1
|
Ying K, Liu H, Tarkhov AE, Sadler MC, Lu AT, Moqri M, Horvath S, Kutalik Z, Shen X, Gladyshev VN. Causality-enriched epigenetic age uncouples damage and adaptation. NATURE AGING 2024; 4:231-246. [PMID: 38243142 PMCID: PMC11070280 DOI: 10.1038/s43587-023-00557-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
Machine learning models based on DNA methylation data can predict biological age but often lack causal insights. By harnessing large-scale genetic data through epigenome-wide Mendelian randomization, we identified CpG sites potentially causal for aging-related traits. Neither the existing epigenetic clocks nor age-related differential DNA methylation are enriched in these sites. These CpGs include sites that contribute to aging and protect against it, yet their combined contribution negatively affects age-related traits. We established a new framework to introduce causal information into epigenetic clocks, resulting in DamAge and AdaptAge-clocks that track detrimental and adaptive methylation changes, respectively. DamAge correlates with adverse outcomes, including mortality, while AdaptAge is associated with beneficial adaptations. These causality-enriched clocks exhibit sensitivity to short-term interventions. Our findings provide a detailed landscape of CpG sites with putative causal links to lifespan and healthspan, facilitating the development of aging biomarkers, assessing interventions, and studying reversibility of age-associated changes.
Collapse
Affiliation(s)
- Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Hanna Liu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy, Massachusetts General Hospital, Boston, MA, USA
| | - Andrei E Tarkhov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Marie C Sadler
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ake T Lu
- Altos Labs, San Diego, CA, USA
- Departments of Human Genetics and Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mahdi Moqri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Steve Horvath
- Altos Labs, San Diego, CA, USA
- Departments of Human Genetics and Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zoltán Kutalik
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xia Shen
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
2
|
Tseng WHS, Chattopadhyay A, Phan NN, Chuang EY, Lee OK. Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank. GeroScience 2024; 46:1211-1228. [PMID: 37523034 PMCID: PMC10828416 DOI: 10.1007/s11357-023-00874-7] [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: 05/05/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Frailty, a prevalent clinical syndrome in aging adults, is characterized by poor health outcomes, represented via a standardized frailty-phenotype (FP), and Frailty Index (FI). While the relevance of the syndrome is gaining awareness, much remains unclear about its underlying biology. Further elucidation of the genetic determinants and possible underlying mechanisms may help improve patients' outcomes allowing healthy aging.Genotype, clinical and demographic data of subjects (aged 60-73 years) from UK Biobank were utilized. FP was defined on Fried's criteria. FI was calculated using electronic-health-records. Genome-wide-association-studies (GWAS) were conducted and polygenic-risk-scores (PRS) were calculated for both FP and FI. Functional analysis provided interpretations of underlying biology. Finally, machine-learning (ML) models were trained using clinical, demographic and PRS towards identifying frail from non-frail individuals.Thirty-one loci were significantly associated with FI accounting for 12% heritability. Seventeen of those were known associations for body-mass-index, coronary diseases, cholesterol-levels, and longevity, while the rest were novel. Significant genes CDKN2B and APOE, previously implicated in aging, were reported to be enriched in lipoprotein-particle-remodeling. Linkage-disequilibrium-regression identified specific regulation in limbic-system, associated with long-term memory and cognitive-function. XGboost was established as the best performing ML model with area-under-curve as 85%, sensitivity and specificity as 0.75 and 0.8, respectively.This study provides novel insights into increased vulnerability and risk stratification of frailty syndrome via a multi-modal approach. The findings suggest frailty as a highly polygenic-trait, enriched in cholesterol-remodeling and metabolism and to be genetically associated with cognitive abilities. ML models utilizing FP and FI + PRS were established that identified frailty-syndrome patients with high accuracy.
Collapse
Affiliation(s)
- Watson Hua-Sheng Tseng
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.
| | - Nam Nhut Phan
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Oscar K Lee
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Center for Translational Genomics and Regenerative Medicine, China Medical University Hospital, Taichung, Taiwan.
- Stem Cell Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Orthopedics, China Medical University Hospital, Taichung, Taiwan.
| |
Collapse
|
3
|
Vladimir K, Perišić MM, Štorga M, Mostashari A, Khanin R. Epigenetics insights from perceived facial aging. Clin Epigenetics 2023; 15:176. [PMID: 37924108 PMCID: PMC10623707 DOI: 10.1186/s13148-023-01590-x] [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: 06/01/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Facial aging is the most visible manifestation of aging. People desire to look younger than others of the same chronological age. Hence, perceived age is often used as a visible marker of aging, while biological age, often estimated by methylation markers, is used as an objective measure of age. Multiple epigenetics-based clocks have been developed for accurate estimation of general biological age and the age of specific organs, including the skin. However, it is not clear whether the epigenetic biomarkers (CpGs) used in these clocks are drivers of aging processes or consequences of aging. In this proof-of-concept study, we integrate data from GWAS on perceived facial aging and EWAS on CpGs measured in blood. By running EW Mendelian randomization, we identify hundreds of putative CpGs that are potentially causal to perceived facial aging with similar numbers of damaging markers that causally drive or accelerate facial aging and protective methylation markers that causally slow down or protect from aging. We further demonstrate that while candidate causal CpGs have little overlap with known epigenetics-based clocks, they affect genes or proteins with known functions in skin aging, such as skin pigmentation, elastin, and collagen levels. Overall, our results suggest that blood methylation markers reflect facial aging processes, and thus can be used to quantify skin aging and develop anti-aging solutions that target the root causes of aging.
Collapse
Affiliation(s)
- Klemo Vladimir
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Electrical Engineering and Computing, University of Zagreb, 10000, Zagreb, Croatia
| | - Marija Majda Perišić
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | - Mario Štorga
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | | | - Raya Khanin
- LifeNome Inc., New York, 10018, NY, USA.
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, 10065, NY, USA.
| |
Collapse
|
4
|
Wu Y, Qi T, Wray NR, Visscher PM, Zeng J, Yang J. Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes. CELL GENOMICS 2023; 3:100344. [PMID: 37601976 PMCID: PMC10435383 DOI: 10.1016/j.xgen.2023.100344] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 08/22/2023]
Abstract
Molecular quantitative trait loci (xQTLs) are often harnessed to prioritize genes or functional elements underpinning variant-trait associations identified from genome-wide association studies (GWASs). Here, we introduce OPERA, a method that jointly analyzes GWAS and multi-omics xQTL summary statistics to enhance the identification of molecular phenotypes associated with complex traits through shared causal variants. Applying OPERA to summary-level GWAS data for 50 complex traits (n = 20,833-766,345) and xQTL data from seven omics layers (n = 100-31,684) reveals that 50% of the GWAS signals are shared with at least one molecular phenotype. GWAS signals shared with multiple molecular phenotypes, such as those at the MSMB locus for prostate cancer, are particularly informative for understanding the genetic regulatory mechanisms underlying complex traits. Future studies with more molecular phenotypes, measured considering spatiotemporal effects in larger samples, are required to obtain a more saturated map linking molecular intermediates to GWAS signals.
Collapse
Affiliation(s)
- Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter M. Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| |
Collapse
|
5
|
Juvinao-Quintero DL, Sharp GC, Sanderson ECM, Relton CL, Elliott HR. Investigating causality in the association between DNA methylation and type 2 diabetes using bidirectional two-sample Mendelian randomisation. Diabetologia 2023; 66:1247-1259. [PMID: 37202507 PMCID: PMC10244277 DOI: 10.1007/s00125-023-05914-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/25/2023] [Indexed: 05/20/2023]
Abstract
AIMS/HYPOTHESIS Several studies have identified associations between type 2 diabetes and DNA methylation (DNAm). However, the causal role of these associations remains unclear. This study aimed to provide evidence for a causal relationship between DNAm and type 2 diabetes. METHODS We used bidirectional two-sample Mendelian randomisation (2SMR) to evaluate causality at 58 CpG sites previously detected in a meta-analysis of epigenome-wide association studies (meta-EWAS) of prevalent type 2 diabetes in European populations. We retrieved genetic proxies for type 2 diabetes and DNAm from the largest genome-wide association study (GWAS) available. We also used data from the Avon Longitudinal Study of Parents and Children (ALSPAC, UK) when associations of interest were not available in the larger datasets. We identified 62 independent SNPs as proxies for type 2 diabetes, and 39 methylation quantitative trait loci as proxies for 30 of the 58 type 2 diabetes-related CpGs. We applied the Bonferroni correction for multiple testing and inferred causality based on p<0.001 for the type 2 diabetes to DNAm direction and p<0.002 for the opposing DNAm to type 2 diabetes direction in the 2SMR analysis. RESULTS We found strong evidence of a causal effect of DNAm at cg25536676 (DHCR24) on type 2 diabetes. An increase in transformed residuals of DNAm at this site was associated with a 43% (OR 1.43, 95% CI 1.15, 1.78, p=0.001) higher risk of type 2 diabetes. We inferred a likely causal direction for the remaining CpG sites assessed. In silico analyses showed that the CpGs analysed were enriched for expression quantitative trait methylation sites (eQTMs) and for specific traits, dependent on the direction of causality predicted by the 2SMR analysis. CONCLUSIONS/INTERPRETATION We identified one CpG mapping to a gene related to the metabolism of lipids (DHCR24) as a novel causal biomarker for risk of type 2 diabetes. CpGs within the same gene region have previously been associated with type 2 diabetes-related traits in observational studies (BMI, waist circumference, HDL-cholesterol, insulin) and in Mendelian randomisation analyses (LDL-cholesterol). Thus, we hypothesise that our candidate CpG in DHCR24 may be a causal mediator of the association between known modifiable risk factors and type 2 diabetes. Formal causal mediation analysis should be implemented to further validate this assumption.
Collapse
Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eleanor C M Sanderson
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| |
Collapse
|
6
|
Howell AE, Relton C, Martin RM, Zheng J, Kurian KM. Role of DNA methylation in the relationship between glioma risk factors and glioma incidence: a two-step Mendelian randomization study. Sci Rep 2023; 13:6590. [PMID: 37085538 PMCID: PMC10121678 DOI: 10.1038/s41598-023-33621-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 04/15/2023] [Indexed: 04/23/2023] Open
Abstract
Genetic evidence suggests glioma risk is altered by leukocyte telomere length, allergic disease (asthma, hay fever or eczema), alcohol consumption, childhood obesity, low-density lipoprotein cholesterol (LDLc) and triglyceride levels. DNA methylation (DNAm) variation influences many of these glioma-related traits and is an established feature of glioma. Yet the causal relationship between DNAm variation with both glioma incidence and glioma risk factors is unknown. We applied a two-step Mendelian randomization (MR) approach and several sensitivity analyses (including colocalization and Steiger filtering) to assess the association of DNAm with glioma risk factors and glioma incidence. We used data from a recently published catalogue of germline genetic variants robustly associated with DNAm variation in blood (32,851 participants) and data from a genome-wide association study of glioma risk (12,488 cases and 18,169 controls, sub-divided into 6191 glioblastoma cases and 6305 non-glioblastoma cases). MR evidence indicated that DNAm at 3 CpG sites (cg01561092, cg05926943, cg01584448) in one genomic region (HEATR3) had a putative association with glioma and glioblastoma risk (False discovery rate [FDR] < 0.05). Steiger filtering provided evidence against reverse causation. Colocalization presented evidence against genetic confounding and suggested that differential DNAm at the 3 CpG sites and glioma were driven by the same genetic variant. MR provided little evidence to suggest that DNAm acts as a mediator on the causal pathway between risk factors previously examined and glioma onset. To our knowledge, this is the first study to use MR to appraise the causal link of DNAm with glioma risk factors and glioma onset. Subsequent analyses are required to improve the robustness of our results and rule out horizontal pleiotropy.
Collapse
Affiliation(s)
- Amy E Howell
- Brain Tumour Research Centre, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Kathreena M Kurian
- Brain Tumour Research Centre, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK.
| |
Collapse
|
7
|
Elucidating the genetic architecture of DNA methylation to identify promising molecular mechanisms of disease. Sci Rep 2022; 12:19564. [PMID: 36380121 PMCID: PMC9664436 DOI: 10.1038/s41598-022-24100-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
DNA methylation commonly occurs at cytosine-phosphate-guanine sites (CpGs) that can serve as biomarkers for many diseases. We analyzed whole genome sequencing data to identify DNA methylation quantitative trait loci (mQTLs) in 4126 Framingham Heart Study participants. Our mQTL mapping identified 94,362,817 cis-mQTLvariant-CpG pairs (for 210,156 unique autosomal CpGs) at P < 1e-7 and 33,572,145 trans-mQTL variant-CpG pairs (for 213,606 unique autosomal CpGs) at P < 1e-14. Using cis-mQTL variants for 1258 CpGs associated with seven cardiovascular disease (CVD) risk factors, we found 104 unique CpGs that colocalized with at least one CVD trait. For example, cg11554650 (PPP1R18) colocalized with type 2 diabetes, and was driven by a single nucleotide polymorphism (rs2516396). We performed Mendelian randomization (MR) analysis and demonstrated 58 putatively causal relations of CVD risk factor-associated CpGs to one or more risk factors (e.g., cg05337441 [APOB] with LDL; MR P = 1.2e-99, and 17 causal associations with coronary artery disease (e.g. cg08129017 [SREBF1] with coronary artery disease; MR P = 5e-13). We also showed that three CpGs, e.g., cg14893161 (PM20D1), are putatively causally associated with COVID-19 severity. To assist in future analyses of the role of DNA methylation in disease pathogenesis, we have posted a comprehensive summary data set in the National Heart, Lung, and Blood Institute's BioData Catalyst.
Collapse
|
8
|
Tekola-Ayele F, Zeng X, Chatterjee S, Ouidir M, Lesseur C, Hao K, Chen J, Tesfaye M, Marsit CJ, Workalemahu T, Wapner R. Placental multi-omics integration identifies candidate functional genes for birthweight. Nat Commun 2022; 13:2384. [PMID: 35501330 PMCID: PMC9061712 DOI: 10.1038/s41467-022-30007-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 04/11/2022] [Indexed: 12/27/2022] Open
Abstract
Abnormal birthweight is associated with increased risk for cardiometabolic diseases in later life. Although the placenta is critical to fetal development and later life health, it has not been integrated into largescale functional genomics initiatives, and mechanisms of birthweight-associated variants identified by genome wide association studies (GWAS) are unclear. The goal of this study is to provide functional mechanistic insight into the causal pathway from a genetic variant to birthweight by integrating placental methylation and gene expression with established GWAS loci for birthweight. We identify placental DNA methylation and gene expression targets for several birthweight GWAS loci. The target genes are broadly enriched in cardiometabolic, immune response, and hormonal pathways. We find that methylation causally influences WNT3A, CTDNEP1, and RANBP2 expression in placenta. Multi-trait colocalization identifies PLEKHA1, FES, CTDNEP1, and PRMT7 as likely functional effector genes. These findings reveal candidate functional pathways that underpin the genetic regulation of birthweight via placental epigenetic and transcriptomic mechanisms. Clinical trial registration; ClinicalTrials.gov, NCT00912132.
Collapse
Affiliation(s)
- Fasil Tekola-Ayele
- Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Xuehuo Zeng
- Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Suvo Chatterjee
- Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marion Ouidir
- Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Markos Tesfaye
- Section of Sensory Science and Metabolism (SenSMet), National Institute on Alcohol Abuse and Alcoholism & National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health of Emory University, Atlanta, GA, USA
| | - Tsegaselassie Workalemahu
- Department of Obstetrics and Gynecology, Maternal-Fetal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| |
Collapse
|
9
|
Leyden GM, Shapland CY, Davey Smith G, Sanderson E, Greenwood MP, Murphy D, Richardson TG. Harnessing tissue-specific genetic variation to dissect putative causal pathways between body mass index and cardiometabolic phenotypes. Am J Hum Genet 2022; 109:240-252. [PMID: 35090585 DOI: 10.1016/j.ajhg.2021.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/14/2021] [Indexed: 12/11/2022] Open
Abstract
Body mass index (BMI) is a complex disease risk factor known to be influenced by genes acting via both metabolic pathways and appetite regulation. In this study, we aimed to gain insight into the phenotypic consequences of BMI-associated genetic variants, which may be mediated by their expression in different tissues. First, we harnessed meta-analyzed gene expression datasets derived from subcutaneous adipose (n = 1257) and brain (n = 1194) tissue to identify 86 and 140 loci, respectively, which provided evidence of genetic colocalization with BMI. These two sets of tissue-partitioned loci had differential effects with respect to waist-to-hip ratio, suggesting that the way they influence fat distribution might vary despite their having very similar average magnitudes of effect on BMI itself (adipose = 0.0148 and brain = 0.0149 standard deviation change in BMI per effect allele). For instance, BMI-associated variants colocalized with TBX15 expression in adipose tissue (posterior probability [PPA] = 0.97), but not when we used TBX15 expression data derived from brain tissue (PPA = 0.04) This gene putatively influences BMI via its role in skeletal development. Conversely, there were loci where BMI-associated variants provided evidence of colocalization with gene expression in brain tissue (e.g., NEGR1, PPA = 0.93), but not when we used data derived from adipose tissue, suggesting that these genes might be more likely to influence BMI via energy balance. Leveraging these tissue-partitioned variant sets through a multivariable Mendelian randomization framework provided strong evidence that the brain-tissue-derived variants are predominantly responsible for driving the genetically predicted effects of BMI on cardiovascular-disease endpoints (e.g., coronary artery disease: odds ratio = 1.05, 95% confidence interval = 1.04-1.07, p = 4.67 × 10-14). In contrast, our analyses suggested that the adipose tissue variants might predominantly be responsible for the underlying relationship between BMI and measures of cardiac function, such as left ventricular stroke volume (beta = 0.21, 95% confidence interval = 0.09-0.32, p = 6.43 × 10-4).
Collapse
|
10
|
Richardson TG, Mykkänen J, Pahkala K, Ala-Korpela M, Bell JA, Taylor K, Viikari J, Lehtimäki T, Raitakari O, Davey Smith G. Evaluating the direct effects of childhood adiposity on adult systemic metabolism: a multivariable Mendelian randomization analysis. Int J Epidemiol 2021; 50:1580-1592. [PMID: 33783488 PMCID: PMC8580280 DOI: 10.1093/ije/dyab051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Individuals who are obese in childhood have an elevated risk of disease in adulthood. However, whether childhood adiposity directly impacts intermediate markers of this risk, independently of adult adiposity, is unclear. In this study, we have simultaneously evaluated the effects of childhood and adulthood body size on 123 systemic molecular biomarkers representing multiple metabolic pathways. METHODS Two-sample Mendelian randomization (MR) was conducted to estimate the causal effect of childhood body size on a total of 123 nuclear magnetic resonance-based metabolic markers using summary genome-wide association study (GWAS) data from up to 24 925 adults. Multivariable MR was then applied to evaluate the direct effects of childhood body size on these metabolic markers whilst accounting for adult body size. Further MR analyses were undertaken to estimate the potential mediating effects of these circulating metabolites on the risk of coronary artery disease (CAD) in adulthood using a sample of 60 801 cases and 123 504 controls. RESULTS Univariable analyses provided evidence that childhood body size has an effect on 42 of the 123 metabolic markers assessed (based on P < 4.07 × 10-4). However, the majority of these effects (35/42) substantially attenuated when accounting for adult body size using multivariable MR. We found little evidence that the biomarkers that were potentially influenced directly by childhood body size (leucine, isoleucine and tyrosine) mediate this effect onto adult disease risk. Very-low-density lipoprotein markers provided the strongest evidence of mediating the long-term effect of adiposity on CAD risk. CONCLUSIONS Our findings suggest that childhood adiposity predominantly exerts its detrimental effect on adult systemic metabolism along a pathway that involves adulthood body size.
Collapse
Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Juha Mykkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Joshua A Bell
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Kurt Taylor
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Jorma Viikari
- Department of Medicine, University of Turku and Division of Medicine, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| |
Collapse
|
11
|
Do WL, Gohar J, McCullough LE, Galaviz KI, Conneely KN, Narayan KMV. Examining the association between adiposity and DNA methylation: A systematic review and meta-analysis. Obes Rev 2021; 22:e13319. [PMID: 34278703 DOI: 10.1111/obr.13319] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Obesity is associated with widespread differential DNA methylation (DNAm) patterns, though there have been limited overlap in the obesity-associated cytosine-guanine nucleotide pair (CpG) sites that have been identified in the literature. We systematically searched four databases for studies published until January 2020. Eligible studies included cross-sectional, longitudinal, or intervention studies examining adiposity and genome-wide DNAm in non-pregnant adults aged 18-75 in all tissue types. Study design and results were extracted in the descriptive review. Blood-based DNAm results in body mass index (BMI) and waist circumference (WC) were meta-analyzed using weighted sum of Z-score meta-analysis. Of the 10,548 studies identified, 46 studies were included in the systematic review with 18 and nine studies included in the meta-analysis of BMI and WC, respectively. In the blood, 77 and four CpG sites were significant in three or more studies of BMI and WC, respectively. Using a genome-wide threshold for significance, 52 blood-based CpG sites were significantly associated with BMI. These sites have previously been associated with many obesity-related diseases including type 2 diabetes, cardiovascular disease, Crohn's disease, and depression. Our study shows that DNAm at 52 CpG sites represent potential mediators of obesity-associated chronic diseases and may be novel intervention or therapeutic targets to protect against obesity-associated chronic diseases.
Collapse
Affiliation(s)
- Whitney L Do
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jazib Gohar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lauren E McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Karla I Galaviz
- Department of Applied Health Science, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - K M Venkat Narayan
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
12
|
Zhang T, Choi J, Dilshat R, Einarsdóttir BÓ, Kovacs MA, Xu M, Malasky M, Chowdhury S, Jones K, Bishop DT, Goldstein AM, Iles MM, Landi MT, Law MH, Shi J, Steingrímsson E, Brown KM. Cell-type-specific meQTLs extend melanoma GWAS annotation beyond eQTLs and inform melanocyte gene-regulatory mechanisms. Am J Hum Genet 2021; 108:1631-1646. [PMID: 34293285 PMCID: PMC8456160 DOI: 10.1016/j.ajhg.2021.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023] Open
Abstract
Although expression quantitative trait loci (eQTLs) have been powerful in identifying susceptibility genes from genome-wide association study (GWAS) findings, most trait-associated loci are not explained by eQTLs alone. Alternative QTLs, including DNA methylation QTLs (meQTLs), are emerging, but cell-type-specific meQTLs using cells of disease origin have been lacking. Here, we established an meQTL dataset by using primary melanocytes from 106 individuals and identified 1,497,502 significant cis-meQTLs. Multi-QTL colocalization with meQTLs, eQTLs, and mRNA splice-junction QTLs from the same individuals together with imputed methylome-wide and transcriptome-wide association studies identified candidate susceptibility genes at 63% of melanoma GWAS loci. Among the three molecular QTLs, meQTLs were the single largest contributor. To compare melanocyte meQTLs with those from malignant melanomas, we performed meQTL analysis on skin cutaneous melanomas from The Cancer Genome Atlas (n = 444). A substantial proportion of meQTL probes (45.9%) in primary melanocytes is preserved in melanomas, while a smaller fraction of eQTL genes is preserved (12.7%). Integration of melanocyte multi-QTLs and melanoma meQTLs identified candidate susceptibility genes at 72% of melanoma GWAS loci. Beyond GWAS annotation, meQTL-eQTL colocalization in melanocytes suggested that 841 unique genes potentially share a causal variant with a nearby methylation probe in melanocytes. Finally, melanocyte trans-meQTLs identified a hotspot for rs12203592, a cis-eQTL of a transcription factor, IRF4, with 131 candidate target CpGs. Motif enrichment and IRF4 ChIP-seq analysis demonstrated that these target CpGs are enriched in IRF4 binding sites, suggesting an IRF4-mediated regulatory network. Our study highlights the utility of cell-type-specific meQTLs.
Collapse
Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Berglind Ósk Einarsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Malasky
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Salma Chowdhury
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - D Timothy Bishop
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
13
|
Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nat Genet 2021; 53:1311-1321. [PMID: 34493871 PMCID: PMC7612069 DOI: 10.1038/s41588-021-00923-x] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022]
Abstract
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
Collapse
Affiliation(s)
- Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - René Luijk
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Gemma Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Biostatistics and Health Informatics, King's College London, London, UK
| | - Wendy L McArdle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Karen M Ho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Chronic Disease Epidemiology unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Soriano-Tárraga
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Karen Sugden
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Silva Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Michael Lerro
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Richa Gupta
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pooja Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Vanessa Schmoll
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yvonne Awaloff
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Marine Germain
- INSERM UMR_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Dylan Aïssi
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Ramona Zwamborn
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristel van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annelot Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
- CiiM and TWINCORE, Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Guillermo Barturen
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Francesc Català-Moll
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Carol Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Phillip Melton
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
- School of Global Population Health, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Manon Bernard
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | | | - Chris Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
| | - Ammar Al Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
- United Kingdom Dementia Research Institute, King's College London, London, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jaume Roquer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Terrie E Moffitt
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Carlotta Sacerdote
- Italian Institute for Genomic Medicine, Turin, Italy
- Piemonte Centre for Cancer Prevention, Turin, Italy
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Avshalom Caspi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Miina Ollikainen
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - 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
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Clinical, Educational and Health Psychology, Division on Psychology and Language Sciences, Faculty of Brain Sciences, University College London, London, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, 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
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Alison Murray
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical research, University of Southern Denmark, Odense, Denmark
- Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health (Section of Epidemiology), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S Morgen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Susanne Lucae
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Juan Ramon Gonzalez
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Universiteit Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | | | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Tomas Paus
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Canada
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| |
Collapse
|
14
|
Liu D, Wang Y, Jing H, Meng Q, Yang J. Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer's dementia: a network Mendelian randomization analysis. Epigenetics 2021; 17:746-758. [PMID: 34461811 DOI: 10.1080/15592294.2021.1959735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Previous genome-wide association studies (GWAS) have identified potential genetic variants involved in the risk of Alzheimer's dementia, but their underlying biological interpretation remains largely unclear. In addition, the effects of DNA methylation and gene expression on Alzheimer's dementia are not well understood. A network summary data-based Mendelian randomization (SMR) analysis was performed integrating cis- DNA methylation quantitative trait loci (mQTL) /cis- gene expression QTL (eQTL) data in the brain and blood, as well as GWAS summarized data for Alzheimer's dementia to evaluate the pleiotropic associations of DNA methylation and gene expression with Alzheimer's dementia and to explore the complex mechanisms underpinning Alzheimer's dementia. After correction for multiple testing (false discovery rate [FDR] P < 0.05) and filtering using the heterogeneity in dependent instruments (HEIDI) test (PHEIDI>0.01), we identified dozens of DNA methylation sites and genes showing pleiotropic associations with Alzheimer's dementia. We found 22 and 16 potentially causal pathways of Alzheimer's dementia (i.e., SNP→DNA methylation→Gene expression→Alzheimer's dementia) in the brain and blood, respectively. Approximately two-thirds of the identified DNA methylation sites had an influence on gene expression and the expression of almost all the identified genes was regulated by DNA methylation. Our network SMR analysis provided evidence supporting the pleiotropic association of some novel DNA methylation sites and genes with Alzheimer's dementia and revealed possible causal pathways underlying the pathogenesis of Alzheimer's dementia. Our findings shed light on the role of DNA methylation in gene expression and in the development of Alzheimer's dementia.
Collapse
Affiliation(s)
- Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Centre for Biomedical Information Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Huiquan Jing
- School of Public Health, Capital Medical University, Beijing, China
| | - Qun Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| |
Collapse
|
15
|
Porcu E, Sjaarda J, Lepik K, Carmeli C, Darrous L, Sulc J, Mounier N, Kutalik Z. Causal Inference Methods to Integrate Omics and Complex Traits. Cold Spring Harb Perspect Med 2021; 11:a040493. [PMID: 32816877 PMCID: PMC8091955 DOI: 10.1101/cshperspect.a040493] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Major biotechnological advances have facilitated a tremendous boost to the collection of (gen-/transcript-/prote-/methyl-/metabol-)omics data in very large sample sizes worldwide. Coordinated efforts have yielded a deluge of studies associating diseases with genetic markers (genome-wide association studies) or with molecular phenotypes. Whereas omics-disease associations have led to biologically meaningful and coherent mechanisms, the identified (non-germline) disease biomarkers may simply be correlates or consequences of the explored diseases. To move beyond this realm, Mendelian randomization provides a principled framework to integrate information on omics- and disease-associated genetic variants to pinpoint molecular traits causally driving disease development. In this review, we show the latest advances in this field, flag up key challenges for the future, and propose potential solutions.
Collapse
Affiliation(s)
- Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Jennifer Sjaarda
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Kaido Lepik
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
- Institute of Computer Science, University of Tartu, Tartu 50409, Estonia
| | - Cristian Carmeli
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Liza Darrous
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Jonathan Sulc
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Ninon Mounier
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5AX, United Kingdom
| |
Collapse
|
16
|
Villicaña S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol 2021; 22:127. [PMID: 33931130 PMCID: PMC8086086 DOI: 10.1186/s13059-021-02347-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression. In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs. We also discuss challenges in this field and future areas of research geared to generate insights into molecular processes underlying human complex traits.
Collapse
Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| |
Collapse
|
17
|
Korologou-Linden R, Leyden GM, Relton CL, Richmond RC, Richardson TG. Multi-omics analyses of cognitive traits and psychiatric disorders highlights brain-dependent mechanisms. Hum Mol Genet 2021; 32:ddab016. [PMID: 33481009 PMCID: PMC9990996 DOI: 10.1093/hmg/ddab016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/02/2020] [Accepted: 12/23/2020] [Indexed: 01/03/2023] Open
Abstract
Integrating findings from genome-wide association studies with molecular datasets can develop insight into the underlying functional mechanisms responsible for trait-associated genetic variants. We have applied the principles of Mendelian randomization (MR) to investigate whether brain-derived gene expression (n = 1194) may be responsible for mediating the effect of genetic variants on eight cognitive and psychological outcomes (attention deficit hyperactivity disorder (ADHD), Alzheimer's disease, bipolar disorder, depression, intelligence, insomnia, neuroticism and schizophrenia). Transcriptome-wide analyses identified 83 genes associated with at least one outcome (PBonferroni < 6.72 × 10-6), with multiple-trait colocalization also implicating changes to brain-derived DNA methylation at nine of these loci. Comparing effects between outcomes identified evidence of enrichment which may reflect putative causal relationships, such as an inverse relationship between genetic liability towards schizophrenia risk and cognitive ability in later life. Repeating these analyses in whole blood (n = 31 684), we replicated 58.2% of brain-derived effects (based on P < 0.05). Finally, we undertook phenome-wide evaluations at associated loci to investigate pleiotropic effects with 700 complex traits. This highlighted pleiotropic loci such as FURIN (initially implicated in schizophrenia risk (P = 1.05 × 10-7)) which had evidence of an effect on 28 other outcomes, as well as genes which may have a more specific role in disease pathogenesis (e.g. SLC12A5 which only provided evidence of an effect on depression (P = 7.13 × 10-10)). Our results support the utility of whole blood as a valuable proxy for informing initial target identification but also suggest that gene discovery in a tissue-specific manner may be more informative. Finally, non-pleiotropic loci highlighted by our study may be of use for therapeutic translational endeavours.
Collapse
Affiliation(s)
- Roxanna Korologou-Linden
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Genevieve M Leyden
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Bristol Medical School, Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol BS1 3NY, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| |
Collapse
|
18
|
Baird DA, Liu JZ, Zheng J, Sieberts SK, Perumal T, Elsworth B, Richardson TG, Chen CY, Carrasquillo MM, Allen M, Reddy JS, De Jager PL, Ertekin-Taner N, Mangravite LM, Logsdon B, Estrada K, Haycock PC, Hemani G, Runz H, Smith GD, Gaunt TR. Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome. PLoS Genet 2021; 17:e1009224. [PMID: 33417599 PMCID: PMC7819609 DOI: 10.1371/journal.pgen.1009224] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/21/2021] [Accepted: 10/26/2020] [Indexed: 11/26/2022] Open
Abstract
Discovering drugs that efficiently treat brain diseases has been challenging. Genetic variants that modulate the expression of potential drug targets can be utilized to assess the efficacy of therapeutic interventions. We therefore employed Mendelian Randomization (MR) on gene expression measured in brain tissue to identify drug targets involved in neurological and psychiatric diseases. We conducted a two-sample MR using cis-acting brain-derived expression quantitative trait loci (eQTLs) from the Accelerating Medicines Partnership for Alzheimer’s Disease consortium (AMP-AD) and the CommonMind Consortium (CMC) meta-analysis study (n = 1,286) as genetic instruments to predict the effects of 7,137 genes on 12 neurological and psychiatric disorders. We conducted Bayesian colocalization analysis on the top MR findings (using P<6x10-7 as evidence threshold, Bonferroni-corrected for 80,557 MR tests) to confirm sharing of the same causal variants between gene expression and trait in each genomic region. We then intersected the colocalized genes with known monogenic disease genes recorded in Online Mendelian Inheritance in Man (OMIM) and with genes annotated as drug targets in the Open Targets platform to identify promising drug targets. 80 eQTLs showed MR evidence of a causal effect, from which we prioritised 47 genes based on colocalization with the trait. We causally linked the expression of 23 genes with schizophrenia and a single gene each with anorexia, bipolar disorder and major depressive disorder within the psychiatric diseases and 9 genes with Alzheimer’s disease, 6 genes with Parkinson’s disease, 4 genes with multiple sclerosis and two genes with amyotrophic lateral sclerosis within the neurological diseases we tested. From these we identified five genes (ACE, GPNMB, KCNQ5, RERE and SUOX) as attractive drug targets that may warrant follow-up in functional studies and clinical trials, demonstrating the value of this study design for discovering drug targets in neuropsychiatric diseases. Genetic association studies have been successful in identifying many genetic variants associated with disease risk, but it has been far more challenging to determine the genes through which these act. This is important, because such genes may encode effective drug targets for these diseases. We used Mendelian randomization (MR) and colocalization, two methods which in combination exploit these genetic variants to estimate the causal effects of individual genes. We applied this approach to 12 neurological and psychiatric diseases using data from the AMP-AD and CMC brain expression quantitative locus dataset, which is large enough to provide robust evidence for the relationship between genetic variants and gene expression. We found a causal relationship between the change in expression of 47 genes and increased disease risk across the 12 diseases we tested. As drug targets with human genetic evidence are far more likely to be approved in clinical trials, these findings provide a valuable list of potential therapeutic targets, including the ACE, GPNMB, KCNQ5, RERE and SUOX genes.
Collapse
Affiliation(s)
- Denis A. Baird
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail: (DAB); (TRG)
| | - Jimmy Z. Liu
- Translational Biology, Research and Development, Cambridge, Massachusetts, United States of America
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | | | | | - Benjamin Elsworth
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Tom G. Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Chia-Yen Chen
- Translational Biology, Research and Development, Cambridge, Massachusetts, United States of America
| | - Minerva M. Carrasquillo
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida, United States of America
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida, United States of America
| | - Joseph S. Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, Florida, United States of America
| | - Philip L. De Jager
- Centre for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Centre, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Centre, New York, New York, United States of America
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida, United States of America
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, United States of America
| | | | - Ben Logsdon
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Karol Estrada
- Translational Biology, Research and Development, Cambridge, Massachusetts, United States of America
- BioMarin Pharmaceuticals, San Rafael, California, United States of America
| | - Philip C. Haycock
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Heiko Runz
- Translational Biology, Research and Development, Cambridge, Massachusetts, United States of America
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Oakfield House, University of Bristol, Bristol, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Oakfield House, University of Bristol, Bristol, United Kingdom
- * E-mail: (DAB); (TRG)
| | | |
Collapse
|
19
|
Liu D, Wang Y, Jing H, Meng Q, Yang J. Mendelian randomization integrating GWAS and mQTL data identified novel pleiotropic DNA methylation loci for neuropathology of Alzheimer's disease. Neurobiol Aging 2020; 97:18-27. [PMID: 33120085 DOI: 10.1016/j.neurobiolaging.2020.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/04/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
The pathogenesis of Alzheimer's disease (AD) remains largely unclear. Exploring the genetic/epigenetic loci showing pleiotropic association with the neuropathologies of AD may greatly enhance understanding of the mechanisms underlying the development of AD. In this study, using data from the Religious Orders Study and the Rush Memory and Aging Project, we undertook a Mendelian randomization approach integrating genome-wide association studies (GWASs) and DNA methylation quantitative trait locus data to explore pleiotropic epigenetic loci for AD neuropathologies, including amyloid-β (Aβ) load and tau-containing neurofibrillary tangle density. We performed GWASs of DNA methylation in brain tissues from 592 participants and mapped 60,595 cis-SNP-CpG pairs after correction for multiple testing. By linking cis-DNA methylation quantitative trait locus with GWAS results for Aβ load and tau tangles, we identified 47 CpGs showing pleiotropic association with Aβ load by the Mendelian randomization analysis. We then used gene expression data from 537 individuals and performed quantitative trait methylation analysis. We found that 18 of the 47 CpGs were in cis associated with 25 mRNAs/genes, comprising 41 unique CpG-mRNA/gene pairs. Our findings shed light on the role of DNA methylation in the pathogenesis of Aβ.
Collapse
Affiliation(s)
- Di Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Youxin Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Huiquan Jing
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Qun Meng
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China.
| | - Jingyun Yang
- Division of Statistics, School of Economics, Shanghai University, Shanghai, China; Research Center of Financial Information, Shanghai University, Shanghai, China; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| |
Collapse
|
20
|
Zheng J, Haberland V, Baird D, Walker V, Haycock PC, Hurle MR, Gutteridge A, Erola P, Liu Y, Luo S, Robinson J, Richardson TG, Staley JR, Elsworth B, Burgess S, Sun BB, Danesh J, Runz H, Maranville JC, Martin HM, Yarmolinsky J, Laurin C, Holmes MV, Liu JZ, Estrada K, Santos R, McCarthy L, Waterworth D, Nelson MR, Smith GD, Butterworth AS, Hemani G, Scott RA, Gaunt TR. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases. Nat Genet 2020; 52:1122-1131. [PMID: 32895551 PMCID: PMC7610464 DOI: 10.1038/s41588-020-0682-6] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2020] [Indexed: 01/23/2023]
Abstract
The human proteome is a major source of therapeutic targets. Recent genetic association analyses of the plasma proteome enable systematic evaluation of the causal consequences of variation in plasma protein levels. Here we estimated the effects of 1,002 proteins on 225 phenotypes using two-sample Mendelian randomization (MR) and colocalization. Of 413 associations supported by evidence from MR, 130 (31.5%) were not supported by results of colocalization analyses, suggesting that genetic confounding due to linkage disequilibrium is widespread in naïve phenome-wide association studies of proteins. Combining MR and colocalization evidence in cis-only analyses, we identified 111 putatively causal effects between 65 proteins and 52 disease-related phenotypes ( https://www.epigraphdb.org/pqtl/ ). Evaluation of data from historic drug development programs showed that target-indication pairs with MR and colocalization support were more likely to be approved, evidencing the value of this approach in identifying and prioritizing potential therapeutic targets.
Collapse
Affiliation(s)
- Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.
- Proteome MR writing group, .
| | - Valeriia Haberland
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Denis Baird
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Venexia Walker
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Mark R Hurle
- Human Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Pau Erola
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Yi Liu
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Shan Luo
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, Hong Kong, China
| | - Jamie Robinson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - James R Staley
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Benjamin Elsworth
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Benjamin B Sun
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- BHF Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Heiko Runz
- Translational Biology, Biogen, Cambridge, MA, USA
| | - Joseph C Maranville
- Informatics and Predictive Sciences, Celgene Corporation, Cambridge, MA, USA
| | - Hannah M Martin
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - James Yarmolinsky
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Charles Laurin
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael V Holmes
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, UK
| | - Jimmy Z Liu
- Translational Biology, Biogen, Cambridge, MA, USA
| | | | - Rita Santos
- Functional Genomics, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | | | | | | | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Adam S Butterworth
- Proteome MR writing group
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- BHF Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Robert A Scott
- Proteome MR writing group, .
- Human Genetics, GlaxoSmithKline, Stevenage, UK.
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.
- Proteome MR writing group, .
- NIHR Bristol Biomedical Research Centre, Bristol, UK.
| |
Collapse
|
21
|
Allum F, Grundberg E. Capturing functional epigenomes for insight into metabolic diseases. Mol Metab 2020; 38:100936. [PMID: 32199819 PMCID: PMC7300388 DOI: 10.1016/j.molmet.2019.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied. SCOPE OF THE REVIEW We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and their utility in complex disease dissection with a focus on DNA methylation. We contrast DNA methylation profiling methods and discuss the advantages of using targeted methods for single-base resolution assessments of methylation levels across tissue-specific regulatory regions to deepen our understanding of contributing factors leading to complex diseases. MAJOR CONCLUSIONS Large-scale assessments of DNA methylation patterns in metabolic disease-linked study cohorts have provided insight into the impact of variable epigenetic variants in disease etiology. In-depth profiling of epigenetic marks at regulatory regions, particularly at tissue-specific elements, will be key to dissect the genetic and environmental components contributing to metabolic disease onset and progression.
Collapse
Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0C7, Canada; McGill University and Genome Quebec Innovation Centre, Montréal, Québec, H3A 0G1, Canada
| | - Elin Grundberg
- Children's Mercy Kansas City, Kansas City, MO, 64108, United States.
| |
Collapse
|
22
|
Diels S, Vanden Berghe W, Van Hul W. Insights into the multifactorial causation of obesity by integrated genetic and epigenetic analysis. Obes Rev 2020; 21:e13019. [PMID: 32170999 DOI: 10.1111/obr.13019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022]
Abstract
Obesity is a highly heritable multifactorial disease that places an enormous burden on human health. Its increasing prevalence and the concomitant-reduced life expectancy has intensified the search for new analytical methods that can reduce the knowledge gap between genetic susceptibility and functional consequences of the disease pathology. Although the influence of genetics and epigenetics has been studied independently in the past, there is increasing evidence that genetic variants interact with environmental factors through epigenetic regulation. This suggests that a combined analysis of genetic and epigenetic variation may be more effective in characterizing the obesity phenotype. To date, limited genome-wide integrative analyses have been performed. In this review, we provide an overview of the latest findings, advantages, and challenges and discuss future perspectives.
Collapse
Affiliation(s)
- Sara Diels
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
23
|
Kibinge NK, Relton CL, Gaunt TR, Richardson TG. Characterizing the Causal Pathway for Genetic Variants Associated with Neurological Phenotypes Using Human Brain-Derived Proteome Data. Am J Hum Genet 2020; 106:885-892. [PMID: 32413284 PMCID: PMC7273531 DOI: 10.1016/j.ajhg.2020.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Leveraging high-dimensional molecular datasets can help us develop mechanistic insight into associations between genetic variants and complex traits. In this study, we integrated human proteome data derived from brain tissue to evaluate whether targeted proteins putatively mediate the effects of genetic variants on seven neurological phenotypes (Alzheimer disease, amyotrophic lateral sclerosis, depression, insomnia, intelligence, neuroticism, and schizophrenia). Applying the principles of Mendelian randomization (MR) systematically across the genome highlighted 43 effects between genetically predicted proteins derived from the dorsolateral prefrontal cortex and these outcomes. Furthermore, genetic colocalization provided evidence that the same causal variant at 12 of these loci was responsible for variation in both protein and neurological phenotype. This included genes such as DCC, which encodes the netrin-1 receptor and has an important role in the development of the nervous system (p = 4.29 × 10-11 with neuroticism), as well as SARM1, which has been previously implicated in axonal degeneration (p = 1.76 × 10-08 with amyotrophic lateral sclerosis). We additionally conducted a phenome-wide MR study for each of these 12 genes to assess potential pleiotropic effects on 700 complex traits and diseases. Our findings suggest that genes such as SNX32, which was initially associated with increased risk of Alzheimer disease, may potentially influence other complex traits in the opposite direction. In contrast, genes such as CTSH (which was also associated with Alzheimer disease) and SARM1 may make worthwhile therapeutic targets because they did not have genetically predicted effects on any of the other phenotypes after correcting for multiple testing.
Collapse
Affiliation(s)
- Nelson K Kibinge
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Caroline L Relton
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Tom R Gaunt
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Tom G Richardson
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom.
| |
Collapse
|
24
|
Guerrero TP, Fickel J, Benhaiem S, Weyrich A. Epigenomics and gene regulation in mammalian social systems. Curr Zool 2020; 66:307-319. [PMID: 32440291 PMCID: PMC7233906 DOI: 10.1093/cz/zoaa005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.
Collapse
Affiliation(s)
- Tania P Guerrero
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Tennenbacher Str. 4, Freiburg, D-79085, Germany
| | - Jörns Fickel
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Sarah Benhaiem
- Department Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
| | - Alexandra Weyrich
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
| |
Collapse
|
25
|
Agliata I, Fernandez-Jimenez N, Goldsmith C, Marie JC, Bilbao JR, Dante R, Hernandez-Vargas H. The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells. Epigenetics 2020; 15:1068-1082. [PMID: 32281463 PMCID: PMC7518701 DOI: 10.1080/15592294.2020.1748916] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abnormal DNA methylation has been described in human inflammatory conditions of the gastrointestinal tract, such as inflammatory bowel disease (IBD). As other complex diseases, IBD results from the balance between genetic predisposition and environmental exposures. As such, DNA methylation may be the consequence (and potential effector) of both, genetic susceptibility variants and/or environmental signals such as cytokine exposure. We attempted to discern between these two non-excluding possibilities by performing a combined analysis of published DNA methylation data in intestinal mucosal cells of IBD and control samples. We identified abnormal DNA methylation at different levels: deviation from mean methylation signals at site and region levels, and differential variability. A fraction of such changes is associated with genetic polymorphisms linked to IBD susceptibility. In addition, by comparing with another intestinal inflammatory condition (i.e., coeliac disease) we propose that aberrant DNA methylation can also be the result of unspecific processes such as chronic inflammation. Our characterization suggests that IBD methylomes combine intrinsic and extrinsic responses in intestinal mucosal cells, and could point to knowledge-based biomarkers of IBD detection and progression.
Collapse
Affiliation(s)
- Iolanda Agliata
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain
| | - Chloe Goldsmith
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Julien C Marie
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Jose R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain.,Ciber de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) , Madrid, Spain
| | - Robert Dante
- Department of Signaling of Tumoral Escape, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon , Lyon, France
| | - Hector Hernandez-Vargas
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France.,Department of Translational Research and Innovation, Centre Léon Bérard , Lyon, France
| |
Collapse
|
26
|
Jamieson E, Korologou-Linden R, Wootton RE, Guyatt AL, Battram T, Burrows K, Gaunt TR, Tobin MD, Munafò M, Davey Smith G, Tilling K, Relton C, Richardson TG, Richmond RC. Smoking, DNA Methylation, and Lung Function: a Mendelian Randomization Analysis to Investigate Causal Pathways. Am J Hum Genet 2020; 106:315-326. [PMID: 32084330 PMCID: PMC7058834 DOI: 10.1016/j.ajhg.2020.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
Whether smoking-associated DNA methylation has a causal effect on lung function has not been thoroughly evaluated. We first investigated the causal effects of 474 smoking-associated CpGs on forced expiratory volume in 1 s (FEV1) in UK Biobank (n = 321,047) by using two-sample Mendelian randomization (MR) and then replicated this investigation in the SpiroMeta Consortium (n = 79,055). Second, we used two-step MR to investigate whether DNA methylation mediates the effect of smoking on FEV1. Lastly, we evaluated the presence of horizontal pleiotropy and assessed whether there is any evidence for shared causal genetic variants between lung function, DNA methylation, and gene expression by using a multiple-trait colocalization ("moloc") framework. We found evidence of a possible causal effect for DNA methylation on FEV1 at 18 CpGs (p < 1.2 × 10-4). Replication analysis supported a causal effect at three CpGs (cg21201401 [LIME1 and ZGPAT], cg19758448 [PGAP3], and cg12616487 [EML3 and AHNAK] [p < 0.0028]). DNA methylation did not clearly mediate the effect of smoking on FEV1, although DNA methylation at some sites might influence lung function via effects on smoking. By using "moloc", we found evidence of shared causal variants between lung function, gene expression, and DNA methylation. These findings highlight potential therapeutic targets for improving lung function and possibly smoking cessation, although larger, tissue-specific datasets are required to confirm these results.
Collapse
Affiliation(s)
- Emily Jamieson
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Roxanna Korologou-Linden
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Robyn E Wootton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Thomas Battram
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Kimberley Burrows
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Tom R Gaunt
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Marcus Munafò
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol National Health Service Foundation Trust and University of Bristol, Bristol, UK
| | - Kate Tilling
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Tom G Richardson
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| |
Collapse
|
27
|
Yang Y, Wu L, Shu XO, Cai Q, Shu X, Li B, Guo X, Ye F, Michailidou K, Bolla MK, Wang Q, Dennis J, Andrulis IL, Brenner H, Chenevix-Trench G, Campa D, Castelao JE, Gago-Dominguez M, Dörk T, Hollestelle A, Lophatananon A, Muir K, Neuhausen SL, Olsson H, Sandler DP, Simard J, Kraft P, Pharoah PDP, Easton DF, Zheng W, Long J. Genetically Predicted Levels of DNA Methylation Biomarkers and Breast Cancer Risk: Data From 228 951 Women of European Descent. J Natl Cancer Inst 2020; 112:295-304. [PMID: 31143935 PMCID: PMC7073907 DOI: 10.1093/jnci/djz109] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Using a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (n = 1595). The prediction models were validated using data from the Women's Health Initiative (n = 883). We applied these models to genomewide association study (GWAS) data of 122 977 breast cancer patients and 105 974 controls to evaluate if the genetically predicted DNA methylation levels at CpG sites (CpGs) are associated with breast cancer risk. All statistical tests were two-sided. RESULTS Of the 62 938 CpG sites CpGs investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P less than 7.94 × 10-7, including 45 CpGs residing in 18 genomic regions, that have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation, and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.
Collapse
Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Kyriaki Michailidou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Irene L Andrulis
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (HB) and German Cancer Consortium (HB), German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Biomedica Orense-Pontevedra-Vigo, Xerencia de Xestión Integrada de Vigo-SERGAS, Vigo, Spain
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, QC, Canada
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health (PK) and Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Paul D P Pharoah
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
28
|
Howey R, Shin SY, Relton C, Davey Smith G, Cordell HJ. Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data. PLoS Genet 2020; 16:e1008198. [PMID: 32119656 PMCID: PMC7067488 DOI: 10.1371/journal.pgen.1008198] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 03/12/2020] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
Mendelian randomization (MR) implemented through instrumental variables analysis is an increasingly popular causal inference tool used in genetic epidemiology. But it can have limitations for evaluating simultaneous causal relationships in complex data sets that include, for example, multiple genetic predictors and multiple potential risk factors associated with the same genetic variant. Here we use real and simulated data to investigate Bayesian network analysis (BN) with the incorporation of directed arcs, representing genetic anchors, as an alternative approach. A Bayesian network describes the conditional dependencies/independencies of variables using a graphical model (a directed acyclic graph) with an accompanying joint probability. In real data, we found BN could be used to infer simultaneous causal relationships that confirmed the individual causal relationships suggested by bi-directional MR, while allowing for the existence of potential horizontal pleiotropy (that would violate MR assumptions). In simulated data, BN with two directional anchors (mimicking genetic instruments) had greater power for a fixed type 1 error than bi-directional MR, while BN with a single directional anchor performed better than or as well as bi-directional MR. Both BN and MR could be adversely affected by violations of their underlying assumptions (such as genetic confounding due to unmeasured horizontal pleiotropy). BN with no directional anchor generated inference that was no better than by chance, emphasizing the importance of directional anchors in BN (as in MR). Under highly pleiotropic simulated scenarios, BN outperformed both MR (and its recent extensions) and two recently-proposed alternative approaches: a multi-SNP mediation intersection-union test (SMUT) and a latent causal variable (LCV) test. We conclude that BN incorporating genetic anchors is a useful complementary method to conventional MR for exploring causal relationships in complex data sets such as those generated from modern "omics" technologies.
Collapse
Affiliation(s)
- Richard Howey
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - So-Youn Shin
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| |
Collapse
|
29
|
Neumeyer S, Hemani G, Zeggini E. Strengthening Causal Inference for Complex Disease Using Molecular Quantitative Trait Loci. Trends Mol Med 2020; 26:232-241. [PMID: 31718940 DOI: 10.1016/j.molmed.2019.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023]
Abstract
Large genome-wide association studies (GWAS) have identified loci that are associated with complex traits and diseases, but index variants are often not causal and reside in non-coding regions of the genome. To gain a better understanding of the relevant biological mechanisms, intermediate traits such as gene expression and protein levels are increasingly being investigated because these are likely mediators between genetic variants and disease outcome. Genetic variants associated with intermediate traits, termed molecular quantitative trait loci (molQTLs), can then be used as instrumental variables in a Mendelian randomization (MR) approach to identify the causal features and mechanisms of complex traits. Challenges such as pleiotropy and the non-specificity of molQTLs remain, and further approaches and methods need to be developed.
Collapse
Affiliation(s)
- Sonja Neumeyer
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gibran Hemani
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| |
Collapse
|
30
|
Richardson TG, Hemani G, Gaunt TR, Relton CL, Davey Smith G. A transcriptome-wide Mendelian randomization study to uncover tissue-dependent regulatory mechanisms across the human phenome. Nat Commun 2020; 11:185. [PMID: 31924771 PMCID: PMC6954187 DOI: 10.1038/s41467-019-13921-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/26/2019] [Indexed: 11/09/2022] Open
Abstract
Developing insight into tissue-specific transcriptional mechanisms can help improve our understanding of how genetic variants exert their effects on complex traits and disease. In this study, we apply the principles of Mendelian randomization to systematically evaluate transcriptome-wide associations between gene expression (across 48 different tissue types) and 395 complex traits. Our findings indicate that variants which influence gene expression levels in multiple tissues are more likely to influence multiple complex traits. Moreover, detailed investigations of our results highlight tissue-specific associations, drug validation opportunities, insight into the likely causal pathways for trait-associated variants and also implicate putative associations at loci yet to be implicated in disease susceptibility. Similar evaluations can be conducted at http://mrcieu.mrsoftware.org/Tissue_MR_atlas/.
Collapse
Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| |
Collapse
|
31
|
Elliott HR, Sharp GC, Relton CL, Lawlor DA. Epigenetics and gestational diabetes: a review of epigenetic epidemiology studies and their use to explore epigenetic mediation and improve prediction. Diabetologia 2019; 62:2171-2178. [PMID: 31624900 PMCID: PMC6861541 DOI: 10.1007/s00125-019-05011-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
Epigenetics encapsulates a group of molecular mechanisms including DNA methylation, histone modification and microRNAs (miRNAs). Gestational diabetes (GDM) increases the risk of adverse perinatal outcomes and is associated with future offspring risk of obesity and type 2 diabetes. It has been hypothesised that epigenetic mechanisms mediate an effect of GDM on offspring adiposity and type 2 diabetes and this could provide a modifiable mechanism to reduce type 2 diabetes in the next generation. Evidence for this hypothesis is lacking. Epigenetic epidemiology could also contribute to reducing type 2 diabetes by identifying biomarkers that accurately predict risk of GDM and its associated future adverse outcomes. We reviewed published human studies that explored associations between any of maternal GDM, type 2 diabetes, gestational fasting or post-load glucose and any epigenetic marker (DNA methylation, histone modification or miRNA). Of the 81 relevant studies we identified, most focused on the potential role of epigenetic mechanisms in mediating intrauterine effects of GDM on offspring outcomes. Studies were small (median total number of participants 58; median number of GDM cases 27) and most did not attempt replication. The most common epigenetic measure analysed was DNA methylation. Most studies that aimed to explore epigenetic mediation examined associations of in utero exposure to GDM with offspring cord or infant blood/placenta DNA methylation. Exploration of any causal effect, or effect on downstream offspring outcomes, was lacking. There is a need for more robust methods to explore the role of epigenetic mechanisms as possible mediators of effects of exposure to GDM on future risk of obesity and type 2 diabetes. Research to identify epigenetic biomarkers to improve identification of women at risk of GDM and its associated adverse (maternal and offspring) outcomes is currently rare but could contribute to future tools for accurate risk stratification.
Collapse
Affiliation(s)
- Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Bristol NIHR Biomedical Research Centre, University of Bristol, Bristol, UK.
| |
Collapse
|
32
|
Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. CURRENT GENETIC MEDICINE REPORTS 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
Collapse
Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| |
Collapse
|
33
|
Fan Y, Vilgalys TP, Sun S, Peng Q, Tung J, Zhou X. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biol 2019; 20:220. [PMID: 31651351 PMCID: PMC6813132 DOI: 10.1186/s13059-019-1813-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
Identifying genetic variants that are associated with methylation variation-an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping-is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.
Collapse
Affiliation(s)
- Yue Fan
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tauras P Vilgalys
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
| | - Shiquan Sun
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Qinke Peng
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Jenny Tung
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
- Duke University Population Research Institute, Duke University, Durham, NC, 27708, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
34
|
Richardson TG, Richmond RC, North TL, Hemani G, Davey Smith G, Sharp GC, Relton CL. An integrative approach to detect epigenetic mechanisms that putatively mediate the influence of lifestyle exposures on disease susceptibility. Int J Epidemiol 2019; 48:887-898. [PMID: 31257439 PMCID: PMC6659375 DOI: 10.1093/ije/dyz119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There is mounting evidence that our environment and lifestyle has an impact on epigenetic regulatory mechanisms, such as DNA methylation. It has been suggested that these molecular processes may mediate the effect of risk factors on disease susceptibility, although evidence in this regard has been challenging to uncover. Using genetic variants as surrogate variables, we have used two-sample Mendelian randomization (2SMR) to investigate the potential implications of putative changes to DNA methylation levels on disease susceptibility. METHODS To illustrate our approach, we identified 412 CpG sites where DNA methylation was associated with prenatal smoking. We then applied 2SMR to investigate potential downstream effects of these putative changes on 643 complex traits using findings from large-scale genome-wide association studies. To strengthen evidence of mediatory mechanisms, we used multiple-trait colocalization to assess whether DNA methylation, nearby gene expression and complex trait variation were all influenced by the same causal genetic variant. RESULTS We identified 22 associations that survived multiple testing (P < 1.89 × 10-7). In-depth follow-up analyses of particular note suggested that the associations between DNA methylation at the ASPSCR1 and REST/POL2RB gene regions, both linked with reduced lung function, may be mediated by changes in gene expression. We validated associations between DNA methylation and traits using independent samples from different stages across the life course. CONCLUSION Our approach should prove valuable in prioritizing CpG sites that may mediate the effect of causal risk factors on disease. In-depth evaluations of findings are necessary to robustly disentangle causality from alternative explanations such as horizontal pleiotropy.
Collapse
Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Teri-Louise North
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| |
Collapse
|
35
|
Hatcher C, Relton CL, Gaunt TR, Richardson TG. Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of complex traits and disease. Transl Psychiatry 2019; 9:105. [PMID: 30820025 PMCID: PMC6395652 DOI: 10.1038/s41398-019-0437-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 12/23/2022] Open
Abstract
Integrative approaches that harness large-scale molecular datasets can help develop mechanistic insight into findings from genome-wide association studies (GWAS). We have performed extensive analyses to uncover transcriptional and epigenetic processes which may play a role in complex trait variation. This was undertaken by applying Bayesian multiple-trait colocalization systematically across the genome to identify genetic variants responsible for influencing intermediate molecular phenotypes as well as complex traits. In this analysis, we leveraged high-dimensional quantitative trait loci data derived from the prefrontal cortex tissue (concerning gene expression, DNA methylation and histone acetylation) and GWAS findings for five complex traits (Neuroticism, Schizophrenia, Educational Attainment, Insomnia and Alzheimer's disease). There was evidence of colocalization for 118 associations, suggesting that the same underlying genetic variant influenced both nearby gene expression as well as complex trait variation. Of these, 73 associations provided evidence that the genetic variant also influenced proximal DNA methylation and/or histone acetylation. These findings support previous evidence at loci where epigenetic mechanisms may putatively mediate effects of genetic variants on traits, such as KLC1 and schizophrenia. We also uncovered evidence implicating novel loci in disease susceptibility, including genes expressed predominantly in the brain tissue, such as MDGA1, KIRREL3 and SLC12A5. An inverse relationship between DNA methylation and gene expression was observed more than can be accounted for by chance, supporting previous findings implicating DNA methylation as a transcriptional repressor. Our study should prove valuable in helping future studies prioritize candidate genes and epigenetic mechanisms for in-depth functional follow-up analyses.
Collapse
Affiliation(s)
- Charlie Hatcher
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| |
Collapse
|
36
|
Cazaly E, Saad J, Wang W, Heckman C, Ollikainen M, Tang J. Making Sense of the Epigenome Using Data Integration Approaches. Front Pharmacol 2019; 10:126. [PMID: 30837884 PMCID: PMC6390500 DOI: 10.3389/fphar.2019.00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.
Collapse
Affiliation(s)
- Emma Cazaly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Joseph Saad
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Wenyu Wang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
37
|
Yang Y, Wu L, Shu X, Lu Y, Shu XO, Cai Q, Beeghly-Fadiel A, Li B, Ye F, Berchuck A, Anton-Culver H, Banerjee S, Benitez J, Bjørge L, Brenton JD, Butzow R, Campbell IG, Chang-Claude J, Chen K, Cook LS, Cramer DW, deFazio A, Dennis J, Doherty JA, Dörk T, Eccles DM, Edwards DV, Fasching PA, Fortner RT, Gayther SA, Giles GG, Glasspool RM, Goode EL, Goodman MT, Gronwald J, Harris HR, Heitz F, Hildebrandt MA, Høgdall E, Høgdall CK, Huntsman DG, Kar SP, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Koushik A, Lambrechts D, Le ND, Levine DA, Massuger LF, Matsuo K, May T, McNeish IA, Menon U, Modugno F, Monteiro AN, Moorman PG, Moysich KB, Ness RB, Nevanlinna H, Olsson H, Onland-Moret NC, Park SK, Paul J, Pearce CL, Pejovic T, Phelan CM, Pike MC, Ramus SJ, Riboli E, Rodriguez-Antona C, Romieu I, Sandler DP, Schildkraut JM, Setiawan VW, Shan K, Siddiqui N, Sieh W, Stampfer MJ, Sutphen R, Swerdlow AJ, Szafron LM, Teo SH, Tworoger SS, Tyrer JP, Webb PM, Wentzensen N, White E, Willett WC, Wolk A, Woo YL, Wu AH, Yan L, Yannoukakos D, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long J. Genetic Data from Nearly 63,000 Women of European Descent Predicts DNA Methylation Biomarkers and Epithelial Ovarian Cancer Risk. Cancer Res 2019; 79:505-517. [PMID: 30559148 PMCID: PMC6359948 DOI: 10.1158/0008-5472.can-18-2726] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
DNA methylation is instrumental for gene regulation. Global changes in the epigenetic landscape have been recognized as a hallmark of cancer. However, the role of DNA methylation in epithelial ovarian cancer (EOC) remains unclear. In this study, high-density genetic and DNA methylation data in white blood cells from the Framingham Heart Study (N = 1,595) were used to build genetic models to predict DNA methylation levels. These prediction models were then applied to the summary statistics of a genome-wide association study (GWAS) of ovarian cancer including 22,406 EOC cases and 40,941 controls to investigate genetically predicted DNA methylation levels in association with EOC risk. Among 62,938 CpG sites investigated, genetically predicted methylation levels at 89 CpG were significantly associated with EOC risk at a Bonferroni-corrected threshold of P < 7.94 × 10-7. Of them, 87 were located at GWAS-identified EOC susceptibility regions and two resided in a genomic region not previously reported to be associated with EOC risk. Integrative analyses of genetic, methylation, and gene expression data identified consistent directions of associations across 12 CpG, five genes, and EOC risk, suggesting that methylation at these 12 CpG may influence EOC risk by regulating expression of these five genes, namely MAPT, HOXB3, ABHD8, ARHGAP27, and SKAP1. We identified novel DNA methylation markers associated with EOC risk and propose that methylation at multiple CpG may affect EOC risk via regulation of gene expression. SIGNIFICANCE: Identification of novel DNA methylation markers associated with EOC risk suggests that methylation at multiple CpG may affect EOC risk through regulation of gene expression.
Collapse
Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, California
| | - Susana Banerjee
- Gynaecology Unit, Royal Marsden Hospital, London, United Kingdom
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Line Bjørge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Center for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ralf Butzow
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ian G Campbell
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kexin Chen
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Linda S Cook
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico
- Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Alberta, Canada
| | - Daniel W Cramer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Digna Velez Edwards
- Vanderbilt Epidemiology Center, Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | | | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Holly R Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Michelle A Hildebrandt
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
- OVCARE, Vancouver Coastal Health Research Centre, Vancouver General Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Linda E Kelemen
- Hollings Cancer Center and Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anita Koushik
- CHUM Research Centre (CRCHUM) and Département de Médicine Sociale et Préventive, Université de Montréal, Montréal, Quebec, Canada
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB and Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Gynecologic Oncology, Laura and Isaac Pearlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Leon F Massuger
- Department of Gynaecology, Radboud Institute for Molecular Life sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Iain A McNeish
- Department Surgery & Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, United Kingdom
| | - Francesmary Modugno
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Patricia G Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina
| | - Kirsten B Moysich
- Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Roberta B Ness
- School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Utrecht, UMC Utrecht, Utrecht, the Netherlands
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - James Paul
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales Sydney, Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Elio Riboli
- Imperial College London, London, United Kingdom
| | - Cristina Rodriguez-Antona
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Isabelle Romieu
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Veronica W Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kang Shan
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Meir J Stampfer
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, Florida
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Lukasz M Szafron
- Department of Immunology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
- Research Institute and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Walter C Willett
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yin Ling Woo
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Li Yan
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
| |
Collapse
|
38
|
Plotnikov D, Guggenheim JA. Mendelian randomisation and the goal of inferring causation from observational studies in the vision sciences. Ophthalmic Physiol Opt 2019; 39:11-25. [DOI: 10.1111/opo.12596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Denis Plotnikov
- School of Optometry & Vision Sciences Cardiff University Cardiff UK
| | | |
Collapse
|
39
|
Cecil CAM, Walton E, Pingault JB, Provençal N, Pappa I, Vitaro F, Côté S, Szyf M, Tremblay RE, Tiemeier H, Viding E, McCrory EJ. DRD4 methylation as a potential biomarker for physical aggression: An epigenome-wide, cross-tissue investigation. Am J Med Genet B Neuropsychiatr Genet 2018; 177:746-764. [PMID: 30411855 DOI: 10.1002/ajmg.b.32689] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 08/23/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022]
Abstract
Epigenetic processes that regulate gene expression, such as DNA methylation (DNAm), have been linked to individual differences in physical aggression. Yet, it is currently unclear whether: (a) DNAm patterns in humans associate with physical aggression independently of other co-occurring psychiatric and behavioral symptoms; (b) whether these patterns are observable across multiple tissues; and (c) whether they may function as a causal versus noncausal biomarker of physical aggression. Here, we used a multisample, cross-tissue design to address these questions. First, we examined genome-wide DNAm patterns (buccal swabs; Illumina 450k) associated with engagement in physical fights in a sample of high-risk youth (n = 119; age = 16-24 years; 53% female). We identified one differentially methylated region in DRD4, which survived genome-wide correction, associated with physical aggression above and beyond co-occurring symptomatology (e.g., ADHD, substance use), and showed strong cross-tissue concordance with both blood and brain. Second, we found that DNAm sites within this region were also differentially methylated in an independent sample of young adults, between individuals with a history of chronic-high versus low physical aggression (peripheral T cells; ages 26-28). Finally, we ran a Mendelian randomization analysis using GWAS data from the EAGLE consortium to test for a causal association of DRD4 methylation with physical aggression. Only one genetic instrument was eligible for the analysis, and results provided no evidence for a causal association. Overall, our findings lend support for peripheral DRD4 methylation as a potential biomarker of physically aggressive behavior, with no evidence yet of a causal relationship.
Collapse
Affiliation(s)
- Charlotte A M Cecil
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Jean-Baptiste Pingault
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Nadine Provençal
- Faculty of Health Sciences, Simon Fraser University, Burnaby and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Vitaro
- Department of Psychoeducation, Université de Montréal, Montréal, Québec, Canada
| | - Sylvana Côté
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada
| | - Richard E Tremblay
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Essi Viding
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Eamon J McCrory
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| |
Collapse
|
40
|
Hannon E, Gorrie-Stone TJ, Smart MC, Burrage J, Hughes A, Bao Y, Kumari M, Schalkwyk LC, Mill J. Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits. Am J Hum Genet 2018; 103:654-665. [PMID: 30401456 PMCID: PMC6217758 DOI: 10.1016/j.ajhg.2018.09.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/14/2018] [Indexed: 11/23/2022] Open
Abstract
Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. We undertook a comprehensive analysis of common genetic variation on DNA methylation (DNAm) by using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (p < 6.52 × 10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified by previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits by using summary-data-based Mendelian randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression and thereby identify 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database as a resource to the research community.
Collapse
Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Melissa C Smart
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Amanda Hughes
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom.
| |
Collapse
|
41
|
Unravelling the Roles of Susceptibility Loci for Autoimmune Diseases in the Post-GWAS Era. Genes (Basel) 2018; 9:genes9080377. [PMID: 30060490 PMCID: PMC6115971 DOI: 10.3390/genes9080377] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022] Open
Abstract
Although genome-wide association studies (GWAS) have identified several hundred loci associated with autoimmune diseases, their mechanistic insights are still poorly understood. The human genome is more complex than single nucleotide polymorphisms (SNPs) that are interrogated by GWAS arrays. Apart from SNPs, it also comprises genetic variations such as insertions-deletions, copy number variations, and somatic mosaicism. Although previous studies suggest that common copy number variations do not play a major role in autoimmune disease risk, it is possible that certain rare genetic variations with large effect sizes are relevant to autoimmunity. In addition, other layers of regulations such as gene-gene interactions, epigenetic-determinants, gene and environmental interactions also contribute to the heritability of autoimmune diseases. This review focuses on discussing why studying these elements may allow us to gain a more comprehensive understanding of the aetiology of complex autoimmune traits.
Collapse
|