1
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Carland C, Png G, Malarstig A, Kho PF, Gustafsson S, Michaelsson K, Lind L, Tsafantakis E, Karaleftheri M, Dedoussis G, Ramisch A, Macdonald-Dunlop E, Klaric L, Joshi PK, Chen Y, Björck HM, Eriksson P, Carrasco-Zanini J, Wheeler E, Suhre K, Gilly A, Zeggini E, Viñuela A, Dermitzakis ET, Wilson JF, Langenberg C, Thareja G, Halama A, Schmidt F, Zanetti D, Assimes T. Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases. Clin Proteomics 2023; 20:31. [PMID: 37550624 PMCID: PMC10405520 DOI: 10.1186/s12014-023-09421-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Human plasma contains a wide variety of circulating proteins. These proteins can be important clinical biomarkers in disease and also possible drug targets. Large scale genomics studies of circulating proteins can identify genetic variants that lead to relative protein abundance. METHODS We conducted a meta-analysis on genome-wide association studies of autosomal chromosomes in 22,997 individuals of primarily European ancestry across 12 cohorts to identify protein quantitative trait loci (pQTL) for 92 cardiometabolic associated plasma proteins. RESULTS We identified 503 (337 cis and 166 trans) conditionally independent pQTLs, including several novel variants not reported in the literature. We conducted a sex-stratified analysis and found that 118 (23.5%) of pQTLs demonstrated heterogeneity between sexes. The direction of effect was preserved but there were differences in effect size and significance. Additionally, we annotate trans-pQTLs with nearest genes and report plausible biological relationships. Using Mendelian randomization, we identified causal associations for 18 proteins across 19 phenotypes, of which 10 have additional genetic colocalization evidence. We highlight proteins associated with a constellation of cardiometabolic traits including angiopoietin-related protein 7 (ANGPTL7) and Semaphorin 3F (SEMA3F). CONCLUSION Through large-scale analysis of protein quantitative trait loci, we provide a comprehensive overview of common variants associated with plasma proteins. We highlight possible biological relationships which may serve as a basis for further investigation into possible causal roles in cardiometabolic diseases.
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Affiliation(s)
- Corinne Carland
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anders Malarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Pik Fang Kho
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Karl Michaelsson
- Department of Surgical Sciences, Medical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Anna Ramisch
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hanna M Björck
- Cardiovascular Medicine, Medicine, Karolinska Institute, Stockholm, Sweden
| | - Per Eriksson
- Cardiovascular Medicine, Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Karsten Suhre
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Ana Viñuela
- Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Gaurav Thareja
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Anna Halama
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Frank Schmidt
- Proteomics Core, Research, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA
| | - Themistocles Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA.
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2
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Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Li T, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson Å, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, Göteson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Landén M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Butterworth AS, Mälarstig A, Wilson JF, Navarro P, Shen X. Unraveling Neuro-Proteogenomic Landscape and Therapeutic Implications for Human Behaviors and Psychiatric Disorders. Res Sq 2023:rs.3.rs-2720355. [PMID: 37034613 PMCID: PMC10081382 DOI: 10.21203/rs.3.rs-2720355/v1] [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: 05/04/2023]
Abstract
Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioral traits and the disease etiology of neuropsychiatric disorders. Here, the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,500 individuals for 184 neuro-related proteins in human plasma. The analysis identified 117 cis-regulatory protein quantitative trait loci (cis-pQTL) and 166 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. Mendelian randomization analyses revealed multiple proteins showing potential causal effects on neuro-related traits such as sleeping, smoking, feelings, alcohol intake, mental health, and psychiatric disorders. Integrating with established drug information, we validated 13 out of 13 matched combinations of protein targets and diseases or side effects with available drugs, while suggesting hundreds of re-purposing and new therapeutic targets. This consortium effort provides a large-scale proteogenomic resource for biomedical research on human behaviors and other neuro-related phenotypes.
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Affiliation(s)
- Linda Repetto
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
| | - Jiantao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Paul R. H. J. Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ting Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Emma L. Twait
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrechtand Utrecht University, Utrecht, Netherlands
| | - Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Marisa D. Muckian
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Bram P. Prins
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle USA
| | - Åsa Johansson
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Lu Pan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yazhou He
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Sofia Klasson
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shahzad Ahmad
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
| | - James E. Peters
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle USA
| | - Ulf Gyllensten
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Sarah E. Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, United Kingdom
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Andreas Göteson
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Lagging
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | | | | | - Christina Jern
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Germany
| | - Ian J. Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, United Kingdom
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Stefan Enroth
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center and Department of Epidemiology, University of Washington, Seattle USA
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Adam S. Butterworth
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Emerging Science and Innovation, Pfizer Worldwide Research, Development and Medical, Cambridge, UK
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xia Shen
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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3
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Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Li T, Twait EL, May-Wilson S, Muckian MD, Prins BP, Png G, Kooperberg C, Johansson Å, Hillary RF, Wheeler E, Pan L, He Y, Klasson S, Ahmad S, Peters JE, Gilly A, Karaleftheri M, Tsafantakis E, Haessler J, Gyllensten U, Harris SE, Wareham NJ, Göteson A, Lagging C, Ikram MA, van Duijn CM, Jern C, Landén M, Langenberg C, Deary IJ, Marioni RE, Enroth S, Reiner AP, Dedoussis G, Zeggini E, Butterworth AS, Mälarstig A, Wilson JF, Navarro P, Shen X. Genetic mechanisms of 184 neuro-related proteins in human plasma. medRxiv 2023:2023.02.10.23285650. [PMID: 36824751 PMCID: PMC9949195 DOI: 10.1101/2023.02.10.23285650] [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: 02/16/2023]
Abstract
Understanding the genetic basis of neuro-related proteins is essential for dissecting the disease etiology of neuropsychiatric disorders and other complex traits and diseases. Here, the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,500 individuals for 184 neuro-reiated proteins in human plasma. The analysis identified 117 cis-regulatory protein quantitative trait loci (cis-pQTL) and 166 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. Mendelian randomization analyses revealed multiple proteins showing potential causal effects on neuro-reiated traits as well as complex diseases such as hypertension, high cholesterol, immune-related disorders, and psychiatric disorders. Integrating with established drug information, we validated 13 combinations of protein targets and diseases or side effects with available drugs, while suggesting hundreds of re-purposing and new therapeutic targets for diseases and comorbidities. This consortium effort provides a large-scale proteogenomic resource for biomedical research.
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Affiliation(s)
- Linda Repetto
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
| | - Jiantao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Paul R. H. J. Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ting Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Emma L. Twait
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Marisa D. Muckian
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Bram P. Prins
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle USA
| | - Åsa Johansson
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Lu Pan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yazhou He
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Sofia Klasson
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shahzad Ahmad
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
| | - James E. Peters
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle USA
| | - Ulf Gyllensten
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Sarah E. Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, United Kingdom
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Andreas Göteson
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Lagging
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | | | | | - Christina Jern
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Germany
| | - Ian J. Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, United Kingdom
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Stefan Enroth
- Dept. Immunology, Genetics and Pathology, Science for life laboratory, Uppsala University, Sweden
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center and Department of Epidemiology, University of Washington, Seattle USA
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Adam S. Butterworth
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Emerging Science and Innovation, Pfizer Worldwide Research, Development and Medical, Cambridge, UK
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC Institute of Genetics Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xia Shen
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Division of Public Health Sciences, Fred Hutchinson Cancer Center and Department of Epidemiology, University of Washington, Seattle USA
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4
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Png G, Gerlini R, Hatzikotoulas K, Barysenka A, Rayner NW, Klarić L, Rathkolb B, Aguilar-Pimentel JA, Rozman J, Fuchs H, Gailus-Durner V, Tsafantakis E, Karaleftheri M, Dedoussis G, Pietrzik C, Wilson JF, Angelis MH, Becker-Pauly C, Gilly A, Zeggini E. Identifying causal serum protein-cardiometabolic trait relationships using whole genome sequencing. Hum Mol Genet 2022; 32:1266-1275. [PMID: 36349687 PMCID: PMC10077504 DOI: 10.1093/hmg/ddac275] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/10/2022] Open
Abstract
Cardiometabolic diseases, such as type 2 diabetes and cardiovascular disease, have a high public health burden. Understanding the genetically-determined regulation of proteins that are dysregulated in disease can help to dissect the complex biology underpinning them. Here, we perform a protein quantitative trait locus (pQTL) analysis of 255 serum proteins relevant to cardiometabolic processes in 2893 individuals. Meta-analysing whole-genome sequencing (WGS) data from two Greek cohorts, MANOLIS (n = 1356; 22.5x WGS) and Pomak (n = 1537; 18.4x WGS), we detect 302 independently-associated pQTL variants for 171 proteins, including 12 rare variants (minor allele frequency [MAF] < 1%). We additionally find 15 pQTL variants that are rare in non-Finnish European populations, but have drifted up in frequency in the discovery cohorts here. We identify proteins causally associated with cardiometabolic traits, including MEP1B for high-density lipoprotein levels; and describe a knock-out Mep1b mouse model. Our findings furnish insights into the genetic architecture of the serum proteome, identify new protein-disease relationships, and demonstrate the importance of isolated populations in pQTL analysis.
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Affiliation(s)
- Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrei Barysenka
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - N William Rayner
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Lucija Klarić
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Juan A Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jan Rozman
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Centre for Phenogenomics, Vestec, Czech Republic
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Claus Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin Hrabe Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christoph Becker-Pauly
- Institute of Biochemistry, Unit for Degradomics of the Protease Web, University of Kiel, Kiel, Germany
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
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5
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Gilly A, Klaric L, Park YC, Png G, Barysenka A, Marsh JA, Tsafantakis E, Karaleftheri M, Dedoussis G, Wilson JF, Zeggini E. Gene-based whole genome sequencing meta-analysis of 250 circulating proteins in three isolated European populations. Mol Metab 2022; 61:101509. [PMID: 35504531 PMCID: PMC9118462 DOI: 10.1016/j.molmet.2022.101509] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Deep sequencing offers unparalleled access to rare variants in human populations. Understanding their role in disease is a priority, yet prohibitive sequencing costs mean that many cohorts lack the sample size to discover these effects on their own. Meta-analysis of individual variant scores allows the combination of rare variants across cohorts and study of their aggregated effect at the gene level, boosting discovery power. However, the methods involved have largely not been field-tested. In this study, we aim to perform the first meta-analysis of gene-based rare variant aggregation optimal tests, applied to the human cardiometabolic proteome. METHODS Here, we carry out this analysis across MANOLIS, Pomak and ORCADES, three isolated European cohorts with whole-genome sequencing (total N = 4,422). We examine the genetic architecture of 250 proteomic traits of cardiometabolic relevance. We use a containerised pipeline to harmonise variant lists across cohorts and define four sets of qualifying variants. For every gene, we interrogate protein-damaging variants, exonic variants, exonic and regulatory variants, and regulatory only variants, using the CADD and Eigen scores to weigh variants according to their predicted functional consequence. We perform single-cohort rare variant analysis and meta-analyse variant scores using the SMMAT package. RESULTS We describe 5 rare variant pQTLs (RV-pQTL) which pass our stringent significance threshold (7.45 × 10-11) and quality control procedure. These were split between four cis signals for MARCO, TEK, MMP2 and MPO, and one trans association for GDF2 in the SERPINA11 gene. We show that the cis-MPO association, which was not detectable using the single-point data alone, is driven by 5 missense and frameshift variants. These include rs140636390 and rs119468010, which are specific to MANOLIS and ORCADES, respectively. We show how this kind of signal could improve the predictive accuracy of genetic factors in common complex disease such as stroke and cardiovascular disease. CONCLUSIONS Our proof-of-concept study demonstrates the power of gene-based meta-analyses for discovering disease-relevant associations complementing common-variant signals by incorporating population-specific rare variation.
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Affiliation(s)
- Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Young-Chan Park
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Ismaninger Straße 22, 8167 Munich, Germany
| | - Andrei Barysenka
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 70, El. Venizelou ave. 17671, Kallithea, Greece
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany; TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Ismaninger Straße 22, 8167 Munich, Germany.
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6
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Yang Z, Macdonald-Dunlop E, Chen J, Zhai R, Li T, Richmond A, Klarić L, Pirastu N, Ning Z, Zheng C, Wang Y, Huang T, He Y, Guo H, Ying K, Gustafsson S, Prins B, Ramisch A, Dermitzakis ET, Png G, Eriksson N, Haessler J, Hu X, Zanetti D, Boutin T, Hwang SJ, Wheeler E, Pietzner M, Raffield LM, Kalnapenkis A, Peters JE, Viñuela A, Gilly A, Elmståhl S, Dedoussis G, Petrie JR, Polašek O, Folkersen L, Chen Y, Yao C, Võsa U, Pairo-Castineira E, Clohisey S, Bretherick AD, Rawlik K, Esko T, Enroth S, Johansson Å, Gyllensten U, Langenberg C, Levy D, Hayward C, Assimes TL, Kooperberg C, Manichaikul AW, Siegbahn A, Wallentin L, Lind L, Zeggini E, Schwenk JM, Butterworth AS, Michaëlsson K, Pawitan Y, Joshi PK, Baillie JK, Mälarstig A, Reiner AP, Wilson JF, Shen X. Genetic Landscape of the ACE2 Coronavirus Receptor. Circulation 2022; 145:1398-1411. [PMID: 35387486 PMCID: PMC9047645 DOI: 10.1161/circulationaha.121.057888] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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] [Indexed: 02/02/2023]
Abstract
BACKGROUND SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood. METHODS We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data. RESULTS We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells. CONCLUSIONS Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.
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Affiliation(s)
- Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - Jiantao Chen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Ting Li
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Lucija Klarić
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Human Technopole Viale Rita Levi-Montalcini, Milan, Italy (N.P.)
| | - Zheng Ning
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Yipeng Wang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
| | - Tingting Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Yazhou He
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu (Y.H.)
| | - Huiming Guo
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences, Guangzhou, China (H.G.)
| | - Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA (K.Y.)
- T.H. Chan School of Public Health, Harvard University, Boston, MA (K.Y.)
| | - Stefan Gustafsson
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Bram Prins
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Anna Ramisch
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Technical University of Munich (TUM), School of Medicine, Germany (G.P.)
| | | | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Shih-Jen Hwang
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill (L.M.R.)
| | - Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
- Institute of Molecular and Cell Biology, University of Tartu, Estonia (A.K.)
| | - James E. Peters
- Department of Immunology and Inflammation, Imperial College London, UK (J.E.P.)
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland (A. Ramisch, E.T.D., A.V.)
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK (A.V.)
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
| | - Sölve Elmståhl
- Faculty of Medicine, Lund University, Sweden (S. Elmståhl)
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Greece (G.D.)
| | - John R. Petrie
- Institute of Cardiovascular & Medical Sciences, University of Glasgow, UK (J. Petrie)
| | - Ozren Polašek
- University of Split School of Medicine, Croatia (O.P.)
- Algebra University College, Ilica, Zagreb, Croatia (O.P.)
| | | | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Chen Yao
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | - Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
| | | | | | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia (A.K., U.V., T.E.)
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala Universitet, Science for Life Laboratory, Sweden (S. Enroth, A.J., U.G.)
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, UK (E.W., M.P., C.L.)
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin, Germany (M.P., C.L.)
| | - Daniel Levy
- Framingham Heart Study, MA (S.-J.H., C.Y., D.L.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.)
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Themistocles L. Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (D.Z., T.L.A.)
- Stanford Cardiovascular Institute, Stanford University, CA (D.Z., T.L.A.)
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville (X.H., A.W.M.)
| | - Agneta Siegbahn
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Wallentin
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Sweden (A.S., S.G., L.W., L.L.)
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany (G.P., A.G., E.Z.)
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (A.G., E.Z.)
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Germany (E.Z.)
| | - Jochen M. Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden (J.M.S.)
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, UK (B.P., J.E.P., A.S.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge (B.P., J.E.P., A.S.B.)
- British Heart Foundation Centre of Research Excellence, University of Cambridge, UK (A.S.B.)
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, UK (A.S.B.)
| | - Karl Michaëlsson
- Department of Surgical Sciences, Uppsala University, Sweden (K.M.)
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, UK (E.P.-C., S.C., K.R., J.K.B.)
- Intensive Care Unit, Royal Infirmary of Edinburgh, UK (J.K.B.)
| | - Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden (A.M.)
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K., A.P.R.)
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, UK (A. Richmond, L.K., T.B., E.P.-C., A.D.B., C.H., J.F.W.)
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China (Z.Y., J.C., R.Z., T.L., Z.N., C.Z., Y.W., X.S.)
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China (X.S.)
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, China (Z.Y., J.C., R.Z., T.L., X.S.)
- Centre for Global Health Research, Usher Institute, University of Edinburgh, UK (E.M.-D., N.P., Y.H., P.K.J., J.F.W., X.S.)
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden (Z.N., T.H., Y.C., Y.P., A.M., X.S.)
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7
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Png G, Barysenka A, Repetto L, Navarro P, Shen X, Pietzner M, Wheeler E, Wareham NJ, Langenberg C, Tsafantakis E, Karaleftheri M, Dedoussis G, Mälarstig A, Wilson JF, Gilly A, Zeggini E. Mapping the serum proteome to neurological diseases using whole genome sequencing. Nat Commun 2021; 12:7042. [PMID: 34857772 PMCID: PMC8640022 DOI: 10.1038/s41467-021-27387-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the increasing global burden of neurological disorders, there is a lack of effective diagnostic and therapeutic biomarkers. Proteins are often dysregulated in disease and have a strong genetic component. Here, we carry out a protein quantitative trait locus analysis of 184 neurologically-relevant proteins, using whole genome sequencing data from two isolated population-based cohorts (N = 2893). In doing so, we elucidate the genetic landscape of the circulating proteome and its connection to neurological disorders. We detect 214 independently-associated variants for 107 proteins, the majority of which (76%) are cis-acting, including 114 variants that have not been previously identified. Using two-sample Mendelian randomisation, we identify causal associations between serum CD33 and Alzheimer's disease, GPNMB and Parkinson's disease, and MSR1 and schizophrenia, describing their clinical potential and highlighting drug repurposing opportunities.
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Affiliation(s)
- Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany. .,TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany.
| | - Andrei Barysenka
- grid.4567.00000 0004 0483 2525Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Linda Repetto
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xia Shen
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK ,grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China ,grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Maik Pietzner
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Eleanor Wheeler
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Nicholas J. Wareham
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Claudia Langenberg
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK ,grid.484013.aComputational Medicine, Berlin Institute of Health (BIH), Charité University Medicine, Berlin, Germany
| | | | | | - George Dedoussis
- grid.15823.3d0000 0004 0622 2843Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Anders Mälarstig
- grid.4714.60000 0004 1937 0626Department of Medicine, Karolinska Institute, Solna, Sweden ,Emerging Science & Innovation, Pfizer Worldwide Research, Development and Medical, Cambridge, MA USA
| | - James F. Wilson
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK ,grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arthur Gilly
- grid.4567.00000 0004 0483 2525Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany. .,TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany.
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8
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Png G, Suveges D, Park Y, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Cover Image. Genet Epidemiol 2020. [DOI: 10.1002/gepi.22219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Grace Png
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Department of Medical GeneticsUniversity of Cambridge Cambridge United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
| | - Daniel Suveges
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- European Bioinformatics InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Young‐Chan Park
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Department of Medical GeneticsUniversity of Cambridge Cambridge United Kingdom
| | - Klaudia Walter
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Kousik Kundu
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and DentistryQueen Mary University of London London United Kingdom
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and EducationHarokopio University of Athens Athens Greece
| | - Eleftheria Zeggini
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
| | - Arthur Gilly
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
- Department of Public Health and Primary CareUniversity of Cambridge Cambridge United Kingdom
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9
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Png G, Suveges D, Park YC, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Population-wide copy number variation calling using variant call format files from 6,898 individuals. Genet Epidemiol 2019; 44:79-89. [PMID: 31520489 PMCID: PMC8653900 DOI: 10.1002/gepi.22260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 11/10/2022]
Abstract
Copy number variants (CNVs) play an important role in a number of human diseases, but the accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process. We use a regression tree-based approach to call germline CNVs from whole-genome sequencing (WGS, >18x) variant call sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. Eighty-one percent of detected events have been previously reported in the Database of Genomic Variants. Twenty-three percent of high-quality deletions affect entire genes, and we recapitulate known events such as the GSTM1 and RHD gene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe complex CNV patterns underlying an association with levels of the CCL3 protein (MAF = 0.15, p = 3.6x10-12 ) at the CCL3L3 locus, and a novel cis-association between a low-frequency NOMO1 deletion and NOMO1 protein levels (MAF = 0.02, p = 2.2x10-7 ). This study demonstrates that existing population-wide WGS call sets can be mined for germline CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.
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Affiliation(s)
- Grace Png
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Suveges
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Young-Chan Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Arthur Gilly
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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