhi Yu
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Nasir A Aziz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Andrea Baccarelli
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Hermann Brenner
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Monique M B Breteler
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Cristian Carmeli
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Population Health Laboratory, University of Fribourg, Fribourg, Switzerland
| | - Layal Chaker
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, 39216, MS, USA
| | - Simon R Cox
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-UniversitätErlangen-Nürnberg, 91054, Erlangen, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, 98101, WA, USA
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
| | - Eliza Fraszczyk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xu Gao
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Xīn Gào
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
| | - Allan C Gelber
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sahar Ghasemi
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, 77030, TX, USA
| | - Sarah E Harris
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Munich-Neuherberg, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
- Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA, USA
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Jaspal S Kooner
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Dan Liu
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim and Augsburg, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christoph Nowak
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Ludwig-Maximilians Universität München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Computational Health, Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, 98101, WA, USA
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
- Department of Health Services, University of Washington, Seattle, 98101, WA, USA
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, 98101, WA, USA
| | - Ben Schöttker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sanaz Sedaghat
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
| | - Hannah R Stocker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Silvia Stringhini
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Johan Sundström
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, University of Washington, Seattle, 98101, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Uwe Völker
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Chair Neurogenetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Bavaria, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Owen M Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Alexander Teumer
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
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Schlosser P, Tin A, Matias-Garcia PR, Thio CHL, Joehanes R, Liu H, Weihs A, Yu Z, Hoppmann A, Grundner-Culemann F, Min JL, Adeyemo AA, Agyemang C, Ärnlöv J, Aziz NA, Baccarelli A, Bochud M, Brenner H, Breteler MMB, Carmeli C, Chaker L, Chambers JC, Cole SA, Coresh J, Corre T, Correa A, Cox SR, de Klein N, Delgado GE, Domingo-Relloso A, Eckardt KU, Ekici AB, Endlich K, Evans KL, Floyd JS, Fornage M, Franke L, Fraszczyk E, Gao X, Gào X, Ghanbari M, Ghasemi S, Gieger C, Greenland P, Grove ML, Harris SE, Hemani G, Henneman P, Herder C, Horvath S, Hou L, Hurme MA, Hwang SJ, Jarvelin MR, Kardia SLR, Kasela S, Kleber ME, Koenig W, Kooner JS, Kramer H, Kronenberg F, Kühnel B, Lehtimäki T, Lind L, Liu D, Liu Y, Lloyd-Jones DM, Lohman K, Lorkowski S, Lu AT, Marioni RE, März W, McCartney DL, Meeks KAC, Milani L, Mishra PP, Nauck M, Navas-Acien A, Nowak C, Peters A, Prokisch H, Psaty BM, Raitakari OT, Ratliff SM, Reiner AP, Rosas SE, Schöttker B, Schwartz J, Sedaghat S, Smith JA, Sotoodehnia N, Stocker HR, Stringhini S, Sundström J, Swenson BR, Tellez-Plaza M, van Meurs JBJ, van Vliet-Ostaptchouk JV, Venema A, Verweij N, Walker RM, Wielscher M, Winkelmann J, Wolffenbuttel BHR, Zhao W, Zheng Y, Loh M, Snieder H, Levy D, Waldenberger M, Susztak K, Köttgen A, Teumer A. Meta-analyses identify DNA methylation associated with kidney function and damage. Nat Commun 2021; 12:7174. [PMID: 34887417 PMCID: PMC8660832 DOI: 10.1038/s41467-021-27234-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/08/2021] [Indexed: 12/27/2022] Open
Abstract
Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs.
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Affiliation(s)
- Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Roby Joehanes
- Framingham Heart Study, Framingham, Massachusetts, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, US
| | - Hongbo Liu
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Zhi Yu
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Nasir A Aziz
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Andrea Baccarelli
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Hermann Brenner
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Cristian Carmeli
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Population Health Laboratory, University of Fribourg, Fribourg, Switzerland
| | - Layal Chaker
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
| | | | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Simon R Cox
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Arce Domingo-Relloso
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-UniversitätErlangen-Nürnberg, 91054, Erlangen, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Eliza Fraszczyk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xu Gao
- Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Xīn Gào
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sahar Ghasemi
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Sarah E Harris
- Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Munich-Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, Massachusetts, USA
- Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Holly Kramer
- Departments of Public Health Science and Medicine, Loyola University Chicago, Maywood, IL, USA
- Edward Hines VA Medical Center, Hines, IL, USA
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Dan Liu
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kurt Lohman
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim and Augsburg, Augsburg, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Christoph Nowak
- Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- Ludwig-Maximilians Universität München, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Computational Health, Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Department of Health Services, University of Washington, Seattle, WA, 98101, USA
| | - Olli T Raitakari
- Research centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Sylvia E Rosas
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ben Schöttker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sanaz Sedaghat
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48104, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
| | - Hannah R Stocker
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Silvia Stringhini
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Johan Sundström
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Chair Neurogenetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, US
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alexander Teumer
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland.
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ANGPT1 methylation and delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage patients. EPIGENETICS COMMUNICATIONS 2021; 1. [PMID: 35359917 PMCID: PMC8967216 DOI: 10.1186/s43682-021-00001-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background: Delayed cerebral ischemia (DCI) is a common secondary complication and an important cause of disability and mortality among patients who survive aneurysmal subarachnoid hemorrhage (aSAH). Knowledge on DCI pathogenesis, risk factors, and biomarkers are essential for early detection and improved prognosis. To investigate the role of DNA methylation in DCI risk, we conducted an epigenome-wide association study (EWAS) in 68 patients followed up to 1 year after the initial aneurysm rupture. Blood samples were collected within 48 h post hemorrhage and used for DNA methylation profiling at ~ 450k CpG sites. A separate cohort of 175 patients was sequenced for the top CpG sites from the discovery analysis for a replication of the EWAS findings. Results: EWAS did not identify any epigenome-wide significant CpGs. The top signal, cg18031596, was annotated to ANGPT1, a gene with critical functions in angiogenesis after vascular injury. Post hoc power calculations indicated a well-powered discovery analysis for cg18031596. Analysis of the replication cohort showed that four out of the five CpG sites sequenced at the ANGPT1 locus passed a Bonferroni-adjusted significance threshold. In a pooled analysis of the entire sample, three out of five yielded a significant p-value, and the top association signal (p-value = 0.004) was seen for a CpG that was not originally measured in the discovery EWAS. However, four ANGPT1 CpG sites had an opposite effect direction in the replication analysis compared to the discovery EWAS, marking a failure of replication. We carefully examined this observed flip in directions and propose several possible explanations in addition to that it was a random chance that ANGPT1 ranked at the top in the discovery EWAS. Conclusions: We failed to demonstrate a significant and consistent effect of ANGPT1 methylation in DCI risk in two cohorts. Though the replication attempt to weaken the overall support of this gene, given its relevant function and top rank of significance in the EWAS, our results call for future studies of larger aSAH cohorts to determine its relevance for the occurrence of DCI.
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40
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Barišić A, Stanković A, Stojković L, Pereza N, Ostojić S, Peterlin A, Peterlin B, Vraneković J. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth. Biol Res Nurs 2021; 24:85-93. [PMID: 34727781 DOI: 10.1177/10998004211043571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite considerable effort aimed at decreasing the incidence of spontaneous preterm birth (SPTB), it remains the leading cause of infant mortality and morbidity. The aim of this study was to evaluate maternal LINE-1 DNA methylation (DNAm), along with DNMT polymorphisms and factors proposed to modulate DNAm, in patients who delivered early preterm. This case-control study included women who delivered spontaneously early preterm (23-336/7 weeks of gestation), and control women. DNAm was analyzed in peripheral blood lymphocytes by quantification of LINE-1 DNAm using the MethyLight method. There was no significant difference in LINE-1 DNAm between patients with early PTB and controls. Among the investigated predictors, only the history of previous PTB was significantly associated with LINE-1 DNAm in PTB patients (β = -0.407; R2 = 0.131; p = 0.011). The regression analysis showed the effect of DNMT3B rs1569686 TT+TG genotypes on LINE-1 DNAm in patients with familial PTB (β = -0.524; R2 = 0.275; p = 0.037). Our findings suggest novel associations of maternal LINE-1 DNA hypomethylation with DNMT3B rs1569686 T allele. These results also contribute to the understanding of a complex (epi)genetic and environmental relationship underlying the early PTB.
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Affiliation(s)
- Anita Barišić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Aleksandra Stanković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Ljiljana Stojković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Nina Pereza
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Slovenia
| | - Jadranka Vraneković
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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41
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Zhu J, Yang Y, Kisiel JB, Mahoney DW, Michaud DS, Guo X, Taylor WR, Shu XO, Shu X, Liu D, Li B, Tao R, Cai Q, Zheng W, Long J, Wu L. Integrating Genome and Methylome Data to Identify Candidate DNA Methylation Biomarkers for Pancreatic Cancer Risk. Cancer Epidemiol Biomarkers Prev 2021; 30:2079-2087. [PMID: 34497089 PMCID: PMC8568683 DOI: 10.1158/1055-9965.epi-21-0400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/20/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The role of methylation in pancreatic cancer risk remains unclear. We integrated genome and methylome data to identify CpG sites (CpG) with the genetically predicted methylation to be associated with pancreatic cancer risk. We also studied gene expression to understand the identified associations. METHODS Using genetic data and white blood cell methylation data from 1,595 subjects of European descent, we built genetic models to predict DNA methylation levels. After internal and external validation, we applied prediction models with satisfactory performance to the genetic data of 8,280 pancreatic cancer cases and 6,728 controls of European ancestry to investigate the associations of predicted methylation with pancreatic cancer risk. For associated CpGs, we compared their measured levels in pancreatic tumor versus benign tissue. RESULTS We identified 45 CpGs at nine loci showing an association with pancreatic cancer risk, including 15 CpGs showing an association independent from identified risk variants. We observed significant correlations between predicted methylation of 16 of the 45 CpGs and predicted expression of eight adjacent genes, of which six genes showed associations with pancreatic cancer risk. Of the 45 CpGs, we were able to compare measured methylation of 16 in pancreatic tumor versus benign pancreatic tissue. Of them, six showed differentiated methylation. CONCLUSIONS We identified methylation biomarker candidates associated with pancreatic cancer using genetic instruments and added additional insights into the role of methylation in regulating gene expression in pancreatic cancer development. IMPACT A comprehensive study using genetic instruments identifies 45 CpG sites at nine genomic loci for pancreatic cancer risk.
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Affiliation(s)
- Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Dominique S Michaud
- Department of Public Health and Community Medicine, Tufts University Medical School, Boston, Massachusetts
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Duo Liu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.
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42
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van Dongen J, Gordon SD, McRae AF, Odintsova VV, Mbarek H, Breeze CE, Sugden K, Lundgren S, Castillo-Fernandez JE, Hannon E, Moffitt TE, Hagenbeek FA, van Beijsterveldt CEM, Jan Hottenga J, Tsai PC, Min JL, Hemani G, Ehli EA, Paul F, Stern CD, Heijmans BT, Slagboom PE, Daxinger L, van der Maarel SM, de Geus EJC, Willemsen G, Montgomery GW, Reversade B, Ollikainen M, Kaprio J, Spector TD, Bell JT, Mill J, Caspi A, Martin NG, Boomsma DI. Identical twins carry a persistent epigenetic signature of early genome programming. Nat Commun 2021; 12:5618. [PMID: 34584077 PMCID: PMC8479069 DOI: 10.1038/s41467-021-25583-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/19/2021] [Indexed: 02/08/2023] Open
Abstract
Monozygotic (MZ) twins and higher-order multiples arise when a zygote splits during pre-implantation stages of development. The mechanisms underpinning this event have remained a mystery. Because MZ twinning rarely runs in families, the leading hypothesis is that it occurs at random. Here, we show that MZ twinning is strongly associated with a stable DNA methylation signature in adult somatic tissues. This signature spans regions near telomeres and centromeres, Polycomb-repressed regions and heterochromatin, genes involved in cell-adhesion, WNT signaling, cell fate, and putative human metastable epialleles. Our study also demonstrates a never-anticipated corollary: because identical twins keep a lifelong molecular signature, we can retrospectively diagnose if a person was conceived as monozygotic twin.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands.
| | - Scott D Gordon
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | | | - Karen Sugden
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Catharina E M van Beijsterveldt
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD, USA
| | - Franziska Paul
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Medical Genetics Department, KOC University, School of Medicine, Istanbul, Turkey
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
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43
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Amador C, Zeng Y, Barber M, Walker RM, Campbell A, McIntosh AM, Evans KL, Porteous DJ, Hayward C, Wilson JF, Navarro P, Haley CS. Genome-wide methylation data improves dissection of the effect of smoking on body mass index. PLoS Genet 2021; 17:e1009750. [PMID: 34499657 PMCID: PMC8428545 DOI: 10.1371/journal.pgen.1009750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Variation in obesity-related traits has a genetic basis with heritabilities between 40 and 70%. While the global obesity pandemic is usually associated with environmental changes related to lifestyle and socioeconomic changes, most genetic studies do not include all relevant environmental covariates, so the genetic contribution to variation in obesity-related traits cannot be accurately assessed. Some studies have described interactions between a few individual genes linked to obesity and environmental variables but there is no agreement on their total contribution to differences between individuals. Here we compared self-reported smoking data and a methylation-based proxy to explore the effect of smoking and genome-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain. Our results indicate that exploiting omic measures can improve models for complex traits such as obesity and can be used as a substitute for, or jointly with, environmental records to better understand causes of disease.
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Affiliation(s)
- Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, China
| | - Michael Barber
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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44
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Society to cell: How child poverty gets “Under the Skin” to influence child development and lifelong health. DEVELOPMENTAL REVIEW 2021. [DOI: 10.1016/j.dr.2021.100983] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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45
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Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
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Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
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46
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Breton CV, Landon R, Kahn LG, Enlow MB, Peterson AK, Bastain T, Braun J, Comstock SS, Duarte CS, Hipwell A, Ji H, LaSalle JM, Miller RL, Musci R, Posner J, Schmidt R, Suglia SF, Tung I, Weisenberger D, Zhu Y, Fry R. Exploring the evidence for epigenetic regulation of environmental influences on child health across generations. Commun Biol 2021; 4:769. [PMID: 34158610 PMCID: PMC8219763 DOI: 10.1038/s42003-021-02316-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 02/08/2023] Open
Abstract
Environmental exposures, psychosocial stressors and nutrition are all potentially important influences that may impact health outcomes directly or via interactions with the genome or epigenome over generations. While there have been clear successes in large-scale human genetic studies in recent decades, there is still a substantial amount of missing heritability to be elucidated for complex childhood disorders. Mounting evidence, primarily in animals, suggests environmental exposures may generate or perpetuate altered health outcomes across one or more generations. One putative mechanism for these environmental health effects is via altered epigenetic regulation. This review highlights the current epidemiologic literature and supporting animal studies that describe intergenerational and transgenerational health effects of environmental exposures. Both maternal and paternal exposures and transmission patterns are considered, with attention paid to the attendant ethical, legal and social implications.
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Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Remy Landon
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda G Kahn
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Michelle Bosquet Enlow
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alicia K Peterson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theresa Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Braun
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | - Cristiane S Duarte
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Alison Hipwell
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hong Ji
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Rashelle Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jonathan Posner
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Rebecca Schmidt
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
| | | | - Irene Tung
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yeyi Zhu
- Division of Research, Kaiser Permanente Northern California and Department of Epidemiology and Biostatistics, University of California, San Francisco, Oakland, CA, USA
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, UNC Chapel Hill, Chapel Hill, NC, USA
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47
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Li M, Lyu C, Huang M, Do C, Tycko B, Lupo PJ, MacLeod SL, Randolph CE, Liu N, Witte JS, Hobbs CA. Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. BMC Genom Data 2021; 22:20. [PMID: 34112112 PMCID: PMC8194170 DOI: 10.1186/s12863-021-00975-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Background Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation will enhance our understanding of pathogenesis in this important type of congenital disorder. We investigated cis-acting effects of genetic single nucleotide polymorphisms (SNPs) on local DNA methylation patterns within 83 cardiac tissue samples and prioritized their contributions to CHD risk by leveraging results of CHD genome-wide association studies (GWAS) and their effects on cardiac gene expression. Results We identified 13,901 potential methylation quantitative trait loci (mQTLs) with a false discovery threshold of 5%. Further co-localization analyses and Mendelian randomization indicated that genetic variants near the HLA-DRB6 gene on chromosome 6 may contribute to CHD risk by regulating the methylation status of nearby CpG sites. Additional SNPs in genomic regions on chromosome 10 (TNKS2-AS1 gene) and chromosome 14 (LINC01629 gene) may simultaneously influence epigenetic and transcriptomic variations within cardiac tissues. Conclusions Our results support the hypothesis that genetic variants may influence the risk of CHDs through regulating the changes of DNA methylation and gene expression. Our results can serve as an important source of information that can be integrated with other genetic studies of heart diseases, especially CHDs. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00975-2.
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Affiliation(s)
- Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA.
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | | | | | | | - Nianjun Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - John S Witte
- University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
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48
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Bellon M, Bialuk I, Galli V, Bai XT, Farre L, Bittencourt A, Marçais A, Petrus MN, Ratner L, Waldmann TA, Asnafi V, Gessain A, Matsuoka M, Franchini G, Hermine O, Watanabe T, Nicot C. Germinal epimutation of Fragile Histidine Triad (FHIT) gene is associated with progression to acute and chronic adult T-cell leukemia diseases. Mol Cancer 2021; 20:86. [PMID: 34092254 PMCID: PMC8183032 DOI: 10.1186/s12943-021-01370-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human T cell Leukemia virus type 1 (HTLV-I) is etiologically linked to adult T cell leukemia/lymphoma (ATL) and an inflammatory neurodegenerative disease called HTLV-I-associated myelopathy or tropical spastic paraparesis (HAM/TSP). The exact genetic or epigenetic events and/or environmental factors that influence the development of ATL, or HAM/TSP diseases are largely unknown. The tumor suppressor gene, Fragile Histidine Triad Diadenosine Triphosphatase (FHIT), is frequently lost in cancer through epigenetic modifications and/or deletion. FHIT is a tumor suppressor acting as genome caretaker by regulating cellular DNA repair. Indeed, FHIT loss leads to replicative stress and accumulation of double DNA strand breaks. Therefore, loss of FHIT expression plays a key role in cellular transformation. METHODS Here, we studied over 400 samples from HTLV-I-infected individuals with ATL, TSP/HAM, or asymptomatic carriers (AC) for FHIT loss and expression. We examined the epigenetic status of FHIT through methylation specific PCR and bisulfite sequencing; and correlated these results to FHIT expression in patient samples. RESULTS We found that epigenetic alteration of FHIT is specifically found in chronic and acute ATL but is absent in asymptomatic HTLV-I carriers and TSP/HAM patients' samples. Furthermore, the extent of FHIT methylation in ATL patients was quantitatively comparable in virus-infected and virus non-infected cells. We also found that longitudinal HTLV-I carriers that progressed to smoldering ATL and descendants of ATL patients harbor FHIT methylation. CONCLUSIONS These results suggest that germinal epigenetic mutation of FHIT represents a preexisting mark predisposing to the development of ATL diseases. These findings have important clinical implications as patients with acute ATL are rarely cured. Our study suggests an alternative strategy to the current "wait and see approach" in that early screening of HTLV-I-infected individuals for germinal epimutation of FHIT and early treatment may offer significant clinical benefits.
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Affiliation(s)
- Marcia Bellon
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Izabela Bialuk
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue-Tao Bai
- Comprehensive Cancer Center, Department of Health Sciences, Ohio State University, Columbus, OH, USA
| | - Lourdes Farre
- Program in Molecular Mechanisms and Experimental Therapy in Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Achilea Bittencourt
- Department of Pathology, Prof. Edgard Santos Teaching Hospital, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Ambroise Marçais
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Laboratoire Onco-Hématologie, Paris, France
| | - Michael N Petrus
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lee Ratner
- Division of Oncology, Department of Medicine, Washington University, St Louis, MO, USA
| | - Thomas A Waldmann
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale (INSERM) U1151 Laboratoire Onco-Hematology, Paris, France
| | - Antoine Gessain
- Unité d'épidémiologie et de Physiopathologie des virus Oncogene, Institut Pasteur, 75015, Paris, France.,Centre National de la Recherche Scientifique (CNRS) UMR 3569, 75015, Paris, France
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Department of Hematology, Rheumatology, and Infectious Disease, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olivier Hermine
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Laboratoire Onco-Hématologie, Paris, France
| | - Toshiki Watanabe
- Department of Hematology/Oncology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Christophe Nicot
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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49
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Villicaña S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol 2021; 22:127. [PMID: 33931130 PMCID: PMC8086086 DOI: 10.1186/s13059-021-02347-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression. In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs. We also discuss challenges in this field and future areas of research geared to generate insights into molecular processes underlying human complex traits.
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Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
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50
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Lauby SC, Fleming AS, McGowan PO. Beyond maternal care: The effects of extra-maternal influences within the maternal environment on offspring neurodevelopment and later-life behavior. Neurosci Biobehav Rev 2021; 127:492-501. [PMID: 33905789 DOI: 10.1016/j.neubiorev.2021.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 01/26/2023]
Abstract
The early-life maternal environment has a profound and persistent effect on offspring neuroendocrine function, neurotransmitter systems, and behavior. Studies using rodent models suggest that early-life maternal care can influence the 'developmental programming' of offspring in part through altered epigenetic regulation of specific genes. The exploration of epigenetic regulation of these genes as a biological mechanism has been important to our understanding of how animals adapt to their environments and how these developmental trajectories may be altered. However, other non-maternal factors have been shown to act directly, or to interact with maternal care, to influence later-life phenotype. Based on accumulating evidence, including our research, we discuss other important influences on the developmental programming of offspring. We highlight early-life variations in temperature exposure and offspring genotype x environment interactions as prominent examples. We conclude with recommendations for future investigations on how early-life maternal care and extra-maternal influences lead to persistent changes in the brain and behavior of the offspring throughout development.
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Affiliation(s)
- Samantha C Lauby
- Department of Biological Sciences, University of Toronto Scarborough Campus, Scarborough, ON, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alison S Fleming
- Department of Psychology, University of Toronto, Toronto, ON, Canada; Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada.
| | - Patrick O McGowan
- Department of Biological Sciences, University of Toronto Scarborough Campus, Scarborough, ON, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada; Department of Psychology, University of Toronto, Toronto, ON, Canada; Department of Physiology, University of Toronto, Toronto, ON, Canada.
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