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Ciantar J, Marttila S, Rajić S, Kostiniuk D, Mishra PP, Lyytikäinen LP, Mononen N, Kleber ME, März W, Kähönen M, Raitakari O, Lehtimäki T, Raitoharju E. Identification and functional characterisation of DNA methylation differences between East- and West-originating Finns. Epigenetics 2024; 19:2397297. [PMID: 39217505 PMCID: PMC11382697 DOI: 10.1080/15592294.2024.2397297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/14/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Eastern and Western Finns show a striking difference in coronary heart disease-related mortality; genetics is a known contributor for this discrepancy. Here, we discuss the potential role of DNA methylation in mediating the discrepancy in cardiometabolic disease-risk phenotypes between the sub-populations. We used data from the Young Finns Study (n = 969) to compare the genome-wide DNA methylation levels of East- and West-originating Finns. We identified 21 differentially methylated loci (FDR < 0.05; Δβ >2.5%) and 7 regions (smoothed FDR < 0.05; CpGs ≥ 5). Methylation at all loci and regions associates with genetic variants (p < 5 × 10-8). Independently of genetics, methylation at 11 loci and 4 regions associates with transcript expression, including genes encoding zinc finger proteins. Similarly, methylation at 5 loci and 4 regions associates with cardiometabolic disease-risk phenotypes including triglycerides, glucose, cholesterol, as well as insulin treatment. This analysis was also performed in LURIC (n = 2371), a German cardiovascular patient cohort, and results replicated for the association of methylation at cg26740318 and DMR_11p15 with diabetes-related phenotypes and methylation at DMR_22q13 with triglyceride levels. Our results indicate that DNA methylation differences between East and West Finns may have a functional role in mediating the cardiometabolic disease discrepancy between the sub-populations.
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Affiliation(s)
- Joanna Ciantar
- Molecular Epidemiology (MOLE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology (MOLE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology (MOLE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Daria Kostiniuk
- Molecular Epidemiology (MOLE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Tays Research Services, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Tays Research Services, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Tays Research Services, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- 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
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Tays Research Services, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Emma Raitoharju
- Molecular Epidemiology (MOLE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
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El Sharkawy M, Felix JF, Grote V, Voortman T, Jaddoe VWV, Koletzko B, Küpers LK. Animal and plant protein intake during infancy and childhood DNA methylation: a meta-analysis in the NutriPROGRAM consortium. Epigenetics 2024; 19:2299045. [PMID: 38198623 PMCID: PMC10793674 DOI: 10.1080/15592294.2023.2299045] [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: 03/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Higher early-life animal protein intake is associated with a higher childhood obesity risk compared to plant protein intake. Differential DNA methylation may represent an underlying mechanism. METHODS We analysed associations of infant animal and plant protein intakes with DNA methylation in early (2-6 years, N = 579) and late (7̄-12 years, N = 604) childhood in two studies. Study-specific robust linear regression models adjusted for relevant confounders were run, and then meta-analysed using a fixed-effects model. We also performed sex-stratified meta-analyses. Follow-up analyses included pathway analysis and eQTM look-up. RESULTS Infant animal protein intake was not associated with DNA methylation in early childhood, but was associated with late-childhood DNA methylation at cg21300373 (P = 4.27 × 10¯8, MARCHF1) and cg10633363 (P = 1.09 × 10¯7, HOXB9) after FDR correction. Infant plant protein intake was associated with early-childhood DNA methylation at cg25973293 (P = 2.26 × 10-7, C1orf159) and cg15407373 (P = 2.13 × 10-7, MBP) after FDR correction. There was no overlap between the findings from the animal and plant protein analyses. We did not find enriched functional pathways at either time point using CpGs associated with animal and plant protein. These CpGs were not previously associated with childhood gene expression. Sex-stratified meta-analyses showed sex-specific DNA methylation associations for both animal and plant protein intake. CONCLUSION Infant animal protein intake was associated with DNA methylation at two CpGs in late childhood. Infant plant protein intake was associated with DNA methylation in early childhood at two CpGs. A potential mediating role of DNA methylation at these CpGs between infant protein intake and health outcomes requires further investigation.
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Affiliation(s)
- Mohammed El Sharkawy
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
- Munich Medical Research School, Faculty of Medicine, LMU - Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Leanne K. Küpers
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [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: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I. Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R. Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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Melton HJ, Zhang Z, Deng HW, Wu L, Wu C. MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations. Epigenetics 2024; 19:2370542. [PMID: 38963888 PMCID: PMC11225927 DOI: 10.1080/15592294.2024.2370542] [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: 10/06/2023] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
Although DNA methylation (DNAm) has been implicated in the pathogenesis of numerous complex diseases, from cancer to cardiovascular disease to autoimmune disease, the exact methylation sites that play key roles in these processes remain elusive. One strategy to identify putative causal CpG sites and enhance disease etiology understanding is to conduct methylome-wide association studies (MWASs), in which predicted DNA methylation that is associated with complex diseases can be identified. However, current MWAS models are primarily trained using the data from single studies, thereby limiting the methylation prediction accuracy and the power of subsequent association studies. Here, we introduce a new resource, MWAS Imputing Methylome Obliging Summary-level mQTLs and Associated LD matrices (MIMOSA), a set of models that substantially improve the prediction accuracy of DNA methylation and subsequent MWAS power through the use of a large summary-level mQTL dataset provided by the Genetics of DNA Methylation Consortium (GoDMC). Through the analyses of GWAS (genome-wide association study) summary statistics for 28 complex traits and diseases, we demonstrate that MIMOSA considerably increases the accuracy of DNA methylation prediction in whole blood, crafts fruitful prediction models for low heritability CpG sites, and determines markedly more CpG site-phenotype associations than preceding methods. Finally, we use MIMOSA to conduct a case study on high cholesterol, pinpointing 146 putatively causal CpG sites.
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Affiliation(s)
- Hunter J. Melton
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Zichen Zhang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Lang Wu
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Chong Wu
- Cancer Epidemiology Division, University of Hawaii Cancer Center, Honolulu, HI, USA
- Institute for Data Science in Oncology, The UT MD Anderson Cancer Center
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Zhan ZQ, Li JX, Chen YX, Fang JY. The effects of air and transportation noise pollution-related altered blood gene expression, DNA methylation, and protein abundance levels on gastrointestinal diseases risk. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175633. [PMID: 39163931 DOI: 10.1016/j.scitotenv.2024.175633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/03/2024] [Accepted: 08/17/2024] [Indexed: 08/22/2024]
Abstract
INTRODUCTION Air pollution and transportation noise pollution has been linked to gastrointestinal (GI) diseases, but their relationship remains unclear. METHODS We extracted the significantly modulated genes and CpG sites related to air pollution (PM2.5, PM10, and NOx) and transportation noise pollution (aircraft, railway, and traffic road noise) from previous published studies. Genome-wide methylation analysis and colocalization analysis with these CpG sites and GWAS data of GI diseases were performed to disentangle the relationship between pollution-related blood DNA methylation (DNAm) alterations and GI diseases risk. Summary-based Mendelian randomization (SMR) analysis assessed the impact of pollution-related genes on GI diseases risk across methylation, gene expression, and protein levels. Enrichment analysis investigated the implicated biological pathways and immune cell types. RESULTS DNAm at cg00227781 [CD300A] (modulated by NOx exposure) and cg19215199 [ZMIZ1] (modulated by PM2.5 exposure) was significantly linked to increased noninfective enteritis and colitis risk, while cg08500171 [BAT2] (modulated by NOx exposure) is significantly associated with an increased gastroesophageal reflux disease (GERD) risk. Colocalization analysis provides strong evidence supporting a shared causal variant between these associations. Multi-omics levels SMR analysis revealed that pollution-modulated lower DNAm at 5 specific CpG sites were associated with increased expression of 4 genes (IL21R, EVPL, SYNGR1, and WDR46), subsequently increasing the risk of GERD, ulcerative colitis, and gastric ulcer. 7 circulating proteins coded by pollution-modulated genes were observed to be associated with 6 GI diseases risk. Enrichment analysis implicates immune and inflammatory responses, MAPK signaling, and telomere maintenance in these pollution-induced effects. CONCLUSION We identified potential links between air and transportation noise pollution-related gene methylation, expression, and protein abundance with GI diseases risk, possibly revealing new therapeutic targets.
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Affiliation(s)
- Zhi-Qing Zhan
- Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; NHC Key Laboratory of Digestive Diseases; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Xin Li
- Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; NHC Key Laboratory of Digestive Diseases; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; NHC Key Laboratory of Digestive Diseases; State Key Laboratory for Oncogenes and Related Genes; Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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6
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Izaki A, Verbeke WJMI, Vrticka P, Ein-Dor T. A narrative on the neurobiological roots of attachment-system functioning. COMMUNICATIONS PSYCHOLOGY 2024; 2:96. [PMID: 39406946 DOI: 10.1038/s44271-024-00147-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 10/08/2024] [Indexed: 10/18/2024]
Abstract
Attachment theory is one of the most comprehensive frameworks in social and developmental psychology. It describes how selective, enduring emotional bonds between infants and their caregivers are formed and maintained throughout life. These attachment bonds exhibit distinct characteristics that are intimately tied to fundamental aspects of mammalian life, including pregnancy, birth, lactation, and infant brain development. However, there is a lack of a cohesive biological narrative that explains the psychological forces shaping attachment behavior and the emergence and consolidation of attachment patterns at a neurobiological level. Here, we propose a theoretical narrative focusing on organized attachment patterns that systematically link the two primary purposes of the attachment behavioral system: the provision of tangible protection or support and the corresponding subjective feeling of safety or security. We aim for this detailed delineation of neurobiological circuits to foster more comprehensive and interdisciplinary future research.
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Major TJ, Takei R, Matsuo H, Leask MP, Sumpter NA, Topless RK, Shirai Y, Wang W, Cadzow MJ, Phipps-Green AJ, Li Z, Ji A, Merriman ME, Morice E, Kelley EE, Wei WH, McCormick SPA, Bixley MJ, Reynolds RJ, Saag KG, Fadason T, Golovina E, O'Sullivan JM, Stamp LK, Dalbeth N, Abhishek A, Doherty M, Roddy E, Jacobsson LTH, Kapetanovic MC, Melander O, Andrés M, Pérez-Ruiz F, Torres RJ, Radstake T, Jansen TL, Janssen M, Joosten LAB, Liu R, Gaal OI, Crişan TO, Rednic S, Kurreeman F, Huizinga TWJ, Toes R, Lioté F, Richette P, Bardin T, Ea HK, Pascart T, McCarthy GM, Helbert L, Stibůrková B, Tausche AK, Uhlig T, Vitart V, Boutin TS, Hayward C, Riches PL, Ralston SH, Campbell A, MacDonald TM, Nakayama A, Takada T, Nakatochi M, Shimizu S, Kawamura Y, Toyoda Y, Nakaoka H, Yamamoto K, Matsuo K, Shinomiya N, Ichida K, Lee C, Bradbury LA, Brown MA, Robinson PC, Buchanan RRC, Hill CL, Lester S, Smith MD, Rischmueller M, Choi HK, Stahl EA, Miner JN, Solomon DH, Cui J, Giacomini KM, Brackman DJ, Jorgenson EM, Liu H, Susztak K, Shringarpure S, So A, Okada Y, Li C, Shi Y, Merriman TR. A genome-wide association analysis reveals new pathogenic pathways in gout. Nat Genet 2024:10.1038/s41588-024-01921-5. [PMID: 39406924 DOI: 10.1038/s41588-024-01921-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/21/2024] [Indexed: 10/18/2024]
Abstract
Gout is a chronic disease that is caused by an innate immune response to deposited monosodium urate crystals in the setting of hyperuricemia. Here, we provide insights into the molecular mechanism of the poorly understood inflammatory component of gout from a genome-wide association study (GWAS) of 2.6 million people, including 120,295 people with prevalent gout. We detected 377 loci and 410 genetically independent signals (149 previously unreported loci in urate and gout). An additional 65 loci with signals in urate (from a GWAS of 630,117 individuals) but not gout were identified. A prioritization scheme identified candidate genes in the inflammatory process of gout, including genes involved in epigenetic remodeling, cell osmolarity and regulation of NOD-like receptor protein 3 (NLRP3) inflammasome activity. Mendelian randomization analysis provided evidence for a causal role of clonal hematopoiesis of indeterminate potential in gout. Our study identifies candidate genes and molecular processes in the inflammatory pathogenesis of gout suitable for follow-up studies.
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Affiliation(s)
- Tanya J Major
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Riku Takei
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
- Department of Biomedical Information Management, National Defense Medical College Research Institute, National Defense Medical College, Saitama, Japan
| | - Megan P Leask
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicholas A Sumpter
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ruth K Topless
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Wei Wang
- Genomics R&D, 23andMe, Inc, Sunnyvale, CA, USA
| | - Murray J Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Zhiqiang Li
- The Biomedical Sciences Institute and The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Aichang Ji
- Shandong Provincial Key Laboratory of Metabolic Diseases, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- The Institute of Metabolic Diseases, Qingdao University, Qingdao, Shandong, China
| | - Marilyn E Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Emily Morice
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eric E Kelley
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA
| | - Wen-Hua Wei
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
| | | | - Matthew J Bixley
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Richard J Reynolds
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth G Saag
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tayaza Fadason
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Evgenia Golovina
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
- Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Abhishek Abhishek
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Michael Doherty
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Edward Roddy
- School of Medicine, Keele University, Keele, Staffordshire, United Kingdom
- Haywood Academic Rheumatology Centre, Midlands Partnership University NHS Foundation Trust, Stoke-on-Trent, UK
| | - Lennart T H Jacobsson
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Meliha C Kapetanovic
- Department of Clinical Sciences Lund, Section of Rheumatology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Emergency and Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Mariano Andrés
- Rheumatology Department, Dr Balmis General University Hospital-ISABIAL, Alicante, Spain
- Department of Clinical Medicine, Miguel Hernandez University, Alicante, Spain
| | - Fernando Pérez-Ruiz
- Osakidetza, OSI-EE-Cruces, BIOBizkaia Health Research Institute and Medicine Department of Medicine and Nursery School, University of the Basque Country, Biskay, Spain
| | - Rosa J Torres
- Department of Biochemistry, Hospital La Paz Institute for Health Research (IdiPaz), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Timothy Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center, Utrecht, The Netherlands
| | - Timothy L Jansen
- Department of Rheumatology, VieCuri Medical Centre, Venlo, The Netherlands
| | - Matthijs Janssen
- Department of Rheumatology, VieCuri Medical Centre, Venlo, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Science, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ruiqi Liu
- Department of Internal Medicine and Radboud Institute of Molecular Life Science, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Orsolya I Gaal
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tania O Crişan
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Simona Rednic
- Department of Rheumatology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - René Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frédéric Lioté
- Rheumatology Department, Feel'Gout, GH Paris Saint Joseph, Paris, France
- Rheumatology Department, INSERM U1132, BIOSCAR, University Paris Cité, Lariboisière Hospital, Paris, France
| | - Pascal Richette
- Rheumatology Department, INSERM U1132, BIOSCAR, University Paris Cité, Lariboisière Hospital, Paris, France
| | - Thomas Bardin
- Rheumatology Department, INSERM U1132, BIOSCAR, University Paris Cité, Lariboisière Hospital, Paris, France
| | - Hang Korng Ea
- Rheumatology Department, INSERM U1132, BIOSCAR, University Paris Cité, Lariboisière Hospital, Paris, France
| | - Tristan Pascart
- Department of Rheumatology, Hopital Saint-Philibert, Lille Catholic University, Lille, France
| | - Geraldine M McCarthy
- Department of Rheumatology, Mater Misericordiae University Hospital and School of Medicine, University College, Dublin, Ireland
| | - Laura Helbert
- Department of Rheumatology, Mater Misericordiae University Hospital and School of Medicine, University College, Dublin, Ireland
| | - Blanka Stibůrková
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
- Institute of Rheumatology, Prague, Czech Republic
| | - Anne-K Tausche
- Department of Rheumatology, University Clinic 'Carl Gustav Carus' at the Technical University, Dresden, Germany
| | - Till Uhlig
- Center for Treatment of Rheumatic and Musculoskeletal Diseases, Diakonhjemmet Hospital, Oslo, Norway
| | - Véronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Philip L Riches
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Thomas M MacDonald
- MEMO Research, Division of Molecular and Clinical Medicine, University of Dundee Medical School, Ninewells Hospital, Dundee, United Kingdom
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Yusuke Kawamura
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo, Japan
| | - Yu Toyoda
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology & Prevention, Aichi Cancer Center, Aichi, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Aichi, Japan
- The Japan Multi-Institutional Collaborative Cohort (J-MICC) Study, Tokyo, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
| | - Linda A Bradbury
- Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Philip C Robinson
- School of Clinical Medicine, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | | | - Catherine L Hill
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | - Susan Lester
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Maureen Rischmueller
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
- Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | - Hyon K Choi
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eli A Stahl
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeff N Miner
- Viscient Biosciences, 5752 Oberlin Dr., Suite 111, San Diego, CA, 92121, USA
| | - Daniel H Solomon
- Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jing Cui
- Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Deanna J Brackman
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Eric M Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Hongbo Liu
- Penn / The Children's Hospital of Pennsylvania Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19101, USA
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19101, USA
| | - Katalin Susztak
- Penn / The Children's Hospital of Pennsylvania Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19101, USA
- Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19101, USA
| | | | - Alexander So
- Service of Rheumatology, Center Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Changgui Li
- Shandong Provincial Key Laboratory of Metabolic Diseases, Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- The Institute of Metabolic Diseases, Qingdao University, Qingdao, Shandong, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Tony R Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA.
- The Institute of Metabolic Diseases, Qingdao University, Qingdao, Shandong, China.
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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8
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Koetsier J, Cavill R, Reijnders R, Harvey J, Homann J, Kouhsar M, Deckers K, Köhler S, Eijssen LMT, van den Hove DLA, Demuth I, Düzel S, Smith RG, Smith AR, Burrage J, Walker EM, Shireby G, Hannon E, Dempster E, Frayling T, Mill J, Dobricic V, Johannsen P, Wittig M, Franke A, Vandenberghe R, Schaeverbeke J, Freund-Levi Y, Frölich L, Scheltens P, Teunissen CE, Frisoni G, Blin O, Richardson JC, Bordet R, Engelborghs S, de Roeck E, Martinez-Lage P, Tainta M, Lleó A, Sala I, Popp J, Peyratout G, Verhey F, Tsolaki M, Andreasson U, Blennow K, Zetterberg H, Streffer J, Vos SJB, Lovestone S, Visser PJ, Lill CM, Bertram L, Lunnon K, Pishva E. Blood-based multivariate methylation risk score for cognitive impairment and dementia. Alzheimers Dement 2024; 20:6682-6698. [PMID: 39193899 DOI: 10.1002/alz.14061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION The established link between DNA methylation and pathophysiology of dementia, along with its potential role as a molecular mediator of lifestyle and environmental influences, positions blood-derived DNA methylation as a promising tool for early dementia risk detection. METHODS In conjunction with an extensive array of machine learning techniques, we employed whole blood genome-wide DNA methylation data as a surrogate for 14 modifiable and non-modifiable factors in the assessment of dementia risk in independent dementia cohorts. RESULTS We established a multivariate methylation risk score (MMRS) for identifying mild cognitive impairment cross-sectionally, independent of age and sex (P = 2.0 × 10-3). This score significantly predicted the prospective development of cognitive impairments in independent studies of Alzheimer's disease (hazard ratio for Rey's Auditory Verbal Learning Test (RAVLT)-Learning = 2.47) and Parkinson's disease (hazard ratio for MCI/dementia = 2.59). DISCUSSION Our work shows the potential of employing blood-derived DNA methylation data in the assessment of dementia risk. HIGHLIGHTS We used whole blood DNA methylation as a surrogate for 14 dementia risk factors. Created a multivariate methylation risk score for predicting cognitive impairment. Emphasized the role of machine learning and omics data in predicting dementia. The score predicts cognitive impairment development at the population level.
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Affiliation(s)
- Jarno Koetsier
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Rachel Cavill
- Department of Advanced Computing Sciences (DACS), Faculty of Science and Engineering (FSE), Maastricht University, Maastricht, The Netherlands
| | - Rick Reijnders
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Joshua Harvey
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Jan Homann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Morteza Kouhsar
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Kay Deckers
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Sebastian Köhler
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Lars M T Eijssen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Dr. Manuel Nagel, Würzburg, Germany
| | - Ilja Demuth
- Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BCRT - Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Rebecca G Smith
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Adam R Smith
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Joe Burrage
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Emma M Walker
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Gemma Shireby
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Eilis Hannon
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Emma Dempster
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tim Frayling
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen, Denmark
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | | | - Yvonne Freund-Levi
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Department of Geriatrics, Södertälje Hospital, Södertälje, Sweden
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Central Institute of Mental Health; Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Philip Scheltens
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Giovanni Frisoni
- Memory Center, Geneva University and University Hospitals; on behalf of the AMYPAD Consortium, Genève, Switzerland
| | - Olivier Blin
- Aix-Marseille University-CNRS, Marseille, France
| | - Jill C Richardson
- Neuroscience Therapeutic Area, GlaxoSmithKline R&D, Stevenage, Hertfordshire, UK
| | | | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerpen, Belgium
- Neuroprotection & Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Jette, Brussels, Belgium
| | - Ellen de Roeck
- Department of Biomedical Sciences, University of Antwerp, Antwerpen, Belgium
| | - Pablo Martinez-Lage
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Gipuzkoa, Spain
| | - Mikel Tainta
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Gipuzkoa, Spain
| | - Alberto Lleó
- Neurology Department, Centro de Investigación en Red en enfermedades neurodegenerativas (CIBERNED), Hospital Sant Pau, Sant Antoni Maria Claret, Barcelona, Spain
| | - Isabel Sala
- Neurology Department, Centro de Investigación en Red en enfermedades neurodegenerativas (CIBERNED), Hospital Sant Pau, Sant Antoni Maria Claret, Barcelona, Spain
| | - Julius Popp
- University Hospital of Psychiatry Zürich, University of Zürich, Zürich, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Magda Tsolaki
- 1st Department of Neurology, School of Medicine, `Laboratory of Neurodegenerative Diseases, Center for Interdisciplinary Research and Innovation, Aristotle University of Thessaloniki, and Alzheimer Hellas, Macedonia, Balkan Center, Thessaloniki, Greece
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
- Clinical Neurochemistry Lab, Sahlgrenska University Hospital, Göteborg, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, P.R. China
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, Maple House, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Shatin, N.T., Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johannes Streffer
- AC Immune SA, formerly Janssen R&D, LLC. Beerse, Belgium at the time of study conduct, Lausanne, Switzerland
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Simon Lovestone
- University of Oxford, Oxford, United Kingdom; Currently at Johnson & Johnson Innovative Medicines, Beerse, Belgium
| | - Pieter-Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Geriatrics, Södertälje Hospital, Södertälje, Sweden
| | - Christina M Lill
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College, South Kensington Campus, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Katie Lunnon
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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9
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Carnes MU, Quach BC, Zhou L, Han S, Tao R, Mandal M, Deep-Soboslay A, Marks JA, Page GP, Maher BS, Jaffe AE, Won H, Bierut LJ, Hyde TM, Kleinman JE, Johnson EO, Hancock DB. Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci. Neuropsychopharmacology 2024; 49:1749-1757. [PMID: 38830989 PMCID: PMC11399277 DOI: 10.1038/s41386-024-01885-4] [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: 11/30/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
Smoking is a leading cause of preventable morbidity and mortality. Smoking is heritable, and genome-wide association studies (GWASs) of smoking behaviors have identified hundreds of significant loci. Most GWAS-identified variants are noncoding with unknown neurobiological effects. We used genome-wide genotype, DNA methylation, and RNA sequencing data in postmortem human nucleus accumbens (NAc) to identify cis-methylation/expression quantitative trait loci (meQTLs/eQTLs), investigate variant-by-cigarette smoking interactions across the genome, and overlay QTL evidence at smoking GWAS-identified loci to evaluate their regulatory potential. Active smokers (N = 52) and nonsmokers (N = 171) were defined based on cotinine biomarker levels and next-of-kin reporting. We simultaneously tested variant and variant-by-smoking interaction effects on methylation and expression, separately, adjusting for biological and technical covariates and correcting for multiple testing using a two-stage procedure. We found >2 million significant meQTL variants (padj < 0.05) corresponding to 41,695 unique CpGs. Results were largely driven by main effects, and five meQTLs, mapping to NUDT12, FAM53B, RNF39, and ADRA1B, showed a significant interaction with smoking. We found 57,683 significant eQTL variants for 958 unique eGenes (padj < 0.05) and no smoking interactions. Colocalization analyses identified loci with smoking-associated GWAS variants that overlapped meQTLs/eQTLs, suggesting that these heritable factors may influence smoking behaviors through functional effects on methylation/expression. One locus containing MUSTN1 and ITIH4 colocalized across all data types (GWAS, meQTL, and eQTL). In this first genome-wide meQTL map in the human NAc, the enriched overlap with smoking GWAS-identified genetic loci provides evidence that gene regulation in the brain helps explain the neurobiology of smoking behaviors.
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Affiliation(s)
- Megan Ulmer Carnes
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Bryan C Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Linran Zhou
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Shizhong Han
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Ran Tao
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Meisha Mandal
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | | | - Jesse A Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Grier P Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Brion S Maher
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Eric O Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
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10
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Smith RG, Pishva E, Kouhsar M, Imm J, Dobricic V, Johannsen P, Wittig M, Franke A, Vandenberghe R, Schaeverbeke J, Freund-Levi Y, Frölich L, Scheltens P, Teunissen CE, Frisoni G, Blin O, Richardson JC, Bordet R, Engelborghs S, de Roeck E, Martinez-Lage P, Altuna M, Tainta M, Lleó A, Sala I, Popp J, Peyratout G, Winchester L, Nevado-Holgado A, Verhey F, Tsolaki M, Andreasson U, Blennow K, Zetterberg H, Streffer J, Vos SJB, Lovestone S, Visser PJ, Bertram L, Lunnon K. Blood DNA methylomic signatures associated with CSF biomarkers of Alzheimer's disease in the EMIF-AD study. Alzheimers Dement 2024; 20:6722-6739. [PMID: 39193893 DOI: 10.1002/alz.14098] [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: 12/08/2023] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION We investigated blood DNA methylation patterns associated with 15 well-established cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) pathophysiology, neuroinflammation, and neurodegeneration. METHODS We assessed DNA methylation in 885 blood samples from the European Medical Information Framework for Alzheimer's Disease (EMIF-AD) study using the EPIC array. RESULTS We identified Bonferroni-significant differential methylation associated with CSF YKL-40 (five loci) and neurofilament light chain (NfL; seven loci) levels, with two of the loci associated with CSF YKL-40 levels correlating with plasma YKL-40 levels. A co-localization analysis showed shared genetic variants underlying YKL-40 DNA methylation and CSF protein levels, with evidence that DNA methylation mediates the association between genotype and protein levels. Weighted gene correlation network analysis identified two modules of co-methylated loci correlated with several amyloid measures and enriched in pathways associated with lipoproteins and development. DISCUSSION We conducted the most comprehensive epigenome-wide association study (EWAS) of AD-relevant CSF biomarkers to date. Future work should explore the relationship between YKL-40 genotype, DNA methylation, and protein levels in the brain. HIGHLIGHTS Blood DNA methylation was assessed in the EMIF-AD MBD study. Epigenome-wide association studies (EWASs) were performed for 15 Alzheimer's disease (AD)-relevant cerebrospinal fluid (CSF) biomarker measures. Five Bonferroni-significant loci were associated with YKL-40 levels and seven with neurofilament light chain (NfL). DNA methylation in YKL-40 co-localized with previously reported genetic variation. DNA methylation potentially mediates the effect of single-nucleotide polymorphisms (SNPs) in YKL-40 on CSF protein levels.
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Affiliation(s)
- Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Morteza Kouhsar
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK
| | - Jennifer Imm
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen, Denmark
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Jolien Schaeverbeke
- Laboratory for Cognitive Neurology, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Yvonne Freund-Levi
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Department of Geriatrics, Södertälje Hospital, Södertälje, Sweden
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Central Institut of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Giovanni Frisoni
- Memory center, Geneva University and University Hospitals; on behalf of the AMYPAD consortium, Geneva, Switzerland
| | - Olivier Blin
- Aix-Marseille University-CNRS, Marseille, France
| | - Jill C Richardson
- Neuroscience Therapeutic Area, GlaxoSmithKline R&D, Stevenage, Hertfordshire, UK
| | | | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuroprotection & Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Jette, Brussels, Belgium
| | - Ellen de Roeck
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Pablo Martinez-Lage
- Center for Research and Advanced Therapies, Fundación CITA-Alzhéimer Fundazioa, San Sebastian, Gipuzkoa, Spain
| | - Miren Altuna
- Center for Research and Advanced Therapies, Fundación CITA-Alzhéimer Fundazioa, San Sebastian, Gipuzkoa, Spain
| | - Mikel Tainta
- Center for Research and Advanced Therapies, Fundación CITA-Alzhéimer Fundazioa, San Sebastian, Gipuzkoa, Spain
| | - Alberto Lleó
- Servicio de Neurología, Centre of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Hospital Sant Pau, Barcelona, Spain
| | - Isabel Sala
- Servicio de Neurología, Centre of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Hospital Sant Pau, Barcelona, Spain
| | - Julius Popp
- University Hospital of Psychiatry Zürich, University of Zürich, Zürich, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | | | | | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Magda Tsolaki
- 1st Department of Neurology, School of Medicine, Laboratory of Neurodegenerative Diseases, Center for Interdisciplinary Research and Innovation, Aristotle University of Thessaloniki, and Alzheimer Hellas, Thessaloniki, Greece
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, PR China
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, N.T., Shatin, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johannes Streffer
- Translational Medicine Neuroscience, UCB Biopharma SRL, Brussels, Belgium
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Simon Lovestone
- Department of Psychiatry, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Currently at: Johnson & Johnson Innovative Medicines, Beerse, Belgium
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK
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11
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Kiselev I, Kulakova O, Baturina O, Kabilov M, Boyko A, Favorova O. Different genome-wide DNA methylation patterns in CD4+ T lymphocytes and CD14+ monocytes characterize relapse and remission of multiple sclerosis: Focus on GNAS. Mult Scler Relat Disord 2024; 91:105910. [PMID: 39369632 DOI: 10.1016/j.msard.2024.105910] [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: 05/06/2024] [Revised: 07/31/2024] [Accepted: 09/27/2024] [Indexed: 10/08/2024]
Abstract
BACKGROUND Relapsing-remitting multiple sclerosis (RRMS) is a most common form of multiple sclerosis in which periods of neurological worsening are followed by periods of clinical remission. RRMS relapses are caused by an acute autoimmune inflammatory process, which can occur in any area of the central nervous system. Although development of exacerbation cannot yet be accurately predicted, various external factors are known to affect its risk. These factors may trigger the pathological process through epigenetic mechanisms of gene expression regulation, first of all, through changes in DNA methylation. METHODS In the present work, we for the first time analyzed genome-wide DNA methylation patterns in CD4+ T lymphocytes and CD14+ monocytes of the same RRMS patients in relapse and remission. The effects of the differential methylation on gene expression were studied using qPCR. RESULTS We found 743 differentially methylated CpG positions (DMPs) in CD4+ cells and only 113 DMPs in CD14+ cells. They were mostly hypermethylated in RRMS relapse in both cell populations. However, the proportion of hypermethylated DMPs (as well as DMPs located within or in close proximity to CpG islands) was significantly higher in CD4+ T lymphocytes. In CD4+ and CD14+ cells we identified 469 and 67 DMP-containing genes, respectively; 25 of them were common for two cell populations. When we conducted a search for differentially methylated genomic regions (DMRs), we found a CD4+ specific DMR hypermethylated in RRMS relapse (adj. p = 0.03) within the imprinted GNAS locus. Total level of the protein-coding GNAS transcripts in CD4+ T cells decreased significantly in the row from healthy control to RRMS remission and then to RRMS relapse (adj. p = 3.1 × 10-7 and 0.011, respectively). CONCLUSION Our findings suggest that the epigenetic mechanism of DNA methylation in immune cells contributes to the development of RRMS relapse. Further studies are now required to validate these results and shed light on the molecular mechanisms underlying the observed GNAS methylation and expression changes.
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Affiliation(s)
- Ivan Kiselev
- Pirogov Russian National Research Medical University, 117997, Moscow, Ostrovityanova st. 1, Russia.
| | - Olga Kulakova
- Pirogov Russian National Research Medical University, 117997, Moscow, Ostrovityanova st. 1, Russia
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Lavrentiev ave. 8, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Lavrentiev ave. 8, Russia
| | - Alexey Boyko
- Pirogov Russian National Research Medical University, 117997, Moscow, Ostrovityanova st. 1, Russia
| | - Olga Favorova
- Pirogov Russian National Research Medical University, 117997, Moscow, Ostrovityanova st. 1, Russia
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12
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Tian Y, McDonnell SK, Wu L, Larson NB, Wang L. Fine Mapping Regulatory Variants by Characterizing Native CpG Methylation with Nanopore Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.614715. [PMID: 39386487 PMCID: PMC11463401 DOI: 10.1101/2024.09.27.614715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
5-methylcytosine (5mC) is the most common chemical modification occurring on the CpG sites across the human genome. Bisulfite conversion combined with short-read whole genome sequencing can capture and quantify the modification at single nucleotide resolution. However, the PCR amplification process could lead to duplicative methylation patterns and introduce 5mC detection bias. Additionally, the limited read length also restricts co-methylation analysis between distant CpG sites. The bisulfite conversion process presents a significant challenge for detecting variant-specific methylation due to the destruction of allele information in the sequencing reads. To address these issues, we sought to characterize the human methylation profiling with the nanopore long-read sequencing, aiming to demonstrate its potential for long-range co-methylation analysis with native modification call and intact allele information retained. In this regard, we first analyzed the nanopore demo data in the adaptive sampling sequencing run targeting all human CpG islands. We applied the linkage disequilibrium (LD) R 2 to calculate the co-methylation in nanopore data, and further identified 27,875, 50,481, 26,542 and 51,189 methylation haplotype blocks (MHB) in COLO829, COLO829BL, HCC1395 and HCC1395BL cell lines, respectively. Interestingly, while we found that majority of the co-methylation were in a short range (≤200bp), a small portion (1∼3%) showed long distance (≥1,000bp), suggesting potential remote regulatory mechanisms across the genome. To further characterize the epigenetic changes related to transcription factor binding, we profiled the 5mC percentage changes surrounding various motif sites in JASPAR collection and found that CTCF and KLF5 binding sites showed reduced methylation, while FOXE1 and ZNF354A sites showed increased methylation. To further investigate the allele-specific 5mCG in the prostate genome, we designed a target region covering methylation quantitative trait loci (mQTL) and genome-wide association study (GWAS) risk germline variants and generated long reads with adaptive sampling run in the 22Rv1 cell line. To identify the allele-specific methylation in the 22Rv1 cell line, we performed long-read based phasing and compared the 5mCG signals between the two haplotypes. As a result, we identified 6,390 haplotype-specific methylated regions in the 22Rv1 cell line (p-MWU ≤ 1e-5 and delta ≥ 50%). By examining haplotype-specific methylated regions near the phasing variants, we identified examples of allele-specific methylated regions that showed allele-specific accessibility in the ATAC-seq data. By further integrating the ATAC-seq data of 22Rv1, we found that methylation levels were negatively correlated with chromatin accessibility at the genome-wide scale. Our study has revealed native methylome profiling while preserving haplotype information, offering a novel approach to uncovering the regulatory mechanisms of the human prostate genome.
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13
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Diez-Ahijado L, Cilleros-Portet A, Fernández-Jimenez N, Fernández MF, Guxens M, Julvez J, Llop S, Lopez-Espinosa MJ, Subiza-Pérez M, Lozano M, Ibarluzea J, Sunyer J, Bustamante M, Cosin-Tomas M. Evaluating the association between placenta DNA methylation and cognitive functions in the offspring. Transl Psychiatry 2024; 14:383. [PMID: 39304652 DOI: 10.1038/s41398-024-03094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
The placenta plays a crucial role in protecting the fetus from environmental harm and supports the development of its brain. In fact, compromised placental function could predispose an individual to neurodevelopmental disorders. Placental epigenetic modifications, including DNA methylation, could be considered a proxy of placental function and thus plausible mediators of the association between intrauterine environmental exposures and genetics, and childhood and adult mental health. Although neurodevelopmental disorders such as autism spectrum disorder have been investigated in relation to placenta DNA methylation, no studies have addressed the association between placenta DNA methylation and child's cognitive functions. Thus, our goal here was to investigate whether the placental DNA methylation profile measured using the Illumina EPIC array is associated with three different cognitive domains (namely verbal score, perceptive performance score, and general cognitive score) assessed by the McCarthy Scales of Children's functions in childhood at age 4. To this end, we conducted epigenome-wide association analyses, including data from 255 mother-child pairs within the INMA project, and performed a follow-up functional analysis to help the interpretation of the findings. After multiple-testing correction, we found that methylation at 4 CpGs (cg1548200, cg02986379, cg00866476, and cg14113931) was significantly associated with the general cognitive score, and 2 distinct differentially methylated regions (DMRs) (including 27 CpGs) were significantly associated with each cognitive dimension. Interestingly, the genes annotated to these CpGs, such as DAB2, CEP76, PSMG2, or MECOM, are involved in placenta, fetal, and brain development. Moreover, functional enrichment analyses of suggestive CpGs (p < 1 × 10-4) revealed gene sets involved in placenta development, fetus formation, and brain growth. These findings suggest that placental DNA methylation could be a mechanism contributing to the alteration of important pathways in the placenta that have a consequence on the offspring's brain development and cognitive function.
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Affiliation(s)
- Laia Diez-Ahijado
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Nora Fernández-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Mariana F Fernández
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- University of Granada, Biomedical Research Centre, Instituto de Investigación Biosanitaria (ibs.GRANADA), Granada, Spain
| | - Monica Guxens
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jordi Julvez
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Clinical and Epidemiological Neuroscience, Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Sabrina Llop
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
| | - Maria-Jose Lopez-Espinosa
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Faculty of Nursing and Chiropody, University of Valencia, Valencia, Spain
| | - Mikel Subiza-Pérez
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Department of Clinical and Health Psychology and Research Methods, University of the Basque Country UPV/EHU, Avenida Tolosa 70, 20018, Donostia-San Sebastián, Spain
- Bradford Institute for Health Research, Temple Bank House, Bradford Royal Infirmary, Duckworth Lane, BD9 6RJ, Bradford, UK
- Biodonostia Health Research Institute, Group of Environmental Epidemiology and Child Development, Paseo Doctor Begiristain s/n, 20014, Donostia- San Sebastián, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Jesus Ibarluzea
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Biodonostia Health Research Institute, Group of Environmental Epidemiology and Child Development, Paseo Doctor Begiristain s/n, 20014, Donostia- San Sebastián, Spain
- Ministry of Health of the Basque Government, Sub-Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain
| | - Jordi Sunyer
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Marta Cosin-Tomas
- ISGlobal, Institute for Global Health, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública, Madrid, Spain.
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14
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Melén E, Zar HJ, Siroux V, Shaw D, Saglani S, Koppelman GH, Hartert T, Gern JE, Gaston B, Bush A, Zein J. Asthma Inception: Epidemiologic Risk Factors and Natural History Across the Life Course. Am J Respir Crit Care Med 2024; 210:737-754. [PMID: 38981012 PMCID: PMC11418887 DOI: 10.1164/rccm.202312-2249so] [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: 12/10/2023] [Accepted: 07/09/2024] [Indexed: 07/11/2024] Open
Abstract
Asthma is a descriptive label for an obstructive inflammatory disease in the lower airways manifesting with symptoms including breathlessness, cough, difficulty in breathing, and wheezing. From a clinician's point of view, asthma symptoms can commence at any age, although most patients with asthma-regardless of their age of onset-seem to have had some form of airway problems during childhood. Asthma inception and related pathophysiologic processes are therefore very likely to occur early in life, further evidenced by recent lung physiologic and mechanistic research. Herein, we present state-of-the-art updates on the role of genetics and epigenetics, early viral and bacterial infections, immune response, and pathophysiology, as well as lifestyle and environmental exposures, in asthma across the life course. We conclude that early environmental insults in genetically vulnerable individuals inducing abnormal, pre-asthmatic airway responses are key events in asthma inception, and we highlight disease heterogeneity across ages and the potential shortsightedness of treating all patients with asthma using the same treatments. Although there are no interventions that, at present, can modify long-term outcomes, a precision-medicine approach should be implemented to optimize treatment and tailor follow-up for all patients with asthma.
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Affiliation(s)
- Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Heather J. Zar
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Valerie Siroux
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Dominic Shaw
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Sejal Saglani
- National Heart and Lung Institute, Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Groningen, the Netherlands
| | - Tina Hartert
- Department of Medicine and Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin
| | | | - Andrew Bush
- National Heart and Lung Institute, Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
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15
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Drouard G, Wang Z, Heikkinen A, Foraster M, Julvez J, Kanninen KM, van Kamp I, Pirinen M, Ollikainen M, Kaprio J. Lifestyle differences between co-twins are associated with decreased similarity in their internal and external exposome profiles. Sci Rep 2024; 14:21261. [PMID: 39261679 PMCID: PMC11390871 DOI: 10.1038/s41598-024-72354-7] [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: 02/29/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024] Open
Abstract
Whether differences in lifestyle between co-twins are reflected in differences in their internal or external exposome profiles remains largely underexplored. We therefore investigated whether within-pair differences in lifestyle were associated with within-pair differences in exposome profiles across four domains: the external exposome, proteome, metabolome and epigenetic age acceleration (EAA). For each domain, we assessed the similarity of co-twin profiles using Gaussian similarities in up to 257 young adult same-sex twin pairs (54% monozygotic). We additionally tested whether similarity in one domain translated into greater similarity in another. Results suggest that a lower degree of similarity in co-twins' exposome profiles was associated with greater differences in their behavior and substance use. The strongest association was identified between excessive drinking behavior and the external exposome. Overall, our study demonstrates how social behavior and especially substance use are connected to the internal and external exposomes, while controlling for familial confounders.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Zhiyang Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Foraster
- PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull (URL), Barcelona, Spain
| | - Jordi Julvez
- Clinical and Epidemiological Neuroscience (NeuroÈpia), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- ISGlobal, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irene van Kamp
- Centre for Sustainability, Environment and Health, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
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16
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Shore CJ, Villicaña S, El-Sayed Moustafa JS, Roberts AL, Gunn DA, Bataille V, Deloukas P, Spector TD, Small KS, Bell JT. Genetic effects on the skin methylome in healthy older twins. Am J Hum Genet 2024; 111:1932-1952. [PMID: 39137780 PMCID: PMC11393713 DOI: 10.1016/j.ajhg.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/22/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Whole-skin DNA methylation variation has been implicated in several diseases, including melanoma, but its genetic basis has not yet been fully characterized. Using bulk skin tissue samples from 414 healthy female UK twins, we performed twin-based heritability and methylation quantitative trait loci (meQTL) analyses for >400,000 DNA methylation sites. We find that the human skin DNA methylome is on average less heritable than previously estimated in blood and other tissues (mean heritability: 10.02%). meQTL analysis identified local genetic effects influencing DNA methylation at 18.8% (76,442) of tested CpG sites, as well as 1,775 CpG sites associated with at least one distal genetic variant. As a functional follow-up, we performed skin expression QTL (eQTL) analyses in a partially overlapping sample of 604 female twins. Colocalization analysis identified over 3,500 shared genetic effects affecting thousands of CpG sites (10,067) and genes (4,475). Mediation analysis of putative colocalized gene-CpG pairs identified 114 genes with evidence for eQTL effects being mediated by DNA methylation in skin, including in genes implicating skin disease such as ALOX12 and CSPG4. We further explored the relevance of skin meQTLs to skin disease and found that skin meQTLs and CpGs under genetic influence were enriched for multiple skin-related genome-wide and epigenome-wide association signals, including for melanoma and psoriasis. Our findings give insights into the regulatory landscape of epigenomic variation in skin.
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Affiliation(s)
- Christopher J Shore
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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17
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Islam F, Lisoway A, Oh ES, Fiori LM, Magarbeh L, Elsheikh SSM, Kim HK, Kloiber S, Kennedy JL, Frey BN, Milev R, Soares CN, Parikh SV, Placenza F, Hassel S, Taylor VH, Leri F, Blier P, Uher R, Farzan F, Lam RW, Turecki G, Foster JA, Rotzinger S, Kennedy SH, Müller DJ. Integrative Genetic Variation, DNA Methylation, and Gene Expression Analysis of Escitalopram and Aripiprazole Treatment Outcomes in Depression: A CAN-BIND-1 Study. PHARMACOPSYCHIATRY 2024; 57:232-244. [PMID: 38917846 DOI: 10.1055/a-2313-9979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Little is known about the interplay between genetics and epigenetics on antidepressant treatment (1) response and remission, (2) side effects, and (3) serum levels. This study explored the relationship among single nucleotide polymorphisms (SNPs), DNA methylation (DNAm), and mRNA levels of four pharmacokinetic genes, CYP2C19, CYP2D6, CYP3A4, and ABCB1, and its effect on these outcomes. METHODS The Canadian Biomarker Integration Network for Depression-1 dataset consisted of 177 individuals with major depressive disorder treated for 8 weeks with escitalopram (ESC) followed by 8 weeks with ESC monotherapy or augmentation with aripiprazole. DNAm quantitative trait loci (mQTL), identified by SNP-CpG associations between 20 SNPs and 60 CpG sites in whole blood, were tested for associations with our outcomes, followed by causal inference tests (CITs) to identify methylation-mediated genetic effects. RESULTS Eleven cis-SNP-CpG pairs (q<0.05) constituting four unique SNPs were identified. Although no significant associations were observed between mQTLs and response/remission, CYP2C19 rs4244285 was associated with treatment-related weight gain (q=0.027) and serum concentrations of ESCadj (q<0.001). Between weeks 2-4, 6.7% and 14.9% of those with *1/*1 (normal metabolizers) and *1/*2 (intermediate metabolizers) genotypes, respectively, reported ≥2 lbs of weight gain. In contrast, the *2/*2 genotype (poor metabolizers) did not report weight gain during this period and demonstrated the highest ESCadj concentrations. CITs did not indicate that these effects were epigenetically mediated. DISCUSSION These results elucidate functional mechanisms underlying the established associations between CYP2C19 rs4244285 and ESC pharmacokinetics. This mQTL SNP as a marker for antidepressant-related weight gain needs to be further explored.
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Affiliation(s)
- Farhana Islam
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Amanda Lisoway
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Edward S Oh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Laura M Fiori
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Verdun, Quebec, Canada
| | - Leen Magarbeh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Samar S M Elsheikh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Helena K Kim
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Stefan Kloiber
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - James L Kennedy
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Benicio N Frey
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Roumen Milev
- Department of Psychiatry, Queen's University, Providence Care, Kingston, Ontario, Canada
| | - Claudio N Soares
- Department of Psychiatry, Queen's University, Providence Care, Kingston, Ontario, Canada
| | - Sagar V Parikh
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Franca Placenza
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
| | - Stefanie Hassel
- Department of Psychiatry, University of Calgary, Calgary, Alberta, Canada; Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Valerie H Taylor
- Department of Psychiatry, University of Calgary, Calgary, Alberta, Canada; Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Francesco Leri
- Department of Psychology and Neuroscience, University of Guelph, Guelph, Ontario, Canada
| | - Pierre Blier
- The Royal Institute of Mental Health Research, Ottawa, Ontario, Canada
| | - Rudolf Uher
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Faranak Farzan
- Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia, Canada
| | - Raymond W Lam
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Verdun, Quebec, Canada
| | - Jane A Foster
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Susan Rotzinger
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, St Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sidney H Kennedy
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
- Department of Psychiatry, St Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario, Canada
| | - Daniel J Müller
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Clinic of Würzburg, Würzburg, Germany
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18
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Meeks GL, Scelza B, Asnake HM, Prall S, Patin E, Froment A, Fagny M, Quintana-Murci L, Henn BM, Gopalan S. Common DNA sequence variation influences epigenetic aging in African populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.608843. [PMID: 39253488 PMCID: PMC11383046 DOI: 10.1101/2024.08.26.608843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Aging is associated with genome-wide changes in DNA methylation in humans, facilitating the development of epigenetic age prediction models. However, most of these models have been trained primarily on European-ancestry individuals, and none account for the impact of methylation quantitative trait loci (meQTL). To address these gaps, we analyzed the relationships between age, genotype, and CpG methylation in 3 understudied populations: central African Baka (n = 35), southern African ‡Khomani San (n = 52), and southern African Himba (n = 51). We find that published prediction methods yield higher mean errors in these cohorts compared to European-ancestry individuals, and find that unaccounted-for DNA sequence variation may be a significant factor underlying this loss of accuracy. We leverage information about the associations between DNA genotype and CpG methylation to develop an age predictor that is minimally influenced by meQTL, and show that this model remains accurate across a broad range of genetic backgrounds. Intriguingly, we also find that the older individuals and those exhibiting relatively lower epigenetic age acceleration in our cohorts tend to carry more epigenetic age-reducing genetic variants, suggesting a novel mechanism by which heritable factors can influence longevity.
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Affiliation(s)
- Gillian L Meeks
- Integrative Genetics and Genomics Graduate Program, University of California, Davis, CA 95694, USA
| | - Brooke Scelza
- Department of Anthropology, University of California, Los Angeles, CA, 90095, USA
| | - Hana M Asnake
- Forensic Science Graduate Program, University of California, Davis, CA, 95694, USA
| | - Sean Prall
- Department of Anthropology, University of California, Los Angeles, CA, 90095, USA
| | - Etienne Patin
- Human Evolutionary Genetics Unit, CNRS UMR2000, Paris, 75015, France
| | - Alain Froment
- Institut de Recherche pour le Développement, UMR 208, Muséum National d'Histoire Naturelle, Paris, 75005, France
| | - Maud Fagny
- Human Evolutionary Genetics Unit, CNRS UMR2000, Paris, 75015, France
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Genetique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, 91190, France
| | | | - Brenna M Henn
- Department of Anthropology, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center and Center for Population Biology, University of California, Davis, CA 95694, USA
| | - Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
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19
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Zhang W, Zhang X, Qiu C, Zhang Z, Su KJ, Luo Z, Liu M, Zhao B, Wu L, Tian Q, Shen H, Wu C, Deng HW. An atlas of genetic effects on the monocyte methylome across European and African populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.12.24311885. [PMID: 39211851 PMCID: PMC11361221 DOI: 10.1101/2024.08.12.24311885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Elucidating the genetic architecture of DNA methylation (DNAm) is crucial for decoding the etiology of complex diseases. However, current epigenomic studies often suffer from incomplete coverage of methylation sites and the use of tissues containing heterogeneous cell populations. To address these challenges, we present a comprehensive human methylome atlas based on deep whole-genome bisulfite sequencing (WGBS) and whole-genome sequencing (WGS) of purified monocytes from 298 European Americans (EA) and 160 African Americans (AA) in the Louisiana Osteoporosis Study. Our atlas enables the analysis of over 25 million DNAm sites. We identified 1,383,250 and 1,721,167 methylation quantitative trait loci (meQTLs) in cis -regions for EA and AA populations, respectively, with 880,108 sites shared between ancestries. While cis -meQTLs exhibited population-specific patterns, primarily due to differences in minor allele frequencies, shared cis -meQTLs showed high concordance across ancestries. Notably, cis -heritability estimates revealed significantly higher mean values in the AA population (0.09) compared to the EA population (0.04). Furthermore, we developed population-specific DNAm imputation models using Elastic Net, enabling methylome-wide association studies (MWAS) for 1,976,046 and 2,657,581 methylation sites in EA and AA, respectively. The performance of our MWAS models was validated through a systematic multi-ancestry analysis of 41 complex traits from the Million Veteran Program. Our findings bridge the gap between genomics and the monocyte methylome, uncovering novel methylation-phenotype associations and their transferability across diverse ancestries. The identified meQTLs, MWAS models, and data resources are freely available at www.gcbhub.org and https://osf.io/gct57/ .
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20
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Ji A, Sui Y, Xue X, Ji X, Shi W, Shi Y, Terkeltaub R, Dalbeth N, Takei R, Yan F, Sun M, Li M, Lu J, Cui L, Liu Z, Wang C, Li X, Han L, Fang Z, Sun W, Liang Y, He Y, Zheng G, Wang X, Wang J, Zhang H, Pang L, Qi H, Li Y, Cheng Z, Li Z, Xiao J, Zeng C, Merriman TR, Qu H, Fang X, Li C. Novel Genetic Loci in Early-Onset Gout Derived From Whole-Genome Sequencing of an Adolescent Gout Cohort. Arthritis Rheumatol 2024. [PMID: 39118347 DOI: 10.1002/art.42969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE Mechanisms underlying the adolescent-onset and early-onset gout are unclear. This study aimed to discover variants associated with early-onset gout. METHODS We conducted whole-genome sequencing in a discovery adolescent-onset gout cohort of 905 individuals (gout onset 12 to 19 years) to discover common and low-frequency single-nucleotide variants (SNVs) associated with gout. Candidate common SNVs were genotyped in an early-onset gout cohort of 2,834 individuals (gout onset ≤30 years old), and meta-analysis was performed with the discovery and replication cohorts to identify loci associated with early-onset gout. Transcriptome and epigenomic analyses, quantitative real-time polymerase chain reaction and RNA sequencing in human peripheral blood leukocytes, and knock-down experiments in human THP-1 macrophage cells investigated the regulation and function of candidate gene RCOR1. RESULTS In addition to ABCG2, a urate transporter previously linked to pediatric-onset and early-onset gout, we identified two novel loci (Pmeta < 5.0 × 10-8): rs12887440 (RCOR1) and rs35213808 (FSTL5-MIR4454). Additionally, we found associations at ABCG2 and SLC22A12 that were driven by low-frequency SNVs. SNVs in RCOR1 were linked to elevated blood leukocyte messenger RNA levels. THP-1 macrophage culture studies revealed the potential of decreased RCOR1 to suppress gouty inflammation. CONCLUSION This is the first comprehensive genetic characterization of adolescent-onset gout. The identified risk loci of early-onset gout mediate inflammatory responsiveness to crystals that could mediate gouty arthritis. This study will contribute to risk prediction and therapeutic interventions to prevent adolescent-onset gout.
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Affiliation(s)
- Aichang Ji
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Sui
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Xue
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiapeng Ji
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenrui Shi
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China, and Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Riku Takei
- Asia Pacific Gout Consortium and University of Alabama at Birmingham
| | - Fei Yan
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mingshu Sun
- Shandong Provincial Clinical Research Center for Immune Diseases and Gout & Shandong Provincial Key Laboratory of Metabolic Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Maichao Li
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jie Lu
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lingling Cui
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhen Liu
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Can Wang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xinde Li
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Han
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhanjie Fang
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Wenyan Sun
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yue Liang
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Yuwei He
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guangmin Zheng
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Xuefeng Wang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jiayi Wang
- Development Center for Medical Science & Technology, National Health Commission of the People's Republic of China, Beijing, China
| | - Hui Zhang
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China
| | - Lei Pang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Han Qi
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yushuang Li
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zan Cheng
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhiqiang Li
- The Biomedical Sciences Institute and The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Changqing Zeng
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
| | - Tony R Merriman
- Asia Pacific Gout Consortium, University of Alabama at Birmingham, Institute of Metabolic Diseases, Qingdao University, Qingdao, China, and University of Otago, Dunedin, New Zealand
| | - Hongzhu Qu
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, and Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
| | - Xiangdong Fang
- China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, and Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
| | - Changgui Li
- The Affiliated Hospital of Qingdao University, Qingdao, China, Asia Pacific Gout Consortium, and Institute of Metabolic Diseases, Qingdao University, Qingdao, China
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21
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Giordano A, Pignolet B, Mascia E, Clarelli F, Sorosina M, Misra K, Bucciarelli F, Ferrè L, Moiola L, Liblau R, Filippi M, Esposito F. DNA Methylation in the Anti-Mullerian Hormone Gene and the Risk of Disease Activity in Multiple Sclerosis. Ann Neurol 2024; 96:289-301. [PMID: 38747444 DOI: 10.1002/ana.26959] [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: 01/26/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVE Multiple sclerosis (MS) has a complex pathobiology, with genetic and environmental factors being crucial players. Understanding the mechanisms underlying heterogeneity in disease activity is crucial for tailored treatment. We explored the impact of DNA methylation, a key mechanism in the genetics-environment interplay, on disease activity in MS. METHODS Peripheral immune methylome profiling using Illumina Infinium MethylationEPIC BeadChips was conducted on 249 untreated relapsing-remitting MS patients, sampled at the start of disease-modifying treatment (DMT). A differential methylation analysis compared patients with evidence of disease activity (EDA) to those with no evidence of disease activity (NEDA) over 2 years from DMT start. Utilizing causal inference testing (CIT) and Mendelian randomization (MR), we sought to elucidate the relationships between DNA methylation, gene expression, genetic variation, and disease activity. RESULTS Four differentially methylated regions (DMRs) were identified between EDA and NEDA. Examining the influence of single nucleotide polymorphisms (SNPs), 923 variants were found to account for the observed differences in the 4 DMRs. Importantly, 3 out of the 923 SNPs, affecting DNA methylation in a DMR linked to the anti-Mullerian hormone (AMH) gene, were associated with disease activity risk in an independent cohort of 1,408 MS patients. CIT and MR demonstrated that DNA methylation in AMH acts as a mediator for the genetic risk of disease activity. INTERPRETATION This study uncovered a novel molecular pathway implicating the interaction between DNA methylation and genetic variation in the risk of disease activity in MS, emphasizing the role of sex hormones, particularly the AMH, in MS pathobiology. ANN NEUROL 2024;96:289-301.
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Affiliation(s)
- Antonino Giordano
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology and MS Center, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Béatrice Pignolet
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France
- Neurosciences Department, Toulouse University Hospital, Toulouse, France
| | - Elisabetta Mascia
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ferdinando Clarelli
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Kaalindi Misra
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Florence Bucciarelli
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France
| | - Laura Ferrè
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology and MS Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Lucia Moiola
- Department of Neurology and MS Center, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Roland Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France
- Department of Immunology, Toulouse University Hospitals, Toulouse, France
| | - Massimo Filippi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology and MS Center, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Federica Esposito
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology and MS Center, IRCCS Ospedale San Raffaele, Milan, Italy
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22
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Stefansson OA, Sigurpalsdottir BD, Rognvaldsson S, Halldorsson GH, Juliusson K, Sveinbjornsson G, Gunnarsson B, Beyter D, Jonsson H, Gudjonsson SA, Olafsdottir TA, Saevarsdottir S, Magnusson MK, Lund SH, Tragante V, Oddsson A, Hardarson MT, Eggertsson HP, Gudmundsson RL, Sverrisson S, Frigge ML, Zink F, Holm H, Stefansson H, Rafnar T, Jonsdottir I, Sulem P, Helgason A, Gudbjartsson DF, Halldorsson BV, Thorsteinsdottir U, Stefansson K. The correlation between CpG methylation and gene expression is driven by sequence variants. Nat Genet 2024; 56:1624-1631. [PMID: 39048797 PMCID: PMC11319203 DOI: 10.1038/s41588-024-01851-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation. We used nanopore sequencing to determine haplotype-specific methylation rates of 15.3 million CpG units in 7,179 whole-blood genomes. We identified 189,178 methylation depleted sequences where three or more proximal CpGs were unmethylated on at least one haplotype. A total of 77,789 methylation depleted sequences (~41%) associated with 80,503 cis-acting sequence variants, which we termed allele-specific methylation quantitative trait loci (ASM-QTLs). RNA sequencing of 896 samples from the same blood draws used to perform nanopore sequencing showed that the ASM-QTL, that is, DNA sequence variability, drives most of the correlation found between gene expression and CpG methylation. ASM-QTLs were enriched 40.2-fold (95% confidence interval 32.2, 49.9) among sequence variants associating with hematological traits, demonstrating that ASM-QTLs are important functional units in the noncoding genome.
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Affiliation(s)
| | - Brynja Dogg Sigurpalsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | - Gisli Hreinn Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | - Thorunn Asta Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Karl Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigrun Helga Lund
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Marteinn Thor Hardarson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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23
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Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. Population Diversity at the Single-Cell Level. Annu Rev Genomics Hum Genet 2024; 25:27-49. [PMID: 38382493 DOI: 10.1146/annurev-genom-021623-083207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Population-scale single-cell genomics is a transformative approach for unraveling the intricate links between genetic and cellular variation. This approach is facilitated by cutting-edge experimental methodologies, including the development of high-throughput single-cell multiomics and advances in multiplexed environmental and genetic perturbations. Examining the effects of natural or synthetic genetic variants across cellular contexts provides insights into the mutual influence of genetics and the environment in shaping cellular heterogeneity. The development of computational methodologies further enables detailed quantitative analysis of molecular variation, offering an opportunity to examine the respective roles of stochastic, intercellular, and interindividual variation. Future opportunities lie in leveraging long-read sequencing, refining disease-relevant cellular models, and embracing predictive and generative machine learning models. These advancements hold the potential for a deeper understanding of the genetic architecture of human molecular traits, which in turn has important implications for understanding the genetic causes of human disease.
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Affiliation(s)
| | - Pooja Kathail
- Center for Computational Biology, University of California, Berkeley, California, USA
| | - Bryson Choy
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Min Cheol Kim
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Thomas Mazumder
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Chun Jimmie Ye
- Arc Institute, Palo Alto, California, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
- Bakar Computational Health Sciences Institute, Gladstone-UCSF Institute of Genomic Immunology, Parker Institute for Cancer Immunotherapy, Department of Epidemiology and Biostatistics, Department of Microbiology and Immunology, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA;
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24
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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024; 40:642-667. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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Ruehlmann AK, Cecil KM, Lippert F, Yolton K, Ryan PH, Brunst KJ. Epigenome-wide association study of fluoride exposure during early adolescence and DNA methylation among U.S. children. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174916. [PMID: 39038671 DOI: 10.1016/j.scitotenv.2024.174916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Exposure to fluoride in early childhood has been associated with altered cognition, intelligence, attention, and neurobehavior. Fluoride-related neurodevelopment effects have been shown to vary by sex and very little is known about the mechanistic processes involved. There is limited research on how fluoride exposure impacts the epigenome, potentially leading to changes in DNA methylation of specific genes regulating key developmental processes. In the Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS), urine samples were analyzed using a microdiffusion method to determine childhood urinary fluoride adjusted for specific gravity (CUFsg) concentrations. Whole blood DNA methylation was assessed using the Infinium MethylationEPIC BeadChip 850 k Array. In a cross-sectional analysis, we interrogated epigenome-wide DNA methylation at 775,141 CpG loci across the methylome in relation to CUFsg concentrations in 272 early adolescents at age 12 years. Among all participants, higher concentrations of CUF were associated with differential methylation of one CpG (p < 6 × 10-8) located in the gene body of GBF1 (cg25435255). Among females, higher concentrations of CUFsg were associated with differential methylation of 7 CpGs; only three CpGs were differentially methylated among males with no overlap of significant CpGs observed among females. Secondary analyses revealed several differentially methylated regions (DMRs) and CpG loci mapping to genes with key roles in psychiatric outcomes, social interaction, and cognition, as well as immunologic and metabolic phenotypes. While fluoride exposure may impact the epigenome during early adolescence, the functional consequences of these changes are unclear warranting further investigation.
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Affiliation(s)
- Anna K Ruehlmann
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Kim M Cecil
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA; Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Frank Lippert
- Department of Cariology, Operative Dentistry, and Dental Public Health, Oral Health Research Institute, Indiana University School of Dentistry, Indianapolis, IN, USA
| | - Kimberly Yolton
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of General and Community Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Patrick H Ryan
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kelly J Brunst
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA.
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Huang D, Shang W, Xu M, Wan Q, Zhang J, Tang X, Shen Y, Wang Y, Yu Y. Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension. Circ Res 2024; 135:e76-e93. [PMID: 38841840 DOI: 10.1161/circresaha.124.324455] [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: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. METHODS We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. RESULTS We discovered that DNA methylation-associated genetic effects, especially in non-cytosine-phosphate-guanine (non-CpG) island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 (nuclear receptor subfamily 2 group F member 2) binding at the enhancer locus. CONCLUSIONS Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.
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Affiliation(s)
- Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
- School of Food Science and Technology, Jiangnan University, Wuxi, China (D.H.)
| | - Wenlong Shang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Mengtong Xu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Qiangyou Wan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine (Q.W.)
| | - Jin Zhang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Xiaofeng Tang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Yan Wang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young J, Chen XS, Dietrich ST, Kunkle B, Martin E, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. Database (Oxford) 2024; 2024:baae061. [PMID: 39028752 PMCID: PMC11259044 DOI: 10.1093/database/baae061] [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: 01/19/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledgebase containing manually curated summary statistics from 98 published tables in 38 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels-at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD. Database URL: https://miami-ad.org/.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami, Miller School of Medicine, 7700 W Camino Real, Boca Raton, FL 33433, USA
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Juan Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Eden Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
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28
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Yang Y, Chen Y, Xu S, Guo X, Jia G, Ping J, Shu X, Zhao T, Yuan F, Wang G, Xie Y, Ci H, Liu H, Qi Y, Liu Y, Liu D, Li W, Ye F, Shu XO, Zheng W, Li L, Cai Q, Long J. Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk. Nat Commun 2024; 15:6071. [PMID: 39025880 PMCID: PMC11258330 DOI: 10.1038/s41467-024-50404-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: 09/06/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
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Affiliation(s)
- Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA.
| | - Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuai Xu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianying Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fangcheng Yuan
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gang Wang
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Xie
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Ci
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongmo Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yawen Qi
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Dan Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Li Li
- Department of Family Medicine, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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29
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Castellini-Pérez O, Povedano E, Barturen G, Martínez-Bueno M, Iakovliev A, Kerick M, López-Domínguez R, Marañón C, Martín J, Ballestar E, Borghi MO, Qiu W, Zhu C, Shankara S, Spiliopoulou A, de Rinaldis E, Carnero-Montoro E, Alarcón-Riquelme ME. Molecular subtypes explain lupus epigenomic heterogeneity unveiling new regulatory genetic risk variants. NPJ Genom Med 2024; 9:38. [PMID: 39013887 PMCID: PMC11252280 DOI: 10.1038/s41525-024-00420-0] [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: 04/03/2023] [Accepted: 05/17/2024] [Indexed: 07/18/2024] Open
Abstract
The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel drug targets for SLE. This study reveals possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and novel disease-specific meQTLs. Finally, novel targets for drug development were discovered.
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Affiliation(s)
- Olivia Castellini-Pérez
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- University of Granada, Granada, Spain
| | - Elena Povedano
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- Spanish National Research Council (CSIC), Institute of Economy, Geography and Demography, Madrid (IEGD), Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
| | - Guillermo Barturen
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Manuel Martínez-Bueno
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Andrii Iakovliev
- Usher Institute of Population Health Sciences and Informatics. University of Edinburgh Medical School, EH8 9YL, Edinburgh, UK
| | - Martin Kerick
- IBPLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, 18016, Spain
| | - Raúl López-Domínguez
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Concepción Marañón
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Javier Martín
- IBPLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, 18016, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | | | - Weiliang Qiu
- Sanofi, Early Development and Research, Cambridge, MA, USA
| | - Cheng Zhu
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Srinivas Shankara
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Athina Spiliopoulou
- Usher Institute of Population Health Sciences and Informatics. University of Edinburgh Medical School, EH8 9YL, Edinburgh, UK
| | - Emanuele de Rinaldis
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Elena Carnero-Montoro
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- University of Granada, Granada, Spain.
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- Institute for Environmental Medicine, Karolinska Institutet, 171 67, Solna, Sweden.
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Katrinli S, Wani AH, Maihofer AX, Ratanatharathorn A, Daskalakis NP, Montalvo-Ortiz J, Núñez-Ríos DL, Zannas AS, Zhao X, Aiello AE, Ashley-Koch AE, Avetyan D, Baker DG, Beckham JC, Boks MP, Brick LA, Bromet E, Champagne FA, Chen CY, Dalvie S, Dennis MF, Fatumo S, Fortier C, Galea S, Garrett ME, Geuze E, Grant G, Hauser MA, Hayes JP, Hemmings SM, Huber BR, Jajoo A, Jansen S, Kessler RC, Kimbrel NA, King AP, Kleinman JE, Koen N, Koenen KC, Kuan PF, Liberzon I, Linnstaedt SD, Lori A, Luft BJ, Luykx JJ, Marx CE, McLean SA, Mehta D, Milberg W, Miller MW, Mufford MS, Musanabaganwa C, Mutabaruka J, Mutesa L, Nemeroff CB, Nugent NR, Orcutt HK, Qin XJ, Rauch SAM, Ressler KJ, Risbrough VB, Rutembesa E, Rutten BPF, Seedat S, Stein DJ, Stein MB, Toikumo S, Ursano RJ, Uwineza A, Verfaellie MH, Vermetten E, Vinkers CH, Ware EB, Wildman DE, Wolf EJ, Young RM, Zhao Y, van den Heuvel LL, Uddin M, Nievergelt CM, Smith AK, Logue MW. Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: A meta-analysis of 23 military and civilian cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310422. [PMID: 39072012 PMCID: PMC11275670 DOI: 10.1101/2024.07.15.24310422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background The occurrence of post-traumatic stress disorder (PTSD) following a traumatic event is associated with biological differences that can represent the susceptibility to PTSD, the impact of trauma, or the sequelae of PTSD itself. These effects include differences in DNA methylation (DNAm), an important form of epigenetic gene regulation, at multiple CpG loci across the genome. Moreover, these effects can be shared or specific to both central and peripheral tissues. Here, we aim to identify blood DNAm differences associated with PTSD and characterize the underlying biological mechanisms by examining the extent to which they mirror associations across multiple brain regions. Methods As the Psychiatric Genomics Consortium (PGC) PTSD Epigenetics Workgroup, we conducted the largest cross-sectional meta-analysis of epigenome-wide association studies (EWASs) of PTSD to date, involving 5077 participants (2156 PTSD cases and 2921 trauma-exposed controls) from 23 civilian and military studies. PTSD diagnosis assessments were harmonized following the standardized guidelines established by the PGC-PTSD Workgroup. DNAm was assayed from blood using either Illumina HumanMethylation450 or MethylationEPIC (850K) BeadChips. A common QC pipeline was applied. Within each cohort, DNA methylation was regressed on PTSD, sex (if applicable), age, blood cell proportions, and ancestry. An inverse variance-weighted meta-analysis was performed. We conducted replication analyses in tissue from multiple brain regions, neuronal nuclei, and a cellular model of prolonged stress. Results We identified 11 CpG sites associated with PTSD in the overall meta-analysis (1.44e-09 < p < 5.30e-08), as well as 14 associated in analyses of specific strata (military vs civilian cohort, sex, and ancestry), including CpGs in AHRR and CDC42BPB . Many of these loci exhibit blood-brain correlation in methylation levels and cross-tissue associations with PTSD in multiple brain regions. Methylation at most CpGs correlated with their annotated gene expression levels. Conclusions This study identifies 11 PTSD-associated CpGs, also leverages data from postmortem brain samples, GWAS, and genome-wide expression data to interpret the biology underlying these associations and prioritize genes whose regulation differs in those with PTSD.
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31
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Chen Y, Wang G, Chen J, Wang C, Dong X, Chang HM, Yuan S, Zhao Y, Mu L. Genetic and Epigenetic Landscape for Drug Development in Polycystic Ovary Syndrome. Endocr Rev 2024; 45:437-459. [PMID: 38298137 DOI: 10.1210/endrev/bnae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
The treatment of polycystic ovary syndrome (PCOS) faces challenges as all known treatments are merely symptomatic. The US Food and Drug Administration has not approved any drug specifically for treating PCOS. As the significance of genetics and epigenetics rises in drug development, their pivotal insights have greatly enhanced the efficacy and success of drug target discovery and validation, offering promise for guiding the advancement of PCOS treatments. In this context, we outline the genetic and epigenetic advancement in PCOS, which provide novel insights into the pathogenesis of this complex disease. We also delve into the prospective method for harnessing genetic and epigenetic strategies to identify potential drug targets and ensure target safety. Additionally, we shed light on the preliminary evidence and distinctive challenges associated with gene and epigenetic therapies in the context of PCOS.
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Affiliation(s)
- Yi Chen
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- The First School of Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Guiquan Wang
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen 361003, China
- Xiamen Key Laboratory of Reproduction and Genetics, Xiamen University, Xiamen 361023, China
| | - Jingqiao Chen
- The First School of Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Congying Wang
- The Department of Cardiology, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang 322000, China
| | - Xi Dong
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hsun-Ming Chang
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung 40400, Taiwan
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm 171 65, Sweden
| | - Yue Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing 100007, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University, Beijing 100191, China
| | - Liangshan Mu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Gao F, Tom E, Rydz C, Cho W, Kolesnikov AV, Sha Y, Papadam A, Jafari S, Joseph A, Ahanchi A, Saraei NBS, Lyon D, Foik A, Nie Q, Grassmann F, Kefalov VJ, Skowronska-Krawczyk D. Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601592. [PMID: 39005302 PMCID: PMC11244954 DOI: 10.1101/2024.07.01.601592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), which are primarily localized in cell membranes, where they govern membrane biophysical properties such as diffusion, permeability, domain formation, and curvature generation. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, and this decline is associated with normal age-related visual decline and pathological age-related macular degeneration (AMD). ELOVL2 (Elongation of very-long-chain fatty acids-like 2) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs, and methylation level of its promoter is currently the best predictor of chronological age. Here, we show that mice lacking ELOVL2-specific enzymatic activity (Elovl2 C234W ) have impaired contrast sensitivity and slower rod response recovery following bright light exposure. Intravitreal supplementation with the direct product of ELOVL2, 24:5n-3, in aged animals significantly improved visual function and reduced accumulation of ApoE, HTRA1 and complement proteins in sub-RPE deposits. At the molecular level, the gene expression pattern observed in retinas supplemented with 24:5n-3 exhibited a partial rejuvenation profile, including decreased expression of aging-related genes and a transcriptomic signature of younger retina. Finally, we present the first human genetic data showing significant association of several variants in the human ELOVL2 locus with the onset of intermediate AMD, underlying the translational significance of our findings. In sum, our study identifies novel therapeutic opportunities and defines ELOVL2 as a promising target for interventions aimed at preventing age-related vision loss.
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Affiliation(s)
- Fangyuan Gao
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - Emily Tom
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA
| | - Cezary Rydz
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA
| | - William Cho
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA
| | - Alexander V. Kolesnikov
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - Yutong Sha
- Department of Mathematics, University of California Irvine, CA
| | | | - Samantha Jafari
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - Andrew Joseph
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - Ava Ahanchi
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - Nika Balalaei Someh Saraei
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
| | - David Lyon
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, CA
| | - Andrzej Foik
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Qing Nie
- Department of Mathematics, University of California Irvine, CA
| | - Felix Grassmann
- Institute for Clinical Research and System Medicine, Health and Medical University, Potsdam, Germany
| | - Vladimir J. Kefalov
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA
| | - Dorota Skowronska-Krawczyk
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA
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Huang Z, Peng S, Cen T, Wang X, Ma L, Cao Z. Association between biological ageing and periodontitis: Evidence from a cross-sectional survey and multi-omics Mendelian randomization analysis. J Clin Periodontol 2024. [PMID: 38956929 DOI: 10.1111/jcpe.14040] [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: 03/04/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
AIM To investigate the relationship and potential causality between biological ageing and periodontitis. MATERIALS AND METHODS We obtained the National Health and Nutrition Examination Survey (NHANES) and genome-wide association study (GWAS) summary statistics as well as single-cell sequencing data. Multivariate regression analysis based on cross-sectional data, Mendelian randomization (MR) and multi-omics integration analysis were employed to explore the causal association and potential molecular mechanisms between biological ageing and periodontitis. Additionally, two-step MR mediation analysis explored the risk factors in biological ageing-mediated periodontitis. RESULTS We analysed data from 3189 participants in the NHANES data and found that higher biological age was associated with increased risk of periodontitis. MR analyses revealed causal associations between biological age measures and periodontitis risk. Frailty (odds ratio [OR] = 2.08, 95% confidence interval [CI]: 1.04-4.18, p = .039) and GrimAge acceleration (OR = 1.16, 95% CI: 1.01-1.32, p = .033) were causally associated with periodontitis risk, and these results were validated in a large-scale meta-periodontitis GWAS dataset. Additionally, the risk effects of body mass index, waist circumference and lifetime smoking on periodontitis were partially mediated by frailty and GrimAge acceleration. CONCLUSIONS Evidence from cross-sectional survey and MR analysis suggests that biological ageing increases the risk of periodontitis. Additionally, improving the associated risk factors can help prevent both ageing and periodontitis.
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Affiliation(s)
- Zhendong Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Simin Peng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Ting Cen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiaoxuan Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Li Ma
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhengguo Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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Miller RG, Mychaleckyj JC, Onengut-Gumuscu S, Orchard TJ, Costacou T. An Epigenome-Wide Association Study of DNA Methylation and Proliferative Retinopathy over 28 Years in Type 1 Diabetes. OPHTHALMOLOGY SCIENCE 2024; 4:100497. [PMID: 38601260 PMCID: PMC11004204 DOI: 10.1016/j.xops.2024.100497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024]
Abstract
Purpose To perform a prospective epigenome-wide association study of DNA methylation (DNAm) and 28-year proliferative diabetic retinopathy (PDR) incidence in type 1 diabetes (T1D). Design Prospective observational cohort study. Participants The Pittsburgh Epidemiology of Diabetes Complications (EDC) study of childhood-onset (< 17 years) T1D. Methods Stereoscopic fundus photographs were taken in fields 1, 2, and 4 at baseline, 2, 4, 6, 8, 16, 23, and 28 years after DNAm measurements. The photos were graded using the modified Airlie House System. In those free of PDR at baseline (n = 265; mean T1D duration of 18 years at baseline), whole blood DNAm (EPIC array) at 683 597 CpGs was analyzed in Cox models for time to event. Associations between significant CpGs and clinical risk factors were assessed; genetic variants associated with DNAm were identified (methylation quantitative trait loci [meQTLs]). Mendelian randomization was used to examine evidence of causal associations between DNAm and PDR. Post hoc regional and functional analyses were performed. Main Outcome Measures Proliferative diabetic retinopathy was defined as the first instance of a grade of ≥ 60 in at least 1 eye or pan-retinal photocoagulation for PDR. Follow-up time was calculated from the study visit at which DNAm data were available (baseline) until PDR incidence or censoring (December 31, 2018 or last follow-up). Results PDR incidence was 53% over 28-years' follow-up. Greater DNAm of cg27512687 (KIF16B) was associated with reduced PDR incidence (P = 6.3 × 10-9; false discovery rate [FDR]: < 0.01); 113 cis-meQTLs (P < 5 × 10-8) were identified. Mendelian randomization analysis using the sentinel meQTL as the instrumental variable supported a potentially causal association between cg27512687 and PDR. Cg27512687 was also associated with lower pulse rate and albumin excretion rate and higher estimated glomerular filtration rate, but its association with PDR remained independently significant after adjustment for those factors. In regional analyses, DNAm of FUT4, FKBP1A, and RIN2 was also associated with PDR incidence. Conclusions DNA methylation of KIF16B, FUT4, FKBP1A, and RIN2 was associated with PDR incidence, supporting roles for epigenetic regulation of iron clearance, developmental pathways, and autophagy in PDR pathogenesis. Further study of those loci may provide insight into novel targets for interventions to prevent or delay PDR in T1D. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Rachel G. Miller
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Trevor J. Orchard
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Tina Costacou
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
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Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics 2024; 40:btae423. [PMID: 38963309 PMCID: PMC11233119 DOI: 10.1093/bioinformatics/btae423] [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: 03/19/2024] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION Infinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip. RESULTS We present mLiftOver, a user-friendly tool that harmonizes probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells. AVAILABILITY AND IMPLEMENTATION mLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html. Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz. The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.
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Affiliation(s)
- Brian H Chen
- California Pacific Medical Center Research Institute, Sutter Health, San Francisco, CA 94143, United States
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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Shi X, Li M, Yao J, Li MD, Yang Z. Alcohol drinking, DNA methylation and psychiatric disorders: A multi-omics Mendelian randomization study to investigate causal pathways. Addiction 2024; 119:1226-1237. [PMID: 38523595 DOI: 10.1111/add.16465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/05/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND AND AIMS Whether alcohol-related DNA methylation has a causal effect on psychiatric disorders has not been investigated. Furthermore, a comprehensive investigation into the causal relationship and underlying mechanisms linking alcohol consumption and psychiatric disorders has been lacking. This study aimed to evaluate the causal effect of general alcohol intake and pathological drinking behaviors on psychiatric disorders, alcohol-associated DNA methylation on gene expression and psychiatric disorders, and gene expression on psychiatric disorders. DESIGN Two-sample design Mendelian randomization (MR) analysis. Various sensitivity and validation analyses, including colocalization analysis, were conducted to test the robustness of the results. SETTING Genome-wide association study (GWAS) data mainly from GWAS and Sequencing Consortium of Alcohol and Nicotine use (GSCAN), Genetics of DNA Methylation Consortium (GoDMC) and Psychiatric Genomics Consortium (PGC) with European ancestry. PARTICIPANTS The GWAS summary data on general alcohol intake (drinks per week, n = 941 280), pathological drinking behaviors (including alcohol use disorder [AUD, n = 313 959] and problematic alcohol use [PAU, n = 435 563]) and psychiatric disorders (including schizophrenia, major depressive disorder and bipolar disorder, n = 51 710-500 199) were included. Alcohol-related DNA methylation CpG sites (n = 9643) and mQTL data from blood (n = 27 750) and brain (n = 1160), BrainMeta v2 and GTEx V8 eQTL summary data (n = 73-2865) were also included. MEASUREMENTS Genetic variants were selected as instrumental variables for exposures, including drinks per week, AUD, PAU, alcohol-related DNA methylation CpG sites (mQTL) and genes selected (eQTL). FINDINGS Pathological drinking behaviors were associated with an increased risk of psychiatric disorders after removing outliers or controlling for alcohol consumption. MR analysis identified 10 alcohol-related CpG sites with colocalization evidence that were causally associated with psychiatric disorders (P = 1.65 × 10-4-7.52 × 10-22). Furthermore, the expression of genes (RERE, PTK6, GATAD2B, COG8, PDF and GAS5) mapped to these CpG sites in the brain, led by the cortex, were significantly associated with psychiatric disorders (P = 1.19 × 10-2-3.51 × 10-7). CONCLUSIONS Pathological drinking behavior and alcohol-related DNA methylation appear to have a causal effect on psychiatric disorders. The expression of genes regulated by the alcohol-related DNA methylation sites may underpin this association.
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Affiliation(s)
- Xiaoqiang Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Jianhua Yao
- Joint Institute of Tobacco and Health, Kunming, Yunnan, China
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Elliott HR, Bennett CL, Caramaschi D, English S. Negative association between higher maternal pre-pregnancy body mass index and breastfeeding outcomes is not mediated by DNA methylation. Sci Rep 2024; 14:14675. [PMID: 38918574 PMCID: PMC11199553 DOI: 10.1038/s41598-024-65605-0] [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: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
The benefits of breastfeeding for the health and wellbeing of both infants and mothers are well documented, yet global breastfeeding rates are low. One factor associated with low breast feeding is maternal body mass index (BMI), which is used as a measure of obesity. The negative relationship between maternal obesity and breastfeeding is likely caused by a variety of social, psychological, and physiological factors. Maternal obesity may also have a direct biological association with breastfeeding through changes in maternal DNA methylation. Here, we investigate this potential biological association using data from a UK-based cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC). We find that pre-pregnancy body mass index (BMI) is associated with lower initiation to breastfeed and shorter breastfeeding duration. We conduct epigenome-wide association studies (EWAS) of pre-pregnancy BMI and breastfeeding outcomes, and run candidate-gene analysis of methylation sites associated with BMI identified via previous meta-EWAS. We find that DNA methylation at cg11453712, annotated to PHTP1, is associated with pre-pregnancy BMI. From our results, neither this association nor those at candidate-gene sites are likely to mediate the link between pre-pregnancy BMI and breastfeeding.
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Affiliation(s)
- Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Chloe L Bennett
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Doretta Caramaschi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Faculty of Health and Life Sciences, Department of Psychology, University of Exeter, Exeter, UK
| | - Sinead English
- School of Biological Sciences, University of Bristol, Bristol, UK.
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Singh M, Dolan CV, Lapato DM, Hottenga JJ, Pool R, Verhulst B, Boomsma DI, Breeze CE, de Geus EJC, Hemani G, Min JL, Peterson RE, Maes HHM, van Dongen J, Neale MC. Twin-based Mendelian Randomization Analyses Highlight Smoking's Effects on Blood DNA Methylation, with Putative Reverse Causation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309184. [PMID: 38946972 PMCID: PMC11213072 DOI: 10.1101/2024.06.19.24309184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Epigenome-wide association studies (EWAS) aim to identify differentially methylated loci associated with complex traits and disorders. EWAS of cigarette smoking shows some of the most widespread DNA methylation (DNAm) associations in blood. However, traditional EWAS cannot differentiate between causation and confounding, leading to ambiguity in etiological interpretations. Here, we apply an integrated approach combining Mendelian Randomization and twin-based Direction-of-Causation analyses (MR-DoC) to examine causality underlying smoking-associated blood DNAm changes in the Netherlands Twin Register (N=2577). Evidence across models suggests that current smoking's causal effects on DNAm likely drive many of the previous EWAS findings, implicating functional pathways relevant to several adverse health outcomes of smoking, including hemopoiesis, cell- and neuro-development, and immune regulation. Additionally, we find evidence of potential reverse causal influences at some DNAm sites, with 17 of these sites enriched for gene regulatory functional elements in the brain. The top three sites with evidence of DNAm's effects on smoking annotate to genes involved in G protein-coupled receptor signaling (GNG7, RGS3) and innate immune response (SLC15A4), elucidating potential biological risk factors for smoking. This study highlights the utility of integrating genotypic and DNAm measures in twin cohorts to clarify the causal relationships between health behaviors and blood DNAm.
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Affiliation(s)
- Madhurbain Singh
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
| | - Conor V. Dolan
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Dana M. Lapato
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Brad Verhulst
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, College Station, TX, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Current address: Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
| | - Charles E. Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
- UCL Cancer Institute, University College London, London, UK
| | - Eco J. C. de Geus
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Josine L. Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Roseann E. Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Hermine H. M. Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- These authors jointly supervised this work
| | - Michael C. Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Biological Psychology, Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
- These authors jointly supervised this work
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Shen S, Sobczyk MK, Paternoster L, Brown SJ. From GWASs toward Mechanistic Understanding with Case Studies in Dermatogenetics. J Invest Dermatol 2024; 144:1189-1199.e8. [PMID: 38782533 DOI: 10.1016/j.jid.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 03/06/2024] [Indexed: 05/25/2024]
Abstract
Many human skin diseases result from the complex interplay of genetic and environmental mechanisms that are largely unknown. GWASs have yielded insight into the genetic aspect of complex disease by highlighting regions of the genome or specific genetic variants associated with disease. Leveraging this information to identify causal genes and cell types will provide insight into fundamental biology, inform diagnostics, and aid drug discovery. However, the etiological mechanisms from genetic variant to disease are still unestablished in most cases. There now exists an unprecedented wealth of data and computational methods for variant interpretation in a functional context. It can be challenging to decide where to start owing to a lack of consensus on the best way to identify causal genetic mechanisms. This article highlights 3 key aspects of genetic variant interpretation: prioritizing causal genes, cell types, and pathways. We provide a practical overview of the main methods and datasets, giving examples from recent atopic dermatitis studies to provide a blueprint for variant interpretation. A collection of resources, including brief description and links to the packages and web tools, is provided for researchers looking to start in silico follow-up genetic analysis of associated genetic variants.
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Affiliation(s)
- Silvia Shen
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom; Institute for Evolution and Ecology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
| | - Maria K Sobczyk
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Sara J Brown
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom; Department of Dermatology, NHS Lothian, Edinburgh, United Kingdom
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40
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Liu Y, Liu S, Zhen D, Huang J, He F. Ultrasensitive Detection of Tumor Suppressor Gene Methylation by Piezoelectric Sensing Based on Enrichment of Transcription Activator-Like Effectors. Anal Chem 2024; 96:8534-8542. [PMID: 38743638 DOI: 10.1021/acs.analchem.4c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The detection of DNA methylation at cytosine/guanine dinucleotide (CpG) islands in promoter regions of tumor suppressor genes has great potential for early cancer screening, diagnosis, and prognosis monitoring. Nevertheless, achieving accurate, sensitive, cost-effective, and quantitative detection of target methylated DNA remains challenging. Herein, we propose a novel piezoelectric sensor (series piezoelectric quartz crystal (SPQC)) based on transcription activator-like effectors (TALEs) for detecting DNA methylation of Ras association domain family 1 isoform A (RASSF1A) tumor suppressor genes (R-5mC). The sensor employs TALEs-Ni magnetic beads to specifically recognize and separate the R-5mC, thereby improving the detection selectivity. The TALEs-Ni magnetic beads-R-5mC complex is sheared by a nucleic acid enzyme (DNAzyme) to release the single-stranded DNA (ST). ST initiates a catalyzed hairpin assembly (CHA) reaction on the surface of the electrode, which in turn triggers the hybridization chain reaction (HCR) and silver staining for enhanced detection sensitivity. The strategy exhibits a linear response in the detection of R-5mC in the range of 1 fM to 1 nM with a detection limit of 0.79 fM. R-5mC as low as 0.01% can be detected, even in the presence of large numbers of unmethylated DNA. The detection of R-5mC in circulating cell-free DNA (cfDNA) derived from clinical plasma specimens of lung cancer patients yielded satisfactory results.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Shuyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Deshuai Zhen
- Hunan Key Laboratory of Typical Environment Pollution and Health Hazards, College of Public Health, University of South China, Hengyang 421001, PR China
| | - Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
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Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.
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Affiliation(s)
- David C Goldberg
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Cameron Cloud
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | - Elliot Kim
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | | | | | | | | | | | | | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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42
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Peng Q, Liu X, Li W, Jing H, Li J, Gao X, Luo Q, Breeze CE, Pan S, Zheng Q, Li G, Qian J, Yuan L, Yuan N, You C, Du S, Zheng Y, Yuan Z, Tan J, Jia P, Wang J, Zhang G, Lu X, Shi L, Guo S, Liu Y, Ni T, Wen B, Zeng C, Jin L, Teschendorff AE, Liu F, Wang S. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits. Nat Genet 2024; 56:846-860. [PMID: 38641644 DOI: 10.1038/s41588-023-01494-9] [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: 11/17/2021] [Accepted: 08/02/2023] [Indexed: 04/21/2024]
Abstract
Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height. Trans-mQTL hotspots revealed biological pathways contributing to EA-specific genetic associations, including an ERG-mediated 233 trans-mCpG network, implicated in hematopoietic cell differentiation, which likely reflects binding efficiency modulation of the ERG protein complex. More than 90% of mQTLs were shared between different blood cell lineages, with a smaller fraction of lineage-specific mQTLs displaying preferential hypomethylation in the respective lineages. Our study provides new insights into the mQTL landscape across genetic ancestries and their downstream effects on cellular processes and diseases/traits.
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Affiliation(s)
- Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Wenran Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Han Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xingjian Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Guochao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiaqiang Qian
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liyun Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Chenglong You
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Guoqing Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Xianping Lu
- Shenzhen Chipscreen Biosciences Co. Ltd., Shenzhen, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Bo Wen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Christiansen C, Potier L, Martin TC, Villicaña S, Castillo-Fernandez JE, Mangino M, Menni C, Tsai PC, Campbell PJ, Mullin S, Ordoñana JR, Monteagudo O, Sachdev PS, Mather KA, Trollor JN, Pietilainen KH, Ollikainen M, Dalgård C, Kyvik K, Christensen K, van Dongen J, Willemsen G, Boomsma DI, Magnusson PKE, Pedersen NL, Wilson SG, Grundberg E, Spector TD, Bell JT. Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications. EBioMedicine 2024; 103:105096. [PMID: 38574408 PMCID: PMC11004697 DOI: 10.1016/j.ebiom.2024.105096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) susceptibility is influenced by genetic and environmental factors. Previous findings suggest DNA methylation as a potential mechanism in T2D pathogenesis and progression. METHODS We profiled DNA methylation in 248 blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. FINDINGS We find and replicate 3 previously unreported T2D differentially methylated CpG positions (T2D-DMPs) at FDR 5% in RGL3, NGB and OTX2, and 20 signals at FDR 25%, of which 14 replicated. Integrating genetic variation and T2D-discordant monozygotic twin analyses, we identify both genetic-based and genetic-independent T2D-DMPs. The signals annotate to genes with established GWAS and EWAS links to T2D and its complications, including blood pressure (RGL3) and eye disease (OTX2). INTERPRETATION The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications. FUNDING Funding acknowledgements for each cohort can be found in the Supplementary Note.
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Affiliation(s)
| | - Louis Potier
- APHP, Paris Cité University, INSERM, Paris, France
| | | | | | | | | | | | - Pei-Chien Tsai
- King's College London, UK; Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Purdey J Campbell
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Shelby Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | | | | | | | | | | | - Kirsi H Pietilainen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Finland; HealthyWeightHub, Abdominal Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Miina Ollikainen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Finland
| | | | | | | | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | | | | | - Scott G Wilson
- King's College London, UK; Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
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44
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Lee HS, Kim B, Park T. Genome- and epigenome-wide association studies identify susceptibility of CpG sites and regions for metabolic syndrome in a Korean population. Clin Epigenetics 2024; 16:60. [PMID: 38685121 PMCID: PMC11059751 DOI: 10.1186/s13148-024-01671-5] [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: 11/14/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND While multiple studies have investigated the relationship between metabolic syndrome (MetS) and its related traits (fasting glucose, triglyceride, HDL cholesterol, blood pressure, waist circumference) and DNA methylation, our understanding of the epigenetic mechanisms in MetS remains limited. Therefore, we performed an epigenome-wide meta-analysis of blood DNA methylation to identify differentially methylated probes (DMPs) and differentially methylated regions (DMRs) associated with MetS and its components using two independent cohorts comprising a total of 2,334 participants. We also investigated the specific genetic effects on DNA methylation, identified methylation quantitative trait loci (meQTLs) through genome-wide association studies and further utilized Mendelian randomization (MR) to assess how these meQTLs subsequently influence MetS status. RESULTS We identified 40 DMPs and 27 DMRs that are significantly associated with MetS. In addition, we identified many novel DMPs and DMRs underlying inflammatory and steroid hormonal processes. The most significant associations were observed in 3 DMPs (cg19693031, cg26974062, cg02988288) and a DMR (chr1:145440444-145441553) at the TXNIP, which are involved in lipid metabolism. These CpG sites were identified as coregulators of DNA methylation in MetS, TG and FAG levels. We identified a total of 144 cis-meQTLs, out of which only 13 were found to be associated with DMPs for MetS. Among these, we confirmed the identified causal mediators of genetic effects at CpG sites cg01881899 at ABCG1 and cg00021659 at the TANK genes for MetS. CONCLUSIONS This study observed whether specific CpGs and methylated regions act independently or are influenced by genetic effects for MetS and its components in the Korean population. These associations between the identified DNA methylation and MetS, along with its individual components, may serve as promising targets for the development of preventive interventions for MetS.
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Affiliation(s)
- Ho-Sun Lee
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.
| | - Boram Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Taesung Park
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea
- Department of Statistics, Seoul National University, Seoul, 08826, Korea
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45
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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [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: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Pett L, Li Z, Abrishamcar S, Hodge K, Everson T, Christensen G, Gearing M, Kobor MS, Konwar C, MacIsaac JL, Dever K, Wingo AP, Levey A, Lah JJ, Wingo TS, Hüls A. The association between neighborhood deprivation and DNA methylation in an autopsy cohort. Aging (Albany NY) 2024; 16:6694-6716. [PMID: 38663907 PMCID: PMC11087100 DOI: 10.18632/aging.205764] [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: 09/01/2023] [Accepted: 03/18/2024] [Indexed: 05/08/2024]
Abstract
Previous research has found that living in a disadvantaged neighborhood is associated with poor health outcomes. Living in disadvantaged neighborhoods may alter inflammation and immune response in the body, which could be reflected in epigenetic mechanisms such as DNA methylation (DNAm). We used robust linear regression models to conduct an epigenome-wide association study examining the association between neighborhood deprivation (Area Deprivation Index; ADI), and DNAm in brain tissue from 159 donors enrolled in the Emory Goizueta Alzheimer's Disease Research Center (Georgia, USA). We found one CpG site (cg26514961, gene PLXNC1) significantly associated with ADI after controlling for covariates and multiple testing (p-value=5.0e-8). Effect modification by APOE ε4 was statistically significant for the top ten CpG sites from the EWAS of ADI, indicating that the observed associations between ADI and DNAm were mainly driven by donors who carried at least one APOE ε4 allele. Four of the top ten CpG sites showed a significant concordance between brain tissue and tissues that are easily accessible in living individuals (blood, buccal cells, saliva), including DNAm in cg26514961 (PLXNC1). Our study identified one CpG site (cg26514961, PLXNC1 gene) that was significantly associated with neighborhood deprivation in brain tissue. PLXNC1 is related to immune response, which may be one biological pathway how neighborhood conditions affect health. The concordance between brain and other tissues for our top CpG sites could make them potential candidates for biomarkers in living individuals.
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Affiliation(s)
- Lindsay Pett
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Zhenjiang Li
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kenyaita Hodge
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Todd Everson
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Grace Christensen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Chaini Konwar
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Kristy Dever
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Aliza P. Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA 30033, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Thomas S. Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
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47
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Aguilar-Lacasaña S, Fontes Marques I, de Castro M, Dadvand P, Escribà X, Fossati S, González JR, Nieuwenhuijsen M, Alfano R, Annesi-Maesano I, Brescianini S, Burrows K, Calas L, Elhakeem A, Heude B, Hough A, Isaevska E, W V Jaddoe V, Lawlor DA, Monaghan G, Nawrot T, Plusquin M, Richiardi L, Watmuff A, Yang TC, Vrijheid M, F Felix J, Bustamante M. Green space exposure and blood DNA methylation at birth and in childhood - A multi-cohort study. ENVIRONMENT INTERNATIONAL 2024; 188:108684. [PMID: 38776651 DOI: 10.1016/j.envint.2024.108684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024]
Abstract
Green space exposure has been associated with improved mental, physical and general health. However, the underlying biological mechanisms remain largely unknown. The aim of this study was to investigate the association between green space exposure and cord and child blood DNA methylation. Data from eight European birth cohorts with a total of 2,988 newborns and 1,849 children were used. Two indicators of residential green space exposure were assessed: (i) surrounding greenness (satellite-based Normalized Difference Vegetation Index (NDVI) in buffers of 100 m and 300 m) and (ii) proximity to green space (having a green space ≥ 5,000 m2 within a distance of 300 m). For these indicators we assessed two exposure windows: (i) pregnancy, and (ii) the period from pregnancy to child blood DNA methylation assessment, named as cumulative exposure. DNA methylation was measured with the Illumina 450K or EPIC arrays. To identify differentially methylated positions (DMPs) we fitted robust linear regression models between pregnancy green space exposure and cord blood DNA methylation and between cumulative green space exposure and child blood DNA methylation. Two sensitivity analyses were conducted: (i) without adjusting for cellular composition, and (ii) adjusting for air pollution. Cohort results were combined through fixed-effect inverse variance weighted meta-analyses. Differentially methylated regions (DMRs) were identified from meta-analysed results using the Enmix-combp and DMRcate methods. There was no statistical evidence of pregnancy or cumulative exposures associating with any DMP (False Discovery Rate, FDR, p-value < 0.05). However, surrounding greenness exposure was inversely associated with four DMRs (three in cord blood and one in child blood) annotated to ADAMTS2, KCNQ1DN, SLC6A12 and SDK1 genes. Results did not change substantially in the sensitivity analyses. Overall, we found little evidence of the association between green space exposure and blood DNA methylation. Although we identified associations between surrounding greenness exposure with four DMRs, these findings require replication.
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Affiliation(s)
- Sofia Aguilar-Lacasaña
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain; Universitat de Barcelona, Barcelona, Spain.
| | - Irene Fontes Marques
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Montserrat de Castro
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Xavier Escribà
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Serena Fossati
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Juan R González
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Mark Nieuwenhuijsen
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Isabella Annesi-Maesano
- Desbrest Institute of Epidemiology and Public Health (IDESP), Montpellier University and Inserm, Montpellier, Service des Maladies Allergiques et Respiratoires, CHU, Montpellier, France
| | - Sonia Brescianini
- Centre for Behavioural Science and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Kimberley Burrows
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucinda Calas
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, INRAE, Center for Research in Epidemiology and StatisticS (CRESS), F-75004 Paris, France
| | - Ahmed Elhakeem
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Barbara Heude
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, INRAE, Center for Research in Epidemiology and StatisticS (CRESS), F-75004 Paris, France
| | - Amy Hough
- Born in Bradford, Wolfson Centre for Applied Health Research, Bradford Royal Infirmary, Bradford, UK
| | - Elena Isaevska
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Medical Sciences, University of Turin, CPO-Piemonte, Turin, Italy
| | - Vincent W V Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Deborah A Lawlor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Genevieve Monaghan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tim Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium; Department of Public Health, Leuven University (KU Leuven), Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, CPO-Piemonte, Turin, Italy
| | - Aidan Watmuff
- Born in Bradford, Wolfson Centre for Applied Health Research, Bradford Royal Infirmary, Bradford, UK
| | - Tiffany C Yang
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, UK
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Spain
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48
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Jiang F, Zhao J, Sun J, Chen W, Zhao Y, Zhou S, Yuan S, Timofeeva M, Law PJ, Larsson SC, Chen D, Houlston RS, Dunlop MG, Theodoratou E, Li X. Impact of ambient air pollution on colorectal cancer risk and survival: insights from a prospective cohort and epigenetic Mendelian randomization study. EBioMedicine 2024; 103:105126. [PMID: 38631091 PMCID: PMC11035091 DOI: 10.1016/j.ebiom.2024.105126] [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: 09/03/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND This study investigates the associations between air pollution and colorectal cancer (CRC) risk and survival from an epigenomic perspective. METHODS Using a newly developed Air Pollutants Exposure Score (APES), we utilized a prospective cohort study (UK Biobank) to investigate the associations of individual and combined air pollution exposures with CRC incidence and survival, followed by an up-to-date systematic review with meta-analysis to verify the associations. In epigenetic two-sample Mendelian randomization analyses, we examine the associations between genetically predicted DNA methylation related to air pollution and CRC risk. Further genetic colocalization and gene-environment interaction analyses provided different insights to disentangle pathogenic effects of air pollution via epigenetic modification. FINDINGS During a median 12.97-year follow-up, 5767 incident CRC cases among 428,632 participants free of baseline CRC and 533 deaths in 2401 patients with CRC were documented in the UK Biobank. A higher APES score was associated with an increased CRC risk (HR, 1.03, 95% CI = 1.01-1.06; P = 0.016) and poorer survival (HR, 1.13, 95% CI = 1.03-1.23; P = 0.010), particularly among participants with insufficient physical activity and ever smokers (Pinteraction > 0.05). A subsequent meta-analysis of seven observational studies, including UK Biobank data, corroborated the association between PM2.5 exposure (per 10 μg/m3 increment) and elevated CRC risk (RR,1.42, 95% CI = 1.12-1.79; P = 0.004; I2 = 90.8%). Genetically predicted methylation at PM2.5-related CpG site cg13835894 near TMBIM1/PNKD and cg16235962 near CXCR5, and NO2-related cg16947394 near TMEM110 were associated with an increased CRC risk. Gene-environment interaction analysis confirmed the epigenetic modification of aforementioned CpG sites with CRC risk and survival. INTERPRETATION Our study suggests the association between air pollution and CRC incidence and survival, underscoring the possible modifying roles of epigenomic factors. Methylation may partly mediate pathogenic effects of air pollution on CRC, with annotation to epigenetic alterations in protein-coding genes TMBIM1/PNKD, CXCR5 and TMEM110. FUNDING Xue Li is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001), the National Nature Science Foundation of China (No. 82204019) and Healthy Zhejiang One Million People Cohort (K-20230085). ET is supported by a Cancer Research UK Career Development Fellowship (C31250/A22804). MGD is supported by the MRC Human Genetics Unit Centre Grant (U127527198).
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Affiliation(s)
- Fangyuan Jiang
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhui Zhao
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Sun
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenxi Chen
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyuan Zhao
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Siyun Zhou
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Maria Timofeeva
- Danish Institute for Advanced Study (DIAS), Epidemiology, Biostatistics and Biodemography Research Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden; Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala, Sweden
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang Province, China
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Malcolm G Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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49
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [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: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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50
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Czamara D, Dieckmann L, Lahti-Pulkkinen M, Cruceanu C, Henrich W, Plagemann A, Räikkönen K, Braun T, Binder EB, Lahti J, Entringer S. Sex differences in DNA methylation across gestation: a large scale, cross-cohort, multi-tissue analysis. Cell Mol Life Sci 2024; 81:177. [PMID: 38600394 PMCID: PMC11006734 DOI: 10.1007/s00018-024-05208-0] [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: 10/09/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Biological sex is a key variable influencing many physiological systems. Disease prevalence as well as treatment success can be modified by sex. Differences emerge already early in life and include pregnancy complications and adverse birth outcomes. The placenta is a critical organ for fetal development and shows sex-based differences in the expression of hormones and cytokines. Epigenetic regulation, such as DNA methylation (DNAm), may underlie the previously reported placental sexual dimorphism. We associated placental DNAm with fetal sex in three cohorts. Individual cohort results were meta-analyzed with random-effects modelling. CpG-sites differentially methylated with sex were further investigated regarding pathway enrichment, overlap with methylation quantitative trait loci (meQTLs), and hits from phenome-wide association studies (PheWAS). We evaluated the consistency of findings across tissues (CVS, i.e. chorionic villus sampling from early placenta, and cord blood) as well as with gene expression. We identified 10,320 epigenome-wide significant sex-differentially methylated probes (DMPs) spread throughout the epigenome of the placenta at birth. Most DMPs presented with lower DNAm levels in females. DMPs mapped to genes upregulated in brain, were enriched for neurodevelopmental pathways and significantly overlapped with meQTLs and PheWAS hits. Effect sizes were moderately correlated between CVS and placenta at birth, but only weakly correlated between birth placenta and cord blood. Sex differential gene expression in birth placenta was less pronounced and implicated genetic regions only marginally overlapped with those associated with differential DNAm. Our study provides an integrative perspective on sex-differential DNAm in perinatal tissues underscoring the possible link between placenta and brain.
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Affiliation(s)
- Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany.
| | - Linda Dieckmann
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Marius Lahti-Pulkkinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Cristiana Cruceanu
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Wolfgang Henrich
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Andreas Plagemann
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- Department of Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, HUS Helsinki University Hospital, Helsinki, Finland
| | - Thorsten Braun
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- Department of Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sonja Entringer
- Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany.
- Department of Pediatrics, Health and Disease Research Program, School of Medicine, University of California, Irvine, CA, USA.
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