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Sayeed K, Parameswaran S, Beucler MJ, Edsall LE, VonHandorf A, Crowther A, Donmez O, Hass M, Richards S, Forney C, Wright J, Leong MML, Murray-Nerger LA, Gewurz BE, Kaufman KM, Harley JB, Zhao B, Miller WE, Kottyan LC, Weirauch MT. Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity. bioRxiv 2024:2024.04.12.588762. [PMID: 38645179 PMCID: PMC11030363 DOI: 10.1101/2024.04.12.588762] [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] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Human cytomegalovirus (HCMV) infects up to 80% of the world's population. Here, we show that HCMV infection leads to widespread changes in human chromatin accessibility and chromatin looping, with hundreds of thousands of genomic regions affected 48 hours after infection. Integrative analyses reveal HCMV-induced perturbation of Hippo signaling through drastic reduction of TEAD1 transcription factor activity. We confirm extensive concordant loss of TEAD1 binding, active H3K27ac histone marks, and chromatin looping interactions upon infection. Our data position TEAD1 at the top of a hierarchy involving multiple altered important developmental pathways. HCMV infection reduces TEAD1 activity through four distinct mechanisms: closing of TEAD1-bound chromatin, reduction of YAP1 and phosphorylated YAP1 levels, reduction of TEAD1 transcript and protein levels, and alteration of TEAD1 exon-6 usage. Altered TEAD1-based mechanisms are highly enriched at genetic risk loci associated with eye and ear development, providing mechanistic insight into HCMV's established roles in these processes.
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Affiliation(s)
- Khund Sayeed
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew J. Beucler
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Lee E. Edsall
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Audrey Crowther
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Omer Donmez
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew Hass
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Scott Richards
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jay Wright
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Merrin Man Long Leong
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura A. Murray-Nerger
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Ben E. Gewurz
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kenneth M. Kaufman
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Research Service, Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - John B. Harley
- Research Service, Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bo Zhao
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - William E. Miller
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Leah C. Kottyan
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew T. Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
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Igoe A, Merjanah S, Harley ITW, Clark DH, Sun C, Kaufman KM, Harley JB, Kaelber DC, Scofield RH. Association between systemic lupus erythematosus and myasthenia gravis: A population-based National Study. Clin Immunol 2024; 260:109810. [PMID: 37949200 DOI: 10.1016/j.clim.2023.109810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) and myasthenia gravis (MG) are autoimmune diseases. Previous case reports and case series suggest an association may exist between these diseases, as well as an increased risk of SLE after thymectomy for MG. We undertook this study to determine whether SLE and MG were associated in large cohorts. METHODS We searched the IBM Watson Health Explorys platform and the Department of Veterans Affairs Million Veteran Program (MVP) database for diagnoses of SLE and MG. In addition, we examined subjects enrolled in the Lupus Family Registry and Repository (LFRR) as well as controls for a diagnosis of MG. RESULTS Among 59,780,210 individuals captured in Explorys, there were 25,750 with MG and 65,370 with SLE. 370 subjects had both. Those with MG were >10 times more likely to have SLE than those without MG. Those with both diseases were more likely to be women, African American, and at a younger age than MG subjects without SLE. In addition, the MG patients who underwent thymectomy had an increased risk of SLE compared to MG patients who had not undergone thymectomy (OR 3.11, 95% CI: 2.12 to 4.55). Autoimmune diseases such as pernicious anemia and miscellaneous comorbidities such as chronic kidney disease were significantly more common in MG patients who developed SLE. In the MVP, SLE and MG were also significantly associated. Association of SLE and MG in a large SLE cohort with rigorous SLE classification confirmed the association of SLE with MG at a similar level. CONCLUSION While the number of patients with both MG and SLE is small, SLE and MG are strongly associated together in very large databases and a large SLE cohort.
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Affiliation(s)
- Ann Igoe
- OhioHealth Hospital, Rheumatology Department, Mansfield, OH 44903, USA
| | - Sali Merjanah
- Boston University Medical Center, Section of Rheumatology, Department of Medicine, Boston, MA 02118, USA
| | - Isaac T W Harley
- Division of Rheumatology, Departments of Medicine and Immunology/Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Medicine Service, Rheumatology Section, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO 80045, USA
| | - Dennis H Clark
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Celi Sun
- Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | - Kenneth M Kaufman
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - John B Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA; Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, USA
| | - David C Kaelber
- Departments of Internal Medicine, Pediatrics, and Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine and The Center for Clinical Informatics Research and Education, The MetroHealth System, Cleveland, OH 44109, USA
| | - R Hal Scofield
- Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA; Department of Medicine, University of Oklahoma Health Sciences Center, Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, and Medical/Research Service, and Medicine Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA.
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3
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Chepelev I, Harley IT, Harley JB. Modeling of horizontal pleiotropy identifies possible causal gene expression in systemic lupus erythematosus. Front Lupus 2023; 1:1234578. [PMID: 37799268 PMCID: PMC10554754 DOI: 10.3389/flupu.2023.1234578] [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] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Background Systemic lupus erythematosus (SLE) is a chronic autoimmune condition with complex causes involving genetic and environmental factors. While genome-wide association studies (GWASs) have identified genetic loci associated with SLE, the functional genomic elements responsible for disease development remain largely unknown. Mendelian Randomization (MR) is an instrumental variable approach to causal inference based on data from observational studies, where genetic variants are employed as instrumental variables (IVs). Methods This study utilized a two-step strategy to identify causal genes for SLE. In the first step, the classical MR method was employed, assuming the absence of horizontal pleiotropy, to estimate the causal effect of gene expression on SLE. In the second step, advanced probabilistic MR methods (PMR-Egger, MRAID, and MR-MtRobin) were applied to the genes identified in the first step, considering horizontal pleiotropy, to filter out false positives. PMR-Egger and MRAID analyses utilized whole blood expression quantitative trait loci (eQTL) and SLE GWAS summary data, while MR-MtRobin analysis used an independent eQTL dataset from multiple immune cell types along with the same SLE GWAS data. Results The initial MR analysis identified 142 genes, including 43 outside of chromosome 6. Subsequently, applying the advanced MR methods reduced the number of genes with significant causal effects on SLE to 66. PMR-Egger, MRAID, and MR-MtRobin, respectively, identified 13, 7, and 16 non-chromosome 6 genes with significant causal effects. All methods identified expression of PHRF1 gene as causal for SLE. A comprehensive literature review was conducted to enhance understanding of the functional roles and mechanisms of the identified genes in SLE development. Conclusions The findings from the three MR methods exhibited overlapping genes with causal effects on SLE, demonstrating consistent results. However, each method also uncovered unique genes due to different modelling assumptions and technical factors, highlighting the complementary nature of the approaches. Importantly, MRAID demonstrated a reduced percentage of causal genes from the Major Histocompatibility complex (MHC) region on chromosome 6, indicating its potential in minimizing false positive findings. This study contributes to unraveling the mechanisms underlying SLE by employing advanced probabilistic MR methods to identify causal genes, thereby enhancing our understanding of SLE pathogenesis.
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Affiliation(s)
- Iouri Chepelev
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
| | - Isaac T.W. Harley
- US Department of Veterans Affairs Medical Center, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
| | - John B. Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
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4
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Kiryluk K, Sanchez-Rodriguez E, Zhou XJ, Zanoni F, Liu L, Mladkova N, Khan A, Marasa M, Zhang JY, Balderes O, Sanna-Cherchi S, Bomback AS, Canetta PA, Appel GB, Radhakrishnan J, Trimarchi H, Sprangers B, Cattran DC, Reich H, Pei Y, Ravani P, Galesic K, Maixnerova D, Tesar V, Stengel B, Metzger M, Canaud G, Maillard N, Berthoux F, Berthelot L, Pillebout E, Monteiro R, Nelson R, Wyatt RJ, Smoyer W, Mahan J, Samhar AA, Hidalgo G, Quiroga A, Weng P, Sreedharan R, Selewski D, Davis K, Kallash M, Vasylyeva TL, Rheault M, Chishti A, Ranch D, Wenderfer SE, Samsonov D, Claes DJ, Akchurin O, Goumenos D, Stangou M, Nagy J, Kovacs T, Fiaccadori E, Amoroso A, Barlassina C, Cusi D, Del Vecchio L, Battaglia GG, Bodria M, Boer E, Bono L, Boscutti G, Caridi G, Lugani F, Ghiggeri G, Coppo R, Peruzzi L, Esposito V, Esposito C, Feriozzi S, Polci R, Frasca G, Galliani M, Garozzo M, Mitrotti A, Gesualdo L, Granata S, Zaza G, Londrino F, Magistroni R, Pisani I, Magnano A, Marcantoni C, Messa P, Mignani R, Pani A, Ponticelli C, Roccatello D, Salvadori M, Salvi E, Santoro D, Gembillo G, Savoldi S, Spotti D, Zamboli P, Izzi C, Alberici F, Delbarba E, Florczak M, Krata N, Mucha K, Pączek L, Niemczyk S, Moszczuk B, Pańczyk-Tomaszewska M, Mizerska-Wasiak M, Perkowska-Ptasińska A, Bączkowska T, Durlik M, Pawlaczyk K, Sikora P, Zaniew M, Kaminska D, Krajewska M, Kuzmiuk-Glembin I, Heleniak Z, Bullo-Piontecka B, Liberek T, Dębska-Slizien A, Hryszko T, Materna-Kiryluk A, Miklaszewska M, Szczepańska M, Dyga K, Machura E, Siniewicz-Luzeńczyk K, Pawlak-Bratkowska M, Tkaczyk M, Runowski D, Kwella N, Drożdż D, Habura I, Kronenberg F, Prikhodina L, van Heel D, Fontaine B, Cotsapas C, Wijmenga C, Franke A, Annese V, Gregersen PK, Parameswaran S, Weirauch M, Kottyan L, Harley JB, Suzuki H, Narita I, Goto S, Lee H, Kim DK, Kim YS, Park JH, Cho B, Choi M, Van Wijk A, Huerta A, Ars E, Ballarin J, Lundberg S, Vogt B, Mani LY, Caliskan Y, Barratt J, Abeygunaratne T, Kalra PA, Gale DP, Panzer U, Rauen T, Floege J, Schlosser P, Ekici AB, Eckardt KU, Chen N, Xie J, Lifton RP, Loos RJF, Kenny EE, Ionita-Laza I, Köttgen A, Julian BA, Novak J, Scolari F, Zhang H, Gharavi AG. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nat Genet 2023; 55:1091-1105. [PMID: 37337107 DOI: 10.1038/s41588-023-01422-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/05/2023] [Indexed: 06/21/2023]
Abstract
IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular deposition of IgA. Here we performed a genome-wide association study of 10,146 kidney-biopsy-diagnosed IgAN cases and 28,751 controls across 17 international cohorts. We defined 30 genome-wide significant risk loci explaining 11% of disease risk. A total of 16 loci were new, including TNFSF4/TNFSF18, REL, CD28, PF4V1, LY86, LYN, ANXA3, TNFSF8/TNFSF15, REEP3, ZMIZ1, OVOL1/RELA, ETS1, IGH, IRF8, TNFRSF13B and FCAR. The risk loci were enriched in gene orthologs causing abnormal IgA levels when genetically manipulated in mice. We also observed a positive genetic correlation between IgAN and serum IgA levels. High polygenic score for IgAN was associated with earlier onset of kidney failure. In a comprehensive functional annotation analysis of candidate causal genes, we observed convergence of biological candidates on a common set of inflammatory signaling pathways and cytokine ligand-receptor pairs, prioritizing potential new drug targets.
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Affiliation(s)
- Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA.
| | - Elena Sanchez-Rodriguez
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Francesca Zanoni
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Lili Liu
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Nikol Mladkova
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Maddalena Marasa
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Jun Y Zhang
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Olivia Balderes
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA
| | - Andrew S Bomback
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Pietro A Canetta
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Gerald B Appel
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Jai Radhakrishnan
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Hernan Trimarchi
- Nephrology Service, Hospital Británico de Buenos Aires, Buenos Aires, Argentina
| | - Ben Sprangers
- Department of Microbiology and Immunology, Laboratory of Molecular Immunology, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Daniel C Cattran
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - Heather Reich
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - York Pei
- Department of Nephrology, University of Toronto, Toronto General Hospital, Toronto, Ontario, Canada
| | - Pietro Ravani
- Division of Nephrology, Department of Internal Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Dita Maixnerova
- 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Vladimir Tesar
- 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Benedicte Stengel
- Centre for Research in Epidemiology and Population Health (CESP), Paris-Saclay University, Versailles Saint Quentin University, INSERM Clinical Epidemiology Team, Villejuif, France
| | - Marie Metzger
- Centre for Research in Epidemiology and Population Health (CESP), Paris-Saclay University, Versailles Saint Quentin University, INSERM Clinical Epidemiology Team, Villejuif, France
| | - Guillaume Canaud
- Université de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Nicolas Maillard
- Nephrology, Dialysis, and Renal Transplantation Department, University North Hospital, Saint Etienne, France
| | - Francois Berthoux
- Nephrology, Dialysis, and Renal Transplantation Department, University North Hospital, Saint Etienne, France
| | | | - Evangeline Pillebout
- Center for Research on Inflammation, University of Paris, INSERM and CNRS, Paris, France
| | - Renato Monteiro
- Center for Research on Inflammation, University of Paris, INSERM and CNRS, Paris, France
| | - Raoul Nelson
- Division of Pediatric Nephrology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Robert J Wyatt
- Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Children's Foundation Research Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - William Smoyer
- Division of Pediatric Nephrology, Nationwide Children's Hospital, Columbus, OH, USA
| | - John Mahan
- Division of Pediatric Nephrology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Al-Akash Samhar
- Division of Pediatric Nephrology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Guillermo Hidalgo
- Division of Pediatric Nephrology, Department of Pediatrics, HMH Hackensack University Medical Center, Hackensack, NJ, USA
| | - Alejandro Quiroga
- Division of Pediatric Nephrology, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Patricia Weng
- Division of Pediatric Nephrology, Mattel Children's Hospital, Los Angeles, CA, USA
| | - Raji Sreedharan
- Division of Pediatric Nephrology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - David Selewski
- Division of Pediatric Nephrology, Mott Children's Hospital, Ann Arbor, MI, USA
| | - Keefe Davis
- Division of Pediatric Nephrology, Department of Pediatrics, The Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Mahmoud Kallash
- Division of Pediatric Nephrology, SUNY Buffalo, Buffalo, NY, USA
| | - Tetyana L Vasylyeva
- Division of Pediatric Nephrology, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Michelle Rheault
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, MN, USA
| | - Aftab Chishti
- Division of Pediatric Nephrology, University of Kentucky, Lexington, KY, USA
| | - Daniel Ranch
- Division of Pediatric Nephrology, Department of Pediatrics, University of Kentucky, Lexington, KY, USA
| | - Scott E Wenderfer
- Division of Pediatric Nephrology, Baylor College of Medicine/Texas Children's Hospital, Houston, TX, USA
| | - Dmitry Samsonov
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, MA, USA
| | - Donna J Claes
- Division of Pediatric Nephrology, Department of Pediatrics, New York Medical College, New York City, NY, USA
| | - Oleh Akchurin
- Division of Pediatric Nephrology, Department of Pediatrics, Weill Cornell Medical College, New York City, NY, USA
| | | | - Maria Stangou
- The Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Judit Nagy
- 2nd Department of Internal Medicine, Nephrological and Diabetological Center, University of Pécs, Pécs, Hungary
| | - Tibor Kovacs
- 2nd Department of Internal Medicine, Nephrological and Diabetological Center, University of Pécs, Pécs, Hungary
| | - Enrico Fiaccadori
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cristina Barlassina
- Renal Division, Dipartimento di Medicina, Chirurgia e Odontoiatria, San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | - Daniele Cusi
- Renal Division, Dipartimento di Medicina, Chirurgia e Odontoiatria, San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | | | | | | | - Emanuela Boer
- Division of Nephrology and Dialysis, Gorizia Hospital, Gorizia, Italy
| | - Luisa Bono
- Nephrology and Dialysis, A.R.N.A.S. Civico and Benfratelli, Palermo, Italy
| | - Giuliano Boscutti
- Nephrology, Dialysis and Renal Transplant Unit, S. Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Gianluca Caridi
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - Francesca Lugani
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - GianMarco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - Rosanna Coppo
- Regina Margherita Children's Hospital, Torino, Italy
| | - Licia Peruzzi
- Regina Margherita Children's Hospital, Torino, Italy
| | | | | | | | | | - Giovanni Frasca
- Division of Nephrology, Dialysis and Renal Transplantation, Riuniti Hospital, Ancona, Italy
| | | | - Maurizio Garozzo
- Unità Operativa di Nefrologia e Dialisi, Ospedale di Acireale, Acireale, Italy
| | - Adele Mitrotti
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Simona Granata
- Renal Unit, Department of Medicine, University of Verona, Verona, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University of Verona, Verona, Italy
| | | | - Riccardo Magistroni
- Department of Surgical, Medical, Dental, Oncologic and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Andrea Magnano
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Piergiorgio Messa
- Nephrology Dialysis and Kidney Transplant Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Renzo Mignani
- Azienda Unità Sanitaria Locale Rimini, Rimini, Italy
| | - Antonello Pani
- Department of Nephrology and Dialysis, G. Brotzu Hospital, Cagliari, Italy
| | | | - Dario Roccatello
- Nephrology and Dialysis Unit, G. Bosco Hub Hospital (ERK-net Member) and University of Torino, Torino, Italy
| | - Maurizio Salvadori
- Division of Nephrology and Renal Transplantation, Carreggi Hospital, Florence, Italy
| | - Erica Salvi
- Renal Division, DMCO (Dipartimento di Medicina, Chirurgia e Odontoiatria), San Paolo Hospital, School of Medicine, University of Milan, Milan, Italy
| | - Domenico Santoro
- Unit of Nephrology and Dialysis, AOU G Martino, University of Messina, Messina, Italy
| | - Guido Gembillo
- Unit of Nephrology and Dialysis, AOU G Martino, University of Messina, Messina, Italy
| | - Silvana Savoldi
- Unit of Nephrology and Dialysis, ASL TO4-Consultorio Cirié, Turin, Italy
| | | | | | - Claudia Izzi
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Federico Alberici
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Elisa Delbarba
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Michał Florczak
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Natalia Krata
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Stanisław Niemczyk
- Department of Internal Disease, Nephrology and Dialysotherapy, Military Institute of Medicine, Warsaw, Poland
| | - Barbara Moszczuk
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Teresa Bączkowska
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Durlik
- Department of Transplantation Medicine, Nephrology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Pawlaczyk
- Department of Nephrology, Transplantology and Internal Medicine, Poznan Medical University, Poznan, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Dorota Kaminska
- Clinical Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Magdalena Krajewska
- Clinical Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Izabella Kuzmiuk-Glembin
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Zbigniew Heleniak
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Bullo-Piontecka
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Liberek
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Alicja Dębska-Slizien
- Department of Nephrology, Transplantology and Internal Diseases, Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Hryszko
- 2nd Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Bialystok, Bialystok, Poland
| | | | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepańska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Dyga
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Edyta Machura
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Siniewicz-Luzeńczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Monika Pawlak-Bratkowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Dariusz Runowski
- Department of Nephrology, Kidney Transplantation and Hypertension, Children's Memorial Health Institute, Warsaw, Poland
| | - Norbert Kwella
- Department of Nephrology, Hypertension and Internal Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Drożdż
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Ireneusz Habura
- Department of Nephrology, Karol Marcinkowski Hospital, Zielona Góra, Poland
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Larisa Prikhodina
- Division of Inherited and Acquired Kidney Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - David van Heel
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Bertrand Fontaine
- Sorbonne University, INSERM, Center of Research in Myology, Institute of Myology, University Hospital Pitie-Salpetriere, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Service of Neuro-Myology, University Hospital Pitie-Salpetriere, Paris, France
| | - Chris Cotsapas
- Departments of Neurology and Genetics, Yale University, New Haven, CT, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Vito Annese
- CBP American Hospital, Dubai, United Arab Emirates
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, North Shore LIJ Health System, New York City, NY, USA
| | | | - Matthew Weirauch
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah Kottyan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John B Harley
- US Department of Veterans Affairs Medical Center and Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, USA
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hajeong Lee
- Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Ki Kim
- Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yon Su Kim
- Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - BeLong Cho
- Department of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- Institute on Aging, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ans Van Wijk
- Amsterdam University Medical Centre, VU University Medical Center (VUMC), Amsterdam, the Netherlands
| | - Ana Huerta
- Hospital Universitario Puerta del Hierro Majadahonda, REDINREN, IISCIII, Madrid, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory and Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, REDINREN, IISCIII, Barcelona, Spain
| | - Jose Ballarin
- Molecular Biology Laboratory and Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, REDINREN, IISCIII, Barcelona, Spain
| | - Sigrid Lundberg
- Department of Nephrology, Danderyd University Hospital, and Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Bruno Vogt
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Laila-Yasmin Mani
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yasar Caliskan
- Division of Nephrology, Saint Louis University, Saint Louis, MO, USA
| | - Jonathan Barratt
- John Walls Renal Unit, University Hospitals of Leicester, Leicester, UK
| | | | | | - Daniel P Gale
- Department of Renal Medicine, University College London, London, UK
| | | | - Thomas Rauen
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nan Chen
- Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jingyuan Xie
- Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York City, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York City, NY, USA
- Center for Population Genomic Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Bruce A Julian
- Departments of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Novak
- Departments of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Francesco Scolari
- Department of Medical and Surgical Specialties and Nephrology Unit, University of Brescia-ASST Spedali Civili, Brescia, Italy
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Ali G Gharavi
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York City, NY, USA.
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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. Author Correction: Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nat Commun 2023; 14:655. [PMID: 36746961 PMCID: PMC9902387 DOI: 10.1038/s41467-023-36340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Lili Liu
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elena Sanchez-Rodriguez
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yifu Li
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Nicholas Steers
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Olivia Balderes
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Robert A LeDesma
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Clara Fischman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - John B Harley
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Halima Moncrieffe
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bahram Namjou-Khales
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rachel Knevel
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth W Karlson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas Rauen
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Jürgen Floege
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Frank Eitner
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
- Kidney Diseases Research, Bayer Pharma AG, Wuppertal, Germany
| | - Zina Moldoveanu
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Colin Reily
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbora Knoppova
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stacy Hall
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Justin T Sheff
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bruce A Julian
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert J Wyatt
- Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jingyuan Xie
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Chen
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xujie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Viktorin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Tatjana Rundek
- Department of Neurology, University of Miami, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, FL, USA
| | - Mitchell S V Elkind
- Department of Neurology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elizabeth C Oelsner
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - R Graham Barr
- Division of General Medicine, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jan Novak
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ali G Gharavi
- Division 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.
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Harley JB, Pyarajan S, Partan ES, Epstein L, Wertheim JA, Diwan A, Woods CW, Davey V, Blair S, Clark DH, Kaufman KM, Khan S, Chepelev I, Devine A, Cameron P, McCann MF, Ammons MCB, Bolz DD, Battles JK, Curtis JL, Holodniy M, Marconi VC, Searles CD, Beenhouwer DO, Brown ST, Moorman JP, Yao ZQ, Rodriguez-Barradas MC, Mohapatra S, Molina De Rodriguez OY, Padiernos EB, McIndoo ER, Price E, Burgoyne HM, Robey I, Schwenke DC, Shive CL, Przygodzki RM, Ramoni RB, Krull HK, Bonomo RA. The US Department of Veterans Affairs Science and Health Initiative to Combat Infectious and Emerging Life-Threatening Diseases (VA SHIELD): A Biorepository Addressing National Health Threats. Open Forum Infect Dis 2022; 9:ofac641. [PMID: 36601554 PMCID: PMC9801224 DOI: 10.1093/ofid/ofac641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 12/15/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has demonstrated the need to share data and biospecimens broadly to optimize clinical outcomes for US military Veterans. Methods In response, the Veterans Health Administration established VA SHIELD (Science and Health Initiative to Combat Infectious and Emerging Life-threatening Diseases), a comprehensive biorepository of specimens and clinical data from affected Veterans to advance research and public health surveillance and to improve diagnostic and therapeutic capabilities. Results VA SHIELD now comprises 12 sites collecting de-identified biospecimens from US Veterans affected by SARS-CoV-2. In addition, 2 biorepository sites, a data processing center, and a coordinating center have been established under the direction of the Veterans Affairs Office of Research and Development. Phase 1 of VA SHIELD comprises 34 157 samples. Of these, 83.8% had positive tests for SARS-CoV-2, with the remainder serving as contemporaneous controls. The samples include nasopharyngeal swabs (57.9%), plasma (27.9%), and sera (12.5%). The associated clinical and demographic information available permits the evaluation of biological data in the context of patient demographics, clinical experience and management, vaccinations, and comorbidities. Conclusions VA SHIELD is representative of US national diversity with a significant potential to impact national healthcare. VA SHIELD will support future projects designed to better understand SARS-CoV-2 and other emergent healthcare crises. To the extent possible, VA SHIELD will facilitate the discovery of diagnostics and therapeutics intended to diminish COVID-19 morbidity and mortality and to reduce the impact of new emerging threats to the health of US Veterans and populations worldwide.
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Affiliation(s)
- John B Harley
- Correspondence: John B. Harley, Cincinnati VA Medical Center, 3200 Vine St., John B. Harley (151), Cincinnati, OH 45220 ()
| | - Saiju Pyarajan
- Center for Data and Computational Sciences, Veterans Affairs Boston Healthcare System, Boston, Massachusetts, USA
| | - Elizabeth S Partan
- Center for Data and Computational Sciences, Veterans Affairs Boston Healthcare System, Boston, Massachusetts, USA
| | - Lauren Epstein
- Infectious Diseases, US Department of Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Jason A Wertheim
- Research & Development, Southern Arizona Veterans Affairs Healthcare System, US Department of Veterans Affairs, Tucson, Arizona, USA
| | - Abhinav Diwan
- Cardiology, Veterans Affairs Saint Louis Healthcare System, US Department of Veterans Affairs,Saint Louis, Missouri, USA
| | - Christopher W Woods
- Medicine, US Department of Veterans Affairs Medical Center, Durham, North Carolina, USA
| | - Victoria Davey
- Office of Research and Development, US Department of Veterans Affairs, Washington, District of Columbia, USA
| | - Sharlene Blair
- Research Services, US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Dennis H Clark
- Research Services, US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Research Services, US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Shagufta Khan
- Research Services, US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Iouri Chepelev
- Research Services, US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Alexander Devine
- Prometheus Federal Services, Titan Alpha, Washington, District of Columbia, USA
| | - Perry Cameron
- Customer Value Partners, Titan Alpha, Washington, District of Columbia, USA
| | - Monica F McCann
- Office of Research and Development, Chesapeake Medical Communications, Contractor for the US Department of Veterans Affairs, Washington, District of Columbia, USA
| | - Mary Cloud B Ammons
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA,Idaho Veterans Research and Education Foundation, Boise, Idaho, USA
| | - Devin D Bolz
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA
| | - Jane K Battles
- Office of Research and Development, US Department of Veterans Affairs, Washington, District of Columbia, USA
| | - Jeffrey L Curtis
- Medicine Service, Veteran Affairs Ann Arbor Healthcare System, US Department of Veterans Affairs, Ann Arbor, Michigan, USA
| | - Mark Holodniy
- Public Health Surveillance, Veterans Affairs Palo Alto Healthcare System, US Department of Veterans Affairs, Palo Alto, California, USA
| | - Vincent C Marconi
- Infectious Diseases, US Department of Veterans Affairs Medical Center, Atlanta, Georgia, USA,Division of Infectious Diseases, Emory School of Medicine and Rollins School of Public Health, Atlanta, Georgia, USA
| | - Charles D Searles
- Infectious Diseases, US Department of Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - David O Beenhouwer
- Medicine, Veterans Affairs Greater Los Angeles Healthcare System, US Department of Veterans Affairs, Los Angeles, California, USA
| | - Sheldon T Brown
- Infectious Diseases, James J. Peters Veterans Affairs Medical Center, US Department of Veterans Affairs, Bronx, New York, USA
| | - Jonathan P Moorman
- Infectious Diseases, James H. Quillen Veterans Affairs Medical Center, US Department of Veterans Affairs, Mountain Home, Tennessee, USA,Center of Excellence in Inflammation, Infectious Diseases, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
| | - Zhi Q Yao
- Infectious Diseases, James H. Quillen Veterans Affairs Medical Center, US Department of Veterans Affairs, Mountain Home, Tennessee, USA,Center of Excellence in Inflammation, Infectious Diseases, and Immunity, East Tennessee State University, Johnson City, Tennessee, USA
| | - Maria C Rodriguez-Barradas
- Infectious Diseases Section, Michael E. DeBakey Veterans Affairs Medical Center, US Department of Veterans Affairs, Houston, Texas, USA,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Shyam Mohapatra
- Medicine, James A. Haley Veterans Hospital, US Department of Veterans Affairs, Tampa, Florida, USA
| | - Osmara Y Molina De Rodriguez
- Research & Development, Southern Arizona Veterans Affairs Healthcare System, US Department of Veterans Affairs, Tucson, Arizona, USA
| | - Emerson B Padiernos
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA
| | - Eric R McIndoo
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA,Idaho Veterans Research and Education Foundation, Boise, Idaho, USA
| | - Emily Price
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA,Idaho Veterans Research and Education Foundation, Boise, Idaho, USA
| | - Hailey M Burgoyne
- Research, US Department of Veterans Affairs Medical Center, Boise, Idaho, USA,Idaho Veterans Research and Education Foundation, Boise, Idaho, USA
| | - Ian Robey
- Research & Development, Southern Arizona Veterans Affairs Healthcare System, US Department of Veterans Affairs, Tucson, Arizona, USA
| | - Dawn C Schwenke
- Research & Development, Southern Arizona Veterans Affairs Healthcare System, US Department of Veterans Affairs, Tucson, Arizona, USA
| | - Carey L Shive
- Medicine, Veterans Affairs Northeast Ohio Healthcare System, US Department of Veterans Affairs, Cleveland, Ohio, USA
| | - Ronald M Przygodzki
- Office of Research and Development, US Department of Veterans Affairs, Washington, District of Columbia, USA
| | - Rachel B Ramoni
- Office of Research and Development, US Department of Veterans Affairs, Washington, District of Columbia, USA
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Ribeiro MSJ, Tripathi P, Namjou B, Harley JB, Chepelev I. 909 Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression at the SLE susceptibility locus FAM167A-BLK. Genetics 2022. [DOI: 10.1136/lupus-2022-lupus21century.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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8
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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: 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] [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.
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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.
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9
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Saint Just Ribeiro M, Tripathi P, Namjou B, Harley JB, Chepelev I. Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1. Front Genet 2022; 13:1008582. [PMID: 36160011 PMCID: PMC9490475 DOI: 10.3389/fgene.2022.1008582] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
A major goal of genetics research is to elucidate mechanisms explaining how genetic variation contributes to phenotypic variation. The genetic variants identified in genome-wide association studies (GWASs) generally explain only a small proportion of heritability of phenotypic traits, the so-called missing heritability problem. Recent evidence suggests that additional common variants beyond lead GWAS variants contribute to phenotypic variation; however, their mechanistic underpinnings generally remain unexplored. Herein, we undertake a study of haplotype-specific mechanisms of gene regulation at 8p23.1 in the human genome, a region associated with a number of complex diseases. The FAM167A-BLK locus in this region has been consistently found in the genome-wide association studies (GWASs) of systemic lupus erythematosus (SLE) in all major ancestries. Our haplotype-specific chromatin interaction (Hi-C) experiments, allele-specific enhancer activity measurements, genetic analyses, and epigenome editing experiments revealed that: 1) haplotype-specific long-range chromatin interactions are prevalent in 8p23.1; 2) BLK promoter and cis-regulatory elements cooperatively interact with haplotype-specificity; 3) genetic variants at distal regulatory elements are allele-specific modifiers of the promoter variants at FAM167A-BLK; 4) the BLK promoter interacts with and, as an enhancer-like promoter, regulates FAM167A expression and 5) local allele-specific enhancer activities are influenced by global haplotype structure due to chromatin looping. Although systemic lupus erythematosus causal variants at the FAM167A-BLK locus are thought to reside in the BLK promoter region, our results reveal that genetic variants at distal regulatory elements modulate promoter activity, changing BLK and FAM167A gene expression and disease risk. Our results suggest that global haplotype-specific 3-dimensional chromatin looping architecture has a strong influence on local allelic BLK and FAM167A gene expression, providing mechanistic details for how regional variants controlling the BLK promoter may influence disease risk.
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Affiliation(s)
- Mariana Saint Just Ribeiro
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Pulak Tripathi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - John B. Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
| | - Iouri Chepelev
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
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10
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Cheng J, Clayton JS, Acemel RD, Zheng Y, Taylor RL, Keleş S, Franke M, Boackle SA, Harley JB, Quail E, Gómez-Skarmeta JL, Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Front Immunol 2022; 13:901747. [PMID: 35769482 PMCID: PMC9235356 DOI: 10.3389/fimmu.2022.901747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/22/2022] [Accepted: 05/05/2022] [Indexed: 12/03/2022] Open
Abstract
The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.
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Affiliation(s)
- Jessica Cheng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Joshua S. Clayton
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States,Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States
| | - Rhonda L. Taylor
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Martin Franke
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Susan A. Boackle
- Department of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States,US Department of Veterans Affairs Medical Centre, US Department of Veterans Affairs, Cincinnati, OH, United States
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,*Correspondence: Daniela Ulgiati,
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11
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Munroe ME, Young KA, Guthridge JM, Kamen DL, Gilkeson GS, Weisman MH, Ishimori ML, Wallace DJ, Karp DR, Harley JB, Norris JM, James JA. Pre-Clinical Autoimmunity in Lupus Relatives: Self-Reported Questionnaires and Immune Dysregulation Distinguish Relatives Who Develop Incomplete or Classified Lupus From Clinically Unaffected Relatives and Unaffected, Unrelated Individuals. Front Immunol 2022; 13:866181. [PMID: 35720322 PMCID: PMC9203691 DOI: 10.3389/fimmu.2022.866181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is propelled by pathogenic autoantibody (AutoAb) and immune pathway dysregulation. Identifying populations at risk of reaching classified SLE is essential to curtail inflammatory damage. Lupus blood relatives (Rel) have an increased risk of developing SLE. We tested factors to identify Rel at risk of developing incomplete lupus (ILE) or classified SLE vs. clinically unaffected Rel and healthy controls (HC), drawing from two unique, well characterized lupus cohorts, the lupus autoimmunity in relatives (LAUREL) follow-up cohort, consisting of Rel meeting <4 ACR criteria at baseline, and the Lupus Family Registry and Repository (LFRR), made up of SLE patients, lupus Rel, and HC. Medical record review determined ACR SLE classification criteria; study participants completed the SLE portion of the connective tissue disease questionnaire (SLE-CSQ), type 2 symptom questions, and provided samples for assessment of serum SLE-associated AutoAb specificities and 52 plasma immune mediators. Elevated SLE-CSQ scores were associated with type 2 symptoms, ACR scores, and serology in both cohorts. Fatigue at BL was associated with transition to classified SLE in the LAUREL cohort (p≤0.01). Increased levels of BLyS and decreased levels of IL-10 were associated with type 2 symptoms (p<0.05). SLE-CSQ scores, ACR scores, and accumulated AutoAb specificities correlated with levels of multiple inflammatory immune mediators (p<0.05), including BLyS, IL-2Rα, stem cell factor (SCF), soluble TNF receptors, and Th-1 type mediators and chemokines. Transition to SLE was associated with increased levels of SCF (p<0.05). ILE Rel also had increased levels of TNF-α and IFN-γ, offset by increased levels of regulatory IL-10 and TGF-β (p<0.05). Clinically unaffected Rel (vs. HC) had higher SLE-CSQ scores (p<0.001), increased serology (p<0.05), and increased inflammatory mediator levels, offset by increased IL-10 and TGF-β (p<0.01). These findings suggest that Rel at highest risk of transitioning to classified SLE have increased inflammation coupled with decreased regulatory mediators. In contrast, clinically unaffected Rel and Rel with ILE demonstrate increased inflammation offset with increased immune regulation, intimating a window of opportunity for early intervention and enrollment in prevention trials.
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Affiliation(s)
- Melissa E. Munroe
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- *Correspondence: Melissa E. Munroe,
| | - Kendra A. Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Medicine, Oklahoma University Health Sciences Center, Oklahoma City, OK, United States
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, United States
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, United States
| | - Michael H. Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Mariko L. Ishimori
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Daniel J. Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - David R. Karp
- Division of Rheumatic Diseases, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - John B. Harley
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
| | - Judith A. James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Medicine, Oklahoma University Health Sciences Center, Oklahoma City, OK, United States
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK, United States
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12
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Laurynenka V, Ding L, Kaufman KM, James JA, Harley JB. A High Prevalence of Anti-EBNA1 Heteroantibodies in Systemic Lupus Erythematosus (SLE) Supports Anti-EBNA1 as an Origin for SLE Autoantibodies. Front Immunol 2022; 13:830993. [PMID: 35251022 PMCID: PMC8892314 DOI: 10.3389/fimmu.2022.830993] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background That Epstein–Barr virus (EBV) infection is associated with systemic lupus erythematosus (SLE) is established. The challenge is to explain mechanistic roles EBV has in SLE pathogenesis. Previous studies identify four examples of autoantibody cross-reactions between SLE autoantigens and Epstein–Barr nuclear antigen 1 (EBNA1). For two of these examples, the earliest detected autoantibody specifically cross-reacts with EBNA1; thereby, defined EBNA1 epitopes induce a robust autoantibody response in animals. These results suggest that the autoantibodies initiating the process leading to SLE may emerge from the anti-EBNA1 heteroimmune response. If this hypothesis is true, then anti-EBNA1 responses would be more frequent in EBV-infected SLE patients than in EBV-infected controls. We tested this prediction. Methods We evaluated published East Asian data by selecting those with a positive anti-viral capsid antigen (VCA) antibody immunoglobulin G (IgG) test and determining whether anti-EBNA1 was more common among the EBV-infected SLE cases than among matched EBV-infected controls with conditional logistic regression analysis. Results All the qualifying SLE patients (100%) in this dataset were EBV-infected compared to age- and sex-matched controls (92.2%) [odds ratio (OR) = 28.6, 95% CI 6.4–∞, p = 8.83 × 10-8], confirming the known close association of EBV infection with SLE. Furthermore, virtually all the SLE cases have both anti-VCA IgG and anti-EBNA1 IgG antibodies [124 of 125 (99.2%)], which are more frequently present than in age- and sex-matched EBV-infected controls [232 of 250 (93.2%)] (OR = 9.7, 95% CI 1.5–414, p = 0.0078) for an 89.7% SLE attributable risk from anti-EBNA1, which is in addition to the 100% SLE risk attributable to EBV infection in these data. Conclusions The association of EBV infection with SLE is reconfirmed. The prediction that anti-EBNA1 is more frequent in these SLE cases than in EBV-infected controls is true, consistent with the hypothesis that anti-EBNA1 contributes to SLE. This second EBV-dependent risk factor is consistent with a molecular mimicry model for the generation of SLE, starting with EBV infection, progressing to anti-EBNA1 response; then molecular mimicry leads to anti-EBNA1 antibodies cross-reacting with an SLE autoantigen, causing autoantibody epitope spreading, and culminating in clinical SLE. These results support the anti-EBNA1 heteroimmune response being a foundation from which pathogenic SLE autoimmunity emerges.
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Affiliation(s)
- Viktoryia Laurynenka
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Lili Ding
- Division of Biostatistics and Epidemiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Medicine, University of Oklahoma Health Science Center, Oklahoma City, OK, United States.,Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - John B Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States.,Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
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13
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Zhou T, Zhu X, Ye Z, Wang YF, Yao C, Xu N, Zhou M, Ma J, Qin Y, Shen Y, Tang Y, Yin Z, Xu H, Zhang Y, Zang X, Ding H, Yang W, Guo Y, Harley JB, Namjou B, Kaufman KM, Kottyan LC, Weirauch MT, Hou G, Shen N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nat Commun 2022; 13:1855. [PMID: 35388006 PMCID: PMC8987079 DOI: 10.1038/s41467-022-29514-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/28/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.
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Affiliation(s)
- Tian Zhou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Xinyi Zhu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Yong-Fei Wang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Chao Yao
- grid.9227.e0000000119573309Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031 China
| | - Ning Xu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Mi Zhou
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - Jianyang Ma
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuting Qin
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yiwei Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuanjia Tang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Hong Xu
- grid.16821.3c0000 0004 0368 8293Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China ,grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China
| | - Yutong Zhang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Xiaoli Zang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Huihua Ding
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Wanling Yang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Ya Guo
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - John B. Harley
- grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229 USA
| | - Bahram Namjou
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kenneth M. Kaufman
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Matthew T. Weirauch
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Guojun Hou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Nan Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China ,grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
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14
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Zouk H, Yu W, Oza A, Hawley M, Vijay Kumar PK, Koch C, Mahanta LM, Harley JB, Jarvik GP, Karlson EW, Leppig KA, Myers MF, Prows CA, Williams MS, Weiss ST, Lebo MS, Rehm HL. Reanalysis of eMERGE phase III sequence variants in 10,500 participants and infrastructure to support the automated return of knowledge updates. Genet Med 2022; 24:454-462. [PMID: 34906510 PMCID: PMC10128874 DOI: 10.1016/j.gim.2021.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The clinical genomics knowledgebase is dynamic with variant classifications changing as newly identified cases, additional population data, and other evidence become available. This is a challenge for the clinical laboratory because of limited resource availability for variant reassessment. METHODS Throughout the Electronic Medical Records and Genomics phase III program, clinical sites associated with the Mass General Brigham/Broad sequencing center received automated, real-time notifications when reported variants were reclassified. In this study, we summarized the nature of these reclassifications and described the proactive reassessment framework we used for the Electronic Medical Records and Genomics program data set to identify variants most likely to undergo reclassification. RESULTS Reanalysis of 1855 variants led to the reclassification of 2% (n = 45) of variants, affecting 0.6% (n = 67) of participants. Of these reclassifications, 78% (n = 35) were high-impact changes affecting reportability, with 8 variants downgraded from likely pathogenic/pathogenic to variants of uncertain significance (VUS) and 27 variants upgraded from VUS to likely pathogenic/pathogenic. Most upgraded variants (67%) were initially classified as VUS-Favor Pathogenic, highlighting the benefit of VUS subcategorization. The most common reason for reclassification was new published case data and/or functional evidence. CONCLUSION Our results highlight the importance of periodic sequence variant reevaluation and the need for automated approaches to advance routine implementation of variant reevaluations in clinical practice.
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Affiliation(s)
- Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Prathik K Vijay Kumar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - John B Harley
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH; US Department of Veteran Affairs Medical Center, Cincinnati, OH
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Scott T Weiss
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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15
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Hong T, Parameswaran S, Donmez OA, Miller D, Forney C, Lape M, Saint Just Ribeiro M, Liang J, Edsall LE, Magnusen AF, Miller W, Chepelev I, Harley JB, Zhao B, Kottyan LC, Weirauch MT. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome Res 2021; 31:2185-2198. [PMID: 34799401 PMCID: PMC8647835 DOI: 10.1101/gr.264705.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we showed that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding in a B cell line that was (1) uninfected, (2) infected with a strain of EBV lacking EBNA2, or (3) infected with a strain that expresses EBNA2. We identified more than 400 EBNA2-dependent differentially expressed human genes and more than 5000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed more than 2000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP data revealed more than 1700 regions where EBNA2 altered chromatin looping interactions. Autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1 Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.
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Affiliation(s)
- Ted Hong
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Michael Lape
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Mariana Saint Just Ribeiro
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Jun Liang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lee E Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Albert F Magnusen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - William Miller
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45267, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio 45229, USA
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
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16
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Fechtner S, Berens H, Bemis E, Johnson RL, Guthridge CJ, Carlson NE, Demoruelle MK, Harley JB, Edison JD, Norris JA, Robinson WH, Deane KD, James JA, Holers VM. Antibody Responses to Epstein-Barr Virus in the Preclinical Period of Rheumatoid Arthritis Suggest the Presence of Increased Viral Reactivation Cycles. Arthritis Rheumatol 2021; 74:597-603. [PMID: 34605217 DOI: 10.1002/art.41994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/16/2021] [Accepted: 09/15/2021] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Patients with established rheumatoid arthritis (RA) demonstrate altered immune responses to Epstein-Barr virus (EBV), but the presence and role(s) of EBV have not been fully explored in the preclinical period. We hypothesized that EBV infection, as evidenced by an altered anti-EBV antibody response, could either play an important role in driving the development or be a result of expanded RA-related autoimmunity. METHODS 83 subjects with RA based on 1987 ACR criteria and 83 matched controls were evaluated. Subject and matched control sera from the pre and post- RA diagnosis periods were tested for 5 anti-EBV antibodies (EBNA-1-IgG, VCA-IgG, EA-IgG, VCA-IgA, and EA-IgA), 7 RA-related autoantibodies (RF-neph, RF-IgA, RF-IgM, RF-IgG, CCP2, CCP3, CCP3.1), 22 cytokine/chemokine, 36 individual APCAs, and CMV-IgG antibodies. Random forest classification, mixed and joint mixed modelling were used to determine differences in anti-EBV antibodies between RA cases and controls. RESULTS Random Forest analysis identified preclinical EBV antibodies that differentiate RA subjects from controls. Specifically, EA-IgG antibody levels are higher in RA cases (0.82 ± 0.72) compared to controls (0.49 ± 0.28). Elevations in EA-IgG levels significantly correlated with increasing RF-IgM levels in future RA cases (p = 0.007) but not in controls (p = 0.150). CMV-IgG antibody levels did not differ between groups. CONCLUSION Subjects who eventually develop classified RA demonstrate elevated EA-IgG antibody levels in the preclinical period, which suggests the presence of increased EBV re-activation cycles. A combination of RF and EBV reactivation may play an important role in the development of RA.
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Affiliation(s)
- Sabrina Fechtner
- University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Heather Berens
- University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Elizabeth Bemis
- Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, USA
| | - Rachel L Johnson
- Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, USA
| | - Carla J Guthridge
- University of Oklahoma Health Sciences Center, Department of Medicine, University of Oklahoma Health Sciences Center, Edmond, OK, USA
| | - Nichole E Carlson
- Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, USA
| | | | - John B Harley
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Jess D Edison
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jill A Norris
- Colorado School of Public Health, Anschutz Medical Campus, Aurora, CO, USA
| | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA.,VA Palo Alto Health Care System, Palo Alto, California, USA
| | - Kevin D Deane
- University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - V Michael Holers
- University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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17
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18
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Yang Z, Slone J, Wang X, Zhan J, Huang Y, Namjou B, Kaufman KM, Pauciulo M, Harley JB, Muglia LJ, Chepelev I, Huang T. Validation of low-coverage whole-genome sequencing for mitochondrial DNA variants suggests mitochondrial DNA as a genetic cause of preterm birth. Hum Mutat 2021; 42:1602-1614. [PMID: 34467602 PMCID: PMC9290920 DOI: 10.1002/humu.24279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/06/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/06/2023]
Abstract
Preterm birth (PTB), or birth that occurs earlier than 37 weeks of gestational age, is a major contributor to infant mortality and neonatal hospitalization. Mutations in the mitochondrial genome (mtDNA) have been linked to various rare mitochondrial disorders and may be a contributing factor in PTB given that maternal genetic factors have been strongly linked to PTB. However, to date, no study has found a conclusive connection between a particular mtDNA variant and PTB. Given the high mtDNA copy number per cell, an automated pipeline was developed for detecting mtDNA variants using low‐coverage whole‐genome sequencing (lcWGS) data. The pipeline was first validated against samples of known heteroplasmy, and then applied to 929 samples from a PTB cohort from diverse ethnic backgrounds with an average gestational age of 27.18 weeks (range: 21–30). Our new pipeline successfully identified haplogroups and a large number of mtDNA variants in this large PTB cohort, including 8 samples carrying known pathogenic variants and 47 samples carrying rare mtDNA variants. These results confirm that lcWGS can be utilized to reliably identify mtDNA variants. These mtDNA variants may make a contribution toward preterm birth in a small proportion of live births.
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Affiliation(s)
- Zeyu Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jack Zhan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Michael Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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19
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Khan A, Shang N, Petukhova L, Zhang J, Shen Y, Hebbring SJ, Moncrieffe H, Kottyan LC, Namjou-Khales B, Knevel R, Raychaudhuri S, Karlson EW, Harley JB, Stanaway IB, Crosslin D, Denny JC, Elkind MS, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical Records-Based Genetic Studies of the Complement System. J Am Soc Nephrol 2021; 32:2031-2047. [PMID: 33941608 PMCID: PMC8455263 DOI: 10.1681/asn.2020091371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/09/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Genetic variants in complement genes have been associated with a wide range of human disease states, but well-powered genetic association studies of complement activation have not been performed in large multiethnic cohorts. METHODS We performed medical records-based genome-wide and phenome-wide association studies for plasma C3 and C4 levels among participants of the Electronic Medical Records and Genomics (eMERGE) network. RESULTS In a GWAS for C3 levels in 3949 individuals, we detected two genome-wide significant loci: chr.1q31.3 (CFH locus; rs3753396-A; β=0.20; 95% CI, 0.14 to 0.25; P=1.52x10-11) and chr.19p13.3 (C3 locus; rs11569470-G; β=0.19; 95% CI, 0.13 to 0.24; P=1.29x10-8). These two loci explained approximately 2% of variance in C3 levels. GWAS for C4 levels involved 3998 individuals and revealed a genome-wide significant locus at chr.6p21.32 (C4 locus; rs3135353-C; β=0.40; 95% CI, 0.34 to 0.45; P=4.58x10-35). This locus explained approximately 13% of variance in C4 levels. The multiallelic copy number variant analysis defined two structural genomic C4 variants with large effect on blood C4 levels: C4-BS (β=-0.36; 95% CI, -0.42 to -0.30; P=2.98x10-22) and C4-AL-BS (β=0.25; 95% CI, 0.21 to 0.29; P=8.11x10-23). Overall, C4 levels were strongly correlated with copy numbers of C4A and C4B genes. In comprehensive phenome-wide association studies involving 102,138 eMERGE participants, we cataloged a full spectrum of autoimmune, cardiometabolic, and kidney diseases genetically related to systemic complement activation. CONCLUSIONS We discovered genetic determinants of plasma C3 and C4 levels using eMERGE genomic data linked to electronic medical records. Genetic variants regulating C3 and C4 levels have large effects and multiple clinical correlations across the spectrum of complement-related diseases in humans.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Lynn Petukhova
- Department of Dermatology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jun Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, New York
| | - Scott J. Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | - Halima Moncrieffe
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Leah C. Kottyan
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Bahram Namjou-Khales
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Elizabeth W. Karlson
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - John B. Harley
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Ian B. Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - David Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee
| | - Mitchell S.V. Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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20
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Kawai VK, Shi M, Liu G, Feng Q, Wei W, Chung CP, Walunas TL, Gordon AS, Linneman JG, Hebbring SJ, Harley JB, Cox NJ, Roden DM, Stein CM, Mosley JD. Pleiotropy of systemic lupus erythematosus risk alleles and cardiometabolic disorders: A phenome-wide association study and inverse-variance weighted meta-analysis. Lupus 2021; 30:1264-1272. [PMID: 33977795 PMCID: PMC8205989 DOI: 10.1177/09612033211014952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
OBJECTIVES To test the hypothesis that genetic predisposition to systemic lupus erythematosus (SLE) increases the risk of cardiometabolic disorders. METHODS Using 41 single nucleotide polymorphisms (SNPs) associated with SLE, we calculated a weighted genetic risk score (wGRS) for SLE. In a large biobank we tested the association between this wGRS and 9 cardiometabolic phenotypes previously associated with SLE: atrial fibrillation, ischemic stroke, coronary artery disease, type 1 and type 2 diabetes, obesity, chronic kidney disease, hypertension, and hypercholesterolemia. Additionally, we performed a phenome-wide association analysis (pheWAS) to discover novel clinical associations with a genetic predisposition to SLE. Findings were replicated in the Electronic Medical Records and Genomics (eMERGE) Network. To further define the association between SLE-related risk alleles and the selected cardiometabolic phenotypes, we performed an inverse variance weighted regression (IVWR) meta-analysis. RESULTS The wGRS for SLE was calculated in 74,759 individuals of European ancestry. Among the pre-selected phenotypes, the wGRS was significantly associated with type 1 diabetes (OR [95%CI] =1.11 [1.06, 1.17], P-value = 1.05x10-5). In the PheWAS, the wGRS was associated with several autoimmune phenotypes, kidney disorders, and skin neoplasm; but only the associations with autoimmune phenotypes were replicated. In the IVWR meta-analysis, SLE-related risk alleles were nominally associated with type 1 diabetes (P = 0.048) but the associations were heterogeneous and did not meet the adjusted significance threshold. CONCLUSION A weighted GRS for SLE was associated with an increased risk of several autoimmune-related phenotypes including type I diabetes but not with cardiometabolic disorders.
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Affiliation(s)
- Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ge Liu
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - WeiQi Wei
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cecilia P. Chung
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Rheumatology, Department of Medicine Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System - Nashville Campus
| | - Theresa L. Walunas
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Adam S. Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - James G. Linneman
- Office of Research, Computing, and Analytics, Marshfield Clinic Research Institute, Marshfield, WI
| | - Scott J. Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin USA
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C. Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan D. Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
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21
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Hall MA, Wallace J, Lucas AM, Bradford Y, Verma SS, Müller-Myhsok B, Passero K, Zhou J, McGuigan J, Jiang B, Pendergrass SA, Zhang Y, Peissig P, Brilliant M, Sleiman P, Hakonarson H, Harley JB, Kiryluk K, Van Steen K, Moore JH, Ritchie MD. Novel EDGE encoding method enhances ability to identify genetic interactions. PLoS Genet 2021; 17:e1009534. [PMID: 34086673 PMCID: PMC8208534 DOI: 10.1371/journal.pgen.1009534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/16/2021] [Accepted: 04/06/2021] [Indexed: 11/26/2022] Open
Abstract
Assumptions are made about the genetic model of single nucleotide polymorphisms (SNPs) when choosing a traditional genetic encoding: additive, dominant, and recessive. Furthermore, SNPs across the genome are unlikely to demonstrate identical genetic models. However, running SNP-SNP interaction analyses with every combination of encodings raises the multiple testing burden. Here, we present a novel and flexible encoding for genetic interactions, the elastic data-driven genetic encoding (EDGE), in which SNPs are assigned a heterozygous value based on the genetic model they demonstrate in a dataset prior to interaction testing. We assessed the power of EDGE to detect genetic interactions using 29 combinations of simulated genetic models and found it outperformed the traditional encoding methods across 10%, 30%, and 50% minor allele frequencies (MAFs). Further, EDGE maintained a low false-positive rate, while additive and dominant encodings demonstrated inflation. We evaluated EDGE and the traditional encodings with genetic data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes: age-related macular degeneration (AMD), age-related cataract, glaucoma, type 2 diabetes (T2D), and resistant hypertension. A multi-encoding genome-wide association study (GWAS) for each phenotype was performed using the traditional encodings, and the top results of the multi-encoding GWAS were considered for SNP-SNP interaction using the traditional encodings and EDGE. EDGE identified a novel SNP-SNP interaction for age-related cataract that no other method identified: rs7787286 (MAF: 0.041; intergenic region of chromosome 7)–rs4695885 (MAF: 0.34; intergenic region of chromosome 4) with a Bonferroni LRT p of 0.018. A SNP-SNP interaction was found in data from the UK Biobank within 25 kb of these SNPs using the recessive encoding: rs60374751 (MAF: 0.030) and rs6843594 (MAF: 0.34) (Bonferroni LRT p: 0.026). We recommend using EDGE to flexibly detect interactions between SNPs exhibiting diverse action. Although traditional genetic encodings are widely implemented in genetics research, including in genome-wide association studies (GWAS) and epistasis, each method makes assumptions that may not reflect the underlying etiology. Here, we introduce a novel encoding method that estimates and assigns an individualized data-driven encoding for each single nucleotide polymorphism (SNP): the elastic data-driven genetic encoding (EDGE). With simulations, we demonstrate that this novel method is more accurate and robust than traditional encoding methods in estimating heterozygous genotype values, reducing the type I error, and detecting SNP-SNP interactions. We further applied the traditional encodings and EDGE to biomedical data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes, and EDGE identified a novel interaction for age-related cataract not detected by traditional methods, which replicated in data from the UK Biobank. EDGE provides an alternative approach to understanding and modeling diverse SNP models and is recommended for studying complex genetics in common human phenotypes.
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Affiliation(s)
- Molly A. Hall
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Penn State Cancer Institute, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - John Wallace
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Anastasia M. Lucas
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shefali S. Verma
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Kristin Passero
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jiayan Zhou
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John McGuigan
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Beibei Jiang
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - Peggy Peissig
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Murray Brilliant
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Patrick Sleiman
- Department of Pediatrics, Center for Applied Genomics, Children’s Hospital of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Department of Pediatrics, Center for Applied Genomics, Children’s Hospital of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- United States Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Kristel Van Steen
- WELBIO, GIGA-R Medical Genomics-BIO3, University of Liège, Liège, Belgium
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Jason H. Moore
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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22
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Singh B, Maiti GP, Zhou X, Fazel-Najafabadi M, Bae SC, Sun C, Terao C, Okada Y, Chua KH, Kochi Y, Guthridge JM, Zhang H, Weirauch M, James JA, Harley JB, Varshney GK, Looger LL, Nath SK. Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis. Arthritis Rheumatol 2021; 73:2303-2313. [PMID: 33982894 DOI: 10.1002/art.41799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 05/04/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVE A recent genome-wide association study (GWAS) reported a significant genetic association between rs34330 of cyclin-dependent kinase inhibitor 1B (CDKN1B) and risk of systemic lupus erythematosus (SLE) in Han Chinese. This study aims to validate the reported association and elucidate the biochemical mechanisms underlying the variant's effect. METHODS We performed allelic association with SLE followed by meta-analysis across 11 independent cohorts (n=28,872). We applied in silico bioinformatics and experimental validation in SLE-relevant cell lines to determine the functional consequences of rs34330. RESULTS We replicated genetic association between SLE and rs34330 (Pmeta =5.29x10-22 , OR (95% CI)=0.84 (0.81-0.87)). Follow-up bioinformatics and eQTL analysis suggest that rs34330 is located in active chromatin and potentially regulates several target genes. Using luciferase and ChIP-qPCR, we demonstrated substantial allele-specific promoter and enhancer activity, and allele-specific binding of three histone marks (H3K27ac, H3K4me3, H3K4me1), RNA pol II, CTCF, and a critical immune transcription factor (IRF-1). Chromosome conformation capture (3C) detected long-range chromatin interactions between rs34330 and the promoters of neighboring genes APOLD1 and DDX47, and effects on CDKN1B and the other target genes were directly validated by CRISPR-based genome editing. Finally, CRISPR-dCas9-based epigenetic activation/silencing confirmed these results. Gene-edited cell lines also showed higher levels of proliferation and apoptosis. CONCLUSION Collectively, these findings suggest a mechanism whereby the rs34330 risk allele (C) influences the presence of histone marks, RNA pol II, and the IRF-1 transcription factor to regulate expression of several target genes linked to proliferation and apoptosis, which potentially underlie the association of rs34330 with SLE.
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Affiliation(s)
- Bhupinder Singh
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Guru P Maiti
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Xujie Zhou
- Renal Division, Peking University First Hospital, Peking University, Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Mehdi Fazel-Najafabadi
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Celi Sun
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.,Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University, Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Matthew Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Gaurav K Varshney
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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23
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Yin X, Kim K, Suetsugu H, Bang SY, Wen L, Koido M, Ha E, Liu L, Sakamoto Y, Jo S, Leng RX, Otomo N, Laurynenka V, Kwon YC, Sheng Y, Sugano N, Hwang MY, Li W, Mukai M, Yoon K, Cai M, Ishigaki K, Chung WT, Huang H, Takahashi D, Lee SS, Wang M, Karino K, Shim SC, Zheng X, Miyamura T, Kang YM, Ye D, Nakamura J, Suh CH, Tang Y, Motomura G, Park YB, Ding H, Kuroda T, Choe JY, Li C, Niiro H, Park Y, Shen C, Miyamoto T, Ahn GY, Fei W, Takeuchi T, Shin JM, Li K, Kawaguchi Y, Lee YK, Wang Y, Amano K, Park DJ, Yang W, Tada Y, Yamaji K, Shimizu M, Atsumi T, Suzuki A, Sumida T, Okada Y, Matsuda K, Matsuo K, Kochi Y, Kottyan LC, Weirauch MT, Parameswaran S, Eswar S, Salim H, Chen X, Yamamoto K, Harley JB, Ohmura K, Kim TH, Yang S, Yamamoto T, Kim BJ, Shen N, Ikegawa S, Lee HS, Zhang X, Terao C, Cui Y, Bae SC. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Ann Rheum Dis 2021; 80:632-640. [PMID: 33272962 PMCID: PMC8053352 DOI: 10.1136/annrheumdis-2020-219209] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [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: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE), an autoimmune disorder, has been associated with nearly 100 susceptibility loci. Nevertheless, these loci only partially explain SLE heritability and their putative causal variants are rarely prioritised, which make challenging to elucidate disease biology. To detect new SLE loci and causal variants, we performed the largest genome-wide meta-analysis for SLE in East Asian populations. METHODS We newly genotyped 10 029 SLE cases and 180 167 controls and subsequently meta-analysed them jointly with 3348 SLE cases and 14 826 controls from published studies in East Asians. We further applied a Bayesian statistical approach to localise the putative causal variants for SLE associations. RESULTS We identified 113 genetic regions including 46 novel loci at genome-wide significance (p<5×10-8). Conditional analysis detected 233 association signals within these loci, which suggest widespread allelic heterogeneity. We detected genome-wide associations at six new missense variants. Bayesian statistical fine-mapping analysis prioritised the putative causal variants to a small set of variants (95% credible set size ≤10) for 28 association signals. We identified 110 putative causal variants with posterior probabilities ≥0.1 for 57 SLE loci, among which we prioritised 10 most likely putative causal variants (posterior probability ≥0.8). Linkage disequilibrium score regression detected genetic correlations for SLE with albumin/globulin ratio (rg=-0.242) and non-albumin protein (rg=0.238). CONCLUSION This study reiterates the power of large-scale genome-wide meta-analysis for novel genetic discovery. These findings shed light on genetic and biological understandings of SLE.
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Affiliation(s)
- Xianyong Yin
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China,Department of Dermatology, China-Japan Friendship Hospital, Beijing, China,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Kwangwoo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Hiroyuki Suetsugu
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Kanagawa, Japan,Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea,Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Leilei Wen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eunji Ha
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Lu Liu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | | | - Sungsin Jo
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Nao Otomo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Kanagawa, Japan,Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Viktoryia Laurynenka
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Young-Chang Kwon
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Yujun Sheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Nobuhiko Sugano
- Department of Orthopaedic Medical Engineering, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Mi Yeong Hwang
- Division of Genome Research, Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Korea
| | - Weiran Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Masaya Mukai
- Department of Rheumatology & Clinical Immunology, Sapporo City General Hospital, Hokkaido, Japan
| | - Kyungheon Yoon
- Division of Genome Research, Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Korea
| | - Minglong Cai
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Center for Data Sciences, Harvard Medical School, Boston, Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Won Tae Chung
- Department of Internal Medicine, Dong-A University Hospital, Busan, Korea
| | - He Huang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Daisuke Takahashi
- Department of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Shin-Seok Lee
- Division of Rheumatology, Department of Internal Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Mengwei Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Kohei Karino
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Seung-Cheol Shim
- Division of Rheumatology, Department of Internal Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Xiaodong Zheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Tomoya Miyamura
- Department of Internal Medicine and Rheumatology, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Young Mo Kang
- Division of Rheumatology, Department of Internal medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Dongqing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Junichi Nakamura
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Suwon, Korea
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, China
| | - Goro Motomura
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, China
| | - Takeshi Kuroda
- Niigata University Health Administration Center, Niigata, Japan
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Chengxu Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Hiroaki Niiro
- Department of Medical Education, Kyushu University Graduate School of Medical Sciences, Fukuoka City, Japan
| | - Youngho Park
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Changbing Shen
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China,Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, China
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ga-Young Ahn
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Wenmin Fei
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Jung-Min Shin
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Keke Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Yasushi Kawaguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yeon-Kyung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Yongfei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Koichi Amano
- Department of Rheumatology & Clinical Immunology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Dae Jin Park
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yoshifumi Tada
- Department of Rheumatology, Faculty of Medicine, Saga University, Saga, Japan
| | - Ken Yamaji
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Masato Shimizu
- Hokkaido Medical Center for Rheumatic Disease, Hokkaido, Japan
| | - Takashi Atsumi
- Department of Orthopaedic Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Takayuki Sumida
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPi-iFReC), Osaka University, Osaka, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Shruti Eswar
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Hanan Salim
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Kyoto University Graduate school of Medicine, Kyoto, Japan
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea,Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Sen Yang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China
| | - Takuaki Yamamoto
- Department of Orthopaedic Surgery, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Korea
| | - Nan Shen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA,Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, China,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Kanagawa, Japan
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea,Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Xuejun Zhang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China,Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China,Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, China,Department of Dermatology, Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan,The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea,Hanyang University Institute for Rheumatology Research, Seoul, Korea
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24
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Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Response to Li and Hopper. Am J Hum Genet 2021; 108:527-529. [PMID: 33667396 PMCID: PMC8008475 DOI: 10.1016/j.ajhg.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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25
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Caster DJ, Korte EA, Merchant ML, Klein JB, Barati MT, Joglekar A, Wilkey DW, Coventry S, Hata J, Rovin BH, Harley JB, Namjou-Khales B, McLeish KR, Powell DW. Patients with Proliferative Lupus Nephritis Have Autoantibodies That React to Moesin and Demonstrate Increased Glomerular Moesin Expression. J Clin Med 2021; 10:jcm10040793. [PMID: 33669337 PMCID: PMC7920286 DOI: 10.3390/jcm10040793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Kidney involvement in systemic lupus erythematosus (SLE)—termed lupus nephritis (LN)—is a severe manifestation of SLE that can lead to end-stage kidney disease (ESKD). LN is characterized by immune complex deposition and inflammation in the glomerulus. We tested the hypothesis that autoantibodies targeting podocyte and glomerular cell proteins contribute to the development of immune complex formation in LN. We used Western blotting with SLE sera from patients with and without LN to identify target antigens in human glomerular and cultured human-derived podocyte membrane proteins. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified the proteins in the gel regions corresponding to reactive bands observed with sera from LN patients. We identified 102 proteins that were present in both the podocyte and glomerular samples. We identified 10 high-probability candidates, including moesin, using bioinformatic analysis. Confirmation of moesin as a target antigen was conducted using immunohistochemical analysis (IHC) of kidney biopsy tissue and enzyme-linked immunosorbent assay (ELISA) to detect circulating antibodies. By IHC, biopsies from patients with proliferative lupus nephritis (PLN, class III/IV) demonstrated significantly increased glomerular expression of moesin (p < 0.01). By ELISA, patients with proliferative LN demonstrated significantly increased antibodies against moesin (p < 0.01). This suggests that moesin is a target glomerular antigen in lupus nephritis.
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Affiliation(s)
- Dawn J. Caster
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
- Correspondence: ; Tel.: +1-502-852-5757
| | - Erik A. Korte
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Michael L. Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Jon B. Klein
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
- Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
| | - Michelle T. Barati
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Ami Joglekar
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Daniel W. Wilkey
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Susan Coventry
- Pathology Department, Norton Children’s Hospital, Louisville, KY 40202, USA; (S.C.); (J.H.)
| | - Jessica Hata
- Pathology Department, Norton Children’s Hospital, Louisville, KY 40202, USA; (S.C.); (J.H.)
| | - Brad H. Rovin
- Department of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.B.H.); (B.N.-K.)
- US Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
| | - Bahram Namjou-Khales
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.B.H.); (B.N.-K.)
| | - Kenneth R. McLeish
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - David W. Powell
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
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Hou G, Harley ITW, Lu X, Zhou T, Xu N, Yao C, Qin Y, Ouyang Y, Ma J, Zhu X, Yu X, Xu H, Dai D, Ding H, Yin Z, Ye Z, Deng J, Zhou M, Tang Y, Namjou B, Guo Y, Weirauch MT, Kottyan LC, Harley JB, Shen N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nat Commun 2021; 12:135. [PMID: 33420081 PMCID: PMC7794586 DOI: 10.1038/s41467-020-20460-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.
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Affiliation(s)
- Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Isaac T W Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ning Xu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Chao Yao
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences(SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ye Ouyang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Hong Xu
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
- Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
| | - Dai Dai
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Jun Deng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Mi Zhou
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Leah C Kottyan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - John B Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, 45229, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China.
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China.
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA.
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Stone HK, Parameswaran S, Eapen AA, Chen X, Harley JB, Devarajan P, Weirauch MT, Kottyan L. Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk. Kidney Int Rep 2020; 6:187-195. [PMID: 33426398 PMCID: PMC7783560 DOI: 10.1016/j.ekir.2020.09.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/21/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction The etiology of steroid-sensitive nephrotic syndrome (SSNS) is not well understood. Genetic studies have established common single nucleotide polymorphisms (SNPs) that are associated with increased SSNS disease risk. We review previous genetic association studies of SSNS and nominate particular transcriptional regulators and immune cells as potential key players in the etiology of this disease. Methods A list of SNPs associated with SSNS was compiled from published genome wide association and candidate gene studies. The Regulatory Element Locus Intersection (RELI) tool was used to calculate the enrichment of the overlap between disease risk SNPs and the genomic coordinates of data from a collection of >10,000 chromatin immunoprecipitation sequencing experiments. Results After linkage disequilibrium expansion of the previously reported tag associated SNPs, we identified 192 genetic variants at 8 independent risk loci. Using the Regulatory Element Locus Intersection algorithm, we identified transcriptional regulators with enriched binding at SSNS risk loci (10-05 < Pcorrected < 10-124), including ZNF530, CIITA, CD74, RFX5, and ZNF425. Many of these regulators have well-described roles in the immune response. RNA polymerase II binding in B cells also demonstrated enriched binding at SSNS risk loci (10-37<Pcorrected<10-5). Conclusion SSNS is a complex disease, and immune dysregulation has been previously implicated as a potential underlying cause. This assessment of established SSNS risk loci and analysis of possible function implicates transcriptional dysregulation, and specifically particular transcriptional regulators with known roles in the immune response, as important in the genetic etiology of SSNS.
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Affiliation(s)
- Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Sreeja Parameswaran
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Amy A Eapen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xiaoting Chen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - John B Harley
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Prasad Devarajan
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Leah Kottyan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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Dominguez D, Kamphuis S, Beyene J, Wither J, Harley JB, Blanco I, Vila-Inda C, Brunner H, Klein-Gitleman M, McCurdy D, Wahezi DM, Lehman T, Jelusic M, Peschken CA, Pope JE, Gladman DD, Hanly JG, Clarke AE, Bernatsky S, Pineau C, Smith CD, Barr S, Boire G, Rich E, Silverman ED. Relationship Between Genetic Risk and Age of Diagnosis in Systemic Lupus Erythematosus. J Rheumatol 2020; 48:852-858. [PMID: 33060314 DOI: 10.3899/jrheum.200002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Specific risk alleles for childhood-onset systemic lupus erythematosus SLE (cSLE) vs adult-onset SLE (aSLE) patients have not been identified. The aims of this study were to determine if there is an association (1) between non-HLA-related genetic risk score (GRS) and age of SLE diagnosis, and (2) between HLA-related GRS and age of SLE diagnosis. METHODS Genomic DNA was obtained from 2001 multiethnic patients and genotyped using the Immunochip. Following quality control, genetic risk counting (GRCS), weighted (GRWS), standardized counting (GRSCS), and standardized weighted (GRSWS) scores were calculated based on independent single-nucleotide polymorphisms from validated SLE loci. Scores were analyzed in a regression model and adjusted by sex and ancestral population. RESULTS The analyzed cohort consisted of 1540 patients: 1351 females and 189 males (675 cSLE and 865 aSLE). There were significant negative associations between all non-HLA GRS and age of SLE diagnosis: P = 0.011 and r2 = 0.175 for GRWS; P = 0.008 and r2 = 0.178 for GRSCS; P = 0.002 and r2 = 0.176 for GRSWS (higher GRS correlated with lower age of diagnosis.) All HLA GRS showed significant positive associations with age of diagnosis: P = 0.049 and r2 = 0.176 for GRCS; P = 0.022 and r2 = 0.176 for GRWS; P = 0.022 and r2 = 0.176 for GRSCS; P = 0.011 and r2 = 0.177 for GRSWS (higher GRS correlated with higher age of diagnosis). CONCLUSION Our data suggest that there is a linear relationship between genetic risk and age of SLE diagnosis and that HLA and non-HLA GRS are associated with age of diagnosis in opposite directions.
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Affiliation(s)
- Daniela Dominguez
- D. Dominguez, MSc, Division of Rheumatology, Hospital for Sick Children, Hospital for Sick Children, Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Sylvia Kamphuis
- S. Kamphuis, MD, PhD, Division of Rheumatology Department of Pediatrics, Sophia Children's Hospital, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Joseph Beyene
- J. Beyene, PhD, Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton
| | - Joan Wither
- J. Wither, MD, PhD, Division of Genetics and Development, Krembil Research Institute, Arthritis Centre of Excellence, Division of Rheumatology, Toronto Western Hospital, University Health Network, Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - John B Harley
- J.B. Harley, MD, PhD, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati, and US Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Irene Blanco
- I. Blanco, MD, C. Vila-Inda, MD, Albert Einstein College of Medicine, Division of Rheumatology, Bronx, New York
| | - Catarina Vila-Inda
- I. Blanco, MD, C. Vila-Inda, MD, Albert Einstein College of Medicine, Division of Rheumatology, Bronx, New York
| | - Hermine Brunner
- H. Brunner, MD, MSc, Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Marissa Klein-Gitleman
- M. Klein-Gitleman, MD, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Deborah McCurdy
- D. McCurdy, MD, Division of Pediaitric Rheumatology, University of California Los Angeles, Los Angeles, California
| | - Dawn M Wahezi
- D.M. Wahezi, MD, Children's Hospital at Montefiore, Division of Pediatric Rheumatology, Albert Einstein College of Medicine, the Bronx, New York
| | - Thomas Lehman
- T. Lehman, MD, Division of Pediatric Rheumatology, Hospital for Special Surgery, New York, New York, USA
| | - Marija Jelusic
- M. Jelusic, MD, Department of Pediatric Rheumatology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Christine A Peschken
- C.A. Peschken, MD, MSc, Departments of Medicine and Community Health Sciences, University of Manitoba, Winnipeg, Manitoba
| | - Janet E Pope
- J.E. Pope, MD, MPH, Professor of Medicine, Department of Medicine, University of Western Ontario, London, Ontario
| | - Dafna D Gladman
- D.D. Gladman, MD, Department of Medicine, University of Toronto, Toronto, Ontario
| | - John G Hanly
- J.G. Hanly, MD, Division of Rheumatology, Department of Medicine and Department of Pathology, Queen Elizabeth II Health Sciences Center and Dalhousie University, Halifax, Nova Scotia
| | - Ann E Clarke
- A.E. Clarke, MD, Cumming School of Medicine, University of Calgary, Calgary, Alberta
| | - Sasha Bernatsky
- S. Bernatsky, MD, PhD, Department of Medicine, McGill University, Montreal, Quebec
| | - Christian Pineau
- C. Pineau, MD, Department of Medicine, McGill University Hospital, Montreal, Quebec
| | - C Douglas Smith
- C.D. Smith, MD, Department of Medicine, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario
| | - Susan Barr
- S. Barr, MD, Division of Rheumatology, Department of Medicine, University of Calgary, Calgary, Alberta
| | - Gilles Boire
- G. Boire, MD, Division of Rheumatology, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec
| | - Eric Rich
- E. Rich, MD, Division of Rheumatology, Centre Hospitalier de l'Université de Montreal, Department of Medicine, University of Montreal School of Medicine, Montreal, Quebec
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29
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Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L. Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk. Am J Hum Genet 2020; 107:432-444. [PMID: 32758450 PMCID: PMC7477007 DOI: 10.1016/j.ajhg.2020.07.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/13/2020] [Indexed: 02/08/2023] Open
Abstract
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
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Affiliation(s)
- Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jeffrey K Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Franzel J B van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen 176700, the Netherlands
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA 90089, USA
| | - Christopher H Dampier
- Department of Surgery, University of Virginia Health System, Charlottesville, VA 22903, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna 1090, Austria
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå 90187, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå 90187, Sweden
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock 18051, Germany
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel D Buchanan
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David C Muller
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ 85003, USA
| | - David R Crosslin
- Department of Bioinformatics and Medical Education, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02108, USA
| | - Eric Larson
- Kaiser Permanente Washington Research Institute, Seattle, WA 98101, USA
| | - Flora Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ian B Stanaway
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica Minnier
- School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg 20246, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden 01062, Germany
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Cincinnati VA Medical Center, Cincinnati, OH 45229, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, NY 10065, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | | | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mathieu Lemire
- PanCuRx Translational Research Initiative, Ontario, Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, NL A1B 3R7, Canada
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon 69372, France
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ 85260, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia; Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC 3004, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona 08007, Spain
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes 44093, France
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 85054, USA
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G1X5, Canada
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona 08908, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08907, Spain; ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Vicente Martín
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain; Biomedicine Institute (IBIOMED), University of León, León 24071, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wendy Chung
- Office of Research & Development, Department of Veterans Affairs, Washington, DC 20420, USA; Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre for Public Health Research, Massey University, Wellington 6140, New Zealand
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA 98195, USA; Genome Sciences, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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30
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Kawai VK, Shi M, Feng Q, Chung CP, Liu G, Cox NJ, Jarvik GP, Lee MTM, Hebbring SJ, Harley JB, Kaufman KM, Namjou B, Larson E, Gordon AS, Roden DM, Stein CM, Mosley JD. Pleiotropy in the Genetic Predisposition to Rheumatoid Arthritis: A Phenome-Wide Association Study and Inverse Variance-Weighted Meta-Analysis. Arthritis Rheumatol 2020; 72:1483-1492. [PMID: 32307929 DOI: 10.1002/art.41291] [Citation(s) in RCA: 6] [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: 11/25/2019] [Accepted: 04/14/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study was undertaken to investigate the hypothesis that a genetic predisposition toward rheumatoid arthritis (RA) increases the risk of 10 cardiometabolic and autoimmune disorders previously associated with RA in epidemiologic studies, and to define new genetic pleiotropy present in RA. METHODS Two approaches were used to test our hypothesis. First, we constructed a weighted genetic risk score (wGRS) and then examined its association with 10 prespecified disorders. Additionally, a phenome-wide association study (PheWAS) was carried out to identify potential new associations. Second, inverse variance-weighted regression (IVWR) meta-analysis was used to characterize the association between genetic susceptibility to RA and the prespecified disorders, with the results expressed as odds ratios (ORs) and 95% confidence intervals (95% CIs). RESULTS The wGRS for RA was significantly associated with type 1 diabetes mellitus (DM) (OR 1.10 [95% CI 1.04-1.16]; P = 9.82 × 10-4 ) and multiple sclerosis (OR 0.82 [95% CI 0.77-0.88]; P = 1.73 × 10-8 ), but not with other cardiometabolic phenotypes. In the PheWAS, wGRS was also associated with an increased risk of several autoimmune phenotypes including RA, thyroiditis, and systemic sclerosis, and with a decreased risk of demyelinating disorders. In the IVWR meta-analyses, RA was significantly associated with an increased risk of type 1 DM (P = 1.15 × 10-14 ), with evidence of horizontal pleiotropy (Mendelian Randomization-Egger intercept estimate P = 0.001) likely driven by rs2476601, a PTPN22 variant. The association between type 1 DM and RA remained significant (P = 9.53 × 10-9 ) after excluding rs2476601, with no evidence of horizontal pleiotropy (intercept estimate P = 0.939). RA was also significantly associated with type 2 DM and C-reactive protein levels. These associations were driven by variation in the major histocompatibility complex region. CONCLUSION This study presents evidence of pleiotropy between the genetic predisposition to RA and associated phenotypes found in other autoimmune and cardiometabolic disorders, including type 1 DM.
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Affiliation(s)
- Vivian K Kawai
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mingjian Shi
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Qiping Feng
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cecilia P Chung
- Vanderbilt University Medical Center, Tennessee Valley Healthcare System Nashville Campus, and Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ge Liu
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Nancy J Cox
- Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, and Cincinnati VA Medical Center, Cincinnati, Ohio
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, and Cincinnati VA Medical Center, Cincinnati, Ohio
| | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Eric Larson
- Kaiser Permanente Washington Health Research Institute, Seattle
| | - Adam S Gordon
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Dan M Roden
- Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Jonathan D Mosley
- Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee
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31
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Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H, Harley JB, Hebbring SJ, Ho K, Jarvik GP, Jones M, Karaderi T, Mentch FD, Meun C, Namjou B, Pendergrass S, Ritchie MD, Stanaway IB, Urbanek M, Walunas TL, Smith M, Chisholm RL, Kho AN, Davis L, Hayes MG. A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies. J Clin Endocrinol Metab 2020; 105:dgz326. [PMID: 31917831 PMCID: PMC7453038 DOI: 10.1210/clinem/dgz326] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/07/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT As many as 75% of patients with polycystic ovary syndrome (PCOS) are estimated to be unidentified in clinical practice. OBJECTIVE Utilizing polygenic risk prediction, we aim to identify the phenome-wide comorbidity patterns characteristic of PCOS to improve accurate diagnosis and preventive treatment. DESIGN, PATIENTS, AND METHODS Leveraging the electronic health records (EHRs) of 124 852 individuals, we developed a PCOS risk prediction algorithm by combining polygenic risk scores (PRS) with PCOS component phenotypes into a polygenic and phenotypic risk score (PPRS). We evaluated its predictive capability across different ancestries and perform a PRS-based phenome-wide association study (PheWAS) to assess the phenomic expression of the heightened risk of PCOS. RESULTS The integrated polygenic prediction improved the average performance (pseudo-R2) for PCOS detection by 0.228 (61.5-fold), 0.224 (58.8-fold), 0.211 (57.0-fold) over the null model across European, African, and multi-ancestry participants respectively. The subsequent PRS-powered PheWAS identified a high level of shared biology between PCOS and a range of metabolic and endocrine outcomes, especially with obesity and diabetes: "morbid obesity", "type 2 diabetes", "hypercholesterolemia", "disorders of lipid metabolism", "hypertension", and "sleep apnea" reaching phenome-wide significance. CONCLUSIONS Our study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins. By utilizing the individual genome-phenome data available from the EHR, our approach also demonstrates that polygenic prediction by PRS can provide valuable opportunities to discover the pleiotropic phenomic network associated with PCOS pathogenesis.
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Affiliation(s)
- Yoonjung Yoonie Joo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ky'Era Actkins
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Anna O Basile
- Department of Biomedical Informatics, Columbia University New York, New York
| | - Robert Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Felix Day
- MRC Epidemiology Unit, Cambridge Biomedical Campus, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Joshua C Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Digna R Velez Edwards
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine; US Department of Veterans Affairs, Cincinnati, Ohio
| | - Scott J Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Kevin Ho
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical School, Seattle, Wahington
| | - Michelle Jones
- Center for Bioinformatics & Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Tugce Karaderi
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy Meun
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sarah Pendergrass
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Theresa L Walunas
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Abel N Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lea Davis
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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32
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Kamitaki N, Sekar A, Handsaker RE, de Rivera H, Tooley K, Morris DL, Taylor KE, Whelan CW, Tombleson P, Loohuis LMO, Boehnke M, Kimberly RP, Kaufman KM, Harley JB, Langefeld CD, Seidman CE, Pato MT, Pato CN, Ophoff RA, Graham RR, Criswell LA, Vyse TJ, McCarroll SA. Complement genes contribute sex-biased vulnerability in diverse disorders. Nature 2020; 582:577-581. [PMID: 32499649 PMCID: PMC7319891 DOI: 10.1038/s41586-020-2277-x] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/28/2020] [Indexed: 12/18/2022]
Abstract
Many common illnesses differentially affect men and women for unknown reasons. The autoimmune diseases lupus and Sjögren’s syndrome affect nine times more women than men1, whereas schizophrenia affects men more frequently and severely2. All three illnesses have their strongest common genetic associations in the Major Histocompatibility Complex (MHC) locus, an association that in lupus and Sjögren’s syndrome has long been thought to arise from alleles of the human leukocyte antigen (HLA) genes at that locus3–6. Here we show that the complement component 4 (C4) genes, which are also in the MHC locus and were recently found to increase risk for schizophrenia7, generate 7-fold variation in risk for lupus (95% CI: 5.88–8.61; p < 10−117 in total) and 16-fold variation in risk for Sjögren’s syndrome (95% CI: 8.59–30.89; p < 10−23 in total) among individuals with common C4 genotypes, with C4A protecting more strongly than C4B in both illnesses. The same alleles that increase risk for schizophrenia greatly reduced risk for lupus and Sjögren’s syndrome. In all three illnesses, C4 alleles acted more strongly in men than in women: common combinations of C4A and C4B generated 14-fold variation in risk for lupus, 31-fold variation in risk for Sjögren’s syndrome, and 1.7-fold variation in schizophrenia risk among men (vs. 6-fold, 15-fold, and 1.26-fold among women respectively). At a protein level, both C4 and its effector C3 were present at greater levels in men than women in cerebrospinal fluid (p < 10−5 for both C4 and C3) and plasma8,9 among adults ages 20–50, corresponding to the ages of differential disease vulnerability. Sex differences in complement protein levels may help explain the larger effects of C4 alleles in men, women’s greater risk of SLE and Sjögren’s, and men’s greater vulnerability in schizophrenia. These results implicate the complement system as a source of sexual dimorphism in vulnerability to diverse illnesses.
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Affiliation(s)
- Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aswin Sekar
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heather de Rivera
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine Tooley
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David L Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Kimberly E Taylor
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, CA, USA
| | - Christopher W Whelan
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip Tombleson
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Loes M Olde Loohuis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Roel A Ophoff
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | - Lindsey A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, CA, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK.
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Laurynenka V, Ho D, Huang Y, Parameswaran S, Kottyan LC, Weirauch MT, Perentesis J, Kaufman KM, Mizukawa B, Harley JB. The Ikaros1, IKZF1, risk locus for Acute Lymphoblastic Leukemia (ALL) at chromosome 7p12.2 regulates the expression of the FIGNL1 gene. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.163.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
ALL, the most common pediatric cancer, originates from progenitor B-cells in ~85% of cases. IKAROS Family Zinc Finger 1 (IKZF1) is an important locus for ALL. Our goal was to identify the functional variants, thereby nominating a potential causal mechanism for ALL.
We evaluated all 27 genetic polymorphisms in disequilibrium at r2>0.8 with the tag, the most highly associated risk variant at IKZF1 locus. They map to intron 7, 3′ UTR and 3′ flanking sequence of IKZF1. Fidgetin-like protein 1 (FIGNL1) is 45,524 bases from the tag variant and is nominated by eQTL and DNA looping data along with IKZF1 as possible targets. Epstein-Barr virus (EBV) transformed GM12878 cells were transduced with lentiviral vectors for stable expression of fusion proteins dead (d) Cas9-VP64 and activator MS2-p65-HSF1 (synergistic activation mediator (SAM) system). We designed 27 single guide (sg) RNAs, one for each of the 27 variants and evaluated expression perturbation in cells transfected with pools and individual sgRNA. Expression of FIGNL1, but not IKZF1, was convincingly altered in this system. The reduction of FIGNL1 expression by ~50% was isolated to two neighboring variants separated by 1 kb. The risk allele at these variants increases FIGNL1 expression in wild type cells, however in EBV transformed B-cells FIGNL1 expression is decreased. Other data show that the EBV encoded DNA binding co-factor EBNA3C binds at or very near this locus in EBV transformed B cells.
Our results nominate two closely located SNPs in the last intron of IKZF1 as potentially causal variants, controlling the expression of FIGNL1, which ordinarily participates in homologous recombination during DNA double-strand break repair, maintenance of genomic stability and prevention of cancer.
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Affiliation(s)
| | - Danielle Ho
- 1Cincinnati Children’s hospital Medical Center
| | | | | | | | | | | | - Kenneth M. Kaufman
- 1Cincinnati Children’s hospital Medical Center
- 2Department of Veterans Affairs Medical Center
| | | | - John B. Harley
- 1Cincinnati Children’s hospital Medical Center
- 2Department of Veterans Affairs Medical Center
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Krishnamurthy D, Seelamneni H, Ochayon D, Harley JB, Waggoner SN. Conditional abrogation of Ddx3x reveals its essential role in lymphocyte development and partial compensation by Y chromosome. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.223.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Ddx3x on the X-chromosome encodes a DEAD-box RNA helicase with putative roles in RNA metabolism, cell cycle progression, apoptosis, and viral immunity. We previously found that hematopoietic-specific hemizygosity of Ddx3x studies caused a marked reduction in the frequencies of natural killer (NK) and B cells in peripheral lymphoid organs of male mice (Liu et al. bioRxiv 2018). No homozygous Ddx3x-deficient female pups were ever obtained, suggesting that hematopoietic loss of this gene contributes to the embryonic lethality observed in germline Ddx3x knockout mice. To assess cell-lineage intrinsic roles for Ddx3x in B-cell and NK-cell development, we bred Ddx3x-floxed mice with Mb1-Cre and Ncr1-iCre mice, respectively. While hemizygous male Ddx3x-deficient mice display mild reductions in B-cell (Mb1-Cre) and NK-cell (Ncr1-iCre) frequencies, homozygous Ddx3x-deficient female mice from each were almost completely devoid of the relevant cell lineages. B-cell loss was evident from the pro-B cells stage, with B cells surviving beyond this stage showing evidence of having escaped deletion of Ddx3x. Ncr1-iCre-mediated deletion of Ddx3x completely abrogated development of both NK cells and other Ncr1-expressing innate lymphoid cells. Thus, DDX3 plays an essential role in the lymphocyte development, where Ddx3y may partially compensate for loss of Ddx3x in these lineages.
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Affiliation(s)
- Durga Krishnamurthy
- 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Harsha Seelamneni
- 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - David Ochayon
- 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - John B. Harley
- 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- 2Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- 3US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Stephen N. Waggoner
- 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- 2Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Laurynenka V, Chen X, Carter M, Parameswaran S, Eswar S, Kaufman KM, Namjou B, Weirauch MT, Kottyan LC, Harley JB. Latency III gene products of Epstein-Barr Virus (EBV) are associated with Systemic Lupus Erythematosus (SLE) genetic risk loci. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.141.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
SLE affects millions with increasing diagnostic prevalence. Genetic studies have identified >600 mostly regulatory variant associations. EBV has been nominated as a causal factor for SLE from immunochemistry and epidemiologic studies. EBNA2 concentrates at SLE risk loci (Nat Genet 50:699 2018) suggesting mechanisms. Additional evidence supporting EBV as an SLE origin would advance this hypothesis of etiology.
Previous simulation using our RELI algorithm revealed an astonishing association with Epstein-Barr virus nuclear antigen 2 (EBNA2) (OR=5.96, Pc=E-25) (Nat Genet 50:699, 2018). The >100 risk alleles associated at p<5E-8 for SLE were curated and reduced to 83 loci by linkage disequilibrium pruning. We evaluated the available 53 virally encoded and 13,051 human TF ChIP-seq (chromatin immunoprecipitation with DNA sequencing) datasets. In addition to EBNA2 (now OR=3.7, Pc=1.96E-18 after Bonferroni correction), two of the 53 viral TF data sets, EBNA3C and EBNALP, each of which are EBV Latency III gene products, were also strongly associated with the SLE risk loci (OR=6.0, Pc=4.19E-18; and OR=3.3, Pc=5.53E-18). Moreover, among the human TF datasets strongly associated with SLE risk loci (Pc<E-6), those from EBV infected and transformed B cells are highly concentrated (OR≈56, P<E-100) and, in addition, the human TFs that are known to form super-enhancers upon B cell transformation by EBV (e.g., NFκB subunits) also tend to be concentrated at the SLE risk loci (OR>30, p<E-25). Meanwhile, genetic associations for depression, anxiety, and schizophrenia show no such relationships.
These new results further the possible validity of the hypothesis that SLE is originally caused by the Latency III expression program of EBV.
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Affiliation(s)
| | | | | | | | | | - Kenneth M. Kaufman
- 1Cincinnati Children’s hospital Medical Center
- 2Department of Veterans Affairs Medical Center
| | | | | | | | - John B. Harley
- 1Cincinnati Children’s hospital Medical Center
- 2Department of Veterans Affairs Medical Center
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Laufer VA, Tiwari HK, Reynolds RJ, Danila MI, Wang J, Edberg JC, Kimberly RP, Kottyan LC, Harley JB, Mikuls TR, Gregersen PK, Absher DM, Langefeld CD, Arnett DK, Bridges SL. Genetic influences on susceptibility to rheumatoid arthritis in African-Americans. Hum Mol Genet 2020; 28:858-874. [PMID: 30423114 DOI: 10.1093/hmg/ddy395] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
Large meta-analyses of rheumatoid arthritis (RA) susceptibility in European (EUR) and East Asian (EAS) populations have identified >100 RA risk loci, but genome-wide studies of RA in African-Americans (AAs) are absent. To address this disparity, we performed an analysis of 916 AA RA patients and 1392 controls and aggregated our data with genotyping data from >100 000 EUR and Asian RA patients and controls. We identified two novel risk loci that appear to be specific to AAs: GPC5 and RBFOX1 (PAA < 5 × 10-9). Most RA risk loci are shared across different ethnicities, but among discordant loci, we observed strong enrichment of variants having large effect sizes. We found strong evidence of effect concordance for only 3 of the 21 largest effect index variants in EURs. We used the trans-ethnic fine-mapping algorithm PAINTOR3 to prioritize risk variants in >90 RA risk loci. Addition of AA data to those of EUR and EAS descent enabled identification of seven novel high-confidence candidate pathogenic variants (defined by posterior probability > 0.8). In summary, our trans-ethnic analyses are the first to include AAs, identified several new RA risk loci and point to candidate pathogenic variants that may underlie this common autoimmune disease. These findings may lead to better ways to diagnose or stratify treatment approaches in RA.
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Affiliation(s)
- Vincent A Laufer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Richard J Reynolds
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Maria I Danila
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jelai Wang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leah C Kottyan
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,United States Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Ted R Mikuls
- VA Nebraska-Western Iowa Health Care System and the Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, NY, USA
| | - Devin M Absher
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Donna K Arnett
- University of Kentucky College of Public Health, Lexington, KY, USA
| | - S Louis Bridges
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Jog NR, McClain MT, Heinlen LD, Gross T, Towner R, Guthridge JM, Axtell RC, Pardo G, Harley JB, James JA. Epstein Barr virus nuclear antigen 1 (EBNA-1) peptides recognized by adult multiple sclerosis patient sera induce neurologic symptoms in a murine model. J Autoimmun 2020; 106:102332. [PMID: 31515129 PMCID: PMC6930324 DOI: 10.1016/j.jaut.2019.102332] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disease with progressive neurodegeneration and complex etiology likely involving genetic and environmental factors. MS has been associated with Epstein Barr virus (EBV) infection, with patients often showing enhanced responses to EBV antigens. To determine whether abnormal EBV nuclear antigen-1 (EBNA-1) humoral immunity can serve as an initiator of autoimmune responses in MS, we investigated the fine specificities of the humoral immune response against EBNA-1 in MS patients using solid phase epitope mapping. Antibodies from MS patients recognized an EBNA-1 epitope spanning amino acids 411-426, previously unknown to be recognized specifically by untreated MS patients. Antibodies against this epitope cross-reacted to myelin basic protein (MBP). Furthermore, animals immunized with this EBNA-1 polypeptide mounted a response against MBP and developed signs of experimental autoimmune encephalitis (EAE). These data support a link between MS and EBV through antibodies that cross-react between EBV proteins and the MBP autoantigen.
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Affiliation(s)
- Neelakshi R Jog
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Micah T McClain
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Latisha D Heinlen
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Timothy Gross
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Rheal Towner
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Robert C Axtell
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Gabriel Pardo
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Veterans Affairs VA Medical Center, Cincinnati, OH, USA
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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38
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Glessner JT, Li J, Desai A, Palmer M, Kim D, Lucas AM, Chang X, Connolly JJ, Almoguera B, Harley JB, Jarvik GP, Ritchie MD, Sleiman PM, Roden DM, Crosslin D, Hakonarson H. CNV Association of Diverse Clinical Phenotypes from eMERGE reveals novel disease biology underlying cardiovascular disease. Int J Cardiol 2020; 298:107-113. [DOI: 10.1016/j.ijcard.2019.07.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/15/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
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Sinner DI, Carey B, Zgherea D, Kaufman KM, Leesman L, Wood RE, Rutter MJ, de Alarcon A, Elluru RG, Harley JB, Whitsett JA, Trapnell BC. Complete Tracheal Ring Deformity. A Translational Genomics Approach to Pathogenesis. Am J Respir Crit Care Med 2019; 200:1267-1281. [PMID: 31215789 PMCID: PMC6857493 DOI: 10.1164/rccm.201809-1626oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Rationale: Complete tracheal ring deformity (CTRD) is a rare congenital abnormality of unknown etiology characterized by circumferentially continuous or nearly continuous cartilaginous tracheal rings, variable degrees of tracheal stenosis and/or shortening, and/or pulmonary arterial sling anomaly.Objectives: To test the hypothesis that CTRD is caused by inherited or de novo mutations in genes required for normal tracheal development.Methods: CTRD and normal tracheal tissues were examined microscopically to define the tracheal abnormalities present in CTRD. Whole-exome sequencing was performed in children with CTRD and their biological parents ("trio analysis") to identify gene variants in patients with CTRD. Mutations were confirmed by Sanger sequencing, and their potential impact on structure and/or function of encoded proteins was examined using human gene mutation databases. Relevance was further examined by comparison with the effects of targeted deletion of murine homologs important to tracheal development in mice.Measurements and Main Results: The trachealis muscle was absent in all of five patients with CTRD. Exome analysis identified six de novo, three recessive, and multiple compound-heterozygous or rare hemizygous variants in children with CTRD. De novo variants were identified in SHH (Sonic Hedgehog), and inherited variants were identified in HSPG2 (perlecan), ROR2 (receptor tyrosine kinase-like orphan receptor 2), and WLS (Wntless), genes involved in morphogenetic pathways known to mediate tracheoesophageal development in mice.Conclusions: The results of the present study demonstrate that absence of the trachealis muscle is associated with CTRD. Variants predicted to cause disease were identified in genes encoding Hedgehog and Wnt signaling pathway molecules, which are critical to cartilage formation and normal upper airway development in mice.
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Affiliation(s)
- Debora I. Sinner
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | | | | | - K. M. Kaufman
- Center for Autoimmune Genomics and Etiology, and
- Department of Pediatrics and
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Lauren Leesman
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | | | - Michael J. Rutter
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Alessandro de Alarcon
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Ravindhra G. Elluru
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, and
- Department of Pediatrics and
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Jeffrey A. Whitsett
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | - Bruce C. Trapnell
- Division of Neonatology
- Division of Pulmonary Biology
- Translational Pulmonary Science Center
- Department of Pediatrics and
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; and
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40
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Harris VM, Koelsch KA, Kurien BT, Harley ITW, Wren JD, Harley JB, Scofield RH. Characterization of cxorf21 Provides Molecular Insight Into Female-Bias Immune Response in SLE Pathogenesis. Front Immunol 2019; 10:2160. [PMID: 31695690 PMCID: PMC6816314 DOI: 10.3389/fimmu.2019.02160] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Ninety percent of systemic lupus erythematosus (SLE) patients are women. X chromosome-dosage increases susceptibility to SLE and primary Sjögren's syndrome (pSS). Chromosome X open reading frame 21 (CXorf21) escapes X-inactivation and is an SLE risk gene of previously unknown function. We undertook the present study to delineate the function of CXorf21 in the immune system as well as investigate a potential role in the sex bias of SLE and pSS. Methods: Western blot protein analysis, qPCR, BioPlex cytokine immunoassay, pHrodo™ assays, as well as in vitro CRISPR-Cas9 knockdown experiments were employed to delineate the role of CXorf21 in relevant immunocytes. Results: Expressed in monocytes and B cells, CXorf21 basal Mrna, and protein expression levels are elevated in female primary monocytes, B cells, and EBV-transformed B cells compared to male cells. We also found CXorf21 mRNA and protein expression is higher in both male and female cells from SLE patients compared to control subjects. TLR7 ligation increased CXorf21 protein expression and CXorf21 knockdown abrogated TLR7-driven increased IFNA1 mRNA expression, and reduced secretion of both TNF-alpha and IL-6 in healthy female monocytes. Similarly, we found increased pH in the lysosomes of CXorf21-deficient female monocytes. Conclusion: CXorf21 is more highly expressed in female compared to male cells and is involved in a sexually dimorphic response to TLR7 activation. In addition, CXorf21 expression regulates lysosomal pH in a sexually dimorphic manner. Thus, sexually dimorphic expression of CXorf21 skews cellular immune responses in manner consistent with expected properties of a mediator of the X chromosome dose risk in SLE and pSS.
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Affiliation(s)
- Valerie M Harris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kristi A Koelsch
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Biji T Kurien
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Isaac T W Harley
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, CO, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,United States Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - R Hal Scofield
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Medical and Research Services, Oklahoma City Department of Veterans Affairs Health Care Center, Oklahoma City, OK, United States
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Namjou B, Lingren T, Huang Y, Parameswaran S, Cobb BL, Stanaway IB, Connolly JJ, Mentch FD, Benoit B, Niu X, Wei WQ, Carroll RJ, Pacheco JA, Harley ITW, Divanovic S, Carrell DS, Larson EB, Carey DJ, Verma S, Ritchie MD, Gharavi AG, Murphy S, Williams MS, Crosslin DR, Jarvik GP, Kullo IJ, Hakonarson H, Li R, Xanthakos SA, Harley JB. GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network. BMC Med 2019; 17:135. [PMID: 31311600 PMCID: PMC6636057 DOI: 10.1186/s12916-019-1364-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [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: 02/19/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition. METHODS First, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI). RESULTS Consistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p = 1.70 × 10- 20). This effect was consistent in both pediatric (p = 9.92 × 10- 6) and adult (p = 9.73 × 10- 15) cohorts. Additionally, this variant was also associated with disease severity and NAFLD Activity Score (NAS) (p = 3.94 × 10- 8, beta = 0.85). PheWAS analysis link this locus to a spectrum of liver diseases beyond NAFLD with a novel negative correlation with gout (p = 1.09 × 10- 4). We also identified novel loci for NAFLD disease severity, including one novel locus for NAS score near IL17RA (rs5748926, p = 3.80 × 10- 8), and another near ZFP90-CDH1 for fibrosis (rs698718, p = 2.74 × 10- 11). Post-GWAS and gene-based analyses identified more than 300 genes that were used for functional and pathway enrichment analyses. CONCLUSIONS In summary, this study demonstrates clear confirmation of a previously described NAFLD risk locus and several novel associations. Further collaborative studies including an ethnically diverse population with well-characterized liver histologic features of NAFLD are needed to further validate the novel findings.
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Affiliation(s)
- Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
| | - Todd Lingren
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Beth L Cobb
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
| | - Barbara Benoit
- Research IS and Computing, Partners HealthCare, Harvard University, Somerville, MA, USA
| | - Xinnan Niu
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Wei-Qi Wei
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Robert J Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Isaac T W Harley
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Senad Divanovic
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, WA, USA
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Shefali Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York City, NY, USA
| | - Shawn Murphy
- Research Information Science and Computing, Partners HealthCare, Boston, MA, USA
| | - Marc S Williams
- Genomic Medicine Institute (M.S.W.), Geisinger, Danville, PA, USA
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Bethesda, MD, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stavra A Xanthakos
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
- College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
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Jog NR, Young KA, Munroe ME, Harmon MT, Guthridge JM, Kelly JA, Kamen DL, Gilkeson GS, Weisman MH, Karp DR, Gaffney PM, Harley JB, Wallace DJ, Norris JM, James JA. Association of Epstein-Barr virus serological reactivation with transitioning to systemic lupus erythematosus in at-risk individuals. Ann Rheum Dis 2019; 78:1235-1241. [PMID: 31217170 PMCID: PMC6692217 DOI: 10.1136/annrheumdis-2019-215361] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022]
Abstract
Objective. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with unknown etiology. Epstein-Barr virus (EBV) is an environmental factor associated with SLE. EBV maintains latency in B cells with frequent reactivation measured by antibodies against viral capsid antigen (VCA) and early antigen (EA). In this study, we determined whether EBV reactivation and single nucleotide polymorphisms (SNPs) in EBV-associated host genes are associated with SLE transition. Methods. SLE patient relatives (n=436) who did not have SLE at baseline were re-contacted after 6.3 (±3.9) years and evaluated for interim transitioning to SLE (≥4 cumulative ACR criteria); 56 (13%) transitioned to SLE prior to the follow-up visit. At both visits, detailed demographic, environmental, clinical information, and blood samples were obtained. Antibodies against viral antigens were measured by ELISA. SNPs in IL10, CR2, TNFAIP3, and CD40 genes were typed by ImmunoChip™. Generalized estimating equations were used to test associations between viral antibody levels and transitioning to SLE. Results. Mean baseline VCA IgG (4.879±1.797 vs 3.866±1.795, p=0.0003) and EA IgG (1.192±1.113 vs 0.7774±0.8484, p=0.0236) levels were higher in transitioned compared to autoantibody negative non-transition relatives. Increased VCA IgG and EA IgG were associated with transitioning to SLE (OR 1.28 95%CI 1.07–1.53 p=0.007, OR 1.43 95%CI 1.06–1.93 p=0.02, respectively). Significant interactions were observed between CD40 variant rs48100485 and VCA IgG levels, and IL10 variant rs3024493 and VCA IgA levels in transitioning to SLE. Conclusion. Heightened serologic reactivation of EBV increases the probability of transitioning to SLE in unaffected SLE relatives.
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Affiliation(s)
- Neelakshi R Jog
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Colorado School of Public Health, Aurora, Colorado, USA
| | - Melissa E Munroe
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Michael T Harmon
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Diane L Kamen
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Gary S Gilkeson
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David R Karp
- Division of Rheumatic Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Daniel J Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jill M Norris
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Colorado School of Public Health, Aurora, Colorado, USA
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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Laurynenka V, Carter M, Parameswaran S, Chen X, Kottyan LC, Weirauch MT, Harley JB. New role of Epstein-Barr virus in pathogenesis of acute and chronic lymphocytic leukemia. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.197.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Acute lymphoblastic leukemia (ALL) is the most common mortal cancer in children. Chronic lymphocytic leukemia (CLL) is the most prevalent form of adult leukemia in western countries. B lymphocytes dominate the origin of both diseases. We have found a possible role for Epstein-Barr virus (EBV) in the origins of both ALL and CLL.
We applied our strategy (Nat Genet 50:699, 2018) to determine whether the binding of EBV transcription factors (TFs) was concentrate at the 84 known risk loci for CLL and 16 loci for ALL. We evaluated 52 virally encoded TF ChIP-seq (chromatin immunoprecipitation with DNA sequencing) datasets and complemented this analysis with the results from 1535 human TF ChIP-seq datasets.
We found that Epstein-Barr nuclear antigen leader protein (EBNALP), EBNA3C and EBNA2 were concentrated in the CLL loci by 3.7, 3.7 and 3.5-fold with p=4.89*10−19, p=2.74*10−11 and p=1.07*10−8, respectively. The viral (n=3) and human TFs (n=40) cluster together in an optimal subset of ~15 of the 84 known loci in CLL at p<10−6. Eighty percent of the most highly associated viral and human TF ChIP-seq datasets were collected from EBV transformed B cell lines in the Latency III program of viral expression, for which EBNALP, EBNA3C and EBNA2 are viral gene products.
In ALL 3 of 16 loci were occupied by EBNA3ABC by a 17.7-fold enrichment with p=2.0*10−10. Among human TFs only c-MYC reached statistical significance binding 2 non-overlapping risk loci with 28.4-fold enrichment with p=2.9*10−10.
These results nominate EBV for a role in the pathogenesis of CLL and ALL by a mechanism operating in transformed B cells through the EBV Latency III program of viral expression.
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Molineros JE, Looger LL, Kim K, Okada Y, Terao C, Sun C, Zhou XJ, Raj P, Kochi Y, Suzuki A, Akizuki S, Nakabo S, Bang SY, Lee HS, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Zuo X, Yamamoto K, Li QZ, Shen N, Porter LL, Harley JB, Chua KH, Zhang H, Wakeland EK, Tsao BP, Bae SC, Nath SK. Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians. PLoS Genet 2019; 15:e1008092. [PMID: 31022184 PMCID: PMC6504188 DOI: 10.1371/journal.pgen.1008092] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/07/2019] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology. The Human leukocyte antigen (HLA) region is a key genetic factor conferring risk of systemic lupus erythematosus (SLE). In spite of multiple SLE association signals identified in the HLA region, only amino-acid residues within HLA-DRB1 have been specifically described previously. In this study, we performed an imputation-based analysis on individuals with East Asian ancestry, and characterized SLE risk within the HLA region for all involved independent genes (HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-A, and HLA-B). Furthermore, we identified a characteristic SLE risk residue signature as well as a pattern of specific nRNP and Ro/La autoantibody residues located in the peptide-binding grooves, suggesting their key involvement in autoantibody production.
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Affiliation(s)
- Julio E. Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Chikashi Terao
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuichiro Nakabo
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Mo Kang
- School of Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University Hospital, Suwon, Korea
| | - Won Tae Chung
- Dong-A University Hospital, Department of Internal Medicine, Busan, Korea
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Seung-Cheol Shim
- Daejeon Rheumatoid & Degenerative Arthritis Center, Chungnam National University Hospital, Daejeon, Korea
| | - Shin-Seok Lee
- Department of Rheumatology, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nan Shen
- Department of Rheumatology and Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lauren L. Porter
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Betty P. Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- * E-mail: (SCB); (SKN)
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail: (SCB); (SKN)
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Hanscombe KB, Morris DL, Noble JA, Dilthey AT, Tombleson P, Kaufman KM, Comeau M, Langefeld CD, Alarcon-Riquelme ME, Gaffney PM, Jacob CO, Sivils KL, Tsao BP, Alarcon GS, Brown EE, Croker J, Edberg J, Gilkeson G, James JA, Kamen DL, Kelly JA, McCune J, Merrill JT, Petri M, Ramsey-Goldman R, Reveille JD, Salmon JE, Scofield H, Utset T, Wallace DJ, Weisman MH, Kimberly RP, Harley JB, Lewis CM, Criswell LA, Vyse TJ. Genetic fine mapping of systemic lupus erythematosus MHC associations in Europeans and African Americans. Hum Mol Genet 2019; 27:3813-3824. [PMID: 30085094 PMCID: PMC6196648 DOI: 10.1093/hmg/ddy280] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/24/2018] [Indexed: 11/14/2022] Open
Abstract
Genetic variation within the major histocompatibility complex (MHC) contributes substantial risk for systemic lupus erythematosus, but high gene density, extreme polymorphism and extensive linkage disequilibrium (LD) have made fine mapping challenging. To address the problem, we compared two association techniques in two ancestrally diverse populations, African Americans (AAs) and Europeans (EURs). We observed a greater number of Human Leucocyte Antigen (HLA) alleles in AA consistent with the elevated level of recombination in this population. In EUR we observed 50 different A-C-B-DRB1-DQA-DQB multilocus haplotype sequences per hundred individuals; in the AA sample, these multilocus haplotypes were twice as common compared to Europeans. We also observed a strong narrow class II signal in AA as opposed to the long-range LD observed in EUR that includes class I alleles. We performed a Bayesian model choice of the classical HLA alleles and a frequentist analysis that combined both single nucleotide polymorphisms (SNPs) and classical HLA alleles. Both analyses converged on a similar subset of risk HLA alleles: in EUR HLA- B*08:01 + B*18:01 + (DRB1*15:01 frequentist only) + DQA*01:02 + DQB*02:01 + DRB3*02 and in AA HLA-C*17:01 + B*08:01 + DRB1*15:03 + (DQA*01:02 frequentist only) + DQA*02:01 + DQA*05:01+ DQA*05:05 + DQB*03:19 + DQB*02:02. We observed two additional independent SNP associations in both populations: EUR rs146903072 and rs501480; AA rs389883 and rs114118665. The DR2 serotype was best explained by DRB1*15:03 + DQA*01:02 in AA and by DRB1*15:01 + DQA*01:02 in EUR. The DR3 serotype was best explained by DQA*05:01 in AA and by DQB*02:01 in EUR. Despite some differences in underlying HLA allele risk models in EUR and AA, SNP signals across the extended MHC showed remarkable similarity and significant concordance in direction of effect for risk-associated variants.
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Affiliation(s)
- Ken B Hanscombe
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - David L Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Janelle A Noble
- CHORI, Children's Hospital Oakland Research Institute, Oakland, California, USA
| | | | - Philip Tombleson
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Mary Comeau
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marta E Alarcon-Riquelme
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Unit of Chronic Inflammation, Institute of Environmental Medicine, Karolinska Institute, Sweden
| | - Patrick M Gaffney
- Arthritis & Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Chaim O Jacob
- Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Kathy L Sivils
- Arthritis & Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Betty P Tsao
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Graciela S Alarcon
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer Croker
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeff Edberg
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gary Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Judith A James
- Arthritis & Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Division of Rheumatology, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Diane L Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Joseph McCune
- Michigan Medicine Rheumatology Clinic,Taubman Center Floor 3 Reception A, 1500 E Medical Center Dr SPC 5358, Ann Arbor, MI, USA
| | - Joan T Merrill
- Oklahoma Medical Research Foundation,825 N.E. 13th Street, Oklahoma City, OK, USA
| | - Michelle Petri
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - John D Reveille
- Department of Internal Medicine, The University of Texas, Fannin, MSB, Houston, TX, USA
| | - Jane E Salmon
- Division of Rheumatology, Hospital for Special Surgery-Weill Cornell Medicine, New York, NY, USA
| | - Hal Scofield
- Arthritis & Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Oklahoma Clinical and Translational Science Institute,University of Oklahoma Health Sciences Center, 920 NE Stanton L. Young, Oklahoma City, OK, USA
| | - Tammy Utset
- University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Daniel J Wallace
- Division of Rheumatology, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Michael H Weisman
- Division of Rheumatology, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, King's College London, London, UK.,MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Lindsey A Criswell
- Rosalind Russell / Ephraim P Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, CA, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
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James JA, Chen H, Young KA, Bemis EA, Seifert J, Bourn RL, Deane KD, Demoruelle MK, Feser M, O'Dell JR, Weisman MH, Keating RM, Gaffney PM, Kelly JA, Langefeld CD, Harley JB, Robinson W, Hafler DA, O'Connor KC, Buckner J, Guthridge JM, Norris JM, Holers VM. Latent autoimmunity across disease-specific boundaries in at-risk first-degree relatives of SLE and RA patients. EBioMedicine 2019; 42:76-85. [PMID: 30952617 PMCID: PMC6491794 DOI: 10.1016/j.ebiom.2019.03.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Autoimmune disease prevention requires tools to assess an individual's risk of developing a specific disease. One tool is disease-associated autoantibodies, which accumulate in an asymptomatic preclinical period. However, patients sometimes exhibit autoantibodies associated with a different disease classification. When and how these alternative autoantibodies first appear remain unknown. This cross-sectional study characterizes alternative autoimmunity, and associated genetic and environmental factors, in unaffected first-degree relatives (FDRs) of patients, who exhibit increased future risk for the same disease. METHODS Samples (n = 1321) from disease-specific autoantibody-positive (aAb+) systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 1 diabetes (T1D) patients; and unaffected aAb+ and autoantibody-negative (aAb-) SLE and RA FDRs were tested for SLE, RA, and T1D aAbs, as well as anti-tissue transglutaminase, anti-cardiolipin and anti-thyroperoxidase. FDR SLE and RA genetic risk scores (GRS) were calculated. FINDINGS Alternative autoimmunity occurred in SLE patients (56%) and FDRs (57·4%), RA patients (32·6%) and FDRs (34·8%), and T1D patients (43%). Expanded autoimmunity, defined as autoantibodies spanning at least two other diseases, occurred in 18·5% of SLE patients, 16·4% of SLE FDRs, 7·8% of RA patients, 5·3% of RA FDRs, and 10·8% of T1D patients. SLE FDRs were more likely to have alternative (odds ratio [OR] 2·44) and expanded (OR 3·27) autoimmunity than RA FDRs. Alternative and expanded autoimmunity were associated with several environmental exposures. Alternative autoimmunity was associated with a higher RA GRS in RA FDRs (OR 1·41), and a higher SLE GRS in aAb+ RA FDRs (OR 1·87), but not in SLE FDRs. INTERPRETATION Autoimmunity commonly crosses disease-specific boundaries in systemic (RA, SLE) and organ-specific (T1D) autoimmune diseases. Alternative autoimmunity is more common in SLE FDRs than RA FDRs, and is influenced by genetic and environmental factors. These findings have substantial implications for preclinical disease pathogenesis and autoimmune disease prevention studies. FUND: NIH U01AI101981, R01AR051394, U19AI082714, P30AR053483, P30GM103510, U54GM104938, U01AI101934, R01AI024717, U01AI130830, I01BX001834, & U01HG008666.
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Affiliation(s)
- Judith A James
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Hua Chen
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | | | - Rebecka L Bourn
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | | | | | | | | | | | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, The University of Cincinnati College of Medicine, and Cincinnati US Department of Veterans Affairs VA Medical Center, Cincinnati, OH, USA
| | | | | | | | - Jane Buckner
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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Young KA, Munroe ME, Guthridge JM, Kamen DL, Gilkensen GS, Harley JB, Weisman MH, Karp DR, Wallace DJ, James JA, Norris JM. Screening characteristics for enrichment of individuals at higher risk for transitioning to classified SLE. Lupus 2019; 28:597-606. [PMID: 30845880 DOI: 10.1177/0961203319834675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Further prospective study is needed to elucidate the etiology and natural history of systemic lupus erythematosus development. The clinical complexity of this heterogeneous disease makes study design challenging. Our objective was to ascertain useful screening factors for identifying at-risk individuals for follow-up rheumatologic assessment or inclusion in prospective studies. METHODS We attempted to re-contact 3823 subjects with a family history of systemic lupus erythematosus, who did not meet American College of Rheumatology systemic lupus erythematosus classification at a baseline study visit; 436 agreed to follow-up participation an average of 6.3 years after baseline. In total, 56 of these individuals had transitioned to classified systemic lupus erythematosus (≥ 4 cumulative American College of Rheumatology criteria, verified by medical record review) by the time of follow up. Generalized estimating equations assessed associations between our dichotomous outcome of transitioning to systemic lupus erythematosus with baseline characteristics, including ANA positivity, Connective Tissue Disease Screening questionnaire systemic lupus erythematosus score, and number of American College of Rheumatology criteria. We analyzed predictive accuracy of characteristics on transitioning. RESULTS ANA positivity, Connective Tissue Disease Screening questionnaire systemic lupus erythematosus score categorization of possible or probable systemic lupus erythematosus, and greater number of American College of Rheumatology criteria at baseline were each associated with transitioning to systemic lupus erythematosus classification. Being ANA positive and having confirmed immunologic criteria at baseline had the highest positive predictive value and specificity for transitioning to systemic lupus erythematosus. American College of Rheumatology Connective Tissue Disease Screening questionnaire systemic lupus erythematosus score categorization of possible or probable systemic lupus erythematosus had a better positive predictive value, negative predictive value, sensitivity, and specificity than ANA positivity. CONCLUSION Given limited resources, identifying individuals for follow up based on the systemic lupus erythematosus portion of the Connective Tissue Disease Screening questionnaire could be an efficient way to identify family members at highest risk of disease transition.
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Affiliation(s)
- K A Young
- 1 Department of Epidemiology, Colorado School of Public Health, Aurora, United States of America
| | - M E Munroe
- 2 Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - J M Guthridge
- 2 Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - D L Kamen
- 3 Division of Rheumatology, Medical University of South Carolina, Charleston, United States of America
| | - G S Gilkensen
- 3 Division of Rheumatology, Medical University of South Carolina, Charleston, United States of America
| | - J B Harley
- 4 Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America.,5 US Department of Veterans Affairs Medical Center, Cincinnati, United States of America
| | - M H Weisman
- 6 Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - D R Karp
- 7 Division of Rheumatic Diseases, University of Texas Southwestern, Dallas, United States of America
| | - D J Wallace
- 6 Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - J A James
- 2 Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America.,8 Departments of Medicine and Pathology, Oklahoma University Health Sciences Center, Oklahoma City, United States of America
| | - J M Norris
- 1 Department of Epidemiology, Colorado School of Public Health, Aurora, United States of America
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Ghodke-Puranik Y, Imgruet M, Dorschner JM, Shrestha P, McCoy K, Kelly JA, Marion M, Guthridge JM, Langefeld CD, Harley JB, James JA, Sivils KL, Niewold TB. Novel genetic associations with interferon in systemic lupus erythematosus identified by replication and fine-mapping of trait-stratified genome-wide screen. Cytokine 2019; 132:154631. [PMID: 30685201 DOI: 10.1016/j.cyto.2018.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND/PURPOSE High serum interferon alpha (IFN-α) is an important heritable phenotype in systemic lupus erythematosus (SLE) which is involved in primary disease pathogenesis. High vs. low levels of IFN-α are associated with disease severity and account for some of the biological heterogeneity between SLE patients. The aim of the study was to replicate and fine-map previously detected genetic associations with serum IFN-α in SLE. METHODS We previously undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci identified in this screen were selected for follow up in a large independent cohort of 1370 SLE patients (703 European-ancestry, 432 African ancestry, and 235 Amerindian ancestry). Each ancestral background was analyzed separately, and ancestry-informative markers were used to control for ancestry and admixture. RESULTS We find a rare haplotype spanning the promoter region of EFNA5 that is strongly associated with serum IFN-α in both African-American and European-American SLE patients (OR = 3.0, p = 3.7 × 10-6). We also find SNPs in the PPM1H, PTPRM, and NRGN regions associated with IFN-α levels in European-American, Amerindian, and African-American SLE patients respectively. Many of these associations are within regulatory regions of the gene, suggesting an impact on transcription. CONCLUSION This study demonstrates the power of molecular sub-phenotypes to reveal genetic factors involved in complex autoimmune disease. The distinct associations observed in different ancestral backgrounds emphasize the heterogeneity of molecular pathogenesis in SLE.
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Affiliation(s)
- Yogita Ghodke-Puranik
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Molly Imgruet
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Kaci McCoy
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Miranda Marion
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Joel M Guthridge
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine and Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kathy L Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Timothy B Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA.
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49
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Martínez-Bueno M, Oparina N, Dozmorov MG, Marion MC, Comeau ME, Gilkeson G, Kamen D, Weisman M, Salmon J, McCune JW, Harley JB, Kimberly R, James JA, Merrill J, Montgomery C, Langefeld CD, Alarcón-Riquelme ME. Trans-Ethnic Mapping of BANK1 Identifies Two Independent SLE-Risk Linkage Groups Enriched for Co-Transcriptional Splicing Marks. Int J Mol Sci 2018; 19:ijms19082331. [PMID: 30096841 PMCID: PMC6121630 DOI: 10.3390/ijms19082331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 11/17/2022] Open
Abstract
BANK1 is a susceptibility gene for several systemic autoimmune diseases in several populations. Using the genome-wide association study (GWAS) data from Europeans (EUR) and African Americans (AA), we performed an extensive fine mapping of ankyrin repeats 1 (BANK1). To increase the SNP density, we used imputation followed by univariate and conditional analysis, combined with a haplotypic and expression quantitative trait locus (eQTL) analysis. The data from Europeans showed that the associated region was restricted to a minimal and dependent set of SNPs covering introns two and three, and exon two. In AA, the signal found in the Europeans was split into two independent effects. All of the major risk associated SNPs were eQTLs, and the risks were associated with an increased BANK1 gene expression. Functional annotation analysis revealed the enrichment of repressive B cell epigenomic marks (EZH2 and H3K27me3) and a strong enrichment of splice junctions. Furthermore, one eQTL located in intron two, rs13106926, was found within the binding site for RUNX3, a transcriptional activator. These results connect the local genome topography, chromatin structure, and the regulatory landscape of BANK1 with co-transcriptional splicing of exon two. Our data defines a minimal set of risk associated eQTLs predicted to be involved in the expression of BANK1 modulated through epigenetic regulation and splicing. These findings allow us to suggest that the increased expression of BANK1 will have an impact on B-cell mediated disease pathways.
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Affiliation(s)
- Manuel Martínez-Bueno
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain.
| | - Nina Oparina
- Unit of Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, 171 67 Solna, Sweden.
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Miranda C Marion
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Mary E Comeau
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Gary Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Diane Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Michael Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Jane Salmon
- Hospital for Special Surgery, New York, NY 10021, USA.
| | - Joseph W McCune
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, OH and US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229, USA.
| | - Robert Kimberly
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35205, USA.
| | - Judith A James
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Joan Merrill
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Courtney Montgomery
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| | - Marta E Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Government, PTS, 18016 Granada, Spain.
- Unit of Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, 171 67 Solna, Sweden.
- Arthritis and Clinical Immunology and Clinical Pharmacology Programs, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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50
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Patel ZH, Lu X, Miller D, Forney CR, Lee J, Lynch A, Schroeder C, Parks L, Magnusen AF, Chen X, Pujato M, Maddox A, Zoller EE, Namjou B, Brunner HI, Henrickson M, Huggins JL, Williams AH, Ziegler JT, Comeau ME, Marion MC, Glenn SB, Adler A, Shen N, Nath SK, Stevens AM, Freedman BI, Pons-Estel BA, Tsao BP, Jacob CO, Kamen DL, Brown EE, Gilkeson GS, Alarcón GS, Martin J, Reveille JD, Anaya JM, James JA, Sivils KL, Criswell LA, Vilá LM, Petri M, Scofield RH, Kimberly RP, Edberg JC, Ramsey-Goldman R, Bang SY, Lee HS, Bae SC, Boackle SA, Cunninghame Graham D, Vyse TJ, Merrill JT, Niewold TB, Ainsworth HC, Silverman ED, Weisman MH, Wallace DJ, Raj P, Guthridge JM, Gaffney PM, Kelly JA, Alarcón-Riquelme ME, Langefeld CD, Wakeland EK, Kaufman KM, Weirauch MT, Harley JB, Kottyan LC. A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Hum Mol Genet 2018; 27:2392-2404. [PMID: 29912393 PMCID: PMC6005081 DOI: 10.1093/hmg/ddy140] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/21/2018] [Accepted: 04/13/2018] [Indexed: 01/01/2023] Open
Abstract
Systemic lupus erythematosus (SLE or lupus) (OMIM: 152700) is a chronic autoimmune disease with debilitating inflammation that affects multiple organ systems. The STAT1-STAT4 locus is one of the first and most highly replicated genetic loci associated with lupus risk. We performed a fine-mapping study to identify plausible causal variants within the STAT1-STAT4 locus associated with increased lupus disease risk. Using complementary frequentist and Bayesian approaches in trans-ancestral Discovery and Replication cohorts, we found one variant whose association with lupus risk is supported across ancestries in both the Discovery and Replication cohorts: rs11889341. In B cell lines from patients with lupus and healthy controls, the lupus risk allele of rs11889341 was associated with increased STAT1 expression. We demonstrated that the transcription factor HMGA1, a member of the HMG transcription factor family with an AT-hook DNA-binding domain, has enriched binding to the risk allele compared with the non-risk allele of rs11889341. We identified a genotype-dependent repressive element in the DNA within the intron of STAT4 surrounding rs11889341. Consistent with expression quantitative trait locus (eQTL) analysis, the lupus risk allele of rs11889341 decreased the activity of this putative repressor. Altogether, we present a plausible molecular mechanism for increased lupus risk at the STAT1-STAT4 locus in which the risk allele of rs11889341, the most probable causal variant, leads to elevated STAT1 expression in B cells due to decreased repressor activity mediated by increased binding of HMGA1.
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Affiliation(s)
- Zubin H Patel
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaoming Lu
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmy R Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua Lee
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Arthur Lynch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Connor Schroeder
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lois Parks
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Albert F Magnusen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Avery Maddox
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erin E Zoller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Hermine I Brunner
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael Henrickson
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jennifer L Huggins
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Adrienne H Williams
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie T Ziegler
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Mary E Comeau
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Miranda C Marion
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Stuart B Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Nan Shen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, P.R. China
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Anne M Stevens
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | | | - Betty P Tsao
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Chaim O Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Elizabeth E Brown
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gary S Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada 18001-18016, Spain
| | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogota 111711, Colombia
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Lindsey A Criswell
- Department of Medicine, Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA 94143-0500, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- United States Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Deborah Cunninghame Graham
- Divisions of Genetics/Molecular Medicine and Immunology, King’s College London, Guy’s Hospital, London SE1 9RT, UK
| | - Timothy J Vyse
- Divisions of Genetics/Molecular Medicine and Immunology, King’s College London, Guy’s Hospital, London SE1 9RT, UK
| | - Joan T Merrill
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
| | - Timothy B Niewold
- Division of Rheumatology, Department of Pathology, New York University, New York, NY 10016, USA
| | - Hannah C Ainsworth
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Earl D Silverman
- Division of Rheumatology, The Hospital for Sick Children, Hospital for Sick Research Institute, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Daniel J Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Marta E Alarcón-Riquelme
- Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17167, Sweden
- Center for Genomics and Oncological Research, Pfizer-University of Granada-Junta de Andalucia, Parque Tecnológica de la Salud, Granada 18016, Spain
| | - Carl D Langefeld
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- United States Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- United States Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
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