1
|
Liu L, Khan A, Sanchez-Rodriguez E, Zanoni F, Li Y, Steers N, Balderes O, Zhang J, Krithivasan P, LeDesma RA, Fischman C, Hebbring SJ, Harley JB, Moncrieffe H, Kottyan LC, Namjou-Khales B, Walunas TL, Knevel R, Raychaudhuri S, Karlson EW, Denny JC, Stanaway IB, Crosslin D, Rauen T, Floege J, Eitner F, Moldoveanu Z, Reily C, Knoppova B, Hall S, Sheff JT, Julian BA, Wyatt RJ, Suzuki H, Xie J, Chen N, Zhou X, Zhang H, Hammarström L, Viktorin A, Magnusson PKE, Shang N, Hripcsak G, Weng C, Rundek T, Elkind MSV, Oelsner EC, Barr RG, Ionita-Laza I, Novak J, Gharavi AG, Kiryluk K. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nat Commun 2022; 13:6859. [PMID: 36369178 PMCID: PMC9651905 DOI: 10.1038/s41467-022-34456-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.
Collapse
Affiliation(s)
- Lili Liu
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Atlas Khan
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Elena Sanchez-Rodriguez
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Francesca Zanoni
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Yifu Li
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Nicholas Steers
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Olivia Balderes
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Junying Zhang
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Priya Krithivasan
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Robert A. LeDesma
- grid.16750.350000 0001 2097 5006Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ USA
| | - Clara Fischman
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Scott J. Hebbring
- grid.280718.40000 0000 9274 7048Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI USA
| | - John B. Harley
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA ,grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH USA
| | - Halima Moncrieffe
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Bahram Namjou-Khales
- grid.239573.90000 0000 9025 8099Center of Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Theresa L. Walunas
- grid.16753.360000 0001 2299 3507Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rachel Knevel
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Soumya Raychaudhuri
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Elizabeth W. Karlson
- grid.62560.370000 0004 0378 8294Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Joshua C. Denny
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Ian B. Stanaway
- grid.34477.330000000122986657Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA USA
| | - David Crosslin
- grid.34477.330000000122986657Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA USA
| | - Thomas Rauen
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Jürgen Floege
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Frank Eitner
- grid.1957.a0000 0001 0728 696XDepartment of Nephrology, RWTH University of Aachen, Aachen, Germany ,grid.420044.60000 0004 0374 4101Kidney Diseases Research, Bayer Pharma AG, Wuppertal, Germany
| | - Zina Moldoveanu
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Colin Reily
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Barbora Knoppova
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Stacy Hall
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Justin T. Sheff
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Bruce A. Julian
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Robert J. Wyatt
- grid.267301.10000 0004 0386 9246Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN USA
| | - Hitoshi Suzuki
- grid.258269.20000 0004 1762 2738Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jingyuan Xie
- grid.16821.3c0000 0004 0368 8293Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Chen
- grid.16821.3c0000 0004 0368 8293Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xujie Zhou
- grid.11135.370000 0001 2256 9319Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Hong Zhang
- grid.11135.370000 0001 2256 9319Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Lennart Hammarström
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Viktorin
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K. E. Magnusson
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ning Shang
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - George Hripcsak
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Chunhua Weng
- grid.21729.3f0000000419368729Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Tatjana Rundek
- grid.26790.3a0000 0004 1936 8606Department of Neurology, University of Miami, Miami, FL USA ,grid.26790.3a0000 0004 1936 8606Evelyn F. McKnight Brain Institute, University of Miami, Miami, FL USA
| | - Mitchell S. V. Elkind
- grid.21729.3f0000000419368729Department of Neurology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Elizabeth C. Oelsner
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - R. Graham Barr
- grid.21729.3f0000000419368729Division of General Medicine, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA ,grid.21729.3f0000000419368729Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY USA
| | - Iuliana Ionita-Laza
- grid.21729.3f0000000419368729Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY USA
| | - Jan Novak
- grid.265892.20000000106344187Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Ali G. Gharavi
- grid.21729.3f0000000419368729Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
| |
Collapse
|
2
|
Grönwall C, Liljefors L, Bang H, Hensvold AH, Hansson M, Mathsson-Alm L, Israelsson L, Joshua V, Svärd A, Stålesen R, Titcombe PJ, Steen J, Piccoli L, Sherina N, Clavel C, Svenungsson E, Gunnarsson I, Saevarsdottir S, Kastbom A, Serre G, Alfredsson L, Malmström V, Rönnelid J, Catrina AI, Lundberg K, Klareskog L. A Comprehensive Evaluation of the Relationship Between Different IgG and IgA Anti-Modified Protein Autoantibodies in Rheumatoid Arthritis. Front Immunol 2021; 12:627986. [PMID: 34093522 PMCID: PMC8173192 DOI: 10.3389/fimmu.2021.627986] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/26/2021] [Indexed: 12/25/2022] Open
Abstract
Seropositive rheumatoid arthritis (RA) is characterized by the presence of rheumatoid factor (RF) and anti-citrullinated protein autoantibodies (ACPA) with different fine-specificities. Yet, other serum anti-modified protein autoantibodies (AMPA), e.g. anti-carbamylated (Carb), -acetylated (KAc), and malondialdehyde acetaldehyde (MAA) modified protein antibodies, have been described. In this comprehensive study, we analyze 30 different IgG and IgA AMPA reactivities to Cit, Carb, KAc, and MAA antigens detected by ELISA and autoantigen arrays in N=1985 newly diagnosed RA patients. Association with patient characteristics such as smoking and disease activity were explored. Carb and KAc reactivities by different assays were primarily seen in patients also positive for anti-citrulline reactivity. Modified vimentin (mod-Vim) peptides were used for direct comparison of different AMPA reactivities, revealing that IgA AMPA recognizing mod-Vim was mainly detected in subsets of patients with high IgG anti-Cit-Vim levels and a history of smoking. IgG reactivity to acetylation was mainly detected in a subset of patients with Cit and Carb reactivity. Anti-acetylated histone reactivity was RA-specific and associated with high anti-CCP2 IgG levels, multiple ACPA fine-specificities, and smoking status. This reactivity was also found to be present in CCP2+ RA-risk individuals without arthritis. Our data further demonstrate that IgG autoreactivity to MAA was increased in RA compared to controls with highest levels in CCP2+ RA, but was not RA-specific, and showed low correlation with other AMPA. Anti-MAA was instead associated with disease activity and was not significantly increased in CCP2+ individuals at risk of RA. Notably, RA patients could be subdivided into four different subsets based on their AMPA IgG and IgA reactivity profiles. Our serology results were complemented by screening of monoclonal antibodies derived from single B cells from RA patients for the same antigens as the RA cohort. Certain CCP2+ clones had Carb or Carb+KAc+ multireactivity, while such reactivities were not found in CCP2- clones. We conclude that autoantibodies exhibiting different patterns of ACPA fine-specificities as well as Carb and KAc reactivity are present in RA and may be derived from multireactive B-cell clones. Carb and KAc could be considered reactivities within the "Cit-umbrella" similar to ACPA fine-specificities, while MAA reactivity is distinctly different.
Collapse
Affiliation(s)
- Caroline Grönwall
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lisa Liljefors
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Aase H. Hensvold
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Monika Hansson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Mathsson-Alm
- Thermo Fisher Scientific, Immuno Diagnostics Division, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lena Israelsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vijay Joshua
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Svärd
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Center for Clinical Research Dalarna, Uppsala University, Uppsala, Sweden
| | - Ragnhild Stålesen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Philip J. Titcombe
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- The Center for Immunology and Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Johanna Steen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Natalia Sherina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Cyril Clavel
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Elisabet Svenungsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Department of Medicine Solna, Division of Clinical Epidemiology, Karolinska Institutet, Stockholm, Sweden
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Alf Kastbom
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Guy Serre
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm Health Region, Stockholm, Sweden
| | - Vivianne Malmström
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anca I. Catrina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Lundberg
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
3
|
Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Med 2020; 12:60. [PMID: 32641083 PMCID: PMC7346642 DOI: 10.1186/s13073-020-00754-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets. METHODS In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). RESULTS We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn's disease. CONCLUSIONS Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.
Collapse
Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel Trejo-Banos
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Athanasios Kousathanas
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Sven Erik Ojavee
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David C Liewald
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Craig W Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at Austin, Austin, TX, 78712, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Matthew R Robinson
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
4
|
Rheumatoid arthritis patients display B-cell dysregulation already in the naïve repertoire consistent with defects in B-cell tolerance. Sci Rep 2019; 9:19995. [PMID: 31882654 PMCID: PMC6934703 DOI: 10.1038/s41598-019-56279-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022] Open
Abstract
B cells are postulated to be central in seropositive rheumatoid arthritis (RA). Here, we use exploratory mass cytometry (n = 23) and next-generation sequencing (n = 19) to study B-cell repertoire shifts in RA patients. Expression of several B-cell markers were significantly different in ACPA+ RA compared to healthy controls, including an increase in HLA-DR across subsets, CD22 in clusters of IgM+ B cells and CD11c in IgA+ memory. Moreover, both IgA+ and IgG+ double negative (IgD− CD27−) CD11c+ B cells were increased in ACPA+ RA, and there was a trend for elevation in a CXCR5/CCR6high transitional B-cell cluster. In the RA BCR repertoire, there were significant differences in subclass distribution and, notably, the frequency of VH with low somatic hypermutation (SHM) was strikingly higher, especially in IgG1 (p < 0.0001). Furthermore, both ACPA+ and ACPA− RA patients had significantly higher total serum IgA and IgM compared to controls, based on serology of larger cohorts (n = 3494 IgA; n = 397 IgM). The observed elevated Ig-levels, distortion in IgM+ B cells, increase in double negative B cells, change in B-cell markers, and elevation of unmutated IgG+ B cells suggests defects in B-cell tolerance in RA. This may represent an underlying cause of increased polyreactivity and autoimmunity in RA.
Collapse
|
5
|
Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Murci L, Duffy D, Albert ML, Fellay J. Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines. Genome Med 2018; 10:59. [PMID: 30053915 PMCID: PMC6063007 DOI: 10.1186/s13073-018-0568-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Humoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that human genetic variation influences (i) serum immunoglobulin levels, (ii) seroconversion rates, and (iii) intensity of antigen-specific immune responses. Here, we evaluated the impact of intrinsic (age and sex), environmental, and genetic factors on the variability of humoral response to common pathogens and vaccines. METHODS We characterized the serological response to 15 antigens from common human pathogens or vaccines, in an age- and sex-stratified cohort of 1000 healthy individuals (Milieu Intérieur cohort). Using clinical-grade serological assays, we measured total IgA, IgE, IgG, and IgM levels, as well as qualitative (serostatus) and quantitative IgG responses to cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1 and 2, varicella zoster virus, Helicobacter pylori, Toxoplasma gondii, influenza A virus, measles, mumps, rubella, and hepatitis B virus. Following genome-wide genotyping of single nucleotide polymorphisms and imputation, we examined associations between ~ 5 million genetic variants and antibody responses using single marker and gene burden tests. RESULTS We identified age and sex as important determinants of humoral immunity, with older individuals and women having higher rates of seropositivity for most antigens. Genome-wide association studies revealed significant associations between variants in the human leukocyte antigen (HLA) class II region on chromosome 6 and anti-EBV and anti-rubella IgG levels. We used HLA imputation to fine map these associations to amino acid variants in the peptide-binding groove of HLA-DRβ1 and HLA-DPβ1, respectively. We also observed significant associations for total IgA levels with two loci on chromosome 2 and with specific KIR-HLA combinations. CONCLUSIONS Using extensive serological testing and genome-wide association analyses in a well-characterized cohort of healthy individuals, we demonstrated that age, sex, and specific human genetic variants contribute to inter-individual variability in humoral immunity. By highlighting genes and pathways implicated in the normal antibody response to frequently encountered antigens, these findings provide a basis to better understand disease pathogenesis. TRIALS REGISTRATION ClinicalTrials.gov , NCT01699893.
Collapse
Affiliation(s)
- Petar Scepanovic
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cécile Alanio
- Immunobiology of Dendritic Cell Unit, Institut Pasteur, Paris, France.,Center for Translational Research, Institut Pasteur, Paris, France.,Inserm U1223, Institut Pasteur, Paris, France
| | - Christian Hammer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Flavia Hodel
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacob Bergstedt
- Department of Automatic Control, Lund University, Lund, Sweden
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA 3012, Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015, Paris, France
| | - Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bruno Charbit
- Center for Translational Research, Institut Pasteur, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker branch, Inserm U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St Giles laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA 3012, Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015, Paris, France
| | - Darragh Duffy
- Immunobiology of Dendritic Cell Unit, Institut Pasteur, Paris, France.,Center for Translational Research, Institut Pasteur, Paris, France.,Inserm U1223, Institut Pasteur, Paris, France
| | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA.
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland.
| | | |
Collapse
|
6
|
Jonsson S, Sveinbjornsson G, de Lapuente Portilla AL, Swaminathan B, Plomp R, Dekkers G, Ajore R, Ali M, Bentlage AEH, Elmér E, Eyjolfsson GI, Gudjonsson SA, Gullberg U, Gylfason A, Halldorsson BV, Hansson M, Holm H, Johansson Å, Johnsson E, Jonasdottir A, Ludviksson BR, Oddsson A, Olafsson I, Olafsson S, Sigurdardottir O, Sigurdsson A, Stefansdottir L, Masson G, Sulem P, Wuhrer M, Wihlborg AK, Thorleifsson G, Gudbjartsson DF, Thorsteinsdottir U, Vidarsson G, Jonsdottir I, Nilsson B, Stefansson K. Identification of sequence variants influencing immunoglobulin levels. Nat Genet 2017. [DOI: 10.1038/ng.3897] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
7
|
GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway. PLoS Genet 2017; 13:e1006609. [PMID: 28187132 PMCID: PMC5328405 DOI: 10.1371/journal.pgen.1006609] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/27/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022] Open
Abstract
Aberrant O-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, in C1GALT1 (rs13226913, P = 3.2 x 10−11) and C1GALT1C1 (rs5910940, P = 2.7 x 10−8). These genes encode molecular partners essential for enzymatic O-glycosylation of IgA1. We demonstrated that these two loci explain approximately 7% of variability in circulating Gd-IgA1 in Europeans, but only 2% in East Asians. Notably, the Gd-IgA1-increasing allele of rs13226913 is common in Europeans, but rare in East Asians. Moreover, rs13226913 represents a strong cis-eQTL for C1GALT1 that encodes the key enzyme responsible for the transfer of galactose to O-linked glycans on IgA1. By in vitro siRNA knock-down studies, we confirmed that mRNA levels of both C1GALT1 and C1GALT1C1 determine the rate of secretion of Gd-IgA1 in IgA1-producing cells. Our findings provide novel insights into the genetic regulation of O-glycosylation and are relevant not only to IgA nephropathy, but also to other complex traits associated with O-glycosylation defects, including inflammatory bowel disease, hematologic disease, and cancer. O-glycosylation is a common type of post-translational modification of proteins; specific abnormalities in the mechanism of O-glycosylation have been implicated in cancer, inflammatory and blood diseases. However, the molecular basis of abnormal O-glycosylation in these complex disorders is not known. We studied the genetic basis of defective O-glycosylation of serum immunoglobulin A1 (IgA1), that represents the key pathogenic defect in IgA nephropathy, the most common form of primary glomerulonephritis worldwide. We report our results of the first genome-wide association study for this trait using serum assays in 2,633 individuals of European and East-Asian ancestry. In our genome scan, we observed two significant signals with large effects, on chromosomes 7p21.3 and Xq24, jointly explaining about 7% of trait variability. These signals implicate two genes that encode molecular partners essential for enzymatic O-glycosylation of IgA1 and mucins, and represent potential new targets for therapy.
Collapse
|
8
|
Lomax-Browne HJ, Visconti A, Pusey CD, Cook HT, Spector TD, Pickering MC, Falchi M. IgA1 Glycosylation Is Heritable in Healthy Twins. J Am Soc Nephrol 2016; 28:64-68. [PMID: 27313232 DOI: 10.1681/asn.2016020184] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/15/2016] [Indexed: 11/03/2022] Open
Abstract
IgA nephropathy (IgAN) is the most common form of primary GN and an important cause of kidney failure. Characteristically, patients with IgAN have increased serum levels of undergalactosylated IgA1 (gd-IgA1). To assess the degree to which serum gd-IgA1 levels are genetically determined in healthy individuals, we determined serum IgA and gd-IgA1 levels by ELISA in a sample of 148 healthy female twins, including 27 monozygotic and 47 dizygotic pairs. Using the classic twin model, we found the heritability of serum gd-IgA1 and IgA levels to be 80% (95% confidence interval, 66% to 89%) and 46% (95% confidence interval, 15% to 69%), respectively. These data indicate that serum gd-IgA1 levels are highly heritable. Elucidating the genetic basis of this heritability will be important in understanding the pathogenesis of IgAN.
Collapse
Affiliation(s)
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Charles D Pusey
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, London, United Kingdom; and
| | | | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| |
Collapse
|
9
|
The higher frequency of IgA deficiency among Swedish twins is not explained by HLA haplotypes. Genes Immun 2015; 16:199-205. [PMID: 25569265 DOI: 10.1038/gene.2014.78] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/21/2022]
Abstract
Serum immunoglobulin A (IgA) concentrations were determined in 12 600 adult Swedish twins, applying a high-throughput reverse-phase protein microarray technique. The prevalence of IgA deficiency (IgAD) was found to be 1:241 in monozygotic (MZ) twins and 1:198 in dizygotic (DZ) twins. Hence, the prevalence in twins is markedly elevated as compared with the normal Swedish adult population (1:600). The twins did not show a difference in the frequency of HLA haplotypes in comparison with almost 40 000 healthy Swedish controls. As expected, the risk-conveying HLA alleles A*01, B*08 and DRB1*01 were overrepresented among the IgAD twins and were also associated with significantly lower mean serum IgA concentrations in the twin cohort. In contrast, significantly higher mean IgA concentrations were found among individuals carrying the protective HLA alleles B*07 and DRB1*15. Exome sequencing data from two MZ twin pairs discordant for the deficiency showed no differences between the siblings. Model fitting analyses derived a heritability of 35% and indicate that genetic influences are modestly important for IgAD. The probandwise concordance rates for IgAD were found to be 31% for MZ and 13% for DZ twins.
Collapse
|