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Christiansen C, Potier L, Martin TC, Villicaña S, Castillo-Fernandez JE, Mangino M, Menni C, Tsai PC, Campbell PJ, Mullin S, Ordoñana JR, Monteagudo O, Sachdev PS, Mather KA, Trollor JN, Pietilainen KH, Ollikainen M, Dalgård C, Kyvik K, Christensen K, van Dongen J, Willemsen G, Boomsma DI, Magnusson PKE, Pedersen NL, Wilson SG, Grundberg E, Spector TD, Bell JT. Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications. EBioMedicine 2024; 103:105096. [PMID: 38574408 PMCID: PMC11004697 DOI: 10.1016/j.ebiom.2024.105096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) susceptibility is influenced by genetic and environmental factors. Previous findings suggest DNA methylation as a potential mechanism in T2D pathogenesis and progression. METHODS We profiled DNA methylation in 248 blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. FINDINGS We find and replicate 3 previously unreported T2D differentially methylated CpG positions (T2D-DMPs) at FDR 5% in RGL3, NGB and OTX2, and 20 signals at FDR 25%, of which 14 replicated. Integrating genetic variation and T2D-discordant monozygotic twin analyses, we identify both genetic-based and genetic-independent T2D-DMPs. The signals annotate to genes with established GWAS and EWAS links to T2D and its complications, including blood pressure (RGL3) and eye disease (OTX2). INTERPRETATION The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications. FUNDING Funding acknowledgements for each cohort can be found in the Supplementary Note.
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Affiliation(s)
| | - Louis Potier
- APHP, Paris Cité University, INSERM, Paris, France
| | | | | | | | | | | | - Pei-Chien Tsai
- King's College London, UK; Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Purdey J Campbell
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Shelby Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | | | | | | | | | | | - Kirsi H Pietilainen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Finland; HealthyWeightHub, Abdominal Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Miina Ollikainen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Finland
| | | | | | | | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | | | | | - Scott G Wilson
- King's College London, UK; Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
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Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung W, Johnston JJ, Barrett C, Feldman K, Cohen AS, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. medRxiv 2024:2024.01.10.24301111. [PMID: 38260377 PMCID: PMC10802745 DOI: 10.1101/2024.01.10.24301111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - impacting the onset and phenotypic presentation of rare diseases. In this study, we quantified individual polygenic liability for 1,151 previously published PGS in a cohort of 2,374 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. We observed increased polygenic burden in probands with variants of unknown significance (VUS) compared to unaffected carrier parents. We further observed an enrichment in overlap between diagnostic and candidate rare disease genes and large-effect PGS genes. Overall, our study supports and expands on previous findings of complex trait associations in rare disease phenotypes and provides a framework for identifying novel candidate rare disease genes and in understanding variable penetrance of candidate Mendelian disease variants.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Marissa R. Keever-Keigher
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Warren Cheung
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J. Johnston
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Cassandra Barrett
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | - Keith Feldman
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Health Outcomes and Health Services Research, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Ana S.A. Cohen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Emily G. Farrow
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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3
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Li X, Shao X, Kou M, Wang X, Ma H, Grundberg E, Bazzano LA, Smith SR, Bray GA, Sacks FM, Qi L. DNA Methylation at ABCG1 and Long-term Changes in Adiposity and Fat Distribution in Response to Dietary Interventions: The POUNDS Lost Trial. Diabetes Care 2023; 46:2201-2207. [PMID: 37770056 DOI: 10.2337/dc23-0748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE To examine whether participants with different levels of diabetes-related DNA methylation at ABCG1 might respond differently to dietary weight loss interventions with long-term changes in adiposity and body fat distribution. RESEARCH DESIGN AND METHODS The current study included overweight/obese participants from the POUNDS Lost trial. Blood levels of regional DNA methylation at ABCG1 were profiled by high-resolution methylC-capture sequencing at baseline among 673 participants, of whom 598 were followed up at 6 months and 543 at 2 years. Two-year changes in adiposity and computed tomography-measured body fat distribution were calculated. RESULTS Regional DNA methylation at ABCG1 showed significantly different associations with long-term changes in body weight and waist circumference at 6 months and 2 years in dietary interventions varying in protein intake (interaction P < 0.05 for all). Among participants assigned to an average-protein (15%) diet, lower baseline regional DNA methylation at ABCG1 was associated with greater reductions in body weight and waist circumference at 6 months and 2 years, whereas opposite associations were found among those assigned to a high-protein (25%) diet. Similar interaction patterns were also observed for body fat distribution, including visceral adipose tissue, subcutaneous adipose tissue, deep subcutaneous adipose tissue, and total adipose tissue at 6 months and 2 years (interaction P < 0.05 for all). CONCLUSIONS Baseline DNA methylation at ABCG1 interacted with dietary protein intake on long-term decreases in adiposity and body fat distribution. Participants with lower methylation at ABCG1 benefitted more in long-term reductions in body weight, waist circumference, and body fat distribution when consuming an average-protein diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | | | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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4
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Mullin BH, Zhu K, Brown SJ, Mullin S, Dudbridge F, Pavlos NJ, Richards JB, Grundberg E, Bell JT, Zeggini E, Walsh JP, Xu J, Wilson SG. Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis. Genetics 2023; 225:iyad150. [PMID: 37579195 PMCID: PMC10550309 DOI: 10.1093/genetics/iyad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - J Brent Richards
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Department of Medicine, Human Genetics, Epidemiology, and Biostatistics, Jewish General Hospital, McGill University, Montreal H3A 0G4, Canada
| | - Elin Grundberg
- Genomic Medicine Center, Children’s Mercy Kansas City, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Eleftheria Zeggini
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Translational Genomics, Neuherberg 85764, Germany
- TUM School of Medicine, Technical University of Munich (TUM) and Klinikum Rechts der Isar, Munich 81675, Germany
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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5
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Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape. Nat Commun 2023; 14:4826. [PMID: 37563143 PMCID: PMC10415281 DOI: 10.1038/s41467-023-40424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
The extravillous trophoblast cell lineage is a key feature of placentation and successful pregnancy. Knowledge of transcriptional regulation driving extravillous trophoblast cell development is limited. Here, we map the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem cells and their transition into extravillous trophoblast cells. We show that integrating chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enables identification of transcription factors and regulatory mechanisms critical for extravillous trophoblast cell development. We elucidate functional roles for TFAP2C, SNAI1, and EPAS1 in the regulation of extravillous trophoblast cell development. EPAS1 is identified as an upstream regulator of key extravillous trophoblast cell transcription factors, including ASCL2 and SNAI1 and together with its target genes, is linked to pregnancy loss and birth weight. Collectively, we reveal activation of a dynamic regulatory network and provide a framework for understanding extravillous trophoblast cell specification in trophoblast cell lineage development and human placentation.
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Affiliation(s)
- Kaela M Varberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Esteban M Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Ross P McNally
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Emily R Wesley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Michael Lydic
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Kristin Holoch
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Courtney Marsh
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Michael J Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
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6
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Li X, Shao X, Xue Q, Kou M, Champagne CM, Koseva BS, Heianza Y, Grundberg E, Bazzano LA, Bray GA, Sacks FM, Qi L. DNA Methylation Near CPT1A and Changes in Triglyceride-rich Lipoproteins in Response to Weight-loss Diet Interventions. J Clin Endocrinol Metab 2023; 108:e542-e549. [PMID: 36800272 PMCID: PMC10348458 DOI: 10.1210/clinem/dgad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
CONTEXT Carnitine palmitoyltransferase-1A, encoded by the CPT1A gene, plays a key role in the oxidation of long-chain fatty acids in the mitochondria and may be important in triglyceride metabolism. Previous work has shown that high fat intake was negatively associated with CPT1A methylation and positively associated with CPT1A expression. OBJECTIVE We aim to investigate the association of DNA methylation (DNAm) at the CPT1A gene with reductions in triglycerides and triglyceride-rich lipoproteins (TRLs) in response to weight-loss diet interventions. METHODS The current study included 538 White participants, who were randomly assigned to 1 of 4 diets varying in macronutrient components. We defined the regional DNAm at CPT1A as the average methylation level over CpGs within 500 bp of the 3 triglyceride-related DNAm sites. RESULTS Dietary fat intake significantly modified the association between baseline DNAm at CPT1A and 2-year changes in total plasma triglycerides, independent of concurrent weight loss. Among participants assigned to a low-fat diet, a higher regional DNAm level at CPT1A was associated with a greater reduction in total plasma triglycerides at 2 years (P = .01), compared with those assigned to a high-fat diet (P = .64) (P interaction = .018). Further investigation on lipids and apolipoproteins in very low-density lipoprotein (VLDL) revealed similar interaction patterns for 2-year changes in VLDL-triglycerides, VLDL-cholesterol, and VLDL-apolipoprotein B (P interaction = .009, .002, and .016, respectively), but not for VLDL-apoC-III (P interaction = .36). CONCLUSION Participants with a higher regional DNAm level at CPT1A benefit more in long-term improvement in triglycerides, particularly in the TRLs and related apolipoproteins when consuming a low-fat weight-loss diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1C 0R6, Canada
| | - Qiaochu Xue
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Catherine M Champagne
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Boryana S Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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7
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Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nat Commun 2023; 14:3090. [PMID: 37248219 DOI: 10.1038/s41467-023-38782-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis of regulatory element activity directly in HiFi reads. We present a comprehensive haplotype resolved 5-base HiFi genome sequencing dataset from a rare disease cohort of 276 samples in 152 families to identify rare (~0.5%) hypermethylation events. We find that 80% of these events are allele-specific and predicted to cause loss of regulatory element activity. We demonstrate heritability of extreme hypermethylation including rare cis variants associated with short (~200 bp) and large hypermethylation events (>1 kb), respectively. We identify repeat expansions in proximal promoters predicting allelic gene silencing via hypermethylation and demonstrate allelic transcriptional events downstream. On average 30-40 rare hypermethylation tiles overlap rare disease genes per patient, providing indications for variation prioritization including a previously undiagnosed pathogenic allele in DIP2B causing global developmental delay. We propose that use of HiFi genome sequencing in unsolved rare disease cases will allow detection of unconventional diseases alleles due to loss of regulatory element activity.
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Affiliation(s)
- Warren A Cheung
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Adam F Johnson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | - Emily Farrow
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | | | - Ana S A Cohen
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - John C Means
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tricia N Zion
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Boryana Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tina K Truong
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Carl Schwendinger-Schreck
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J Johnston
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Margaret Gibson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Gilad Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - William B Rizzo
- Child Health Research Institute, Department of Pediatrics, Nebraska Medical Center, Omaha, NE, USA
| | - Isabelle Thiffault
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Scott T Younger
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO, USA
| | | | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
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8
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Hassan N, Gregson CL, Tang H, van der Kamp M, Leo P, McInerney‐Leo AM, Zheng J, Brandi ML, Tang JCY, Fraser W, Stone MD, Grundberg E, Brown MA, Duncan EL, Tobias JH. Rare and Common Variants in GALNT3 May Affect Bone Mass Independently of Phosphate Metabolism. J Bone Miner Res 2023; 38:678-691. [PMID: 36824040 PMCID: PMC10729283 DOI: 10.1002/jbmr.4795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Anabolic treatment options for osteoporosis remain limited. One approach to discovering novel anabolic drug targets is to identify genetic causes of extreme high bone mass (HBM). We investigated a pedigree with unexplained HBM within the UK HBM study, a national cohort of probands with HBM and their relatives. Whole exome sequencing (WES) in a family with HBM identified a rare heterozygous missense variant (NM_004482.4:c.1657C > T, p.Arg553Trp) in GALNT3, segregating appropriately. Interrogation of data from the UK HBM study and the Anglo-Australasian Osteoporosis Genetics Consortium (AOGC) revealed an unrelated individual with HBM with another rare heterozygous variant (NM_004482.4:c.831 T > A, p.Asp277Glu) within the same gene. In silico protein modeling predicted that p.Arg553Trp would disrupt salt-bridge interactions, causing instability of GALNT3, and that p.Asp277Glu would disrupt manganese binding and consequently GALNT3 catalytic function. Bi-allelic loss-of-function GALNT3 mutations alter FGF23 metabolism, resulting in hyperphosphatemia and causing familial tumoral calcinosis (FTC). However, bone mineral density (BMD) in FTC cases, when reported, has been either normal or low. Common variants in the GALNT3 locus show genome-wide significant associations with lumbar, femoral neck, and total body BMD. However, no significant associations with BMD are observed at loci coding for FGF23, its receptor FGFR1, or coreceptor klotho. Mendelian randomization analysis, using expression quantitative trait loci (eQTL) data from primary human osteoblasts and genome-wide association studies data from UK Biobank, suggested increased expression of GALNT3 reduces total body, lumbar spine, and femoral neck BMD but has no effect on phosphate concentrations. In conclusion, rare heterozygous loss-of-function variants in GALNT3 may cause HBM without altering phosphate concentration. These findings suggest that GALNT3 may affect BMD through pathways other than FGF23 regulation, the identification of which may yield novel anabolic drug targets for osteoporosis. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Celia L. Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Haotian Tang
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Paul Leo
- Faculty of Health, Translational Genomics Group, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Aideen M. McInerney‐Leo
- The Faculty of Medicine, Frazer InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Jie Zheng
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR ChinaShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | | | - Jonathan C. Y. Tang
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Clinical Biochemistry, Departments of Laboratory MedicineNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - William Fraser
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Department of Diabetes, Endocrinology and Clinical BiochemistryNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - Michael D. Stone
- University Hospital LlandoughCardiff & Vale University Health BoardCardiffUK
| | - Elin Grundberg
- Genomic Medicine CenterChildren's Mercy Kansas CityKansas CityMissouriUSA
| | | | | | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Jonathan H. Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
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9
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Zion TN, Berrios CD, Cohen ASA, Bartik L, Cross LA, Engleman KL, Fleming EA, Gadea RN, Hughes SS, Jenkins JL, Kussmann J, Lawson C, Schwager C, Strenk ME, Welsh H, Rush ET, Amudhavalli SM, Sullivan BR, Zhou D, Gannon JL, Heese BA, Moore R, Boillat E, Biswell RL, Louiselle DA, Puckett LMB, Beyer S, Neal SH, Sierant V, McBeth M, Belden B, Walter AM, Gibson M, Cheung WA, Johnston JJ, Thiffault I, Farrow EG, Grundberg E, Pastinen T. Insurance denials and diagnostic rates in a pediatric genomic research cohort. Genet Med 2023; 25:100020. [PMID: 36718845 PMCID: PMC10584034 DOI: 10.1016/j.gim.2023.100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
PURPOSE This study aimed to assess the amount and types of clinical genetic testing denied by insurance and the rate of diagnostic and candidate genetic findings identified through research in patients who faced insurance denials. METHODS Analysis consisted of review of insurance denials in 801 patients enrolled in a pediatric genomic research repository with either no previous genetic testing or previous negative genetic testing result identified through cross-referencing with insurance prior-authorizations in patient medical records. Patients and denials were also categorized by type of insurance coverage. Diagnostic findings and candidate genetic findings in these groups were determined through review of our internal variant database and patient charts. RESULTS Of the 801 patients analyzed, 147 had insurance prior-authorization denials on record (18.3%). Exome sequencing and microarray were the most frequently denied genetic tests. Private insurance was significantly more likely to deny testing than public insurance (odds ratio = 2.03 [95% CI = 1.38-2.99] P = .0003). Of the 147 patients with insurance denials, 53.7% had at least 1 diagnostic or candidate finding and 10.9% specifically had a clinically diagnostic finding. Fifty percent of patients with clinically diagnostic results had immediate medical management changes (5.4% of all patients experiencing denials). CONCLUSION Many patients face a major barrier to genetic testing in the form of lack of insurance coverage. A number of these patients have clinically diagnostic findings with medical management implications that would not have been identified without access to research testing. These findings support re-evaluation of insurance carriers' coverage policies.
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Affiliation(s)
- Tricia N Zion
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO.
| | - Courtney D Berrios
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ana S A Cohen
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; University of Kansas Medical Center, School of Professional Health Sciences, Kansas City, MO
| | - Laura A Cross
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Kendra L Engleman
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Caitlin Lawson
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Eric T Rush
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO
| | - Shivarajan M Amudhavalli
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jennifer L Gannon
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Riley Moore
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Emelia Boillat
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Rebecca L Biswell
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Daniel A Louiselle
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Shanna Beyer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Victoria Sierant
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Macy McBeth
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Bradley Belden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Adam M Walter
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Warren A Cheung
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey J Johnston
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Emily G Farrow
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Tomi Pastinen
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
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10
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Kou M, Li X, Shao X, Grundberg E, Wang X, Ma H, Heianza Y, Alfredo Martinez J, Bray GA, Sacks FM, Qi L. DNA Methylation of Birthweight-Blood Pressure Genes and Changes of Blood Pressure in Response to Weight-Loss Diets in the POUNDS Lost Trial. Hypertension 2023; 80:1223-1230. [PMID: 37039021 DOI: 10.1161/hypertensionaha.123.20864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
BACKGROUND DNA methylation (DNAm) may play a critical role in bridging prenatal adverse events and cardiometabolic disorders including hypertension in later life. METHODS We included 672 adult participants with overweight or obesity, who participated in a 2-year randomized weight-loss dietary intervention study. We defined the regional DNAm levels as the average methylation level of 5'-cytosine-phosphate-guanine-3' within 500 bp of LINC00319 (cg01820192), ATP2B1 (cg00508575), and LMNA (cg12593793), respectively. Generalized linear regression models were used to assess the association between the regional DNAm and 2-year blood pressure changes. Trajectory analysis was used to identify subgroups that shared a similar underlying trajectory of 2-year blood pressure changes. RESULTS The regional DNAm at LINC00319, showed significantly different associations with 2-year changes in systolic blood pressure and diastolic blood pressure among participants assigned to low- or high-fat diets (P for interaction<0.05 for all). In response to the low-fat diet, per SD higher regional DNAm at LINC00319 was associated with greater reductions in both 2-year changes in systolic blood pressure (β, -1.481; P=0.020) and diastolic blood pressure (β, -1.096; P=0.009). Three trajectories of changes in systolic blood pressure or diastolic blood pressure were identified, and participants with higher regional DNAm at LINC00319 were more likely to experience and maintain decreased systolic blood pressure and diastolic blood pressure (odds ratio of being in decrease-stable versus stable [95% CI], 1.542 [1.146-2.076] and 1.463 [1.125-1.902]). CONCLUSIONS Our findings suggest that DNAm could be a metabolic memory bridging early and later life, and an indicator of more benefits from eating a low-fat weight-loss diet.
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Affiliation(s)
- Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada (X.S.)
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, MO (E.G.)
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
| | - J Alfredo Martinez
- Madrid Institute of Advance Studies (IMDEA), Research Institute on Food & Health Sciences, Precision Nutrition Program, Madrid, Spain (J.A.M.)
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge (G.A.B.)
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA (F.M.S., L.Q.)
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA (M.K., X.L., X.W., H.M., Y.H., L.Q.)
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA (F.M.S., L.Q.)
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11
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Li X, Shao X, Xue Q, Kou M, Grundberg E, Bray GA, Sacks FM, Qi L. Abstract 65: DNA Methylation at
ABCG1
and Long-Term Changes in Adiposity in Response to Diet Interventions: The POUNDS Lost Trial. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Introduction:
Epigenome-wide association studies identified that DNA methylation (DNAm) at the
ABCG1
gene (cg06500161) was associated with obesity. However, little is known about whether DNAm at
ABCG1
is associated with long-term changes in adiposity and body fat distribution in response to dietary weight-loss interventions.
Hypothesis:
We hypothesized that participants with varying DNAm at
ABCG1
might respond differently to dietary weight-loss interventions on long-term changes in adiposity and body fat distribution.
Methods:
The current study included 673 participants with overweight/obesity, who were randomly assigned to 1 of 4 diets varying in macronutrient components. Blood DNAm level was profiled by a high-resolution methylC-capture sequencing at baseline. The regional DNAm at
ABCG1
was defined as the average methylation level over CpGs within ± 250 bp of cg06500161. Two-year changes in adiposity and Computed Tomography (CT)-measured body fat distribution were calculated.
Results:
We found that regional DNAm at
ABCG1
significantly interacted with dietary protein intake on long-term changes in body weight and waist circumference (WC) at 6 months and 2 years (P-interaction<0.05 for all,
Figure
). Among participants assigned to an average-protein (15%) diet, lower regional DNAm at
ABCG1
was associated with greater reductions in body weight and WC at 6 months and 2 years, while opposite associations were found among those assigned to a high-protein (25%) diet. Similar interactions were also observed for body fat distribution, including visceral adipose tissue, subcutaneous adipose tissue, deep subcutaneous adipose tissue, and total adipose tissue at 6 months and 2 years (P-interaction<0.05 for all).
Conclusion:
Our data indicate that DNAm at
ABCG1
interacted with dietary protein intake on long-term changes in adiposity and body fat distribution. Participants with hypomethylation at
ABCG1
benefited more in long-term improvement in adiposity and body fat distribution by consuming an average-protein diet.
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Affiliation(s)
| | | | | | | | | | | | | | - Lu Qi
- TULANE UNIVERSITY, New Orleans, LA
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12
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Li X, Shao X, Xue Q, Kou M, Grundberg E, Bray GA, Sacks FM, Qi L. Abstract P619: DNA Methylation at
SREBF1
and Long-Term Changes in Body Composition: The POUNDS Lost Trial. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Introduction:
A previous epigenome-wide association study has causally linked DNA methylation (DNAm) at the
SREBF1
gene (cg11024682) with obesity and lipids. However, little is known about whether DNAm at
SREBF1
is associated with long-term changes in body adiposity and composition.
Hypothesis:
We hypothesized that participants with different DNAm at
SRBF1
might respond differently to dietary weight-loss interventions on changes in body adiposity and composition.
Methods:
The current study included 314 individuals with overweight or obese, who participated in POUNDS Lost: a 2-year randomized dietary weight-loss trial. The blood DNAm level was profiled by methylC-capture sequencing at baseline. Regional DNAm at
SREBF1
was calculated as the average methylation level over CpGs within ±250 bp of cg11024682. Body composition, including total fat mass (FM), percentage of FM (FM%), total fat-free mass (FFM), percentage of FFM (FFM%), and percentage of trunk fat (TF%) were measured by dual-energy X-ray absorptiometry (DEXA) at baseline, 6 months, and 2 years.
Results:
Lower regional DNAm at
SREBF1
was significantly associated with changes in body composition across 2 years (
Table
). At 6 months, per SD lower regional DNAm at
SREBF1
was significantly associated with greater reductions in FM (β [SE] -0.23 [0.07], p=0.002), FM% (-0.30 [0.09], p<0.001), and TF% (-0.44 [0.13], p<0.001), and greater increases in FFM (0.18 [0.08], p=0.028) and FFM% (0.30 [0.09], p<0.001), regardless of dietary intervention groups and independent of concurrent weight loss. Such association remained at 2 years: FM (β [SE] -0.21 [0.10], p=0.045), FM% (-0.32 [0.11], p=0.004), TF% (-0.36 [0.16], p=0.026), FFM (0.22 [0.12], p=0.07) and FFM% (0.32 [0.11], p=0.004).
Conclusions:
Overweight and obese individuals with a lower regional DNAm at
SREBF1
achieved greater improvement in body composition across the 2-year intervention, independent of concurrent weight loss, suggesting DNAm at
SREBF1
is predictive of individuals’ response to treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - Lu Qi
- TULANE UNIVERSITY, New Orleans, LA
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13
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Xia S, Vila Ellis L, Winkley K, Menden H, Mabry SM, Venkatraman A, Louiselle D, Gibson M, Grundberg E, Chen J, Sampath V. Neonatal hyperoxia induces activated pulmonary cellular states and sex-dependent transcriptomic changes in a model of experimental bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol 2023; 324:L123-L140. [PMID: 36537711 PMCID: PMC9902224 DOI: 10.1152/ajplung.00252.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Hyperoxia disrupts lung development in mice and causes bronchopulmonary dysplasia (BPD) in neonates. To investigate sex-dependent molecular and cellular programming involved in hyperoxia, we surveyed the mouse lung using single cell RNA sequencing (scRNA-seq), and validated our findings in human neonatal lung cells in vitro. Hyperoxia-induced inflammation in alveolar type (AT) 2 cells gave rise to damage-associated transient progenitors (DATPs). It also induced a new subpopulation of AT1 cells with reduced expression of growth factors normally secreted by AT1 cells, but increased mitochondrial gene expression. Female alveolar epithelial cells had less EMT and pulmonary fibrosis signaling in hyperoxia. In the endothelium, expansion of Car4+ EC (Cap2) was seen in hyperoxia along with an emergent subpopulation of Cap2 with repressed VEGF signaling. This regenerative response was increased in females exposed to hyperoxia. Mesenchymal cells had inflammatory signatures in hyperoxia, with a new distal interstitial fibroblast subcluster characterized by repressed lipid biosynthesis and a transcriptomic signature resembling myofibroblasts. Hyperoxia-induced gene expression signatures in human neonatal fibroblasts and alveolar epithelial cells in vitro resembled mouse scRNA-seq data. These findings suggest that neonatal exposure to hyperoxia programs distinct sex-specific stem cell progenitor and cellular reparative responses that underpin lung remodeling in BPD.
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Affiliation(s)
- Sheng Xia
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Lisandra Vila Ellis
- Department of Pulmonary Medicine, University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Konner Winkley
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Heather Menden
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Sherry M Mabry
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Aparna Venkatraman
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Daniel Louiselle
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
- Children's Mercy Research Institute, Kansas City, Missouri
| | - Jichao Chen
- Department of Pulmonary Medicine, University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Venkatesh Sampath
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
- Children's Mercy Research Institute, Kansas City, Missouri
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14
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Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, Pospisilik JA. Independent phenotypic plasticity axes define distinct obesity sub-types. Nat Metab 2022; 4:1150-1165. [PMID: 36097183 PMCID: PMC9499872 DOI: 10.1038/s42255-022-00629-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
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Affiliation(s)
- Chih-Hsiang Yang
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | | | - Vanessa Wegert
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
| | - Ilaria Panzeri
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Roche Diagnostics Deutschland, Mannheim, Germany
| | - Till Wörpel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Di Lu
- Van Andel Institute, Grand Rapids, MI, USA
| | - Tao Yang
- Van Andel Institute, Grand Rapids, MI, USA
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Allan A Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, MO, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - J Andrew Pospisilik
- Van Andel Institute, Grand Rapids, MI, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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15
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Fraley E, LeMaster C, Khanal S, Banerjee D, Pastinen T, Grundberg E, Selvarangan R, Bradley T. The Impact of Prior Infection and Age on Antibody Persistence After Severe Acute Respiratory Syndrome Coronavirus 2 Messenger RNA Vaccine. Clin Infect Dis 2022; 75:e902-e904. [PMID: 34551091 PMCID: PMC8522412 DOI: 10.1093/cid/ciab850] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 01/19/2023] Open
Abstract
Determining the duration of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is critical for informing the timing of booster immunization. Many genetic and environmental factors could influence both the magnitude and persistence of the antibody response. Here, we showed that SARS-CoV-2 infection before vaccination and age affected the decay of antibody responses to the SARS-CoV-2 messenger RNA vaccine.
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16
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Christiansen C, Tomlinson M, Eliot M, Nilsson E, Costeira R, Xia Y, Villicaña S, Mompeo O, Wells P, Castillo-Fernandez J, Potier L, Vohl MC, Tchernof A, Moustafa JES, Menni C, Steves CJ, Kelsey K, Ling C, Grundberg E, Small KS, Bell JT. Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers. Genome Med 2022; 14:75. [PMID: 35843982 PMCID: PMC9290282 DOI: 10.1186/s13073-022-01077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND There is considerable evidence for the importance of the DNA methylome in metabolic health, for example, a robust methylation signature has been associated with body mass index (BMI). However, visceral fat (VF) mass accumulation is a greater risk factor for metabolic disease than BMI alone. In this study, we dissect the subcutaneous adipose tissue (SAT) methylome signature relevant to metabolic health by focusing on VF as the major risk factor of metabolic disease. We integrate results with genetic, blood methylation, SAT gene expression, blood metabolomic, dietary intake and metabolic phenotype data to assess and quantify genetic and environmental drivers of the identified signals, as well as their potential functional roles. METHODS Epigenome-wide association analyses were carried out to determine visceral fat mass-associated differentially methylated positions (VF-DMPs) in SAT samples from 538 TwinsUK participants. Validation and replication were performed in 333 individuals from 3 independent cohorts. To assess functional impacts of the VF-DMPs, the association between VF and gene expression was determined at the genes annotated to the VF-DMPs and an association analysis was carried out to determine whether methylation at the VF-DMPs is associated with gene expression. Further epigenetic analyses were carried out to compare methylation levels at the VF-DMPs as the response variables and a range of different metabolic health phenotypes including android:gynoid fat ratio (AGR), lipids, blood metabolomic profiles, insulin resistance, T2D and dietary intake variables. The results from all analyses were integrated to identify signals that exhibit altered SAT function and have strong relevance to metabolic health. RESULTS We identified 1181 CpG positions in 788 genes to be differentially methylated with VF (VF-DMPs) with significant enrichment in the insulin signalling pathway. Follow-up cross-omic analysis of VF-DMPs integrating genetics, gene expression, metabolomics, diet, and metabolic traits highlighted VF-DMPs located in 9 genes with strong relevance to metabolic disease mechanisms, with replication of signals in FASN, SREBF1, TAGLN2, PC and CFAP410. PC methylation showed evidence for mediating effects of diet on VF. FASN DNA methylation exhibited putative causal effects on VF that were also strongly associated with insulin resistance and methylation levels in FASN better classified insulin resistance (AUC=0.91) than BMI or VF alone. CONCLUSIONS Our findings help characterise the adiposity-associated methylation signature of SAT, with insights for metabolic disease risk.
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Affiliation(s)
- Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Max Tomlinson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yujing Xia
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Philippa Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Louis Potier
- Diabetology Department, Bichat Hospital, AP-HP, Université de Paris, Paris, France
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC, Canada
| | - Andre Tchernof
- Québec Heart and Lung Institute, Université Laval, Québec, QC, Canada
| | | | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karl Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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17
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Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon JB, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med 2022; 24:1336-1348. [PMID: 35305867 DOI: 10.1016/j.gim.2022.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Shivarajan M Amudhavalli
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - John T Anderson
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Lalit Bansal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rebecca L Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Keith A Coffman
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Ashley M Cooper
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Laura A Cross
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO
| | - Thuy Tien T Dang
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Mary M Elfrink
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Erin D Fecske
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Cynthia Fieser
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Keely Fitzgerald
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rose N Gelineau-Morel
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey Goldstein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Kelsee Halpin
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Brian S Harvey
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Wendy Hein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Suzanne M Herd
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Mohammed Ilyas
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jill Jacobson
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Kathryn Keeler
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Jonas Korlach
- Pacific Biosciences of California, Inc, Menlo Park, CA
| | | | | | - Caitlin Lawson
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Vicki C Little
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Neil Miller
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Allergy Immunology Pulmonary and Sleep Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Annapoorna Nair
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Donna M Pacicca
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nyshele L Posey
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Nigel Price
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Julio F Quezada
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nikita Raje
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO
| | | | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, MO
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Hospital Kansas City, Kansas City, MO
| | - Carol J Saunders
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Richard M Schwend
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Elizabeth Shaffer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Sarah Soden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Brooke R Sweeney
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Adam M Walter
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Laurel K Willig
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Yun Yan
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Children's Mercy Research Institute, Kansas City, MO.
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Bradley T, Geanes E, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R. Identification of conserved coronavirus epitopes targeted by antibodies after SARS-CoV-2 infection or vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.65.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
SARS-CoV-2 is a novel betacoronavirus that causes coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and antibodies targeting this region reacted with proteins in human fecal protein extracts. This indicated that the composition of the gut microbiota could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicited cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
This work was supported through internal institutional funds from Children’s Mercy Research Institute and Children’s Mercy Kansas City.
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19
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Geanes ES, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R, Bradley T. Cross-reactive antibodies elicited to conserved epitopes on SARS-CoV-2 spike protein after infection and vaccination. Sci Rep 2022; 12:6496. [PMID: 35444221 PMCID: PMC9019795 DOI: 10.1038/s41598-022-10230-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is a novel betacoronavirus that caused coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicit cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA. .,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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20
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Varberg KM, Koseva B, Iqbal K, Vijay J, Biswell R, Gibson M, Cheung WA, Varberg JM, Okae H, Arima T, Soares MJ, Grundberg E. Dynamic Regulation of the Chromatin Landscape during Human Extravillous Trophoblast Cell Lineage Development. Placenta 2021. [DOI: 10.1016/j.placenta.2021.07.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Winkley K, Banerjee D, Bradley T, Koseva B, Cheung WA, Selvarangan R, Pastinen T, Grundberg E. Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range. Sci Rep 2021; 11:15927. [PMID: 34354210 PMCID: PMC8342554 DOI: 10.1038/s41598-021-95532-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Previous studies focusing on the age disparity in COVID-19 severity have suggested that younger individuals mount a more robust innate immune response in the nasal mucosa after infection with SARS-CoV-2. However, it is unclear if this reflects increased immune activation or increased immune residence in the nasal mucosa. We hypothesized that immune residency in the nasal mucosa of healthy individuals may differ across the age range. We applied single-cell RNA-sequencing and measured the cellular composition and transcriptional profile of the nasal mucosa in 35 SARS-CoV-2 negative children and adults, ranging in age from 4 months to 65 years. We analyzed in total of ~ 30,000 immune and epithelial cells and found that age and immune cell proportion in the nasal mucosa are inversely correlated, with little evidence for structural changes in the transcriptional state of a given cell type across the age range. Orthogonal validation by epigenome sequencing indicate that it is especially cells of the innate immune system that underlie the age-association. Additionally, we characterize the predominate immune cell type in the nasal mucosa: a resident T cell like population with potent antiviral properties. These results demonstrate fundamental changes in the immune cell makeup of the uninfected nasal mucosa over the lifespan. The resource we generate here is an asset for future studies focusing on respiratory infection and immunization strategies.
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Affiliation(s)
- Konner Winkley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
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22
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Fraley E, LeMaster C, Geanes E, Banerjee D, Khanal S, Grundberg E, Selvarangan R, Bradley T. Humoral immune responses during SARS-CoV-2 mRNA vaccine administration in seropositive and seronegative individuals. BMC Med 2021; 19:169. [PMID: 34304742 PMCID: PMC8310732 DOI: 10.1186/s12916-021-02055-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/07/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The global pandemic of coronavirus disease 2019 (COVID-19) is caused by infection with the SARS-CoV-2 virus. Currently, there are three approved vaccines against SARS-CoV-2 in the USA, including two based on messenger RNA (mRNA) technology that has demonstrated high vaccine efficacy. We sought to characterize humoral immune responses, at high resolution, during immunization with the BNT162b2 (Pfizer-BioNTech) vaccine in individuals with or without prior history of natural SARS-CoV-2 infection. METHODS We determined antibody responses after each dose of the BNT162b2 SARS-CoV-2 vaccine in individuals who had no prior history of SARS-CoV-2 infection (seronegative) and individuals that had previous viral infection 30-60 days prior to first vaccination (seropositive). To do this, we used both an antibody isotype-specific multiplexed bead-based binding assays targeting multiple SARS-CoV-2 viral protein antigens and an assay that identified potential SARS-CoV-2 neutralizing antibody levels. Moreover, we mapped antibody epitope specificity after immunization using SARS-CoV-2 spike protein peptide arrays. RESULTS Antibody levels were significantly higher after a single dose in seropositive individuals compared to seronegative individuals and were comparable to levels observed in seronegative individuals after two doses. While IgG was boosted by vaccination for both seronegative and seropositive individuals, only seronegative individuals had increased IgA or IgM antibody titers after primary immunization. We identified immunodominant peptides targeted on both SARS-CoV-2 spike S1 and S2 subunits after vaccination. CONCLUSION These findings demonstrated the antibody responses to SARS-CoV-2 immunization in seropositive and seronegative individuals and provide support for the concept of using prior infection history as a guide for the consideration of future vaccination regimens. Moreover, we identified key epitopes on the SARS-CoV-2 spike protein that are targeted by antibodies after vaccination that could guide future vaccine and immune correlate development.
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Affiliation(s)
- Elizabeth Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Eric Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA.
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA. .,Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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23
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Bradley T, Grundberg E, Selvarangan R, LeMaster C, Fraley E, Banerjee D, Belden B, Louiselle D, Nolte N, Biswell R, Pastinen T, Myers A, Schuster J. Antibody Responses after a Single Dose of SARS-CoV-2 mRNA Vaccine. N Engl J Med 2021; 384:1959-1961. [PMID: 33755375 PMCID: PMC8008753 DOI: 10.1056/nejmc2102051] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Nick Nolte
- Children's Mercy Kansas City, Kansas City, MO
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24
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Ostinelli G, Vijay J, Vohl MC, Grundberg E, Tchernof A. AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants. Mol Cell Endocrinol 2021; 527:111220. [PMID: 33675863 PMCID: PMC8052191 DOI: 10.1016/j.mce.2021.111220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Changes in androgen dynamics within adipose tissue have been proposed as modulators of body fat accumulation. In this context, AKR1C2 likely plays a significant role by inactivating 5α-dihydrotestosterone. AIM To characterize AKR1C2 expression patterns across adipose depots and cell populations and to provide insight into the link with body fat distribution and genetic regulation. METHODS We used RNA sequencing data from severely obese patients to assess patterns of AKR1C2 and AKR1C3 expression in abdominal adipose tissue depots and cell fractions. We additionally used data from 856 women to assess AKR1C2 heritability and to link its expression in adipose tissue with body fat distribution. Further, we used public resources to study AKR1C2 genetic regulation as well as reference epigenome data for regulatory element profiling and functional interpretation of genetic data. RESULTS We found that mature adipocytes and adipocyte-committed adipocyte progenitor cells (APCs) had enriched expression of AKR1C2. We found adipose tissue AKR1C2 and AKR1C3 expression to be significantly and positively associated with percentage trunk fat mass in women. We identified strong genetic regulation of AKR1C2 by rs28571848 and rs34477787 located on the binding sites of two nuclear transcription factors, namely retinoid acid-related orphan receptor alpha and the glucocorticoid receptor. CONCLUSION We confirm the link between AKR1C2, adipogenic differentiation and adipose tissue distribution. We provide insight into genetic regulation of AKR1C2 by identifying regulatory variants mapping to binding sites for the glucocorticoid receptor and retinoid acid-related orphan receptor alpha which may in part mediate the effect of AKR1C2 expression on body fat distribution.
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Affiliation(s)
- Giada Ostinelli
- Centre de Recherche de l'Institut Universitaire de Cardiologie et Pneumologie de Québec-Université Laval, 2725 Chemin Sainte-Foy, G1V 4G5, Québec City, Québec, Canada; École de Nutrition, Université Laval, 2425 Rue de l'Agriculture, G1V 0A6, Québec City, Québec, Canada
| | - Jinchu Vijay
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Marie-Claude Vohl
- École de Nutrition, Université Laval, 2425 Rue de l'Agriculture, G1V 0A6, Québec City, Québec, Canada; Centre Nutrition, Santé et Societé (NUTRISS)-Insitut sur la Nutrition et les Aliments Fonctionnells (INAF), Université Laval, Québec City, Québec, Canada
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, USA.
| | - Andre Tchernof
- Centre de Recherche de l'Institut Universitaire de Cardiologie et Pneumologie de Québec-Université Laval, 2725 Chemin Sainte-Foy, G1V 4G5, Québec City, Québec, Canada; École de Nutrition, Université Laval, 2425 Rue de l'Agriculture, G1V 0A6, Québec City, Québec, Canada.
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25
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Winkley K, Koseva B, Banerjee D, Cheung W, Selvarangan R, Pastinen T, Grundberg E. High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection. medRxiv 2021:2021.03.09.21253155. [PMID: 33758880 PMCID: PMC7987039 DOI: 10.1101/2021.03.09.21253155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background DNA methylation patterns of the human genome can be modified by environmental stimuli and provide dense information on gene regulatory circuitries. We studied genome-wide DNA methylation in nasal samples from infants (<6 months) applying whole-genome bisulfite sequencing (WGBS) to characterize epigenome response to 10 different respiratory viral infections including SARS-CoV-2. Results We identified virus-specific differentially methylated regions (vDMR) with human metapneumovirus (hMPV) and SARS-CoV-2 followed by Influenza B (Flu B) causing the weakest vs. strongest epigenome response with 496 vs. 78541 and 14361 vDMR, respectively. We found a strong replication rate of FluB (52%) and SARS-CoV-2 (42%) vDMR in independent samples indicating robust epigenome perturbation upon infection. Among the FluB and SARS-CoV-2 vDMRs, around 70% were hypomethylated and significantly enriched among epithelial cell-specific regulatory elements whereas the hypermethylated vDMRs for these viruses mapped more frequently to immune cell regulatory elements, especially those of the myeloid lineage. The hypermethylated vDMRs were also enriched among genes and genetic loci in monocyte activation pathways and monocyte count. Finally, we perform single-cell RNA-sequencing characterization of nasal mucosa in response to these two viruses to functionally analyze the epigenome perturbations. Which supports the trends we identified in methylation data and highlights and important role for monocytes. Conclusions All together, we find evidence indicating genetic predisposition to innate immune response upon a respiratory viral infection. Our genome-wide monitoring of infant viral response provides first catalogue of associated host regulatory elements. Assessing epigenetic variation in individual patients may reveal evidence for viral triggers of childhood disease.
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Affiliation(s)
- Konner Winkley
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Boryana Koseva
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Warren Cheung
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
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26
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Bradley T, Grundberg E, Selvarangan R. Antibody responses boosted in seropositive healthcare workers after single dose of SARS-CoV-2 mRNA vaccine. medRxiv 2021. [PMID: 33564797 DOI: 10.1101/2021.02.03.21251078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Current guidelines recommend that individuals who have had COVID-19 should receive the identical vaccine regimen as those who have not had the infection. This includes two doses of the mRNA platform vaccines (BNT162b2/Pfizer; mRNA-1273/Moderna) that are approved for use in the United States. In this brief report, we show that after a single dose of the Pfizer SARS-CoV-2 vaccine, individuals that had prior SARS-CoV-2 infection had significantly higher antibody levels than individuals that had no history of infection. This provides the rationale for changing vaccination policy to deliver only a single dose to individuals with recent SARS-CoV-2 infection that may free up additional doses for individuals that have no preexisting immunity to the virus. Future study of other immune parameters such as T cell response and durability of immune response should be rapidly undertaken in individuals that had COVID-19 prior to vaccination.
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27
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Péan N, Le Lay A, Brial F, Wasserscheid J, Rouch C, Vincent M, Myridakis A, Hedjazi L, Dumas ME, Grundberg E, Lathrop M, Magnan C, Dewar K, Gauguier D. Dominant gut Prevotella copri in gastrectomised non-obese diabetic Goto-Kakizaki rats improves glucose homeostasis through enhanced FXR signalling. Diabetologia 2020; 63:1223-1235. [PMID: 32173762 PMCID: PMC7228998 DOI: 10.1007/s00125-020-05122-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022]
Abstract
AIMS/HYPOTHESIS Drug and surgical-based therapies in type 2 diabetes are associated with altered gut microbiota architecture. Here we investigated the role of the gut microbiome in improved glucose homeostasis following bariatric surgery. METHODS We carried out gut microbiome analyses in gastrectomised (by vertical sleeve gastrectomy [VSG]) rats of the Goto-Kakizaki (GK) non-obese model of spontaneously occurring type 2 diabetes, followed by physiological studies in the GK rat. RESULTS VSG in the GK rat led to permanent improvement of glucose tolerance associated with minor changes in the gut microbiome, mostly characterised by significant enrichment of caecal Prevotella copri. Gut microbiota enrichment with P. copri in GK rats through permissive antibiotic treatment, inoculation of gut microbiota isolated from gastrectomised GK rats, and direct inoculation of P. copri, resulted in significant improvement of glucose tolerance, independent of changes in body weight. Plasma bile acids were increased in GK rats following inoculation with P. copri and P. copri-enriched microbiota from VSG-treated rats; the inoculated GK rats then showed increased liver glycogen and upregulated expression of Fxr (also known as Nr1h4), Srebf1c, Chrebp (also known as Mlxipl) and Il10 and downregulated expression of Cyp7a1. CONCLUSIONS Our data underline the impact of intestinal P. copri on improved glucose homeostasis through enhanced bile acid metabolism and farnesoid X receptor (FXR) signalling, which may represent a promising opportunity for novel type 2 diabetes therapeutics.
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Affiliation(s)
- Noémie Péan
- Inserm UMR 1124, Université de Paris, 45 rue des Saint-Pères, 75006, Paris, France
| | - Aurelie Le Lay
- Inserm UMR 1124, Université de Paris, 45 rue des Saint-Pères, 75006, Paris, France
| | - Francois Brial
- Inserm UMR 1124, Université de Paris, 45 rue des Saint-Pères, 75006, Paris, France
| | - Jessica Wasserscheid
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Claude Rouch
- Unit of Functional and Adaptive Biology, UMR 8251, CNRS, Université de Paris, 4 rue Marie Andrée Lagroua Weill-Halle, Paris, France
| | - Mylène Vincent
- Unit of Functional and Adaptive Biology, UMR 8251, CNRS, Université de Paris, 4 rue Marie Andrée Lagroua Weill-Halle, Paris, France
| | - Antonis Myridakis
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | | | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elin Grundberg
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Christophe Magnan
- Unit of Functional and Adaptive Biology, UMR 8251, CNRS, Université de Paris, 4 rue Marie Andrée Lagroua Weill-Halle, Paris, France
| | - Ken Dewar
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
| | - Dominique Gauguier
- Inserm UMR 1124, Université de Paris, 45 rue des Saint-Pères, 75006, Paris, France.
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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28
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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. Changes in epigenetic marks have been linked to metabolic disease phenotypes. Disease-linked sites of variable DNA methylation status are enriched in distal regulatory regions of disease-linked tissues. Distal regulatory elements remain underrepresented in popular array-based methylation profiling technologies. Novel next-generation capture methods provide cost-effective solutions to assess the impact of DNA methylation in metabolic diseases specifically at regulatory elements. Improvements in methodologies to account for tissue heterogeneity and causality will be crucial in future epigenome-wide association studies.
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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.
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29
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Vijay J, Gauthier MF, Biswell RL, Louiselle DA, Johnston JJ, Cheung WA, Belden B, Pramatarova A, Biertho L, Gibson M, Simon MM, Djambazian H, Staffa A, Bourque G, Laitinen A, Nystedt J, Vohl MC, Fraser JD, Pastinen T, Tchernof A, Grundberg E. Single-cell analysis of human adipose tissue identifies depot and disease specific cell types. Nat Metab 2020; 2:97-109. [PMID: 32066997 PMCID: PMC7025882 DOI: 10.1038/s42255-019-0152-6] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between metabolic disease risk and body fat distribution in humans involves cellular characteristics which are specific to body fat compartments. Here we show depot-specific differences in the stromal vascual fraction of visceral and subcutaneous adipose tissue by performing single-cell RNA sequencing of tissue specimen from obese individuals. We characterize multiple immune cells, endothelial cells, fibroblasts, adipose and hematopoietic stem cell progenitors. Subpopulations of adipose-resident immune cells are metabolically active and associated with metabolic disease status and those include a population of potential dysfunctional CD8+ T cells expressing metallothioneins. We identify multiple types of adipocyte progenitors that are common across depots, including a subtype enriched in individuals with type 2 diabetes. Depot-specific analysis reveals a class of adipocyte progenitors unique to visceral adipose tissue, which shares common features with beige preadipocytes. Our human single-cell transcriptome atlas across fat depots provides a resource to dissect functional genomics of metabolic disease.
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Affiliation(s)
- Jinchu Vijay
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | | | - Rebecca L Biswell
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Daniel A Louiselle
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J Johnston
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Warren A Cheung
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Bradley Belden
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Albena Pramatarova
- McGill University and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | - Laurent Biertho
- Québec Heart and Lung Institute, Université Laval, Québec, Québec, Canada
| | - Margaret Gibson
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | - Haig Djambazian
- McGill University and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | - Alfredo Staffa
- McGill University and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | | | | | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, Québec, Canada
| | - Jason D Fraser
- Department of Surgery, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tomi Pastinen
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - André Tchernof
- Québec Heart and Lung Institute, Université Laval, Québec, Québec, Canada.
| | - Elin Grundberg
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.
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30
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Zheng J, Maerz W, Gergei I, Kleber M, Drechsler C, Wanner C, Brandenburg V, Reppe S, Gautvik KM, Medina-Gomez C, Shevroja E, Gilly A, Park YC, Dedoussis G, Zeggini E, Lorentzon M, Henning P, Lerner UH, Nilsson KH, Movérare-Skrtic S, Baird D, Elsworth B, Falk L, Groom A, Capellini TD, Grundberg E, Nethander M, Ohlsson C, Davey Smith G, Tobias JH. Mendelian Randomization Analysis Reveals a Causal Influence of Circulating Sclerostin Levels on Bone Mineral Density and Fractures. J Bone Miner Res 2019; 34:1824-1836. [PMID: 31170332 PMCID: PMC6899787 DOI: 10.1002/jbmr.3803] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/14/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022]
Abstract
In bone, sclerostin is mainly osteocyte-derived and plays an important local role in adaptive responses to mechanical loading. Whether circulating levels of sclerostin also play a functional role is currently unclear, which we aimed to examine by two-sample Mendelian randomization (MR). A genetic instrument for circulating sclerostin, derived from a genomewide association study (GWAS) meta-analysis of serum sclerostin in 10,584 European-descent individuals, was examined in relation to femoral neck bone mineral density (BMD; n = 32,744) in GEFOS and estimated bone mineral density (eBMD) by heel ultrasound (n = 426,824) and fracture risk (n = 426,795) in UK Biobank. Our GWAS identified two novel serum sclerostin loci, B4GALNT3 (standard deviation [SD]) change in sclerostin per A allele (β = 0.20, p = 4.6 × 10-49 ) and GALNT1 (β = 0.11 per G allele, p = 4.4 × 10-11 ). B4GALNT3 is an N-acetyl-galactosaminyltransferase, adding a terminal LacdiNAc disaccharide to target glycocoproteins, found to be predominantly expressed in kidney, whereas GALNT1 is an enzyme causing mucin-type O-linked glycosylation. Using these two single-nucleotide polymorphisms (SNPs) as genetic instruments, MR revealed an inverse causal relationship between serum sclerostin and femoral neck BMD (β = -0.12, 95% confidence interval [CI] -0.20 to -0.05) and eBMD (β = -0.12, 95% CI -0.14 to -0.10), and a positive relationship with fracture risk (β = 0.11, 95% CI 0.01 to 0.21). Colocalization analysis demonstrated common genetic signals within the B4GALNT3 locus for higher sclerostin, lower eBMD, and greater B4GALNT3 expression in arterial tissue (probability >99%). Our findings suggest that higher sclerostin levels are causally related to lower BMD and greater fracture risk. Hence, strategies for reducing circulating sclerostin, for example by targeting glycosylation enzymes as suggested by our GWAS results, may prove valuable in treating osteoporosis. © 2019 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc.
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Affiliation(s)
- Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Winfried Maerz
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany.,Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ingrid Gergei
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marcus Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Christoph Wanner
- Department of Cardiology and Nephrology, Rhein-Maas-Klinikum Würselen, Germany
| | - Vincent Brandenburg
- Department of Cardiology and Nephrology, Rhein-Maas-Klinikum Würselen, Germany
| | - Sjur Reppe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Enisa Shevroja
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Arthur Gilly
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Young-Chan Park
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,University of Cambridge, Cambridge, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Eleftheria Zeggini
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mattias Lorentzon
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Geriatric Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Geriatric Medicine Clinic, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Petra Henning
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Ulf H Lerner
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Karin H Nilsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Movérare-Skrtic
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Denis Baird
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Benjamin Elsworth
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Louise Falk
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Alix Groom
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.,Bristol Bioresource Laboratories, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Terence D Capellini
- Human Evolutionary Biology, Harvard University, Boston, MA, USA.,Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Quebec, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy, Kansas City, MO, USA
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Jonathan H Tobias
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.,Musculoskeletal Research Unit, University of Bristol, Bristol, UK
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31
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Chan D, Shao X, Dumargne MC, Aarabi M, Simon MM, Kwan T, Bailey JL, Robaire B, Kimmins S, San Gabriel MC, Zini A, Librach C, Moskovtsev S, Grundberg E, Bourque G, Pastinen T, Trasler JM. Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism. Environ Health Perspect 2019; 127:87002. [PMID: 31393794 PMCID: PMC6792365 DOI: 10.1289/ehp4812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND The sperm DNA methylation landscape is unique and critical for offspring health. If gamete-derived DNA methylation escapes reprograming in early embryos, epigenetic defects in sperm may be transmitted to the next generation. Current techniques to assess sperm DNA methylation show bias toward CpG-dense regions and do not target areas of dynamic methylation, those predicted to be environmentally sensitive and tunable regulatory elements. OBJECTIVES Our goal was to assess variation in human sperm DNA methylation and design a targeted capture panel to interrogate the human sperm methylome. METHODS To characterize variation in sperm DNA methylation, we performed whole genome bisulfite sequencing (WGBS) on an equimolar pool of sperm DNA from a wide cross section of 30 men varying in age, fertility status, methylenetetrahydrofolate reductase (MTHFR) genotype, and exposures. With our targeted capture panel, in individual samples, we examined the effect of MTHFR genotype ([Formula: see text] 677CC, [Formula: see text] 677TT), as well as high-dose folic acid supplementation ([Formula: see text], per genotype, before and after supplementation). RESULTS Through WGBS we discovered nearly 1 million CpGs possessing intermediate methylation levels (20-80%), termed dynamic sperm CpGs. These dynamic CpGs, along with 2 million commonly assessed CpGs, were used to customize a capture panel for targeted interrogation of the human sperm methylome and test its ability to detect effects of altered folate metabolism. As compared with MTHFR 677CC men, those with the 677TT genotype (50% decreased MTHFR activity) had both hyper- and hypomethylation in their sperm. High-dose folic acid supplement treatment exacerbated hypomethylation in MTHFR 677TT men compared with 677CC. In both cases, [Formula: see text] of altered methylation was found in dynamic sperm CpGs, uniquely measured by our assay. DISCUSSION Our sperm panel allowed the discovery of differential methylation following conditions affecting folate metabolism in novel dynamic sperm CpGs. Improved ability to examine variation in sperm DNA methylation can facilitate comprehensive studies of environment-epigenome interactions. https://doi.org/10.1289/EHP4812.
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Affiliation(s)
- Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Marie-Charlotte Dumargne
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Animal Sciences, McGill University, Montreal, Quebec, Canada
| | - Mahmoud Aarabi
- Medical Genetics & Genomics Laboratories, University of Pittsburgh Medical Center (UPMC) Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Tony Kwan
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Janice L. Bailey
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Faculté des sciences de l’agriculture et de l’alimentation, Quebec, Quebec, Canada
| | - Bernard Robaire
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Animal Sciences, McGill University, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Maria C. San Gabriel
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Urology, Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Armand Zini
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Urology, Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Clifford Librach
- Canadian Reproductive Assisted Technology (CReATe) Fertility Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Sergey Moskovtsev
- Canadian Reproductive Assisted Technology (CReATe) Fertility Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Jacquetta M. Trasler
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
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32
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Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol 2019; 20:89. [PMID: 31064398 PMCID: PMC6503438 DOI: 10.1186/s13059-019-1702-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 11/10/2022] Open
Abstract
Following publication of the original article [1], the authors reported an error in Additional file 1.
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Affiliation(s)
- Warren A Cheung
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Andréanne Morin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Valérie Siroux
- Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Dylan Aïssi
- Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Lu Chen
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Fiona Allum
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Emmanuelle Bouzigon
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | | | - Elodie Boulier
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Adriana Redensek
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.,Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - André Tchernof
- Québec Heart and Lung Institute, Laval University, Québec, QC, G1V 4G5, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Florence Demenais
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Isabelle Pin
- Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France.,Pédiatrie, Centre Hospitalier Universitaire (CHU) Grenoble Alpes, Grenoble, France
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Hendrick G Stunnenberg
- Faculty of Science, Department of Molecular Biology, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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33
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Chechi K, Vijay J, Voisine P, Mathieu P, Bossé Y, Tchernof A, Grundberg E, Richard D. UCP1 expression-associated gene signatures of human epicardial adipose tissue. JCI Insight 2019; 4:123618. [PMID: 30996144 DOI: 10.1172/jci.insight.123618] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple reports of uncoupling protein 1 (UCP1) expression have established its presence in human epicardial adipose tissue (eAT). Its functional relevance to eAT, however, remains largely unknown. In a recent study, we reported that adrenergic stimulation of eAT was associated with downregulation of secreted proteins involved in oxidative stress-related and immune-related pathways. Here, we explored the UCP1-associated features of human eAT using next-generation deep sequencing. Paired biopsies of eAT, mediastinal adipose tissue (mAT), and subcutaneous adipose tissue (sAT) obtained from cardiac surgery patients, with specific criteria of high and low expression of UCP1 in eAT, were subjected to RNA sequencing. Although eAT exhibited a depot-specific upregulation in the immune-related pathways relative to mAT and sAT, high UCP1 expression in eAT was specifically associated with differential gene expression that functionally corresponded with downregulation in the production of reactive oxygen species and immune responses, including T cell homeostasis. Our data indicate that UCP1 and adaptive immunity share a reciprocal relationship at the whole-transcriptome level, thereby supporting a plausible role for UCP1 in maintaining tissue homeostasis in human eAT.
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Affiliation(s)
- Kanta Chechi
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Québec, Canada.,Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada
| | - Jinchu Vijay
- Department of Human Genetics, McGill University, and Genome Québec Innovation Centre, Montreal, Québec, Canada
| | - Pierre Voisine
- Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada.,Department of Cardiovascular Surgery
| | - Patrick Mathieu
- Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada.,Laboratory of Cardiovascular Pathobiology, Department of Surgery, Faculty of Medicine, and
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada.,Department of Molecular Medicine, Université Laval, Québec, Québec, Canada
| | - Andre Tchernof
- Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada.,School of Nutrition, Université Laval, Québec, Québec, Canada
| | - Elin Grundberg
- Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Denis Richard
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Québec, Canada.,Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Chemin Sainte-Foy, Québec, Canada
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34
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Morris JA, Kemp JP, Youlten SE, Laurent L, Logan JG, Chai RC, Vulpescu NA, Forgetta V, Kleinman A, Mohanty ST, Sergio CM, Quinn J, Nguyen-Yamamoto L, Luco AL, Vijay J, Simon MM, Pramatarova A, Medina-Gomez C, Trajanoska K, Ghirardello EJ, Butterfield NC, Curry KF, Leitch VD, Sparkes PC, Adoum AT, Mannan NS, Komla-Ebri DSK, Pollard AS, Dewhurst HF, Hassall TAD, Beltejar MJG, Adams DJ, Vaillancourt SM, Kaptoge S, Baldock P, Cooper C, Reeve J, Ntzani EE, Evangelou E, Ohlsson C, Karasik D, Rivadeneira F, Kiel DP, Tobias JH, Gregson CL, Harvey NC, Grundberg E, Goltzman D, Adams DJ, Lelliott CJ, Hinds DA, Ackert-Bicknell CL, Hsu YH, Maurano MT, Croucher PI, Williams GR, Bassett JHD, Evans DM, Richards JB. Author Correction: An atlas of genetic influences on osteoporosis in humans and mice. Nat Genet 2019; 51:920. [PMID: 30988516 DOI: 10.1038/s41588-019-0415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, in Fig. 5a, the data in the right column of 'DAAM2 gRNA1' were incorrectly plotted as circles indicating 'untreated' rather than as squares indicating 'treated'. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- John A Morris
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John P Kemp
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Scott E Youlten
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Ryan C Chai
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Nicholas A Vulpescu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Aaron Kleinman
- Department of Research, 23andMe, Inc., Mountain View, CA, USA
| | - Sindhu T Mohanty
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - C Marcelo Sergio
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Julian Quinn
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Loan Nguyen-Yamamoto
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Aimee-Lee Luco
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Jinchu Vijay
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | | | - Albena Pramatarova
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elena J Ghirardello
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Katharine F Curry
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Penny C Sparkes
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Anne-Tounsia Adoum
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Naila S Mannan
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Davide S K Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Andrea S Pollard
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Hannah F Dewhurst
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Thomas A D Hassall
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | | | | | - Douglas J Adams
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Stephen Kaptoge
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Baldock
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Jonathan Reeve
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Evangelia E Ntzani
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.,Center for Evidence Synthesis in Health, Department of Health Services, Policy and Practice, School of Public Health, Brown University, Providence, RI, USA
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA
| | - Jonathan H Tobias
- Musculoskeletal Research Unit, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Celia L Gregson
- Musculoskeletal Research Unit, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Elin Grundberg
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada.,Children's Mercy Hospitals and Clinics, Kansas City, MO, USA
| | - David Goltzman
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - David A Hinds
- Department of Research, 23andMe, Inc., Mountain View, CA, USA
| | - Cheryl L Ackert-Bicknell
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, NY, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia. .,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - J Brent Richards
- Department of Human Genetics, McGill University, Montréal, Québec, Canada. .,Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada. .,Department of Medicine, McGill University, Montréal, Québec, Canada. .,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada. .,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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Björk A, Ribom E, Johansson G, Scragg R, Mellström D, Grundberg E, Ohlsson C, Karlsson M, Ljunggren Ö, Kindmark A. Variations in the vitamin D receptor gene are not associated with measures of muscle strength, physical performance, or falls in elderly men. Data from MrOS Sweden. J Steroid Biochem Mol Biol 2019; 187:160-165. [PMID: 30476589 DOI: 10.1016/j.jsbmb.2018.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/17/2018] [Accepted: 11/23/2018] [Indexed: 01/07/2023]
Abstract
The vitamin D receptor (VDR) has been proposed as a candidate gene for several musculoskeletal phenotypes. However, previous results on the associations between genetic variants of the VDR with muscle strength and falls have been contradictory. The MrOS Sweden survey, a prospective population-based cohort study of 3014 elderly men (mean age 75 years, range 69-81) offered the opportunity to further investigate these associations. At baseline, data were collected on muscle strength and also the prevalence of falls during the previous 12 months. Genetic association analysis was performed for 7 Single Nucleotide Polymorphisms (SNPs), covering the genetic region surrounding the VDR gene in 2924 men with available samples of DNA. Genetic variations in the VDR were not associated with five different measurements of muscle strength or physical performance (hand grip strength right and left, 6 m walking test (easy and narrow) and timed-stands test). However, one of the 7 SNPs of the gene for the VDR receptor, rs7136534, was associated with prevalence of falls (33.6% of the AA, 14.6% of the AG and 16.5% of the GG allele). In conclusion, VDR genetic variants are not related to muscle strength or physical performance in elderly Swedish men. The role of the rs7136534 SNP for the occurrence of falls is not clear.
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Affiliation(s)
- A Björk
- Department of Medical Sciences, Endocrinology and Mineral Metabolism, Uppsala University, Uppsala, Sweden.
| | - E Ribom
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - G Johansson
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - R Scragg
- Section of Epidemiology & Biostatistics, School of Population Health, University of Auckland, Auckland, New Zealand
| | - D Mellström
- Geriatric Medicine, Department of Internal Medicine and Clinical, Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - E Grundberg
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - C Ohlsson
- Center for Bone and Arthritis Research at the Sahlgrenska Academy, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - M Karlsson
- Department of Clinical Sciences and Orthopedic Surgery, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Ö Ljunggren
- Department of Medical Sciences, Endocrinology and Mineral Metabolism, Uppsala University, Uppsala, Sweden
| | - A Kindmark
- Department of Medical Sciences, Endocrinology and Mineral Metabolism, Uppsala University, Uppsala, Sweden
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36
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Baird DA, Evans DS, Kamanu FK, Gregory JS, Saunders FR, Giuraniuc CV, Barr RJ, Aspden RM, Jenkins D, Kiel DP, Orwoll ES, Cummings SR, Lane NE, Mullin BH, Williams FMK, Richards JB, Wilson SG, Spector TD, Faber BG, Lawlor DA, Grundberg E, Ohlsson C, Pettersson‐Kymmer U, Capellini TD, Richard D, Beck TJ, Evans DM, Paternoster L, Karasik D, Tobias JH. Identification of Novel Loci Associated With Hip Shape: A Meta-Analysis of Genomewide Association Studies. J Bone Miner Res 2019; 34:241-251. [PMID: 30320955 PMCID: PMC6375741 DOI: 10.1002/jbmr.3605] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 02/05/2023]
Abstract
We aimed to report the first genomewide association study (GWAS) meta-analysis of dual-energy X-ray absorptiometry (DXA)-derived hip shape, which is thought to be related to the risk of both hip osteoarthritis and hip fracture. Ten hip shape modes (HSMs) were derived by statistical shape modeling using SHAPE software, from hip DXA scans in the Avon Longitudinal Study of Parents and Children (ALSPAC; adult females), TwinsUK (mixed sex), Framingham Osteoporosis Study (FOS; mixed), Osteoporotic Fractures in Men study (MrOS), and Study of Osteoporotic Fractures (SOF; females) (total N = 15,934). Associations were adjusted for age, sex, and ancestry. Five genomewide significant (p < 5 × 10-9 , adjusted for 10 independent outcomes) single-nucleotide polymorphisms (SNPs) were associated with HSM1, and three SNPs with HSM2. One SNP, in high linkage disequilibrium with rs2158915 associated with HSM1, was associated with HSM5 at genomewide significance. In a look-up of previous GWASs, three of the identified SNPs were associated with hip osteoarthritis, one with hip fracture, and five with height. Seven SNPs were within 200 kb of genes involved in endochondral bone formation, namely SOX9, PTHrP, RUNX1, NKX3-2, FGFR4, DICER1, and HHIP. The SNP adjacent to DICER1 also showed osteoblast cis-regulatory activity of GSC, in which mutations have previously been reported to cause hip dysplasia. For three of the lead SNPs, SNPs in high LD (r2 > 0.5) were identified, which intersected with open chromatin sites as detected by ATAC-seq performed on embryonic mouse proximal femora. In conclusion, we identified eight SNPs independently associated with hip shape, most of which were associated with height and/or mapped close to endochondral bone formation genes, consistent with a contribution of processes involved in limb growth to hip shape and pathological sequelae. These findings raise the possibility that genetic studies of hip shape might help in understanding potential pathways involved in hip osteoarthritis and hip fracture. © 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Denis A Baird
- Musculoskeletal Research UnitUniversity of BristolBristolUK
| | - Daniel S Evans
- California Pacific Medical Center Research InstituteSan FranciscoCAUSA
| | - Frederick K Kamanu
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
| | | | - Fiona R Saunders
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
| | | | - Rebecca J Barr
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
- MEMO ResearchUniversity of DundeeDundeeUK
| | - Richard M Aspden
- Arthritis and Musculoskeletal MedicineUniversity of AberdeenAberdeenUK
| | | | - Douglas P Kiel
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Broad Institute of MIT and HarvardBostonMAUSA
| | - Eric S Orwoll
- School of MedicineOregon Health and Science UniversityPortlandORUSA
| | - Steven R Cummings
- California Pacific Medical Center Research InstituteSan FranciscoCAUSA
| | - Nancy E Lane
- University of California at DavisSacramentoCAUSA
| | - Benjamin H Mullin
- Department of Endocrinology and DiabetesSir Charles Gairdner HospitalNedlandsAustralia
- School of Biomedical SciencesUniversity of Western AustraliaPerthAustralia
| | - Frances MK Williams
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | - J Brent Richards
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
- Departments of Medicine, Human Genetics, Epidemiology, and BiostatisticsJewish General HospitalMcGill UniversityMontrealCanada
| | - Scott G Wilson
- Department of Endocrinology and DiabetesSir Charles Gairdner HospitalNedlandsAustralia
- School of Biomedical SciencesUniversity of Western AustraliaPerthAustralia
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | - Tim D Spector
- Department of Twin Research and Genetic EpidemiologyKing's College LondonLondonUK
| | | | | | - Elin Grundberg
- Department of Human GeneticsMcGill UniversityMontrealCanada
| | - Claes Ohlsson
- Centre for Bone and Arthritis ResearchInstitute of MedicineUniversity of GothenburgGothenburgSweden
| | | | - Terence D Capellini
- Broad Institute of MIT and HarvardBostonMAUSA
- Human Evolutionary BiologyHarvard UniversityBostonMAUSA
| | | | | | - David M Evans
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
- University of Queensland Diamantina InstituteTranslational Research InstituteBrisbaneAustralia
| | | | - David Karasik
- Institute for Aging ResearchHebrew SeniorLifeDepartment of MedicineBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Azrieli Faculty of MedicineBar Ilan UniversitySafedIsrael
| | - Jonathan H Tobias
- Musculoskeletal Research UnitUniversity of BristolBristolUK
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
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Morris JA, Kemp JP, Youlten SE, Laurent L, Logan JG, Chai RC, Vulpescu NA, Forgetta V, Kleinman A, Mohanty ST, Sergio CM, Quinn J, Nguyen-Yamamoto L, Luco AL, Vijay J, Simon MM, Pramatarova A, Medina-Gomez C, Trajanoska K, Ghirardello EJ, Butterfield NC, Curry KF, Leitch VD, Sparkes PC, Adoum AT, Mannan NS, Komla-Ebri DSK, Pollard AS, Dewhurst HF, Hassall TAD, Beltejar MJG, Adams DJ, Vaillancourt SM, Kaptoge S, Baldock P, Cooper C, Reeve J, Ntzani EE, Evangelou E, Ohlsson C, Karasik D, Rivadeneira F, Kiel DP, Tobias JH, Gregson CL, Harvey NC, Grundberg E, Goltzman D, Adams DJ, Lelliott CJ, Hinds DA, Ackert-Bicknell CL, Hsu YH, Maurano MT, Croucher PI, Williams GR, Bassett JHD, Evans DM, Richards JB. An atlas of genetic influences on osteoporosis in humans and mice. Nat Genet 2019; 51:258-266. [PMID: 30598549 PMCID: PMC6358485 DOI: 10.1038/s41588-018-0302-x] [Citation(s) in RCA: 429] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 11/05/2018] [Indexed: 12/25/2022]
Abstract
Osteoporosis is a common aging-related disease diagnosed primarily using bone mineral density (BMD). We assessed genetic determinants of BMD as estimated by heel quantitative ultrasound in 426,824 individuals, identifying 518 genome-wide significant loci (301 novel), explaining 20% of its variance. We identified 13 bone fracture loci, all associated with estimated BMD (eBMD), in ~1.2 million individuals. We then identified target genes enriched for genes known to influence bone density and strength (maximum odds ratio (OR) = 58, P = 1 × 10-75) from cell-specific features, including chromatin conformation and accessible chromatin sites. We next performed rapid-throughput skeletal phenotyping of 126 knockout mice with disruptions in predicted target genes and found an increased abnormal skeletal phenotype frequency compared to 526 unselected lines (P < 0.0001). In-depth analysis of one gene, DAAM2, showed a disproportionate decrease in bone strength relative to mineralization. This genetic atlas provides evidence linking associated SNPs to causal genes, offers new insight into osteoporosis pathophysiology, and highlights opportunities for drug development.
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Affiliation(s)
- John A Morris
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John P Kemp
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Scott E Youlten
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Ryan C Chai
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Nicholas A Vulpescu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Aaron Kleinman
- Department of Research, 23andMe, Inc., Mountain View, CA, USA
| | - Sindhu T Mohanty
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - C Marcelo Sergio
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Julian Quinn
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Loan Nguyen-Yamamoto
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Aimee-Lee Luco
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Jinchu Vijay
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | | | - Albena Pramatarova
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elena J Ghirardello
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Katharine F Curry
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Penny C Sparkes
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Anne-Tounsia Adoum
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Naila S Mannan
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Davide S K Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Andrea S Pollard
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Hannah F Dewhurst
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - Thomas A D Hassall
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Douglas J Adams
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Stephen Kaptoge
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul Baldock
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Jonathan Reeve
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Evangelia E Ntzani
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Center for Evidence Synthesis in Health, Department of Health Services, Policy and Practice, School of Public Health, Brown University, Providence, RI, USA
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA
| | - Jonathan H Tobias
- Musculoskeletal Research Unit, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Celia L Gregson
- Musculoskeletal Research Unit, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Elin Grundberg
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
- Children's Mercy Hospitals and Clinics, Kansas City, MO, USA
| | - David Goltzman
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - David A Hinds
- Department of Research, 23andMe, Inc., Mountain View, CA, USA
| | - Cheryl L Ackert-Bicknell
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, NY, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Peter I Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London, UK
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - J Brent Richards
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.
- Department of Medicine, McGill University, Montréal, Québec, Canada.
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada.
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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38
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Aïssi D, Shao X, Pin I, Bouzigon E, Boudier A, Boulier E, Lathrop M, Grundberg E, Demenais F, Siroux V. DNA methylation and lung function: an epigenome-wide association study. Genes Environ 2017. [DOI: 10.1183/1393003.congress-2017.oa2941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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39
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Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol 2017; 18:50. [PMID: 28283040 PMCID: PMC5346261 DOI: 10.1186/s13059-017-1173-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
Background The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples. Results We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution. We use information from whole genome and targeted bisulfite sequencing from 910 samples to perform genotype-dependent analyses of allele-specific methylation (ASM) and non-allelic methylation (mQTL). In addition, we introduce a novel genotype-independent test to detect methylation imbalance between chromosomes. Of the ~2.2 million CpGs tested for ASM, mQTL, and genotype-independent effects, we identify ~32% as being genetically regulated (ASM or mQTL) and ~14% as being putatively epigenetically regulated. We also show that epigenetically driven effects are strongly enriched in repressed regions and near transcription start sites, whereas the genetically regulated CpGs are enriched in enhancers. Known imprinted regions are enriched among epigenetically regulated loci, but we also observe several novel genomic regions (e.g., HOX genes) as being epigenetically regulated. Finally, we use our ASM datasets for functional interpretation of disease-associated loci and show the advantage of utilizing naïve T cells for understanding autoimmune diseases. Conclusions Our rich catalogue of haploid methylomes across multiple tissues will allow validation of epigenome association studies and exploration of new biological models for allelic exclusion in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1173-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Warren A Cheung
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Andréanne Morin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Valérie Siroux
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Dylan Aïssi
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Lu Chen
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Fiona Allum
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Emmanuelle Bouzigon
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | | | - Elodie Boulier
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Adriana Redensek
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.,Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - André Tchernof
- Québec Heart and Lung Institute, Laval University, Québec, QC, G1V 4G5, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Florence Demenais
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Isabelle Pin
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France.,Pédiatrie, Centre Hospitalier Universitaire (CHU) Grenoble Alpes, Grenoble, France
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Hendrick G Stunnenberg
- Faculty of Science, Department of Molecular Biology, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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40
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Love-Gregory L, Kraja AT, Allum F, Aslibekyan S, Hedman ÅK, Duan Y, Borecki IB, Arnett DK, McCarthy MI, Deloukas P, Ordovas JM, Hopkins PN, Grundberg E, Abumrad NA. Higher chylomicron remnants and LDL particle numbers associate with CD36 SNPs and DNA methylation sites that reduce CD36. J Lipid Res 2016; 57:2176-2184. [PMID: 27729386 DOI: 10.1194/jlr.p065250] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 09/28/2016] [Indexed: 12/18/2022] Open
Abstract
Cluster of differentiation 36 (CD36) variants influence fasting lipids and risk of metabolic syndrome, but their impact on postprandial lipids, an independent risk factor for cardiovascular disease, is unclear. We determined the effects of SNPs within a ∼410 kb region encompassing CD36 and its proximal and distal promoters on chylomicron (CM) remnants and LDL particles at fasting and at 3.5 and 6 h following a high-fat meal (Genetics of Lipid Lowering Drugs and Diet Network study, n = 1,117). Five promoter variants associated with CMs, four with delayed TG clearance and five with LDL particle number. To assess mechanisms underlying the associations, we queried expression quantitative trait loci, DNA methylation, and ChIP-seq datasets for adipose and heart tissues that function in postprandial lipid clearance. Several SNPs that associated with higher serum lipids correlated with lower adipose and heart CD36 mRNA and aligned to active motifs for PPARγ, a major CD36 regulator. The SNPs also associated with DNA methylation sites that related to reduced CD36 mRNA and higher serum lipids, but mixed-model analyses indicated that the SNPs and methylation independently influence CD36 mRNA. The findings support contributions of CD36 SNPs that reduce adipose and heart CD36 RNA expression to inter-individual variability of postprandial lipid metabolism and document changes in CD36 DNA methylation that influence both CD36 expression and lipids.
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Affiliation(s)
- Latisha Love-Gregory
- Department of Medicine, Center for Human Nutrition Washington University School of Medicine, St. Louis, MO 63110
| | - Aldi T Kraja
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Fiona Allum
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama, Birmingham, AL 35294
| | - Åsa K Hedman
- Departments of Medical Sciences and Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Uppsala 75185, Sweden
| | - Yanan Duan
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Ingrid B Borecki
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Donna K Arnett
- Department of Epidemiology, University of Alabama, Birmingham, AL 35294
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK, and Oxford Centre for Diabetes, Endocrinology, and Metabolism and Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford OX3 7JU, UK
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Jose M Ordovas
- JM-USDA-Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111
| | - Paul N Hopkins
- Cardiovascular Genetics Research, University of Utah, Salt Lake City, UT 84132
| | - Elin Grundberg
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Nada A Abumrad
- Department of Medicine, Center for Human Nutrition Washington University School of Medicine, St. Louis, MO 63110
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41
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Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Barrett A, Bell JT, McCarthy MI, Deloukas P, Blanchette M, Bourque G, Spector TD, Lathrop M, Pastinen T, Grundberg E. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol 2015; 16:290. [PMID: 26699896 PMCID: PMC4699357 DOI: 10.1186/s13059-015-0856-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
Background CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution. Results Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15–20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs. Conclusions Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0856-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephan Busche
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Maxime Caron
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Fiona Allum
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Warren A Cheung
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Bing Ge
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Susan Westfall
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada.
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | | | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK. .,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University of London, London, UK. .,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
| | - Mathieu Blanchette
- School of Computer Science, McGill University, Montreal, Quebec, Canada.
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Mark Lathrop
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Elin Grundberg
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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42
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Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C, Kleinman A, Styrkarsdottir U, Liu CT, Uggla C, Evans DS, Nielson CM, Walter K, Pettersson-Kymmer U, McCarthy S, Eriksson J, Kwan T, Jhamai M, Trajanoska K, Memari Y, Min J, Huang J, Danecek P, Wilmot B, Li R, Chou WC, Mokry LE, Moayyeri A, Claussnitzer M, Cheng CH, Cheung W, Medina-Gómez C, Ge B, Chen SH, Choi K, Oei L, Fraser J, Kraaij R, Hibbs MA, Gregson CL, Paquette D, Hofman A, Wibom C, Tranah GJ, Marshall M, Gardiner BB, Cremin K, Auer P, Hsu L, Ring S, Tung JY, Thorleifsson G, Enneman AW, van Schoor NM, de Groot LCPGM, van der Velde N, Melin B, Kemp JP, Christiansen C, Sayers A, Zhou Y, Calderari S, van Rooij J, Carlson C, Peters U, Berlivet S, Dostie J, Uitterlinden AG, Williams SR, Farber C, Grinberg D, LaCroix AZ, Haessler J, Chasman DI, Giulianini F, Rose LM, Ridker PM, Eisman JA, Nguyen TV, Center JR, Nogues X, Garcia-Giralt N, Launer LL, Gudnason V, Mellström D, Vandenput L, Amin N, van Duijn CM, Karlsson MK, Ljunggren Ö, Svensson O, Hallmans G, Rousseau F, Giroux S, Bussière J, Arp PP, Koromani F, Prince RL, Lewis JR, Langdahl BL, Hermann AP, Jensen JEB, Kaptoge S, Khaw KT, Reeve J, Formosa MM, Xuereb-Anastasi A, Åkesson K, McGuigan FE, Garg G, Olmos JM, Zarrabeitia MT, Riancho JA, Ralston SH, Alonso N, Jiang X, Goltzman D, Pastinen T, Grundberg E, Gauguier D, Orwoll ES, Karasik D, Davey-Smith G, Smith AV, Siggeirsdottir K, Harris TB, Zillikens MC, van Meurs JBJ, Thorsteinsdottir U, Maurano MT, Timpson NJ, Soranzo N, Durbin R, Wilson SG, Ntzani EE, Brown MA, Stefansson K, Hinds DA, Spector T, Cupples LA, Ohlsson C, Greenwood CMT, Jackson RD, Rowe DW, Loomis CA, Evans DM, Ackert-Bicknell CL, Joyner AL, Duncan EL, Kiel DP, Rivadeneira F, Richards JB. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature 2015; 526:112-117. [PMID: 26367794 PMCID: PMC4755714 DOI: 10.1038/nature14878 10.1016/j.ajhg.2017.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2015] [Indexed: 04/02/2024]
Abstract
The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants, as well as rare, population-specific, coding variants. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 × 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 × 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 × 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.
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Affiliation(s)
- Hou-Feng Zheng
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
| | - Vincenzo Forgetta
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts 02115, USA
| | - Karol Estrada
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts 02115, USA
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alberto Rosello-Diez
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Paul J Leo
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Chitra L Dahia
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA
- Tissue Engineering, Regeneration and Repair Program, Hospital for Special Surgery, New York 10021, USA
| | - Kyung Hyun Park-Min
- Rheumatology Divison, Hospital for Special Surgery New York, New York 10021, USA
| | - Jonathan H Tobias
- School of Clinical Science, University of Bristol, Bristol BS10 5NB, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | | | - Aaron Kleinman
- Department of Research, 23andMe, Mountain View, California 94041, USA
| | | | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
| | - Charlotta Uggla
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, California 94158, USA
| | - Carrie M Nielson
- Department of Public Health and Preventive Medicine, Oregon Health &Science University, Portland, Oregon 97239, USA
- Bone &Mineral Unit, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Klaudia Walter
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Ulrika Pettersson-Kymmer
- Departments of Pharmacology and Clinical Neurosciences, Umeå University, Umeå S-901 87, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå SE-901 87, Sweden
| | - Shane McCarthy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Joel Eriksson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
| | - Tony Kwan
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
| | - Mila Jhamai
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Yasin Memari
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Josine Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Jie Huang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Petr Danecek
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Beth Wilmot
- Oregon Clinical and Translational Research Institute, Oregon Health &Science University, Portland, Oregon 97239, USA
- Department of Medical and Clinical Informatics, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Rui Li
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
| | - Wen-Chi Chou
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lauren E Mokry
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
| | - Alireza Moayyeri
- Farr Institute of Health Informatics Research, University College London, London NW1 2DA, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Melina Claussnitzer
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Chia-Ho Cheng
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
| | - Warren Cheung
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada
| | - Carolina Medina-Gómez
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - Bing Ge
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
| | - Shu-Huang Chen
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
| | - Kwangbom Choi
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York 14642, USA
| | - Ling Oei
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - James Fraser
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - Matthew A Hibbs
- Center for Musculoskeletal Research, University of Rochester, Rochester, New York 14642, USA
- Department of Computer Science, Trinity University, San Antonio, Texas 78212, USA
| | - Celia L Gregson
- Musculoskeletal Research Unit, University of Bristol, Bristol BS10 5NB, UK
| | - Denis Paquette
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - Carl Wibom
- Department of Radiation Sciences, Umeå University, Umeå S-901 87, Sweden
| | - Gregory J Tranah
- Department of Public Health and Preventive Medicine, Oregon Health &Science University, Portland, Oregon 97239, USA
- Bone &Mineral Unit, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Mhairi Marshall
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Brooke B Gardiner
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Katie Cremin
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Paul Auer
- School of Public Health, University of Wisconsin, Milwaukee, Wisconsin 53726, USA
| | - Li Hsu
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sue Ring
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Joyce Y Tung
- Department of Research, 23andMe, Mountain View, California 94041, USA
| | | | - Anke W Enneman
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Natasja M van Schoor
- Department of Epidemiology and Biostatistics and the EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | | | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Internal Medicine, Section Geriatrics, Academic Medical Center, Amsterdam 1105, The Netherlands
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå S-901 87, Sweden
| | - John P Kemp
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | | | - Adrian Sayers
- Musculoskeletal Research Unit, University of Bristol, Bristol BS10 5NB, UK
| | - Yanhua Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
| | - Sophie Calderari
- Cordeliers Research Centre, INSERM UMRS 1138, Paris 75006, France
- Institute of Cardiometabolism and Nutrition, University Pierre &Marie Curie, Paris 75013, France
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - Chris Carlson
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Soizik Berlivet
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - Stephen R Williams
- Departments of Medicine (Cardiovascular Medicine), Centre for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Charles Farber
- Departments of Medicine (Cardiovascular Medicine), Centre for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Daniel Grinberg
- Department of Genetics, University of Barcelona, Barcelona 08028, Spain
- U-720, Centre for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona 28029, Spain
- Department of Human Molecular Genetics, The Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona 08028, Spain
| | - Andrea Z LaCroix
- Women's Health Center of Excellence Family Medicine and Public Health, University of California - San Diego, San Diego, California 92093, USA
| | - Jeff Haessler
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Daniel I Chasman
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Paul M Ridker
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - John A Eisman
- Osteoporosis &Bone Biology Program, Garvan Institute of Medical Research, Sydney 2010, Australia
- School of Medicine Sydney, University of Notre Dame Australia, Sydney 6959, Australia
- St. Vincent's Hospital &Clinical School, NSW University, Sydney 2010, Australia
| | - Tuan V Nguyen
- Osteoporosis &Bone Biology Program, Garvan Institute of Medical Research, Sydney 2010, Australia
- St. Vincent's Hospital &Clinical School, NSW University, Sydney 2010, Australia
| | - Jacqueline R Center
- Osteoporosis &Bone Biology Program, Garvan Institute of Medical Research, Sydney 2010, Australia
- St. Vincent's Hospital &Clinical School, NSW University, Sydney 2010, Australia
| | - Xavier Nogues
- Musculoskeletal Research Group, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona 08003, Spain
- Cooperative Research Network on Aging and Fragility (RETICEF), Institute of Health Carlos III, 28029, Spain
- Department of Internal Medicine, Hospital del Mar, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Natalia Garcia-Giralt
- Musculoskeletal Research Group, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona 08003, Spain
- Cooperative Research Network on Aging and Fragility (RETICEF), Institute of Health Carlos III, 28029, Spain
| | - Lenore L Launer
- Neuroepidemiology Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Vilmunder Gudnason
- Icelandic Heart Association, Kopavogur IS-201, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
| | - Liesbeth Vandenput
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
| | - Najaf Amin
- Genetic epidemiology unit, Department of Epidemiology, Erasmus MC, Rotterdam 3000CA, The Netherlands
| | - Cornelia M van Duijn
- Genetic epidemiology unit, Department of Epidemiology, Erasmus MC, Rotterdam 3000CA, The Netherlands
| | - Magnus K Karlsson
- Department of Orthopaedics, Skåne University Hospital Malmö 205 02, Sweden
| | - Östen Ljunggren
- Department of Medical Sciences, University of Uppsala, Uppsala 751 85, Sweden
| | - Olle Svensson
- Department of Surgical and Perioperative Sciences, Umeå Unviersity, Umeå 901 85, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umeå University, Umeå SE-901 87, Sweden
| | - François Rousseau
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec City G1V 0A6, Canada
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de recherche du CHU de Québec, Québec City G1V 4G2, Canada
| | - Sylvie Giroux
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de recherche du CHU de Québec, Québec City G1V 4G2, Canada
| | - Johanne Bussière
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de recherche du CHU de Québec, Québec City G1V 4G2, Canada
| | - Pascal P Arp
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Fjorda Koromani
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Richard L Prince
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands 6009, Australia
- Department of Medicine, University of Western Australia, Perth 6009, Australia
| | - Joshua R Lewis
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands 6009, Australia
- Department of Medicine, University of Western Australia, Perth 6009, Australia
| | - Bente L Langdahl
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus C 8000, Denmark
| | - A Pernille Hermann
- Department of Endocrinology, Odense University Hospital, Odense C 5000, Denmark
| | - Jens-Erik B Jensen
- Department of Endocrinology, Hvidovre University Hospital, Hvidovre 2650, Denmark
| | - Stephen Kaptoge
- Farr Institute of Health Informatics Research, University College London, London NW1 2DA, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge CB2 2QQ, UK
| | - Jonathan Reeve
- Medicine and Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Institute of Musculoskeletal Sciences, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Melissa M Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Angela Xuereb-Anastasi
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD 2080, Malta
| | - Kristina Åkesson
- Department of Orthopaedics, Skåne University Hospital Malmö 205 02, Sweden
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Sweden
| | - Fiona E McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Sweden
| | - Gaurav Garg
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Sweden
| | - Jose M Olmos
- Department of Medicine and Psychiatry, University of Cantabria, Santander 39011, Spain
- Department of Internal Medicine, Hospital U.M. Valdecilla- IDIVAL, Santander 39008, Spain
| | - Maria T Zarrabeitia
- Department of Legal Medicine, University of Cantabria, Santander 39011, Spain
| | - Jose A Riancho
- Department of Medicine and Psychiatry, University of Cantabria, Santander 39011, Spain
- Department of Internal Medicine, Hospital U.M. Valdecilla- IDIVAL, Santander 39008, Spain
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nerea Alonso
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Xi Jiang
- Department of Reconstructive Sciences, College of Dental Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - David Goltzman
- Department of Medicine and Physiology, McGill University, Montréal H4A 3J1, Canada
| | - Tomi Pastinen
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada
| | - Elin Grundberg
- McGill University and Genome Quebec Innovation Centre, Montréal H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada
| | - Dominique Gauguier
- Cordeliers Research Centre, INSERM UMRS 1138, Paris 75006, France
- Institute of Cardiometabolism and Nutrition, University Pierre &Marie Curie, Paris 75013, France
| | - Eric S Orwoll
- Bone &Mineral Unit, Oregon Health &Science University, Portland, Oregon 97239, USA
- Department of Medicine, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed 13010, Israel
| | - George Davey-Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur IS-201, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
| | | | - Tamara B Harris
- Laboratory of Epidemiology, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
| | - Unnur Thorsteinsdottir
- Department of Population Genomics, deCODE Genetics, Reykjavik IS-101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
| | - Matthew T Maurano
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Scott G Wilson
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands 6009, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley 6009, Australia
| | - Evangelia E Ntzani
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece
- Department of Health Services, Policy and Practice, Brown University School of Public Health, Providence, Rhode Island 02903, USA
| | - Matthew A Brown
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
| | - Kari Stefansson
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
- deCODE Genetics, Reykjavik IS-101, Iceland
| | - David A Hinds
- Department of Research, 23andMe, Mountain View, California 94041, USA
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
- Framingham Heart Study, Framingham, Massachusetts 01702, USA
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg S-413 45, Sweden
| | - Celia M T Greenwood
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal H3A 1A2, Canada
- Department of Oncology, Gerald Bronfman Centre, McGill University, Montréal H2W 1S6, Canada
| | - Rebecca D Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, Ohio 43210, USA
| | - David W Rowe
- Department of Reconstructive Sciences, College of Dental Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Cynthia A Loomis
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - David M Evans
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | | | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Emma L Duncan
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane 4102, Australia
- Department of Diabetes and Endocrinology, Royal Brisbane and Women's Hospital, Brisbane 4029, Australia
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts 02115, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden 2300RC, The Netherlands
| | - J Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada
- Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal H3T 1E2, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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Laxman N, Rubin CJ, Mallmin H, Nilsson O, Pastinen T, Grundberg E, Kindmark A. Global miRNA expression and correlation with mRNA levels in primary human bone cells. RNA 2015; 21:1433-1443. [PMID: 26078267 PMCID: PMC4509933 DOI: 10.1261/rna.049148.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators that have recently introduced an additional level of intricacy to our understanding of gene regulation. The aim of this study was to investigate miRNA-mRNA interactions that may be relevant for bone metabolism by assessing correlations and interindividual variability in miRNA levels as well as global correlations between miRNA and mRNA levels in a large cohort of primary human osteoblasts (HOBs) obtained during orthopedic surgery in otherwise healthy individuals. We identified differential expression (DE) of 24 miRNAs, and found 9 miRNAs exhibiting DE between males and females. We identified hsa-miR-29b, hsa-miR-30c2, and hsa-miR-125b and their target genes as important modulators of bone metabolism. Further, we used an integrated analysis of global miRNA-mRNA correlations, mRNA-expression profiling, DE, bioinformatics analysis, and functional studies to identify novel target genes for miRNAs with the potential to regulate osteoblast differentiation and extracellular matrix production. Functional studies by overexpression and knockdown of miRNAs showed that, the differentially expressed miRNAs hsa-miR-29b, hsa-miR-30c2, and hsa-miR-125b target genes highly relevant to bone metabolism, e.g., collagen, type I, α1 (COL1A1), osteonectin (SPARC), Runt-related transcription factor 2 (RUNX2), osteocalcin (BGLAP), and frizzled-related protein (FRZB). These miRNAs orchestrate the activities of key regulators of osteoblast differentiation and extracellular matrix proteins by their convergent action on target genes and pathways to control the skeletal gene expression.
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Affiliation(s)
- Navya Laxman
- Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185 Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Hans Mallmin
- Department of Surgical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Olle Nilsson
- Department of Surgical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 1B1 Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 1B1 Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Andreas Kindmark
- Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden Science for Life Laboratory, Department of Medical Sciences, Uppsala University Hospital, SE-75185 Uppsala, Sweden
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44
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Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman ÅK, Kwan T, Ge B, Rönnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Erratum: Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 2015. [PMID: 26219997 DOI: 10.1038/ncomms9016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Viñuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, Erdmann J, Schunkert H, Goodall AH, Ouwehand WH, Dermitzakis E, Spector TD, Samani NJ, Deloukas P. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2015; 9:1382-96. [PMID: 25424692 DOI: 10.4161/15592294.2014.969637] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis P < 5 × 10(-8). All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at CPOX near GPR15. In addition, we found 6 new loci at PRSS23, AVPR1B, PSEN2, LINC00299, RPS6KA2, and KIAA0087. Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or/and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the CHRND gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
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Key Words
- AHRR, aryl-hydrocarbon receptor repressor
- ALPP, alkaline phosphatase, placental
- AVPR1B, arginine vasopressin
- CHRND
- CHRND, cholinergic nicotinic receptor
- COPD, chronic obstructive pulmonary disease
- CPOX
- CPOX, coproporphyrinogen oxidase
- DNA methylation
- DNMT, DNA methyltransferase
- EWAS, epigenome wide association study
- FDR, false discovery rate
- GWAS, genome-wide association studies
- PRSS23, serine protease 23
- PSEN2, presenilin-2 gene
- RPS6KA2, ribosomal protein S6 kinase
- epigenome-wide screen
- gene network
- metQTL, methylation quantitative trait loci
- metQTLs
- rs2697768
- smoking
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Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman ÅK, Kwan T, Ge B, Rönnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 2015; 6:7211. [PMID: 26021296 PMCID: PMC4544751 DOI: 10.1038/ncomms8211] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/17/2015] [Indexed: 02/02/2023] Open
Abstract
Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.
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Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Université Laval, 2440 Hochelaga Boulevard, Québec, Québec, Canada G1V 0A6
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Stephan Busche
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Maxime Caron
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - John Lambourne
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Julie Lessard
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Karolina Tandre
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset Ingång 40, Uppsala 75185, Sweden
| | - Åsa K. Hedman
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Dag Hammarskjölds väg 14B, Uppsala 75185, Sweden,Science for Life Laboratory, Uppsala University, Dag Hammarskjölds väg 14B, Uppsala 75185, Sweden
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Bing Ge
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Lars Rönnblom
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset Ingång 40, Uppsala 75185, Sweden
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7JU, UK,Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford OX3 7JU, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK,William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Todd Richmond
- Roche NimbleGen, 500 South Rosa Road, Madison, Wisconsin 53719, USA
| | - Daniel Burgess
- Roche NimbleGen, 500 South Rosa Road, Madison, Wisconsin 53719, USA
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Lambeth Palace Road, London SE17EH, UK
| | - André Tchernof
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Simon Marceau
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Mark Lathrop
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, 2440 Hochelaga Boulevard, Québec, Québec, Canada G1V 0A6
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Elin Grundberg
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1,
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47
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Park HW, Ge B, Tse S, Grundberg E, Pastinen T, Kelly HW, Tantisira KG. Genetic risk factors for decreased bone mineral accretion in children with asthma receiving multiple oral corticosteroid bursts. J Allergy Clin Immunol 2015; 136:1240-6.e1-8. [PMID: 26025128 DOI: 10.1016/j.jaci.2015.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND Long-term intermittent oral corticosteroid (OCS) use in children with asthma leads to significant decreases in bone mineral accretion (BMA). OBJECTIVE We aimed to identify genetic factors influencing OCS dose effects on BMA in children with asthma. METHODS We first performed a gene-by-OCS interaction genome-wide association study (GWAS) of BMA in 489 white participants in the Childhood Asthma Management Program trial who took short-term oral prednisone bursts when they experienced acute asthma exacerbations. We selected the top-ranked 2000 single nucleotide polymorphisms (SNPs) in the GWAS and determined whether these SNPs also had cis-regulatory effects on dexamethasone-induced gene expression in osteoblasts. RESULTS We identified 2 SNPs (rs9896933 and rs2074439) associated with decreased BMA and related to the tubulin γ pathway. The rs9896933 variant met the criteria for genome-wide significance (P = 3.15 × 10(-8) in the GWAS) and is located on the intron of tubulin folding cofactor D (TBCD) gene. The rs2074439 variant (P = 2.74 × 10(-4) in the GWAS) showed strong cis-regulatory effects on dexamethasone-induced tubulin γ gene expression in osteoblasts (P = 8.64 × 10(-4)). Interestingly, we found that BMA worsened with increasing prednisone dose as the number of mutant alleles of the 2 SNPs increased. CONCLUSIONS We have identified 2 novel tubulin γ pathway SNPs, rs9896933 and rs2074439, showing independent interactive effects with cumulative corticosteroid dose on BMA in children with asthma receiving multiple OCS bursts.
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Affiliation(s)
- Heung-Woo Park
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Bing Ge
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Szeman Tse
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Sainte-Justine University Health Center, University of Montreal, Montreal, Quebec, Canada
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Medical Genetics, McGill University, Montreal, Quebec, Canada
| | - H William Kelly
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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48
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Saferali A, Grundberg E, Berlivet S, Beauchemin H, Morcos L, Polychronakos C, Pastinen T, Graham J, McNeney B, Naumova AK. Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines. Epigenetics 2014; 5:50-60. [DOI: 10.4161/epi.5.1.10436] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ng MCY, Shriner D, Chen BH, Li J, Chen WM, Guo X, Liu J, Bielinski SJ, Yanek LR, Nalls MA, Comeau ME, Rasmussen-Torvik LJ, Jensen RA, Evans DS, Sun YV, An P, Patel SR, Lu Y, Long J, Armstrong LL, Wagenknecht L, Yang L, Snively BM, Palmer ND, Mudgal P, Langefeld CD, Keene KL, Freedman BI, Mychaleckyj JC, Nayak U, Raffel LJ, Goodarzi MO, Chen YDI, Taylor HA, Correa A, Sims M, Couper D, Pankow JS, Boerwinkle E, Adeyemo A, Doumatey A, Chen G, Mathias RA, Vaidya D, Singleton AB, Zonderman AB, Igo RP, Sedor JR, Kabagambe EK, Siscovick DS, McKnight B, Rice K, Liu Y, Hsueh WC, Zhao W, Bielak LF, Kraja A, Province MA, Bottinger EP, Gottesman O, Cai Q, Zheng W, Blot WJ, Lowe WL, Pacheco JA, Crawford DC, Grundberg E, Rich SS, Hayes MG, Shu XO, Loos RJF, Borecki IB, Peyser PA, Cummings SR, Psaty BM, Fornage M, Iyengar SK, Evans MK, Becker DM, Kao WHL, Wilson JG, Rotter JI, Sale MM, Liu S, Rotimi CN, Bowden DW. Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes. PLoS Genet 2014; 10:e1004517. [PMID: 25102180 PMCID: PMC4125087 DOI: 10.1371/journal.pgen.1004517] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/05/2014] [Indexed: 12/11/2022] Open
Abstract
Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10−94<P<5×10−8, odds ratio (OR) = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2×10−23 < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies. Despite the higher prevalence of type 2 diabetes (T2D) in African Americans than in Europeans, recent genome-wide association studies (GWAS) were examined primarily in individuals of European ancestry. In this study, we performed meta-analysis of 17 GWAS in 8,284 cases and 15,543 controls to explore the genetic architecture of T2D in African Americans. Following replication in additional 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry, we identified two novel and three previous reported T2D loci reaching genome-wide significance. We also examined 158 loci previously reported to be associated with T2D or regulating glucose homeostasis. While 56% of these loci were shared between African Americans and the other populations, the strongest associations in African Americans are often found in nearby single nucleotide polymorphisms (SNPs) instead of the original SNPs reported in other populations due to differential genetic architecture across populations. Our results highlight the importance of performing genetic studies in non-European populations to fine map the causal genetic variants.
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Affiliation(s)
- Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Brian H. Chen
- Program on Genomics and Nutrition, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Center for Metabolic Disease Prevention, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jiang Li
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jiankang Liu
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Suzette J. Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Lisa R. Yanek
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mary E. Comeau
- Center for Public Health Genomics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Richard A. Jensen
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel S. Evans
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Yan V. Sun
- Department of Epidemiology and Biomedical Informatics, Emory University, Atlanta, Georgia, United States of America
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanjay R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Loren L. Armstrong
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Lynne Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Lingyao Yang
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Beverly M. Snively
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Poorva Mudgal
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Carl D. Langefeld
- Center for Public Health Genomics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Keith L. Keene
- Department of Biology, Center for Health Disparities, East Carolina University, Greenville, North Carolina, United States of America
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Leslie J. Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Mark O. Goodarzi
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Y-D Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Herman A. Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Jackson State University, Tougaloo College, Jackson, Mississippi, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - David Couper
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Rasika A. Mathias
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dhananjay Vaidya
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John R. Sedor
- Department of Medicine, Case Western Reserve University, MetroHealth System campus, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | - Edmond K. Kabagambe
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David S. Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Barbara McKnight
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Kenneth Rice
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wen-Chi Hsueh
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Aldi Kraja
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael A. Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee; International Epidemiology Institute, Rockville, Maryland, United States of America
| | - William L. Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jennifer A. Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Dana C. Crawford
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | | | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - M. Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ingrid B. Borecki
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Steven R. Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Health Services, University of Washington, Seattle, Washington, United States of America
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michele K. Evans
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Baltimore Maryland, United States of America
| | - Diane M. Becker
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - W. H. Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Michèle M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Simin Liu
- Program on Genomics and Nutrition, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Epidemiology, University of California Los Angeles, Los Angeles, California, United States of America
- Departments of Epidemiology and Medicine, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SL); (CNR); (DWB)
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
- * E-mail: (SL); (CNR); (DWB)
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail: (SL); (CNR); (DWB)
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50
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Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP, Walter K, Menni C, Chen L, Vasquez L, Valdes AM, Hyde CL, Wang V, Ziemek D, Roberts P, Xi L, Grundberg E, Waldenberger M, Richards JB, Mohney RP, Milburn MV, John SL, Trimmer J, Theis FJ, Overington JP, Suhre K, Brosnan MJ, Gieger C, Kastenmüller G, Spector TD, Soranzo N. An atlas of genetic influences on human blood metabolites. Nat Genet 2014; 46:543-550. [PMID: 24816252 PMCID: PMC4064254 DOI: 10.1038/ng.2982] [Citation(s) in RCA: 868] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 04/14/2014] [Indexed: 02/07/2023]
Abstract
Genome-wide association scans with high-throughput metabolic profiling provide unprecedented insights into how genetic variation influences metabolism and complex disease. Here we report the most comprehensive exploration of genetic loci influencing human metabolism to date, including 7,824 adult individuals from two European population studies. We report genome-wide significant associations at 145 metabolic loci and their biochemical connectivity regarding more than 400 metabolites in human blood. We extensively characterize the resulting in vivo blueprint of metabolism in human blood by integrating it with information regarding gene expression, heritability, overlap with known drug targets, previous association with complex disorders and inborn errors of metabolism. We further developed a database and web-based resources for data mining and results visualization. Our findings contribute to a greater understanding of the role of inherited variation in blood metabolic diversity, and identify potential new opportunities for pharmacologic development and disease understanding.
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Affiliation(s)
- So-Youn Shin
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Eric B Fauman
- Pfizer Worldwide Research and Development, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Cambridge MA, 02140, USA
| | - Ann-Kristin Petersen
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Jan Krumsiek
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Rita Santos
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Jie Huang
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Matthias Arnold
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Idil Erte
- Department of Twin research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Vincenzo Forgetta
- Department of Human Genetics, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal H3A 1A5, Canada
| | - Tsun-Po Yang
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Cristina Menni
- Department of Twin research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Lu Chen
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK.,Department of Hematology, University of Cambridge, Long Road, Cambridge CB2 2PT, UK
| | - Louella Vasquez
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Ana M Valdes
- Department of Twin research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK.,School of Medicine, University of Nottingham, Nottingham NG5 1PB, UK
| | - Craig L Hyde
- Pfizer Worldwide Research and Development, Clinical Research Statistics, 558 Eastern Point Rd, Groton CT 06340, USA
| | - Vicky Wang
- Pfizer Worldwide Research and Development, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Cambridge MA, 02140, USA
| | - Daniel Ziemek
- Pfizer Worldwide Research and Development, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Cambridge MA, 02140, USA
| | - Phoebe Roberts
- Pfizer Worldwide Research and Development, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Cambridge MA, 02140, USA
| | - Li Xi
- Pfizer Worldwide Research and Development, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Cambridge MA, 02140, USA
| | - Elin Grundberg
- Department of Human Genetics, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal H3A 1A5, Canada.,Genome Quebec Innovation Centre, McGill University, Montreal QCH3A 1A5, Canada
| | | | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - J Brent Richards
- Department of Human Genetics, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal H3A 1A5, Canada.,Department of Medicine, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal H3A 1A5, Canada
| | | | | | - Sally L John
- Pfizer Worldwide Research and Development, Cardiovascular and Metabolic Diseases, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - Jeff Trimmer
- Pfizer Worldwide Research and Development, Cardiovascular and Metabolic Diseases, 620 Memorial Drive, Cambridge, MA 02139, USA
| | - Fabian J Theis
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Department of Mathematics, Technische Universität München, Garching, Germany
| | - John P Overington
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - M Julia Brosnan
- Pfizer Worldwide Research and Development, Clinical Research Statistics, 558 Eastern Point Rd, Groton CT 06340, USA
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Tim D Spector
- Department of Twin research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK.,Department of Hematology, Long Road, Cambridge CB2 0PT, UK
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