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Carmichael OT, Singh M, Bashir A, Russell AM, Bolding M, Redden DT, Storrs J, Willoughby WR, Howard-Claudio C, Hsia DS, Kimberly RP, Gray ME, Ravussin E, Denney TS. Harmonized Multisite MRI-Based Quantification of Human Liver Fat and Stiffness: A Pilot Study. J Magn Reson Imaging 2024; 59:1070-1073. [PMID: 37246446 DOI: 10.1002/jmri.28790] [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: 09/29/2022] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is a leading cause of end-stage liver disease. NAFLD diagnosis and follow-up relies on a combination of clinical data, liver imaging, and/or liver biopsy. However, intersite imaging differences impede diagnostic consistency and reduce the repeatability of the multisite clinical trials necessary to develop effective treatments. PURPOSE/HYPOTHESIS The goal of this pilot study was to harmonize commercially available 3 T magnetic resonance imaging (MRI) measurements of liver fat and stiffness in human participants across academic sites and MRI vendors. STUDY TYPE Cohort. SUBJECTS Four community-dwelling adults with obesity. FIELD STRENGTH/SEQUENCE 1.5 and 3 T, multiecho 3D imaging, PRESS, and GRE. ASSESSMENT Harmonized proton density fat fraction (PDFF) and magnetic resonance spectroscopy (MRS) protocols were used to quantify the FF of synthetic phantoms and human participants with obesity using standard acquisition parameters at four sites that had four different 3 T MRI instruments. In addition, a harmonized magnetic resonance elastography (MRE) protocol was used to quantify liver stiffness among participants at two different sites at 1.5 and 3 T field strengths. Data were sent to a single data coordinating site for postprocessing. STATISTICAL TESTS Linear regression in MATLAB, ICC analyses using SAS 9.4, one-sided 95% confidence intervals for the ICC. RESULTS PDFF and MRS FF measurements were highly repeatable among sites in both humans and phantoms. MRE measurements of liver stiffness in three individuals at two sites using one 1.5 T and one 3 T instrument showed repeatability that was high although lower than that of MRS and PDFF. CONCLUSIONS We demonstrated harmonization of PDFF, MRS, and MRE-based quantification of liver fat and stiffness through synthetic phantoms, traveling participants, and standardization of postprocessing analysis. Multisite MRI harmonization could contribute to multisite clinical trials assessing the efficacy of interventions and therapy for NAFLD. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY STAGE: 2.
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Affiliation(s)
- Owen T Carmichael
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, 70808, USA
| | - Maninder Singh
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, 70808, USA
| | - Adil Bashir
- Auburn University, Samuel Ginn College of Engineering, Auburn, Alabama, 36849, USA
| | - Anne M Russell
- The University of Alabama, Birmingham, Alabama, 35294, USA
| | - Mark Bolding
- The University of Alabama, Birmingham, Alabama, 35294, USA
- The University of Alabama Medical Center, Birmingham, Alabama, 35233, USA
| | - David T Redden
- The University of Alabama, Birmingham, Alabama, 35294, USA
- School of Public Health, The University of Alabama, Birmingham, Alabama, 35233, USA
| | - Judd Storrs
- The University of Mississippi Medical Center, Jackson, Mississippi, 39216, USA
| | - William R Willoughby
- The University of Alabama, Birmingham, Alabama, 35294, USA
- The University of Alabama Medical Center, Birmingham, Alabama, 35233, USA
| | | | - Daniel S Hsia
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, 70808, USA
| | - Robert P Kimberly
- The University of Alabama, Birmingham, Alabama, 35294, USA
- School of Medicine, The University of Alabama, Birmingham, Alabama, 35233, USA
| | - Meagan E Gray
- The University of Alabama, Birmingham, Alabama, 35294, USA
- School of Medicine, The University of Alabama, Birmingham, Alabama, 35233, USA
- The University of Alabama Hospital, Birmingham, Alabama, 35205, USA
| | - Eric Ravussin
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, 70808, USA
- The University of Alabama, Birmingham, Alabama, 35294, USA
| | - Thomas S Denney
- Auburn University, Samuel Ginn College of Engineering, Auburn, Alabama, 36849, USA
- The University of Alabama, Birmingham, Alabama, 35294, USA
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2
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Hurst C, Leeth TR, Benveniste EN, Kimberly RP, Hoesley C, Mack L, Fouad MN, Rogers DA, Vickers SM, Agarwal A. The Pittman Scholar Program for junior faculty recognition at the University of Alabama at Birmingham Heersink School of Medicine. Med Educ Online 2023; 28:2182188. [PMID: 36861296 PMCID: PMC9987741 DOI: 10.1080/10872981.2023.2182188] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/08/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The University of Alabama at Birmingham Heersink School of Medicine established the Pittman Scholars Program in 2015 to elevate scientific impact and to support the recruitment and retention of highly competitive junior faculty. The authors examined the impact of this program on research productivity and on faculty retention. The authors evaluated publications and extramural grant awards and available demographic data for the Pittman Scholars compared to all junior faculty in the Heersink School of Medicine. From 2015 to 2021, the program awarded a diverse group of 41 junior faculty members across the institution. For this cohort, ninety-four new extramural grants were awarded and 146 grant applications were submitted since the inception of the scholar award. Pittman Scholars published a total of 411 papers during the term of the award. The faculty retention rate of the scholars was 95%, comparable to that of all Heersink junior faculty, with 2 recipients being recruited to other institutions. The implementation of the Pittman Scholars Program has been an effective strategy to celebrate scientific impact and acknowledge junior faculty members as outstanding scientists at our institution. The Pittman Scholars award allows junior faculty to use funds for their research program, publications, collaborations, and career advancement. The Pittman Scholars are recognized at local, regional, and national levels for the work they are contributing to academic medicine. The program has served as an important pipeline faculty development program and an avenue for individual recognition for research-intensive faculty.
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Affiliation(s)
- Cayla Hurst
- Administrative Fellow, UAB Academic Medicine and Ambulatory Operations, Birmingham, AL, USA
| | - Toni R. Leeth
- Strategic Planning and Administration for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Etty N. Benveniste
- Research for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert P. Kimberly
- Clinical and Translational Research for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Craig Hoesley
- Medical Education for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - LaKisha Mack
- Administration and Finance for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mona N. Fouad
- Diversity and Inclusion for the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - David A. Rogers
- Wellness Officer for UAB Medicine and the Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Selwyn M. Vickers
- Medicine and Dean of the Heersink School of Medicine and Chief Executive Officer of the UAB Health System, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anupam Agarwal
- The Heersink School of Medicine, the University of Alabama at Birmingham, Birmingham, AL, USA
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3
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Karkanitsa M, Li Y, Valenti S, Spathies J, Kelly S, Hunsberger S, Yee L, Croker JA, Wang J, Alfonso AL, Faust M, Mehalko J, Drew M, Denson JP, Putman Z, Fathi P, Ngo TB, Siripong N, Baus HA, Petersen B, Ford EW, Sundaresan V, Josyula A, Han A, Giurgea LT, Rosas LA, Bean R, Athota R, Czajkowski L, Klumpp-Thomas C, Cervantes-Medina A, Gouzoulis M, Reed S, Graubard B, Hall MD, Kalish H, Esposito D, Kimberly RP, Reis S, Sadtler K, Memoli MJ. Dynamics of SARS-CoV-2 Seroprevalence in a Large US population Over a Period of 12 Months. medRxiv 2023:2023.10.20.23297329. [PMID: 37904956 PMCID: PMC10614993 DOI: 10.1101/2023.10.20.23297329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Due to a combination of asymptomatic or undiagnosed infections, the proportion of the United States population infected with SARS-CoV-2 was unclear from the beginning of the pandemic. We previously established a platform to screen for SARS-CoV-2 positivity across a representative proportion of the US population, from which we reported that almost 17 million Americans were estimated to have had undocumented infections in the Spring of 2020. Since then, vaccine rollout and prevalence of different SARS-CoV-2 variants have further altered seropositivity trends within the United States population. To explore the longitudinal impacts of the pandemic and vaccine responses on seropositivity, we re-enrolled participants from our baseline study in a 6- and 12- month follow-up study to develop a longitudinal antibody profile capable of representing seropositivity within the United States during a critical period just prior to and during the initiation of vaccine rollout. Initial measurements showed that, since July 2020, seropositivity elevated within this population from 4.8% at baseline to 36.2% and 89.3% at 6 and 12 months, respectively. We also evaluated nucleocapsid seropositivity and compared to spike seropositivity to identify trends in infection versus vaccination relative to baseline. These data serve as a window into a critical timeframe within the COVID-19 pandemic response and serve as a resource that could be used in subsequent respiratory illness outbreaks.
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Affiliation(s)
- Maria Karkanitsa
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Yan Li
- Joint Program in Survey Methodology, Department of Epidemiology and Biostatistics, University of Maryland College Park, College Park, MD 20742
| | - Shannon Valenti
- Clinical and Translational Science Institute (CTSI), University of Pittsburgh, Pittsburgh, PA 15213
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science (BEPS), NIBIB, NIH, Bethesda MD 20894
| | - Sophie Kelly
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science (BEPS), NIBIB, NIH, Bethesda MD 20894
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20894
| | - Laura Yee
- Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), NIH, MD 20894
| | - Jennifer A. Croker
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jing Wang
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Andrea Lucia Alfonso
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Mondreakest Faust
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Jennifer Mehalko
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Matthew Drew
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - John-Paul Denson
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Zoe Putman
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Parinaz Fathi
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Tran B. Ngo
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Nalyn Siripong
- Clinical and Translational Science Institute (CTSI), University of Pittsburgh, Pittsburgh, PA 15213
| | - Holly Ann Baus
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda MD 20894
| | - Brian Petersen
- Clinical and Translational Science Institute (CTSI), University of Pittsburgh, Pittsburgh, PA 15213
| | - Eric W. Ford
- Department of Health Care Organization, and Policy, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vanathi Sundaresan
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Aditya Josyula
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Alison Han
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Luca T. Giurgea
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Luz Angela Rosas
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Rachel Bean
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Rani Athota
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Lindsay Czajkowski
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD 20850
| | | | - Monica Gouzoulis
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Susan Reed
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
| | - Barry Graubard
- Division of Cancer Epidemiology & Genetics, Biostatistics Branch, NCI, NIH, Bethesda, MD 20894
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD 20850
| | - Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science (BEPS), NIBIB, NIH, Bethesda MD 20894
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702
| | - Robert P. Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven Reis
- Clinical and Translational Science Institute (CTSI), University of Pittsburgh, Pittsburgh, PA 15213
| | - Kaitlyn Sadtler
- Section on Immunoengineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda MD 20894
| | - Matthew J Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20894
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4
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Harris PA, Dunsmore SE, Atkinson JC, Benjamin DK, Bernard GR, Dean JM, Dwyer JP, Ford DF, Selker HP, Waddy SP, Wiley KL, Wilkins CH, Cook SK, Burr JS, Edwards TL, Huvane J, Kennedy N, Lane K, Majkowski R, Nelson S, Palm ME, Stroud M, Thompson DD, Busacca L, Elkind MSV, Kimberly RP, Reilly MP, Hanley DF. Leveraging the Expertise of the CTSA Program to Increase the Impact and Efficiency of Clinical Trials. JAMA Netw Open 2023; 6:e2336470. [PMID: 37796498 PMCID: PMC10773966 DOI: 10.1001/jamanetworkopen.2023.36470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Importance Multicenter clinical trials play a critical role in the translational processes that enable new treatments to reach all people and improve public health. However, conducting multicenter randomized clinical trials (mRCT) presents challenges. The Trial Innovation Network (TIN), established in 2016 to partner with the Clinical and Translational Science Award (CTSA) Consortium of academic medical institutions in the implementation of mRCTs, consists of 3 Trial Innovation Centers (TICs) and 1 Recruitment Innovation Center (RIC). This unique partnership has aimed to address critical roadblocks that impede the design and conduct of mRCTs, in expectation of accelerating the translation of novel interventions to clinical practice. The TIN's challenges and achievements are described in this article, along with examples of innovative resources and processes that may serve as useful models for other clinical trial networks providing operational and recruitment support. Observations The TIN has successfully integrated more than 60 CTSA institution program hubs into a functional network for mRCT implementation and optimization. A unique support system for investigators has been created that includes the development and deployment of novel tools, operational and recruitment services, consultation models, and rapid communication pathways designed to reduce delays in trial start-up, enhance recruitment, improve engagement of diverse research participants and communities, and streamline processes that improve the quality, efficiency, and conduct of mRCTs. These resources and processes span the clinical trial spectrum and enable the TICs and RIC to serve as coordinating centers, data centers, and recruitment specialists to assist trials across the National Institutes of Health and other agencies. The TIN's impact has been demonstrated through its response to both historical operational challenges and emerging public health emergencies, including the national opioid public health crisis and the COVID-19 pandemic. Conclusions and Relevance The TIN has worked to reduce barriers to implementing mRCTs and to improve mRCT processes and operations by providing needed clinical trial infrastructure and resources to CTSA investigators. These resources have been instrumental in more quickly and efficiently translating research discoveries into beneficial patient treatments.
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Affiliation(s)
- Paul A Harris
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sarah E Dunsmore
- National Center for Advancing Translational Sciences, Bethesda, Maryland
| | - Jane C Atkinson
- National Center for Advancing Translational Sciences, Bethesda, Maryland
| | - Daniel Kelly Benjamin
- Duke University School of Medicine, Durham, North Carolina
- Duke Clinical Research Institute, Durham, North Carolina
| | - Gordon R Bernard
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Jamie P Dwyer
- University of Utah Health, Salt Lake City
- Utah Clinical and Translational Sciences Institute, Salt Lake City
| | - Daniel F Ford
- Johns Hopkins Institute for Clinical and Translational Research, Baltimore, Maryland
| | - Harry P Selker
- Department of Medicine, Tufts University, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Salina P Waddy
- National Center for Advancing Translational Sciences, Bethesda, Maryland
| | - Kenneth L Wiley
- National Center for Advancing Translational Sciences, Bethesda, Maryland
| | - Consuelo H Wilkins
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee
| | - Sarah K Cook
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
| | | | - Terri L Edwards
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
| | | | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
| | - Karen Lane
- Johns Hopkins Institute for Clinical and Translational Research, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ryan Majkowski
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah Nelson
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
| | - Marisha E Palm
- Department of Medicine, Tufts University, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Mary Stroud
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee
| | - Dixie D Thompson
- University of Utah Health, Salt Lake City
- Utah Clinical and Translational Sciences Institute, Salt Lake City
| | - Linda Busacca
- Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York
| | - Mitchell S V Elkind
- Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham
| | - Muredach P Reilly
- Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York
| | - Daniel F Hanley
- Johns Hopkins Institute for Clinical and Translational Research, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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5
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Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet 2022; 54:1640-1651. [PMID: 36333501 PMCID: PMC10165422 DOI: 10.1038/s41588-022-01213-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 12/01/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chun Lai Too
- Immunogenetics Unit, Allergy and Immunology Research Center, Institute for Medical Research, National Institutes of Health Complex, Ministry of Health, Kuala Lumpur, Malaysia
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vincent A Laufer
- Department of Clinical Immunology and Rheumatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Ian C Scott
- Haywood Academic Rheumatology Centre, Haywood Hospital, Midlands Partnership NHS Foundation Trust, Burslem, UK
- Primary Care Centre Versus Arthritis, School of Medicine, Keele University, Keele, UK
| | - Sebastien Viatte
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Murasawa
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Mohammed Hammoudeh
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Samar Al Emadi
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Basel K Masri
- Department of Internal Medicine, Jordan Hospital, Amman, Jordan
| | - Hussein Halabi
- Section of Rheumatology, Department of Internal Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical Center, Emirates Hospital, Dubai, United Arab Emirates
| | - Imad W Uthman
- Department of Rheumatology, American University of Beirut, Beirut, Lebanon
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | | | - Suguru Honda
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Eiichi Tanaka
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Jinyi Zhang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center (ARC), Reade, Amsterdam, the Netherlands
| | - Irene van der Horst-Bruinsma
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Niek de Vries
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location AMC/University of Amsterdam, Amsterdam, the Netherlands
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Robert P Kimberly
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, Assistance Pubique - Hôpitaux de Paris, Hôpital Bicêtre, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Tom Huizinga
- Leiden University Medical Center, Leiden, the Netherlands
| | - Philippe Dieudé
- University of Paris Cité, Inserm, PHERE, F-75018, Paris, France
- Department of Rheumatology, Hôpital Bichat, APHP, Paris, France
| | - Matthias Schneider
- Department of Rheumatology & Hiller Research Unit Rheumatology, UKD, Heinrich-Heine University, Düsseldorf, Germany
| | - Martin Kerick
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- All of Us Research Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - 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, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Matthew Traylor
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
- School of Clinical Medicine Tsinghua University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Thurayya Arayssi
- Department of Internal Medicine, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Orthopedic Surgery, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
- Division of Multidisciplinary Management of Rheumatic Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayoshi Harigai
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Weill Cornell Medicine, New York, NY, USA
| | - Leonid Padyukov
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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6
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Vickers SM, Agarwal A, Patel N, Benveniste EN, Bulgarella D, Fouad MN, Hoesley C, Jones K, Kimberly RP, Rogers DA, Larson JA, Leeth TR, Mack L, Dorman P, Furgerson T, Longshore J, Watts RL. Returning to Growth: One Academic Medical Center's Successful Five-Step Approach to Change Management. Acad Med 2021; 96:1401-1407. [PMID: 33830950 DOI: 10.1097/acm.0000000000004116] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The University of Alabama at Birmingham academic medical center (UAB AMC) had achieved great success and growth during the 50 years since its founding. However, the challenging and more competitive environment of the 2000s left the UAB AMC on a downward trajectory. The UAB AMC had to overcome difficult internal cultural and structural barriers that stood in the way of the transformational change needed to remain competitive. Competition rather than collaborative and strategic financial investment were the primary cultural barriers for the UAB AMC, while people were the primary structural barrier. Leadership identified 5 steps that were critical for the transformation that occurred between 2013 and 2018: alignment of leadership; creating a compelling and credible shared vision; identifying cultural and structural barriers; creating a thoughtful, data-driven intervention; and improved communication and accountability. Following these steps enabled the UAB AMC to transform its institutional structure and culture. As a result, the UAB AMC thrived, returning to substantial growth in research and clinical care. UAB AMC School of Medicine grew by $100 million in National Institutes of Health funding and moved up 10 spots in ranking. In 2018, UAB Hospital had 10 specialties ranked by U.S. News & World Report, 7 more than in 2013. This article outlines the approach taken and provides a conceptual framework for other AMCs eager to transform their structure and culture and position themselves for growth.
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Affiliation(s)
- Selwyn M Vickers
- S.M. Vickers is senior vice president for medicine and dean, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Anupam Agarwal
- A. Agarwal is executive vice dean, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama; ORCID: https://orcid.org/0000-0003-4276-5186
| | - Nisha Patel
- N. Patel is executive director of operations, wellness, and administration, Dean's Office, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Etty N Benveniste
- E.N. Benveniste is senior vice dean for research, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Dawn Bulgarella
- D. Bulgarella is chief financial officer, UAB Health System, Birmingham, Alabama
| | - Mona N Fouad
- M.N. Fouad is senior associate dean for diversity and inclusion, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Craig Hoesley
- C. Hoesley is senior associate dean for medical education, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama; ORCID: https://orcid.org/0000-0003-2654-9141
| | - Keith Jones
- K. Jones is senior associate dean for clinical affairs, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Robert P Kimberly
- R.P. Kimberly is senior associate dean for clinical and translational research, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - David A Rogers
- D.A. Rogers is senior associate dean for faculty affairs and professional development, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Jean Ann Larson
- J.A. Larson is senior associate dean for leadership development, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Toni R Leeth
- T.R. Leeth is associate dean for strategic planning and administration, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - LaKisha Mack
- L. Mack is senior associate dean for administration and finance, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Paige Dorman
- P. Dorman is executive director of communications, Dean's Office, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Tyler Furgerson
- T. Furgerson is web communications specialist, Dean's Office, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Jane Longshore
- J. Longshore is managing editor, Dean's Office, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Ray L Watts
- R.L. Watts is president, University of Alabama at Birmingham, Birmingham, Alabama
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7
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Zhang Y, Li X, Gibson A, Edberg J, Kimberly RP, Absher DM. Skewed allelic expression on X chromosome associated with aberrant expression of XIST on systemic lupus erythematosus lymphocytes. Hum Mol Genet 2021; 29:2523-2534. [PMID: 32628254 DOI: 10.1093/hmg/ddaa131] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/27/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
A common feature of autoimmune diseases, including systemic lupus erythematosus (SLE), is an increased prevalence in women. However, the molecular basis for sex disparity in SLE remains poorly understood. To examine the role of X-linked transcription in SLE adaptive immune cells, we performed RNA-seq in T cell and B cell subsets from either healthy donors or patients with SLE. Analyses of allelic expression (AE) profiles identified a pattern of increased allelic imbalance across the entire X chromosome in SLE lymphocytes. X-linked genes exhibiting AE in SLE had an extensive overlap with genes known to escape X chromosome inactivation (XCI). XIST RNA was overexpressed in SLE patients. Differential XIST expression correlated with AE profiles more positively at X-linked genes than the genome-wide background. Analysis of three independent RNA-seq data verified the XIST-associated skewed AE on X chromosome in SLE. Integrative analyses of DNA methylation profiles showed an increased variability of DNA methylation levels at these AE-related X-linked genes. In cultured lymphoblastic cells, knockdown of XIST specifically altered allelic imbalance patterns between X chromosomes. Our study provides genetic evidence that upregulation of XIST accompanied with more skewed allelic expression on X chromosome is associated with the pathogenesis of SLE and may provide mechanistic insights into the increased incidence of SLE in females.
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Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Xinrui Li
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Andrew Gibson
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeffrey Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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8
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Kalish H, Klumpp-Thomas C, Hunsberger S, Baus HA, Fay MP, Siripong N, Wang J, Hicks J, Mehalko J, Travers J, Drew M, Pauly K, Spathies J, Ngo T, Adusei KM, Karkanitsa M, Croker JA, Li Y, Graubard BI, Czajkowski L, Belliveau O, Chairez C, Snead KR, Frank P, Shunmugavel A, Han A, Giurgea LT, Rosas LA, Bean R, Athota R, Cervantes-Medina A, Gouzoulis M, Heffelfinger B, Valenti S, Caldararo R, Kolberg MM, Kelly A, Simon R, Shafiq S, Wall V, Reed S, Ford EW, Lokwani R, Denson JP, Messing S, Michael SG, Gillette W, Kimberly RP, Reis SE, Hall MD, Esposito D, Memoli MJ, Sadtler K. Undiagnosed SARS-CoV-2 seropositivity during the first 6 months of the COVID-19 pandemic in the United States. Sci Transl Med 2021; 13:eabh3826. [PMID: 34158410 PMCID: PMC8432952 DOI: 10.1126/scitranslmed.abh3826] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [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: 03/04/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022]
Abstract
Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the U.S. population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. Most blood samples (88.7%) were collected between 10 May and 31 July 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI, 2.6 to 6.5%), with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%. The highest seropositivity estimates were in African American participants; younger, female, and Hispanic participants; and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.
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Affiliation(s)
- Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Holly Ann Baus
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Nalyn Siripong
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jing Wang
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kyle Pauly
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tran Ngo
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kenneth M Adusei
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Maria Karkanitsa
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jennifer A Croker
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yan Li
- Joint Program in Survey Methodology, Department of Epidemiology and Biostatistics, University of Maryland College Park, College Park, MD 20742, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, Biostatistics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lindsay Czajkowski
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olivia Belliveau
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Cheryl Chairez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kelly R Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Alison Han
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Luca T Giurgea
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Luz Angela Rosas
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rachel Bean
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rani Athota
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Adriana Cervantes-Medina
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Monica Gouzoulis
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Brittany Heffelfinger
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shannon Valenti
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rocco Caldararo
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Michelle M Kolberg
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Andrew Kelly
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Reid Simon
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Saifullah Shafiq
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Susan Reed
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric W Ford
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ravi Lokwani
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sam G Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert P Kimberly
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven E Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Memoli
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA.
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9
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Robertson CC, Inshaw JRJ, Onengut-Gumuscu S, Chen WM, Santa Cruz DF, Yang H, Cutler AJ, Crouch DJM, Farber E, Bridges SL, Edberg JC, Kimberly RP, Buckner JH, Deloukas P, Divers J, Dabelea D, Lawrence JM, Marcovina S, Shah AS, Greenbaum CJ, Atkinson MA, Gregersen PK, Oksenberg JR, Pociot F, Rewers MJ, Steck AK, Dunger DB, Wicker LS, Concannon P, Todd JA, Rich SS. Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes. Nat Genet 2021; 53:962-971. [PMID: 34127860 PMCID: PMC8273124 DOI: 10.1038/s41588-021-00880-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [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: 06/19/2020] [Accepted: 05/05/2021] [Indexed: 12/13/2022]
Abstract
We report the largest and most diverse genetic study of type 1 diabetes (T1D) to date (61,427 participants), yielding 78 genome-wide-significant (P < 5 × 10-8) regions, including 36 that are new. We define credible sets of T1D-associated variants and show that they are enriched in immune-cell accessible chromatin, particularly CD4+ effector T cells. Using chromatin-accessibility profiling of CD4+ T cells from 115 individuals, we map chromatin-accessibility quantitative trait loci and identify five regions where T1D risk variants co-localize with chromatin-accessibility quantitative trait loci. We highlight rs72928038 in BACH2 as a candidate causal T1D variant leading to decreased enhancer accessibility and BACH2 expression in T cells. Finally, we prioritize potential drug targets by integrating genetic evidence, functional genomic maps and immune protein-protein interactions, identifying 12 genes implicated in T1D that have been targeted in clinical trials for autoimmune diseases. These findings provide an expanded genomic landscape for T1D.
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Affiliation(s)
- Catherine C Robertson
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jamie R J Inshaw
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - David Flores Santa Cruz
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Hanzhi Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Antony J Cutler
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Daniel J M Crouch
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - S Louis Bridges
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jane H Buckner
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jasmin Divers
- Division of Health Services Research, Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, USA
| | - Dana Dabelea
- Colorado School of Public Health and Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jean M Lawrence
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Santica Marcovina
- Northwest Lipid Metabolism and Diabetes Research Laboratories, University of Washington, Seattle, WA, USA
- Medpace Reference Laboratories, Cincinnati, OH, USA
| | - Amy S Shah
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati, Cincinnati, OH, USA
| | - Carla J Greenbaum
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
- Diabetes Program, Benaroya Research Institute, Seattle, WA, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jorge R Oksenberg
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA
| | - Flemming Pociot
- Department of Pediatrics, Herlev University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Type 1 Diabetes Biology, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea K Steck
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David B Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Wellcome Trust Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Linda S Wicker
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Patrick Concannon
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
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10
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Coller BS, Buse JB, Kimberly RP, Powderly WG, Zand MS. Re-engineering The Clinical Research Enterprise in Response to COVID-19: The Clinical Translational Science Award (CTSA) experience and proposed playbook for future pandemics. J Clin Transl Sci 2021; 5:e96. [PMID: 34192053 PMCID: PMC8137226 DOI: 10.1017/cts.2021.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/18/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
The 2020 COVID-19 pandemic has had a profound impact on the clinical research enterprises at the 60 Clinical and Translational Science Award (CTSA) Hubs throughout the nation. There was simultaneously a need to expand research to obtain crucial data about disease prognosis and therapy and enormous limitations on conducting research as localities and institutions limited travel and person-to-person contact. These imperatives resulted in major changes in the way research was conducted, including expediting Institutional Review Board review, shifting to remote interactions with participants, centralizing decision-making in prioritizing research protocols, establishing biobanks, adopting novel informatics platforms, and distributing study drugs in unconventional ways. National CTSA Steering Committee meetings provided an opportunity to share best practices and develop the idea of capturing the CTSA program experiences in a series of papers. Here we bring together the recommendations from those papers in a list of specific actions that research sites can take to strengthen operations and prepare for similar future public health emergencies. Most importantly, creative innovations developed in response to the COVID-19 pandemic deserve serious consideration for adoption as new standards, thus converting the painful trauma of the pandemic into "post-traumatic growth" that makes the clinical research enterprise stronger, more resilient, and more effective.
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Affiliation(s)
- Barry S. Coller
- Allen and Frances Adler Laboratory of Vascular Biology, Rockefeller University, New York, NY, USA
| | - John B. Buse
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William G. Powderly
- Division of Infectious Diseases and Institute for Public Health, Washington University in St. Louis, St. Louis, MO, USA
| | - Martin S. Zand
- Department of Medicine, University of Rochester Medical Center, Department of Medicine, Nephrology, Rochester, NY, USA
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11
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Croker JA, Patel R, Campbell KS, Barton-Baxter M, Wallet S, Firestein GS, Kimberly RP, Elemento O. Building biorepositories in the midst of a pandemic. J Clin Transl Sci 2021; 5:e92. [PMID: 34192049 PMCID: PMC8134891 DOI: 10.1017/cts.2021.6] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/07/2022] Open
Abstract
Biospecimen repositories play a vital role in enabling investigation of biologic mechanisms, identification of disease-related biomarkers, advances in diagnostic assays, recognition of microbial evolution, and characterization of new therapeutic targets for intervention. They rely on the complex integration of scientific need, regulatory oversight, quality control in collection, processing and tracking, and linkage to robust phenotype information. The COVID-19 pandemic amplified many of these considerations and illuminated new challenges, all while academic health centers were trying to adapt to unprecedented clinical demands and heightened research constraints not witnessed in over 100 years. The outbreak demanded rapid understanding of SARS-CoV-2 to develop diagnostics and therapeutics, prompting the immediate need for access to high quality, well-characterized COVID-19-associated biospecimens. We surveyed 60 Clinical and Translational Science Award (CTSA) hubs to better understand the strategies and barriers encountered in biobanking before and in response to the COVID-19 pandemic. Feedback revealed a major shift in biorepository model, specimen-acquisition and consent process from a combination of investigator-initiated and institutional protocols to an enterprise-serving strategy. CTSA hubs were well equipped to leverage established capacities and expertise to quickly respond to the scientific needs of this crisis through support of institutional approaches in biorepository management.
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Affiliation(s)
- Jennifer A. Croker
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robin Patel
- Division of Clinical Microbiology, Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Kenneth S. Campbell
- Center for Clinical and Translational Science, University of Kentucky, Lexington, KY, USA
| | - Marietta Barton-Baxter
- Center for Clinical and Translational Science, University of Kentucky, Lexington, KY, USA
| | - Shannon Wallet
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Gary S. Firestein
- Altman Clinical & Translational Science Institute, University of California San Diego, San Diego, CA, USA
| | - Robert P. Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olivier Elemento
- Clinical & Translational Science Center, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
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12
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Kalish H, Klumpp-Thomas C, Hunsberger S, Baus HA, Fay MP, Siripong N, Wang J, Hicks J, Mehalko J, Travers J, Drew M, Pauly K, Spathies J, Ngo T, Adusei KM, Karkanitsa M, Croker JA, Li Y, Graubard BI, Czajkowski L, Belliveau O, Chairez C, Snead K, Frank P, Shunmugavel A, Han A, Giurgea LT, Rosas LA, Bean R, Athota R, Cervantes-Medina A, Gouzoulis M, Heffelfinger B, Valenti S, Caldararo R, Kolberg MM, Kelly A, Simon R, Shafiq S, Wall V, Reed S, Ford EW, Lokwani R, Denson JP, Messing S, Michael SG, Gillette W, Kimberly RP, Reis SE, Hall MD, Esposito D, Memoli MJ, Sadtler K. Mapping a Pandemic: SARS-CoV-2 Seropositivity in the United States. medRxiv 2021:2021.01.27.21250570. [PMID: 33532807 PMCID: PMC7852277 DOI: 10.1101/2021.01.27.21250570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population (n = 11,382) and who had not previously been diagnosed with COVID-19 were selected by quota sampling from 241,424 volunteers (ClinicalTrials.gov NCT04334954). Enrolled participants provided medical, geographic, demographic, and socioeconomic information and 9,028 blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. Samples were analyzed via ELISA for anti-Spike and anti-RBD antibodies. Estimation of seroprevalence was performed by using a weighted analysis to reflect the US population. We detected an undiagnosed seropositivity rate of 4.6% (95% CI: 2.6 - 6.5%). There was distinct regional variability, with heightened seropositivity in locations of early outbreaks. Subgroup analysis demonstrated that the highest estimated undiagnosed seropositivity within groups was detected in younger participants (ages 18-45, 5.9%), females (5.5%), Black/African American (14.2%), Hispanic (6.1%), and Urban residents (5.3%), and lower undiagnosed seropositivity in those with chronic diseases. During the first wave of infection over the spring/summer of 2020 an estimate of 4.6% of adults had a prior undiagnosed SARS-CoV-2 infection. These data indicate that there were 4.8 (95% CI: 2.8-6.8) undiagnosed cases for every diagnosed case of COVID-19 during this same time period in the United States, and an estimated 16.8 million undiagnosed cases by mid-July 2020.
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Affiliation(s)
- Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Holly Ann Baus
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Nalyn Siripong
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jing Wang
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Kyle Pauly
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Tran Ngo
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Kenneth M. Adusei
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Maria Karkanitsa
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jennifer A Croker
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Yan Li
- Joint Program in Survey Methodology, Department of Epidemiology and Biostatistics, University of Maryland College Park, College Park, MD 20742
| | - Barry I. Graubard
- Division of Cancer Epidemiology & Genetics, Biostatistics Branch, National Cancer Institute, National Institutes of Health, Bethesda MD 20894
| | - Lindsay Czajkowski
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Olivia Belliveau
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Cheryl Chairez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Alison Han
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Luca T. Giurgea
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Luz Angela Rosas
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Rachel Bean
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Rani Athota
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Adriana Cervantes-Medina
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Monica Gouzoulis
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Brittany Heffelfinger
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Shannon Valenti
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rocco Caldararo
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick MD 21702
| | - Michelle M. Kolberg
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Andrew Kelly
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Reid Simon
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Saifullah Shafiq
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Susan Reed
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Eric W Ford
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ravi Lokwani
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Sam G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Robert P. Kimberly
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Steven E. Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Matthew J. Memoli
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
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13
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Xu P, Kennell T, Gao M, Kimberly RP, Chong Z. MRLR: unraveling high-resolution meiotic recombination by linked reads. Bioinformatics 2020; 36:10-16. [PMID: 31214684 PMCID: PMC6956785 DOI: 10.1093/bioinformatics/btz503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/30/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Meiotic recombination facilitates the transmission of exchanged genetic material between homologous chromosomes and plays a crucial role in increasing the genetic variations in eukaryotic organisms. In humans, thousands of crossover events have been identified by genotyping related family members. However, most of these crossover regions span tens to hundreds of kb, which is not sufficient resolution to accurately identify the crossover breakpoints in a typical trio family. RESULTS We have developed MRLR, a software using 10X linked reads to identify crossover events at a high resolution. By reconstructing the gamete genome, MRLR only requires a trio family dataset and can efficiently discover the crossover events. Using MRLR, we revealed a fine-scale pattern of crossover regions in six human families. From the two closest heterozygous alleles around the crossovers, we determined that MRLR achieved a median resolution 4.5 kb. This method can delineate a genome-wide landscape of crossover events at a precise scale, which is important for both functional and genomic features analysis of meiotic recombination. AVAILABILITY AND IMPLEMENTATION MRLR is freely available at https://github.com/ChongLab/MRLR, implemented in Perl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peng Xu
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Timothy Kennell
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Min Gao
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Robert P Kimberly
- Department of Medicine, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zechen Chong
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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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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15
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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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16
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Breitbach ME, Ramaker RC, Roberts K, Kimberly RP, Absher D. Population-Specific Patterns of Epigenetic Defects in the B Cell Lineage in Patients With Systemic Lupus Erythematosus. Arthritis Rheumatol 2019; 72:282-291. [PMID: 31430064 DOI: 10.1002/art.41083] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine the stage of B cell development at which a systemic lupus erythematosus (SLE)-associated DNA methylation signature originates in African American (AA) and European American (EA) subjects, and to assess whether epigenetic defects in B cell development patterns could be predictive of SLE status in individual and mixed immune cell populations. METHODS B cells from AA patients (n = 31) and EA patients (n = 49) with or without SLE were sorted using fluorescence-activated cell sorting into 5 B cell subsets. DNA methylation, measured at ~460,000 CpG sites, was interrogated in each subset. Enrichment analysis of transcription factor interaction at SLE-associated methylation sites was performed. A random forests algorithm was used to identify an epigenetic signature of SLE in the B cell subsets, which was then validated in an independent cohort of AA and EA patients and healthy controls. RESULTS Regression analysis across all B cell stages resulted in identification of 60 CpGs that reached genome-wide significance for SLE-associated methylation differences (P ≤ 1.07 × 10-7 ). Interrogation of ethnicity-specific CpGs associated with SLE revealed a hypomethylated pattern that was enriched for interferon (IFN)-regulated genes and binding of EBF1 in AA patients (each P < 0.001). AA patients with SLE could be distinguished from healthy controls when the predictive model developed with the transitional B cell subset was applied to other B cell subsets (mean receiver operating characteristic [ROC] area under the curve [AUC] 0.98), and when applied to CD19+ pan-B cells (mean ROC AUC 0.95) and CD4+ pan-T cells (mean ROC AUC 0.97) from the independent validation cohort. CONCLUSION These results indicate that SLE-specific methylation patterns are ethnicity dependent. A pattern of epigenetic changes near IFN-regulated genes early in B cell development is a hallmark of SLE in AA female subjects. EBF1 binding sites are highly enriched for significant methylation changes, implying that this may be a potential regulator of SLE-associated epigenetic changes.
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Affiliation(s)
- Megan E Breitbach
- University of Alabama at Huntsville and HudsonAlpha Institute for Biotechnology
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, and University of Alabama at Birmingham
| | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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17
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Kimberly RP. Translational Research-For the Individual and the Community. J Health Care Poor Underserved 2019; 30:79-85. [PMID: 31735721 DOI: 10.1353/hpu.2019.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The potential for translational research to improve human health is unprecedented, as the integration of genetic health risks with other data influencing health provides substantial opportunities for improvement. However, how integrating these data sources in a fair, unbiased and appropriate way without reinforcing pre-existing assumptions requires thoughtful implementation. Furthermore, integration of new technologies requires assessment of needs and benefits for the individual balanced with community needs and goals. Thus, examination of values, goals and implicit assumptions through transparent, authentic engagement of individuals and communities is essential.
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18
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Spiliopoulou A, Colombo M, Plant D, Nair N, Cui J, Coenen MJ, Ikari K, Yamanaka H, Saevarsdottir S, Padyukov L, Bridges SL, Kimberly RP, Okada Y, van Riel PLC, Wolbink G, van der Horst-Bruinsma IE, de Vries N, Tak PP, Ohmura K, Canhão H, Guchelaar HJ, Huizinga TW, Criswell LA, Raychaudhuri S, Weinblatt ME, Wilson AG, Mariette X, Isaacs JD, Morgan AW, Pitzalis C, Barton A, McKeigue P. Association of response to TNF inhibitors in rheumatoid arthritis with quantitative trait loci for CD40 and CD39. Ann Rheum Dis 2019; 78:1055-1061. [PMID: 31036624 PMCID: PMC6669378 DOI: 10.1136/annrheumdis-2018-214877] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES We sought to investigate whether genetic effects on response to TNF inhibitors (TNFi) in rheumatoid arthritis (RA) could be localised by considering known genetic susceptibility loci for relevant traits and to evaluate the usefulness of these genetic loci for stratifying drug response. METHODS We studied the relation of TNFi response, quantified by change in swollen joint counts ( Δ SJC) and erythrocyte sedimentation rate ( Δ ESR) with locus-specific scores constructed from genome-wide assocation study summary statistics in 2938 genotyped individuals: 37 scores for RA; scores for 19 immune cell traits; scores for expression or methylation of 93 genes with previously reported associations between transcript level and drug response. Multivariate associations were evaluated in penalised regression models by cross-validation. RESULTS We detected a statistically significant association between Δ SJC and the RA score at the CD40 locus (p=0.0004) and an inverse association between Δ SJC and the score for expression of CD39 on CD4 T cells (p=0.00005). A previously reported association between CD39 expression on regulatory T cells and response to methotrexate was in the opposite direction. In stratified analysis by concomitant methotrexate treatment, the inverse association was stronger in the combination therapy group and dissipated in the TNFi monotherapy group. Overall, ability to predict TNFi response from genotypic scores was limited, with models explaining less than 1% of phenotypic variance. CONCLUSIONS The association with the CD39 trait is difficult to interpret because patients with RA are often prescribed TNFi after failing to respond to methotrexate. The CD39 and CD40 pathways could be relevant for targeting drug therapy.
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Affiliation(s)
- Athina Spiliopoulou
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marco Colombo
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Darren Plant
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Nisha Nair
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Jing Cui
- Division of Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marieke Jh Coenen
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katsunori Ikari
- Department of Orthopedic Surgery, Tokyo Women's Medical University, Tokyo, Japan
- The Centers of Research Excellence in Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Hisashi Yamanaka
- Department of Rheumatology, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Saedis Saevarsdottir
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - 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, Suita, Japan
| | - Piet L Cm van Riel
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gertjan Wolbink
- Amsterdam Rheumatology and Immunology Centre, Reade, Amsterdam, The Netherlands
| | - Irene E van der Horst-Bruinsma
- Department of Rheumatology, VU University Medical Centre, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P Tak
- Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Helena Canhão
- CEDOC, EpiDoC Unit, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom Wj Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lindsey A Criswell
- Rosalind Russell / Ephraim P Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Center for Data Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael E Weinblatt
- Division of Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Anthony G Wilson
- EULAR Centre of Excellence/UCD Centre for Arthritis Research, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Xavier Mariette
- y Université Paris-Sud, INSERM UMR1184, Hôpitaux Universitaire Paris-Sud, AP-HP, Le Kremlin Bicêtre, Paris, France
| | - John D Isaacs
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ann W Morgan
- School of Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Paul McKeigue
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
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19
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Zumaquero E, Stone SL, Scharer CD, Jenks SA, Nellore A, Mousseau B, Rosal-Vela A, Botta D, Bradley JE, Wojciechowski W, Ptacek T, Danila MI, Edberg JC, Bridges SL, Kimberly RP, Chatham WW, Schoeb TR, Rosenberg AF, Boss JM, Sanz I, Lund FE. IFNγ induces epigenetic programming of human T-bet hi B cells and promotes TLR7/8 and IL-21 induced differentiation. eLife 2019; 8:e41641. [PMID: 31090539 PMCID: PMC6544433 DOI: 10.7554/elife.41641] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [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: 09/01/2018] [Accepted: 05/10/2019] [Indexed: 12/24/2022] Open
Abstract
Although B cells expressing the IFNγR or the IFNγ-inducible transcription factor T-bet promote autoimmunity in Systemic Lupus Erythematosus (SLE)-prone mouse models, the role for IFNγ signaling in human antibody responses is unknown. We show that elevated levels of IFNγ in SLE patients correlate with expansion of the T-bet expressing IgDnegCD27negCD11c+CXCR5neg (DN2) pre-antibody secreting cell (pre-ASC) subset. We demonstrate that naïve B cells form T-bethi pre-ASCs following stimulation with either Th1 cells or with IFNγ, IL-2, anti-Ig and TLR7/8 ligand and that IL-21 dependent ASC formation is significantly enhanced by IFNγ or IFNγ-producing T cells. IFNγ promotes ASC development by synergizing with IL-2 and TLR7/8 ligands to induce genome-wide epigenetic reprogramming of B cells, which results in increased chromatin accessibility surrounding IRF4 and BLIMP1 binding motifs and epigenetic remodeling of IL21R and PRDM1 loci. Finally, we show that IFNγ signals poise B cells to differentiate by increasing their responsiveness to IL-21.
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Affiliation(s)
- Esther Zumaquero
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Sara L Stone
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Division of RheumatologyEmory UniversityAtlantaUnited States
| | - Scott A Jenks
- Department of Medicine, Division of RheumatologyEmory UniversityAtlantaUnited States
| | - Anoma Nellore
- Department of Medicine, Division of Infectious DiseaseThe University of Alabama at BirminghamBirminghamUnited States
| | - Betty Mousseau
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Antonio Rosal-Vela
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Davide Botta
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
| | - John E Bradley
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Wojciech Wojciechowski
- Center for Pediatric Biomedical Research, Flow Cytometry Shared Resource LaboratoryUniversity of Rochester School of Medicine and DentistryRochesterUnited States
| | - Travis Ptacek
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
- Informatics Group, Center for Clinical and Translational ScienceThe University of Alabama at BirminghamBirminghamUnited States
| | - Maria I Danila
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Jeffrey C Edberg
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - S Louis Bridges
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Robert P Kimberly
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - W Winn Chatham
- Department of Medicine, Division of Clinical Immunology and RheumatologyThe University of Alabama at BirminghamBirminghamUnited States
| | - Trenton R Schoeb
- Department of Genetics, Animal Resources ProgramThe University of Alabama at BirminghamBirminghamUnited States
| | - Alexander F Rosenberg
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
- The Informatics InstituteThe University of Alabama at BirminghamBirminghamUnited States
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Division of RheumatologyEmory UniversityAtlantaUnited States
| | - Ignacio Sanz
- Department of Medicine, Division of RheumatologyEmory UniversityAtlantaUnited States
| | - Frances E Lund
- Department of MicrobiologyThe University of Alabama at BirminghamBirminghamUnited States
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20
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Singh JA, Fraenkel L, Green C, Alarcón GS, Barton JL, Saag KG, Hanrahan LM, Raymond SC, Kimberly RP, Leong AL, Reyes E, Street RL, Suarez-Almazor ME, Eakin GS, Marrow L, Morgan CJ, Caro B, Sloan JA, Jandali B, Garcia SR, Grossman J, Winthrop KL, Trupin L, Dall’Era M, Meara A, Rizvi T, Chatham WW, Yazdany J. Individualized decision aid for diverse women with lupus nephritis (IDEA-WON): A randomized controlled trial. PLoS Med 2019; 16:e1002800. [PMID: 31067237 PMCID: PMC6505936 DOI: 10.1371/journal.pmed.1002800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/04/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Treatment decision-making regarding immunosuppressive therapy is challenging for individuals with lupus. We assessed the effectiveness of a decision aid for immunosuppressive therapy in lupus nephritis. METHODS AND FINDINGS In a United States multicenter, open-label, randomized controlled trial (RCT), adult women with lupus nephritis, mostly from racial/ethnic minority backgrounds with low socioeconomic status (SES), seen in in- or outpatient settings, were randomized to an individualized, culturally tailored, computerized decision aid versus American College of Rheumatology (ACR) lupus pamphlet (1:1 ratio), using computer-generated randomization. We hypothesized that the co-primary outcomes of decisional conflict and informed choice regarding immunosuppressive medications would improve more in the decision aid group. Of 301 randomized women, 298 were analyzed; 47% were African-American, 26% Hispanic, and 15% white. Mean age (standard deviation [SD]) was 37 (12) years, 57% had annual income of <$40,000, and 36% had a high school education or less. Compared with the provision of the ACR lupus pamphlet (n = 147), participants randomized to the decision aid (n = 151) had (1) a clinically meaningful and statistically significant reduction in decisional conflict, 21.8 (standard error [SE], 2.5) versus 12.7 (SE, 2.0; p = 0.005) and (2) no difference in informed choice in the main analysis, 41% versus 31% (p = 0.08), but clinically meaningful and statistically significant difference in sensitivity analysis (net values for immunosuppressives positive [in favor] versus negative [against]), 50% versus 35% (p = 0.006). Unresolved decisional conflict was lower in the decision aid versus pamphlet groups, 22% versus 44% (p < 0.001). Significantly more patients in the decision aid versus pamphlet group rated information to be excellent for understanding lupus nephritis (49% versus 33%), risk factors (43% versus 27%), medication options (50% versus 33%; p ≤ 0.003 for all); and the ease of use of materials was higher in the decision aid versus pamphlet groups (51% versus 38%; p = 0.006). Key study limitations were the exclusion of men, short follow-up, and the lack of clinical outcomes, including medication adherence. CONCLUSIONS An individualized decision aid was more effective than usual care in reducing decisional conflict for choice of immunosuppressive medications in women with lupus nephritis. TRIAL REGISTRATION Clinicaltrials.gov, NCT02319525.
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Affiliation(s)
- Jasvinder A. Singh
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Birmingham VA Medical Center, Birmingham, Alabama, United States of America
- * E-mail:
| | - Liana Fraenkel
- Yale University, New Haven, Connecticut, United States of America
| | - Candace Green
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Graciela S. Alarcón
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jennifer L. Barton
- Oregon Health Science University, Portland, Oregon, United States of America
- VA Portland Health Care System, Portland, Oregon, United States of America
| | - Kenneth G. Saag
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | - Sandra C. Raymond
- Lupus Foundation of America, Washington, DC, United States of America
| | - Robert P. Kimberly
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amye L. Leong
- Healthy Motivation, Inc., Los Angeles, California, United States of America
| | - Elyse Reyes
- Elyse Reyes Consulting, Los Angeles, California, United States of America
| | - Richard L. Street
- Texas A&M University, College Station, Texas, United States of America
| | | | - Guy S. Eakin
- Arthritis Foundation, Atlanta, Georgia, United States of America
| | - Laura Marrow
- Arthritis Foundation, Atlanta, Georgia, United States of America
| | - Charity J. Morgan
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brennda Caro
- Georgia State University, Atlanta, Georgia, United States of America
| | - Jeffrey A. Sloan
- Mayo Clinic School of Medicine, Rochester, Minnesota, United States of America
| | - Bochra Jandali
- Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Jennifer Grossman
- University of California, Los Angeles (UCLA), Los Angeles, California, United States of America
| | - Kevin L. Winthrop
- Oregon Health Science University, Portland, Oregon, United States of America
| | - Laura Trupin
- University of California at San Francisco (UCSF), San Francisco, California, United States of America
| | - Maria Dall’Era
- University of California at San Francisco (UCSF), San Francisco, California, United States of America
| | - Alexa Meara
- Ohio State University, Columbus, Ohio, United States of America
| | - Tara Rizvi
- Baylor College of Medicine, Houston, Texas, United States of America
| | - W. Winn Chatham
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jinoos Yazdany
- University of California at San Francisco (UCSF), San Francisco, California, United States of America
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21
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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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22
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Onengut-Gumuscu S, Chen WM, Robertson CC, Bonnie JK, Farber E, Zhu Z, Oksenberg JR, Brant SR, Bridges SL, Edberg JC, Kimberly RP, Gregersen PK, Rewers MJ, Steck AK, Black MH, Dabelea D, Pihoker C, Atkinson MA, Wagenknecht LE, Divers J, Bell RA, Erlich HA, Concannon P, Rich SS. Type 1 Diabetes Risk in African-Ancestry Participants and Utility of an Ancestry-Specific Genetic Risk Score. Diabetes Care 2019; 42:406-415. [PMID: 30659077 PMCID: PMC6385701 DOI: 10.2337/dc18-1727] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/14/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Genetic risk scores (GRS) have been developed that differentiate individuals with type 1 diabetes from those with other forms of diabetes and are starting to be used for population screening; however, most studies were conducted in European-ancestry populations. This study identifies novel genetic variants associated with type 1 diabetes risk in African-ancestry participants and develops an African-specific GRS. RESEARCH DESIGN AND METHODS We generated single nucleotide polymorphism (SNP) data with the ImmunoChip on 1,021 African-ancestry participants with type 1 diabetes and 2,928 control participants. HLA class I and class II alleles were imputed using SNP2HLA. Logistic regression models were used to identify genome-wide significant (P < 5.0 × 10-8) SNPs associated with type 1 diabetes in the African-ancestry samples and validate SNPs associated with risk in known European-ancestry loci (P < 2.79 × 10-5). RESULTS African-specific (HLA-DQA1*03:01-HLA-DQB1*02:01) and known European-ancestry HLA haplotypes (HLA-DRB1*03:01-HLA-DQA1*05:01-HLA-DQB1*02:01, HLA-DRB1*04:01-HLA-DQA1*03:01-HLA-DQB1*03:02) were significantly associated with type 1 diabetes risk. Among European-ancestry defined non-HLA risk loci, six risk loci were significantly associated with type 1 diabetes in subjects of African ancestry. An African-specific GRS provided strong prediction of type 1 diabetes risk (area under the curve 0.871), performing significantly better than a European-based GRS and two polygenic risk scores in independent discovery and validation cohorts. CONCLUSIONS Genetic risk of type 1 diabetes includes ancestry-specific, disease-associated variants. The GRS developed here provides improved prediction of type 1 diabetes in African-ancestry subjects and a means to identify groups of individuals who would benefit from immune monitoring for early detection of islet autoimmunity.
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Affiliation(s)
- Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | | | - Jessica K Bonnie
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Zhennan Zhu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jorge R Oksenberg
- Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, and Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics & Human Genetics, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | | | - Dana Dabelea
- Colorado School of Public Health, University of Colorado Denver, Aurora, CO
| | | | - Mark A Atkinson
- Diabetes Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Lynne E Wagenknecht
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Jasmin Divers
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Ronny A Bell
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA
| | - Patrick Concannon
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
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23
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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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24
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Langefeld CD, Comeau ME, Ng MCY, Guan M, Dimitrov L, Mudgal P, Spainhour MH, Julian BA, Edberg JC, Croker JA, Divers J, Hicks PJ, Bowden DW, Chan GC, Ma L, Palmer ND, Kimberly RP, Freedman BI. Genome-wide association studies suggest that APOL1-environment interactions more likely trigger kidney disease in African Americans with nondiabetic nephropathy than strong APOL1-second gene interactions. Kidney Int 2018; 94:599-607. [PMID: 29885931 DOI: 10.1016/j.kint.2018.03.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/01/2018] [Accepted: 03/22/2018] [Indexed: 12/25/2022]
Abstract
African Americans carrying two apolipoprotein L1 gene (APOL1) renal risk variants have a high risk for nephropathy. However, only a minority develops end-stage renal disease (ESRD). Hence, modifying factors likely contribute to initiation of kidney disease such as endogenous (HIV infection) or exogenous (interferon treatment) environmental modifiers. In this report, genome-wide association studies and a meta-analysis were performed to identify novel loci for nondiabetic ESRD in African Americans and to detect genetic modifiers in APOL1-associated nephropathy. Two African American cohorts were analyzed, 1749 nondiabetic ESRD cases and 1136 controls from Wake Forest and 901 lupus nephritis (LN)-ESRD cases and 520 controls with systemic lupus erythematosus but lacking nephropathy from the LN-ESRD Consortium. Association analyses adjusting for APOL1 G1/G2 renal-risk variants were completed and stratified by APOL1 risk genotype status. Individual genome-wide association studies and meta-analysis results of all 2650 ESRD cases and 1656 controls did not detect significant genome-wide associations with ESRD beyond APOL1. Similarly, no single nucleotide polymorphism showed significant genome-wide evidence of an interaction with APOL1 risk variants. Thus, although variants with small individual effects cannot be ruled out and are likely to exist, our results suggest that APOL1-environment interactions may be of greater clinical importance in triggering nephropathy in African Americans than APOL1 interactions with other single nucleotide polymorphisms.
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Affiliation(s)
- Carl D Langefeld
- Division of Public Health Sciences, Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Mary E Comeau
- Division of Public Health Sciences, Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Maggie C Y Ng
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Meijian Guan
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Latchezar Dimitrov
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Poorva Mudgal
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Mitzie H Spainhour
- Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Bruce A Julian
- Department of Medicine, Division of Nephrology; University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Jeffrey C Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology; University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Jennifer A Croker
- Department of Medicine, Division of Clinical Immunology and Rheumatology; University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Jasmin Divers
- Division of Public Health Sciences, Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Pamela J Hicks
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Donald W Bowden
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Gary C Chan
- Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Lijun Ma
- Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Nicholette D Palmer
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Robert P Kimberly
- Department of Medicine, Division of Clinical Immunology and Rheumatology; University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Barry I Freedman
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Department of Internal Medicine, Section on Nephrology; Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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25
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Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res 2018; 24:2092-2099. [PMID: 29490987 PMCID: PMC5932113 DOI: 10.1158/1078-0432.ccr-17-1960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 07/07/2017] [Revised: 01/02/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
Purpose: Colorectal cancer is the third most common cancer worldwide, causing approximately 700,000 deaths each year. The majority of colorectal cancers begin as adenomas. Definitive screening for colorectal adenomas is currently accomplished through colonoscopy but, owing largely to costs and invasiveness, is typically limited to patient groups at higher risk by virtue of age or family history. We sought to determine if blood-based small RNA markers could detect colorectal adenoma.Experimental Design: We applied high-depth small RNA sequencing to plasma from a large (n = 189) cohort of patients, balanced for age, sex, and ancestry. Our analytical methodology allowed for the detection of both microRNAs and other small RNA species. We replicated sequencing results by qPCR on plasma samples from an independent cohort (n = 140).Results: We found several small RNA species with significant associations to colorectal adenoma, including both microRNAs and non-microRNA small RNAs. These associations were robust to correction for patient covariates, including age. Among the adenoma-associated small RNAs, two, a miR-335-5p isoform and an un-annotated small RNA, were validated by qPCR in an independent cohort. A classifier trained on measures of these two RNAs in the discovery cohort yields an AUC of 0.755 (0.775 with age) for adenoma detection in the independent cohort. This classifier accurately detects adenomas in patients under 50 and is robust to sex or ancestry.Conclusions: Circulating small RNAs (including but not limited to miRNAs) discovered by sequencing and validated by qPCR identify patients with colorectal adenomas effectively. Clin Cancer Res; 24(9); 2092-9. ©2018 AACR.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.
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26
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Liu K, Kurien BT, Zimmerman SL, Kaufman KM, Taft DH, Kottyan LC, Lazaro S, Weaver CA, Ice JA, Adler AJ, Chodosh J, Radfar L, Rasmussen A, Stone DU, Lewis DM, Li S, Koelsch KA, Igoe A, Talsania M, Kumar J, Maier-Moore JS, Harris VM, Gopalakrishnan R, Jonsson R, Lessard JA, Lu X, Gottenberg JE, Anaya JM, Cunninghame-Graham DS, Huang AJW, Brennan MT, Hughes P, Illei GG, Miceli-Richard C, Keystone EC, Bykerk VP, Hirschfield G, Xie G, Ng WF, Nordmark G, Eriksson P, Omdal R, Rhodus NL, Rischmueller M, Rohrer M, Segal BM, Vyse TJ, Wahren-Herlenius M, Witte T, Pons-Estel B, Alarcon-Riquelme ME, Guthridge JM, James JA, Lessard CJ, Kelly JA, Thompson SD, Gaffney PM, Montgomery CG, Edberg JC, Kimberly RP, Alarcón GS, Langefeld CL, Gilkeson GS, Kamen DL, Tsao BP, McCune WJ, Salmon JE, Merrill JT, Weisman MH, Wallace DJ, Utset TO, Bottinger EP, Amos CI, Siminovitch KA, Mariette X, Sivils KL, Harley JB, Scofield RH. X Chromosome Dose and Sex Bias in Autoimmune Diseases: Increased Prevalence of 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome. Arthritis Rheumatol 2017; 68:1290-1300. [PMID: 26713507 DOI: 10.1002/art.39560] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47,XXX; occurring in ∼1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls. METHODS All subjects in this study were female. We identified subjects with 47,XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47,XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction. RESULTS We found 47,XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67-86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18-123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47,XXX. There was an excess of 47,XXX among SLE and SS patients. CONCLUSION The estimated prevalence of SLE and SS in women with 47,XXX was ∼2.5 and ∼2.9 times higher, respectively, than that in women with 46,XX and ∼25 and ∼41 times higher, respectively, than that in men with 46,XY. No statistically significant increase of 47,XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity.
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Affiliation(s)
- Ke Liu
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Biji T Kurien
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,U.S. Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | - Sarah L Zimmerman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Diana H Taft
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara Lazaro
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Carrie A Weaver
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - John A Ice
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Adam J Adler
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,U.S. Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Lida Radfar
- Department of Oral Diagnosis and Radiology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Astrid Rasmussen
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Donald U Stone
- Dean McGee Eye Institute and Department of Ophthalmology, University of Oklahoma College of Medicine, Oklahoma City, OK, USA
| | - David M Lewis
- Department of Oral Diagnosis and Radiology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Shibo Li
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kristi A Koelsch
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ann Igoe
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Mitali Talsania
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jay Kumar
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jacen S Maier-Moore
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,U.S. Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA.,Department of Clinical Laboratory Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Valerie M Harris
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Rajaram Gopalakrishnan
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Department of Rheumatology, Haukeland University Hospital, Bergen 5021, Norway
| | - James A Lessard
- Valley Bone & Joint Clinic, 3035 DeMers Avenue, Grand Forks, ND 58201, USA
| | - Xianglan Lu
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | | | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Deborah S Cunninghame-Graham
- Division of Genetics and Molecular Medicine and Division of Immunology, Infection and Inflammatory Disease, King's College London, London
| | - Andrew J W Huang
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Michael T Brennan
- Department of Oral Medicine, Carolinas Medical Center, Charlotte, NC 28232, USA
| | - Pamela Hughes
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Gabor G Illei
- Sjögren's Syndrome Clinic, National Institute of Dental and Craniofacial Research, Molecular Physiology and Therapeutics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Corinne Miceli-Richard
- Department of Rheumatology, Université Paris-Sud, AP-HP, INSERM U1012, Le Kremlin-Bicêtre, France
| | - Edward C Keystone
- Department of Medicine, Mount Sinai Hospital and University of Toronto, Toronto, Ontario
| | | | | | - Gang Xie
- Lunenfeld Tanenbaum and Toronto General Research Institutes, Departments of Medicine, Immunology and Molecular Genetics, University of Toronto, Toronto Ontario
| | - Wan-Fai Ng
- Musculoskeletal Research Group, Institute of Cellular Medicine & NIHR Newcastle Biomedical Research Centre, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gunnel Nordmark
- Section of Rheumatology, Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Eriksson
- Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Nelson L Rhodus
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, USA
| | - Maureen Rischmueller
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Michael Rohrer
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Barbara M Segal
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine and Division of Immunology, Infection and Inflammatory Disease, King's College London, London
| | | | - Torsten Witte
- Clinic for Immunology and Rheumatology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Marta E Alarcon-Riquelme
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,Center Pfizer, University of Granada, Andalusian Government for Genomics and Oncological Research, PTS Granada, 18016, Spain
| | - Joel M Guthridge
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Judith A James
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Christopher J Lessard
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Susan D Thompson
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Patrick M Gaffney
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Courtney G Montgomery
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, University of Alabama, Birmingham, AL
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama, Birmingham, AL
| | - Graciela S Alarcón
- Division of Clinical Immunology and Rheumatology, University of Alabama, Birmingham, AL
| | - Carl L Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University, Winston-Salem, NC
| | - Gary S Gilkeson
- Division of Rheumatology & Immunology, Medical University of South Carolina, Charleston, SC.,Ralph H. Johnson VA Medical Center, Charleston, SC
| | - Diane L Kamen
- Division of Rheumatology & Immunology, Medical University of South Carolina, Charleston, SC
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, UCLA School of Medicine
| | - W Joseph McCune
- Division of Rheumatology, Department of Medicine, University of Michigan College of Medicine, Ann Arbor, Michigan
| | - Jane E Salmon
- Division of Rheumatology, Hospital for Special Surgery and Weill Cornell Medical College, New York, NY
| | - Joan T Merrill
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Daniel J Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Tammy O Utset
- University of Chicago Pritzker School of Medicine, Chicago, IL
| | - Erwin P Bottinger
- Charles R. Bronfman Institute for personalized medicine, Mount Sinai Hospital, 1468 Madison Avenue, New York, NY 10029
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Katherine A Siminovitch
- Lunenfeld Tanenbaum and Toronto General Research Institutes, Departments of Medicine, Immunology and Molecular Genetics, University of Toronto, Toronto Ontario
| | - Xavier Mariette
- Rhumatologie, Responsable de l'Unité de Recherche Clinique Hôpitaux Universitaire Paris-Sud Université Paris-Sud, INSERM U1184 Head of Autoimmunity team, IMVA : Immunology of viral Infections and Autoimmune Diseases
| | - Kathy L Sivils
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA.,U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - R Hal Scofield
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,U.S. Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
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27
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Shah S, Gibson AW, Ji C, Darrington E, Mobley J, Kojima K, Edberg JC, Kimberly RP. Regulation of FcRγ function by site-specific serine phosphorylation. J Leukoc Biol 2016; 101:421-428. [PMID: 27630214 DOI: 10.1189/jlb.2ab0516-228r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 05/13/2016] [Revised: 08/03/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
The common FcRγ, an immunoreceptor tyrosine-based activation motif (ITAM)- containing adaptor protein, associates with multiple leukocyte receptor complexes and mediates signal transduction through the ITAM in the cytoplasmic domain. The presence of multiple serine and threonine residues within this motif suggests the potential for serine/threonine phosphorylation in modulating signaling events. Single-site mutational analysis of these residues in RBL-2H3 cells indicates that each may contribute to net FcRγ-mediated signaling, and mass spectrometry of WT human FcRγ from receptor-stimulated cells shows consistent preferential phosphorylation of the serine residue at position 51. Immunoblot analysis, mass spectrometry, and mutational analyses showed that phosphorylation of serine 51 in the 7-residue spacer between the 2 YxxL sequences regulates FcRγ signaling by inhibiting tyrosine phosphorylation at the membrane proximal Y47 position of the ITAM, but not phosphorylation at position Y58. This inhibition results in reduced Syk recruitment and activation. With in vitro kinase assays, PKC-δ and PKA show preferential phosphorylation of S51. Serine/threonine phosphorylation of the FcRγ ITAM, which functions as an integrator of multiple signaling elements, may explain in part the contribution of variants in PKC-δ and other PKC isoforms to some autoimmune phenotypes.
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Affiliation(s)
- Spandan Shah
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Andrew W Gibson
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Chuanyi Ji
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Eric Darrington
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kyoko Kojima
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
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Alarcón-Riquelme ME, Ziegler JT, Molineros J, Howard TD, Moreno-Estrada A, Sánchez-Rodríguez E, Ainsworth HC, Ortiz-Tello P, Comeau ME, Rasmussen A, Kelly JA, Adler A, Acevedo-Vázquez EM, Cucho-Venegas JM, García-De la Torre I, Cardiel MH, Miranda P, Catoggio LJ, Maradiaga-Ceceña M, Gaffney PM, Vyse TJ, Criswell LA, Tsao BP, Sivils KL, Bae SC, James JA, Kimberly RP, Kaufman KM, Harley JB, Esquivel-Valerio JA, Moctezuma JF, García MA, Berbotto GA, Babini AM, Scherbarth H, Toloza S, Baca V, Nath SK, Aguilar Salinas C, Orozco L, Tusié-Luna T, Zidovetzki R, Pons-Estel BA, Langefeld CD, Jacob CO. Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture. Arthritis Rheumatol 2016; 68:932-43. [PMID: 26606652 DOI: 10.1002/art.39504] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a strong genetic component. We undertook the present work to perform the first genome-wide association study on individuals from the Americas who are enriched for Native American heritage. METHODS We analyzed 3,710 individuals from the US and 4 countries of Latin America who were diagnosed as having SLE, and healthy controls. Samples were genotyped with HumanOmni1 BeadChip. Data on out-of-study controls genotyped with HumanOmni2.5 were also included. Statistical analyses were performed using SNPtest and SNPGWA. Data were adjusted for genomic control and false discovery rate. Imputation was performed using Impute2 and, for classic HLA alleles, HiBag. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. RESULTS The IRF5-TNPO3 region showed the strongest association and largest OR for SLE (rs10488631: genomic control-adjusted P [Pgcadj ] = 2.61 × 10(-29), OR 2.12 [95% CI 1.88-2.39]), followed by HLA class II on the DQA2-DQB1 loci (rs9275572: Pgcadj = 1.11 × 10(-16), OR 1.62 [95% CI 1.46-1.80] and rs9271366: Pgcadj = 6.46 × 10(-12), OR 2.06 [95% CI 1.71-2.50]). Other known SLE loci found to be associated in this population were ITGAM, STAT4, TNIP1, NCF2, and IRAK1. We identified a novel locus on 10q24.33 (rs4917385: Pgcadj = 1.39 × 10(-8)) with an expression quantitative trait locus (eQTL) effect (Peqtl = 8.0 × 10(-37) at USMG5/miR1307), and several new suggestive loci. SLE risk loci previously identified in Europeans and Asians were corroborated. Local ancestry estimation showed that the HLA allele risk contribution is of European ancestral origin. Imputation of HLA alleles suggested that autochthonous Native American haplotypes provide protection against development of SLE. CONCLUSION Our results demonstrate that studying admixed populations provides new insights in the delineation of the genetic architecture that underlies autoimmune and complex diseases.
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Affiliation(s)
| | - Julie T Ziegler
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | | | - Andrés Moreno-Estrada
- Stanford University School of Medicine, Stanford, California, and Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | | | | | - Patricia Ortiz-Tello
- Stanford University School of Medicine, Stanford, California, and Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Mary E Comeau
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | | | - Adam Adler
- Oklahoma Medical Research Foundation, Oklahoma City
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sang-Cheol Bae
- Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Judith A James
- Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City
| | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jorge A Esquivel-Valerio
- Hospital Universitario Dr. José Eleuterio González Universidad Autonoma de Nuevo León, Monterrey, Mexico
| | | | - Mercedes A García
- Hospital Interzonal General de Agudos General San Martin, La Plata, Argentina
| | | | | | - Hugo Scherbarth
- Hospital Interzonal General de Agudos Oscar E. Alende, Mar del Plata, Argentina
| | - Sergio Toloza
- Hospital Interzonal San Juan Bautista, San Fernando del Valle de Catamarca, Argentina
| | - Vicente Baca
- Hospital de Peditaria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Carlos Aguilar Salinas
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán and Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | | | - Chaim O Jacob
- University of Southern California School of Medicine, Los Angeles
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Lessard CJ, Sajuthi S, Zhao J, Kim K, Ice JA, Li H, Ainsworth H, Rasmussen A, Kelly JA, Marion M, Bang SY, Joo YB, Choi J, Lee HS, Kang YM, Suh CH, Chung WT, Lee SK, Choe JY, Shim SC, Oh JH, Kim YJ, Han BG, Shen N, Howe HS, Wakeland EK, Li QZ, Song YW, Gaffney PM, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Vyse TJ, Harley JB, Sivils KL, Bae SC, Langefeld CD, Tsao BP. Identification of a Systemic Lupus Erythematosus Risk Locus Spanning ATG16L2, FCHSD2, and P2RY2 in Koreans. Arthritis Rheumatol 2016; 68:1197-1209. [PMID: 26663301 PMCID: PMC4981330 DOI: 10.1002/art.39548] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 05/06/2015] [Accepted: 12/08/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder whose etiology is incompletely understood, but likely involves environmental triggers in genetically susceptible individuals. Using an unbiased genome-wide association (GWA) scan and replication analysis, we sought to identify the genetic loci associated with SLE in a Korean population. METHODS A total of 1,174 SLE cases and 4,246 population controls from Korea were genotyped and analyzed with a GWA scan to identify single-nucleotide polymorphisms (SNPs) significantly associated with SLE, after strict quality control measures were applied. For select variants, replication of SLE risk loci was tested in an independent data set of 1,416 SLE cases and 1,145 population controls from Korea and China. RESULTS Eleven regions outside the HLA exceeded the genome-wide significance level (P = 5 × 10(-8) ). A novel SNP-SLE association was identified between FCHSD2 and P2RY2, peaking at rs11235667 (P = 1.03 × 10(-8) , odds ratio [OR] 0.59) on a 33-kb haplotype upstream of ATG16L2. In the independent replication data set, the SNP rs11235667 continued to show a significant association with SLE (replication meta-analysis P = 0.001, overall meta-analysis P = 6.67 × 10(-11) ; OR 0.63). Within the HLA region, the SNP-SLE association peaked in the class II region at rs116727542, with multiple independent effects observed in this region. Classic HLA allele imputation analysis identified HLA-DRB1*1501 and HLA-DQB1*0602, each highly correlated with one another, as most strongly associated with SLE. Ten previously established SLE risk loci were replicated: STAT1-STAT4, TNFSF4, TNFAIP3, IKZF1, HIP1, IRF5, BLK, WDFY4, ETS1, and IRAK1-MECP2. Of these loci, previously unreported, independent second risk effects of SNPs in TNFAIP3 and TNFSF4, as well as differences in the association with a putative causal variant in the WDFY4 region, were identified. CONCLUSION Further studies are needed to identify true SLE risk effects in other loci suggestive of a significant association, and to identify the causal variants in the regions of ATG16L2, FCHSD2, and P2RY2.
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Affiliation(s)
- Christopher J. Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satria Sajuthi
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157-106, USA
| | - Jian Zhao
- Division of Rheumatology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kwangwoo Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - John A. Ice
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - He Li
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73014, USA
| | - Hannah Ainsworth
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157-106, USA
| | - Astrid Rasmussen
- 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
| | - Mindy Marion
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157-106, USA
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - Young Bin Joo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - Jeongim Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - Young Mo Kang
- Kyungpook National University Hospital, Daegu 700-721, Republic of Korea
| | - Chang-Hee Suh
- Ajou University Hospital, Suwon 443-380, Republic of Korea
| | - Won Tae Chung
- Dong-A University Hospital, Busan 602-715, Republic of Korea
| | - Soo-Kon Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-749, Republic of Korea
| | - Jung-Yoon Choe
- Department of Internal Medicine, Catholic University of Daegu School of Medicine, Daegu 705-718, Republic of Korea
| | - Seung Cheol Shim
- Daejeon Rheumatoid & Degenerative Arthritis Center, Chungnam National University Hospital, Daejeon 305-764, Republic of Korea
| | - Ji Hee Oh
- Korea National Institute of Health, Osong 361-709, Republic of Korea
| | - Young Jin Kim
- Korea National Institute of Health, Osong 361-709, Republic of Korea
| | - Bok-Ghee Han
- Korea National Institute of Health, Osong 361-709, Republic of Korea
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai, China 200001
- Shanghai JiaoTong University School of Medicine, Shanghai, China 200025
| | - Hwee Siew Howe
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore 308433
| | | | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yeong Wook Song
- Department of Internal Medicine, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 110-744, Republic of Korea
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Centro de Genómica e Investigaciones Oncológicas, Pfizer-Universidad de Granada-Junta de Andalućıa, Granada 18100, Spain
| | - Lindsey A. Criswell
- Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA, 94117, USA
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA 90095
| | - Robert P. Kimberly
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Timothy J. Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, Infection and Inflammatory Disease, King's College London, London, UK WC2R 2LS
| | - John B. Harley
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
| | - Kathy L. Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73014, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 133-792, Republic of Korea
| | - Carl D. Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157-106, USA
| | - Betty P. Tsao
- Division of Rheumatology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Waite LL, Weaver B, Day K, Li X, Roberts K, Gibson AW, Edberg JC, Kimberly RP, Absher DM, Tiwari HK. Estimation of Cell-Type Composition Including T and B Cell Subtypes for Whole Blood Methylation Microarray Data. Front Genet 2016; 7:23. [PMID: 26925097 PMCID: PMC4757643 DOI: 10.3389/fgene.2016.00023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 09/16/2015] [Accepted: 02/03/2016] [Indexed: 01/31/2023] Open
Abstract
DNA methylation levels vary markedly by cell-type makeup of a sample. Understanding these differences and estimating the cell-type makeup of a sample is an important aspect of studying DNA methylation. DNA from leukocytes in whole blood is simple to obtain and pervasive in research. However, leukocytes contain many distinct cell types and subtypes. We propose a two-stage model that estimates the proportions of six main cell types in whole blood (CD4+ T cells, CD8+ T cells, monocytes, B cells, granulocytes, and natural killer cells) as well as subtypes of T and B cells. Unlike previous methods that only estimate overall proportions of CD4+ T cell, CD8+ T cells, and B cells, our model is able to estimate proportions of naïve, memory, and regulatory CD4+ T cells as well as naïve and memory CD8+ T cells and naïve and memory B cells. Using real and simulated data, we are able to demonstrate that our model is able to reliably estimate proportions of these cell types and subtypes. In studies with DNA methylation data from Illumina's HumanMethylation450k arrays, our estimates will be useful both for testing for associations of cell type and subtype composition with phenotypes of interest as well as for adjustment purposes to prevent confounding in epigenetic association studies. Additionally, our method can be easily adapted for use with whole genome bisulfite sequencing (WGBS) data or any other genome-wide methylation data platform.
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Affiliation(s)
- Lindsay L Waite
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at BirminghamBirmingham, AL, USA; HudsonAlpha Institute for BiotechnologyHuntsville, AL, USA
| | | | - Kenneth Day
- HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Xinrui Li
- Division of Clinical Immunology and Rheumatology, Department of Medicine, School of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Andrew W Gibson
- Division of Clinical Immunology and Rheumatology, Department of Medicine, School of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, School of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, School of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham Birmingham, AL, USA
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Deng Y, Zhao J, Sakurai D, Sestak AL, Osadchiy V, Langefeld CD, Kaufman KM, Kelly JA, James JA, Petri MA, Bae SC, Alarcón-Riquelme ME, Alarcón GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, Merrill JT, Gaffney PM, Sivils KM, Niewold TB, Ramsey-Goldman R, Reveille JD, Scofield RH, Stevens AM, Boackle SA, Vilá LM, Sohn IIW, Lee S, Chang DM, Song YW, Vyse TJ, Harley JB, Brown EE, Edberg JC, Kimberly RP, Cantor RM, Hahn BH, Grossman JM, Tsao BP. Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production. Ann Rheum Dis 2016; 75:2007-2013. [PMID: 26783109 DOI: 10.1136/annrheumdis-2015-208441] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 08/18/2015] [Accepted: 12/14/2015] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Following up the systemic lupus erythematosus (SLE) genome-wide association studies (GWAS) identification of NMNAT2 at rs2022013, we fine-mapped its 150 kb flanking regions containing NMNAT2 and SMG7 in a 15 292 case-control multi-ancestry population and tested functions of identified variants. METHODS We performed genotyping using custom array, imputation by IMPUTE 2.1.2 and allele specific functions using quantitative real-time PCR and luciferase reporter transfections. SLE peripheral blood mononuclear cells (PBMCs) were cultured with small interfering RNAs to measure antinuclear antibody (ANA) and cyto/chemokine levels in supernatants using ELISA. RESULTS We confirmed association at NMNAT2 in European American (EA) and Amerindian/Hispanic ancestries, and identified independent signal at SMG7 tagged by rs2702178 in EA only (p=2.4×10-8, OR=1.23 (95% CI 1.14 to 1.32)). In complete linkage disequilibrium with rs2702178, rs2275675 in the promoter region robustly associated with SMG7 mRNA levels in multiple expression quantitative trait locus (eQTL) datasets. Its risk allele was dose-dependently associated with decreased SMG7 mRNA levels in PBMCs of 86 patients with SLE and 119 controls (p=1.1×10-3 and 6.8×10-8, respectively) and conferred reduced transcription activity in transfected HEK-293 (human embryonic kidney cell line) and Raji cells (p=0.0035 and 0.0037, respectively). As a critical component in the nonsense-mediated mRNA decay pathway, SMG7 could regulate autoantigens including ribonucleoprotein (RNP) and Smith (Sm). We showed SMG7 mRNA levels in PBMCs correlated inversely with ANA titres of patients with SLE (r=-0.31, p=0.01), and SMG7 knockdown increased levels of ANA IgG and chemokine (C-C motif) ligand 19 in SLE PBMCs (p=2.0×10-5 and 2.0×10-4, respectively). CONCLUSION We confirmed NMNAT2 and identified independent SMG7 association with SLE. The inverse relationship between levels of the risk allele-associated SMG7 mRNAs and ANA suggested the novel contribution of mRNA surveillance pathway to SLE pathogenesis.
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Affiliation(s)
- Yun Deng
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Jian Zhao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Daisuke Sakurai
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Andrea L Sestak
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Vadim Osadchiy
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Michelle A Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Marta E Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Lindsey A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Gary S Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, California, USA
| | - Joan T Merrill
- Department of Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - John D Reveille
- Department of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - Anne M Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, USA Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA US Department of Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - I I Woong Sohn
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Seung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | | | - Yeong Wook Song
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine and Immunology, King's College London, London, UK
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Elizabeth E Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rita M Cantor
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Bevra H Hahn
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Jennifer M Grossman
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Betty P Tsao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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Huang C, Haritunians T, Okou DT, Cutler DJ, Zwick ME, Taylor KD, Datta LW, Maranville JC, Liu Z, Ellis S, Chopra P, Alexander JS, Baldassano RN, Cross RK, Dassopoulos T, Dhere TA, Duerr RH, Hanson JS, Hou JK, Hussain SZ, Isaacs KL, Kachelries KE, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kumar A, Kwon JH, Lazarev M, Mannon P, Moulton DE, Osuntokun BO, Patel A, Rioux JD, Rotter JI, Saeed S, Scherl EJ, Silverberg MS, Silverman A, Targan SR, Valentine JF, Wang MH, Simpson CL, Bridges SL, Kimberly RP, Rich SS, Cho JH, Rienzo AD, Kao LW, McGovern DP, Brant SR, Kugathasan S. Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. Gastroenterology 2015; 149:1575-1586. [PMID: 26278503 PMCID: PMC4685036 DOI: 10.1053/j.gastro.2015.07.065] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) has familial aggregation in African Americans (AAs), but little is known about the molecular genetic susceptibility. Mapping studies using the Immunochip genotyping array expand the number of susceptibility loci for IBD in Caucasians to 163, but the contribution of the 163 loci and European admixture to IBD risk in AAs is unclear. We performed a genetic mapping study using the Immunochip to determine whether IBD susceptibility loci in Caucasians also affect risk in AAs and identify new associated loci. METHODS We recruited AAs with IBD and without IBD (controls) from 34 IBD centers in the United States; additional controls were collected from 4 other Immunochip studies. Association and admixture loci were mapped for 1088 patients with Crohn's disease, 361 with ulcerative colitis, 62 with IBD type unknown, and 1797 controls; 130,241 autosomal single-nucleotide polymorphisms (SNPs) were analyzed. RESULTS The strongest associations were observed between ulcerative colitis and HLA rs9271366 (P = 7.5 × 10(-6)), Crohn's disease and 5p13.1 rs4286721 (P = 3.5 × 10(-6)), and IBD and KAT2A rs730086 (P = 2.3 × 10(-6)). Additional suggestive associations (P < 4.2 × 10(-5)) were observed between Crohn's disease and IBD and African-specific SNPs in STAT5A and STAT3; between IBD and SNPs in IL23R, IL12B, and C2orf43; and between ulcerative colitis and SNPs near HDAC11 and near LINC00994. The latter 3 loci have not been previously associated with IBD, but require replication. Established Caucasian associations were replicated in AAs (P < 3.1 × 10(-4)) at NOD2, IL23R, 5p15.3, and IKZF3. Significant admixture (P < 3.9 × 10(-4)) was observed for 17q12-17q21.31 (IZKF3 through STAT3), 10q11.23-10q21.2, 15q22.2-15q23, and 16p12.2-16p12.1. Network analyses showed significant enrichment (false discovery rate <1 × 10(-5)) in genes that encode members of the JAK-STAT, cytokine, and chemokine signaling pathways, as well those involved in pathogenesis of measles. CONCLUSIONS In a genetic analysis of 3308 AA IBD cases and controls, we found that many variants associated with IBD in Caucasians also showed association evidence with these diseases in AAs; we also found evidence for variants and loci not previously associated with IBD. The complex genetic factors that determine risk for or protection against IBD in different populations require further study.
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Affiliation(s)
- Chengrui Huang
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,90502, USA
| | - Lisa W. Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Joseph C. Maranville
- Committee on Clinical Pharmacology and Pharmacogenomics, and the Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - Shannon Ellis
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Robert N. Baldassano
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Raymond K. Cross
- Division of Gastroenterology, University of Maryland, Baltimore, MD 21201, USA
| | | | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, PLLC, Charlotte, NC 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for Innovations in Quality, Effectiveness and Safety , Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, LA 71118, USA
| | - Kim L. Isaacs
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kelly E Kachelries
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jeffrey Katz
- Division of Gastroenterology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, TX, 77030
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - John F. Kuemmerle
- Departments of Medicine and Physiology and Biophysics, VCU Program in Enteric Neuromuscular Sciences, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond VA 23298, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John H. Kwon
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Mark Lazarev
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dedrick E. Moulton
- Division of Gastroenterology, Vanderbilt Children's Hospital, Nashville TN 37212, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Ashish Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Rioux
- Universite de Montreal and the Montreal Heart Institute, Research Center, Montreal, Quebec H1T 1C8, Canada
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences and Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA,90502, USA
| | - Shehzad Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ellen J. Scherl
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mark S. Silverberg
- Departments of Medicine, Surgery, Public Health Sciences, Immunology, and Molecular and Medical Genetics, University of Toronto, Samuel Lunenfeld Research Institute and Mount Sinai Hospital, Toronto General Hospital Research Institute, Toronto, Ontario M5S 2J7, Canada
| | - Ann Silverman
- Department of Gastroenterology, Henry Ford Health System Detroit, MI 48208, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - John F. Valentine
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah, Salt Lake City, Utah
| | - Ming-Hsi Wang
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Claire L. Simpson
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - S. Louis Bridges
- Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P. Kimberly
- Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Judy H. Cho
- Department of Medicine and Genetics, Yale University, New Haven, CT 06520, USA
| | - Anna Di Rienzo
- Committee on Clinical Pharmacology and Pharmacogenomics, and the Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Linda W.H. Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90049, USA
| | - Steven R. Brant
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21231, USA, Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA, Corresponding author Steven R. Brant, M.D., Johns Hopkins University School of Medicine, Meyerhoff Inflammatory Bowel Disease Center, 1501 E. Jefferson St., B136, Baltimore, MD 21231. ; Phone: 410-955-9679; Fax: 410-502-9913
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Zhao J, Wu H, Langefeld CD, Kaufman KM, Kelly JA, Bae SC, Alarcón GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, James JA, Merrill JT, Gaffney PM, Sivils KM, Niewold TB, Petri MA, Song ST, Jeong HJ, Ramsey-Goldman R, Reveille JD, Scofield RH, Stevens AM, Boackle SA, Vilá LM, Chang DM, Song YW, Vyse TJ, Harley JB, Brown EE, Edberg JC, Kimberly RP, Hahn BH, Grossman JM, Tsao BP, La Cava A. Genetic associations of leptin-related polymorphisms with systemic lupus erythematosus. Clin Immunol 2015; 161:157-62. [PMID: 26385092 DOI: 10.1016/j.clim.2015.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 09/12/2015] [Accepted: 09/12/2015] [Indexed: 11/28/2022]
Abstract
Leptin is abnormally elevated in the plasma of patients with systemic lupus erythematosus (SLE), where it is thought to promote and/or sustain pro-inflammatory responses. Whether this association could reflect an increased genetic susceptibility to develop SLE is not known, and studies of genetic associations with leptin-related polymorphisms in SLE patients have been so far inconclusive. Here we genotyped DNA samples from 15,706 SLE patients and healthy matched controls from four different ancestral groups, to correlate polymorphisms of genes of the leptin pathway to risk for SLE. It was found that although several SNPs showed weak associations, those associations did not remain significant after correction for multiple testing. These data do not support associations between defined leptin-related polymorphisms and increased susceptibility to develop SLE.
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Affiliation(s)
- Jian Zhao
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Hui Wu
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | | | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research, Universidad del Rosario, Bogotá, Colombia
| | - Lindsey A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA, United States
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Diane L Kamen
- Medical University of South Carolina, Charleston, SC, United States
| | - Gary S Gilkeson
- Medical University of South Carolina, Charleston, SC, United States
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States; Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Joan T Merrill
- Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Kathy Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | | | - Michelle A Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Seung Taek Song
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Hye-Jin Jeong
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | | | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States; Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States; US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
| | - Anne M Stevens
- Department of Pediatrics, University of Washington, Seattle, WA, United States; Center for Immunity and Immunotherapies, Seattle Children's Research Institute Seattle, WA, United States
| | - Susan A Boackle
- University of Colorado School of Medicine, Aurora, CO, United States; US Department of Veterans Affairs Medical Center, Denver, CO, United States
| | - Luis M Vilá
- Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | | | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Elizabeth E Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bevra H Hahn
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Jennifer M Grossman
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Betty P Tsao
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
| | - Antonio La Cava
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
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Roberts BS, Hardigan AA, Kirby MK, Fitz-Gerald MB, Wilcox CM, Kimberly RP, Myers RM. Blocking of targeted microRNAs from next-generation sequencing libraries. Nucleic Acids Res 2015. [PMID: 26209131 PMCID: PMC4666382 DOI: 10.1093/nar/gkv724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Highly abundant microRNAs (miRNAs) in small RNA sequencing libraries make it difficult to obtain efficient measurements of more lowly expressed species. We present a new method that allows for the selective blocking of specific, abundant miRNAs during preparation of sequencing libraries. This technique is specific with little off-target effects and has no impact on the reproducibility of the measurement of non-targeted species. In human plasma samples, we demonstrate that blocking of highly abundant hsa-miR-16–5p leads to improved detection of lowly expressed miRNAs and more precise measurement of differential expression overall. Furthermore, we establish the ability to target a second abundant miRNA and to multiplex the blocking of two miRNAs simultaneously. For small RNA sequencing, this technique could fill a similar role as do ribosomal or globin removal technologies in messenger RNA sequencing.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Marie K Kirby
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Kimberly RP. The Road Traveled: Genomics and Biomarkers in Antineutrophil Cytoplasmic Antibody-Associated Vasculitis. Arthritis Rheumatol 2015; 67:1700-2. [PMID: 25891203 DOI: 10.1002/art.39148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/07/2015] [Indexed: 11/06/2022]
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Arroyo-Ávila M, Santiago-Casas Y, McGwin G, Cantor RS, Petri M, Ramsey-Goldman R, Reveille JD, Kimberly RP, Alarcón GS, Vilá LM, Brown EE. Clinical associations of anti-Smith antibodies in PROFILE: a multi-ethnic lupus cohort. Clin Rheumatol 2015; 34:1217-23. [PMID: 25896533 DOI: 10.1007/s10067-015-2941-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/24/2015] [Accepted: 04/12/2015] [Indexed: 01/19/2023]
Abstract
The aim of this study was to determine the association of anti-Sm antibodies with clinical manifestations, comorbidities, and disease damage in a large multi-ethnic SLE cohort. SLE patients (per American College of Rheumatology criteria), age ≥16 years, disease duration ≤10 years at enrollment, and defined ethnicity (African American, Hispanic or Caucasian), from a longitudinal US cohort were studied. Socioeconomic-demographic features, cumulative clinical manifestations, comorbidities, and disease damage (as per the Systemic Lupus International Collaborating Clinics Damage Index [SDI]) were determined. The association of anti-Sm antibodies with clinical features was examined using multivariable logistic regression analyses adjusting for age, gender, ethnicity, disease duration, level of education, health insurance, and smoking. A total of 2322 SLE patients were studied. The mean (standard deviation, SD) age at diagnosis was 34.4 (12.8) years and the mean (SD) disease duration was 9.0 (7.9) years; 2127 (91.6%) were women. Anti-Sm antibodies were present in 579 (24.9%) patients. In the multivariable analysis, anti-Sm antibodies were significantly associated with serositis, renal involvement, psychosis, vasculitis, Raynaud's phenomenon, hemolytic anemia, leukopenia, lymphopenia, and arterial hypertension. No significant association was found for damage accrual. In this cohort of SLE patients, anti-Sm antibodies were associated with several clinical features including serious manifestations such as renal, neurologic, and hematologic disorders as well as vasculitis.
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Affiliation(s)
- Mariangelí Arroyo-Ávila
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, PO Box 365067, San Juan, PR, 00936-5067, USA
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Pennison MJ, Zeng Q, Buckhaults PJ, Kaklamani VG, Lindor NM, Hopper JL, Le Marchand L, Gallinger S, Newcomb PA, Haile RW, Baron JA, Stram DO, Zhang HT, Manne U, Edberg JC, Kimberly RP, Xu J, Zhang K, Yi N, Pasche B. Dual role of TGFBR1 as a modifier of colorectal cancer risk. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.3_suppl.600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
600 Background: Experimental and clinical evidence suggests that constitutively decreased Transforming Growth Factor Beta type I receptor (TGFBR1) signaling predisposes to colorectal cancer (CRC) development. However, associations between TGFBR1 variants and CRC risk in case-control studies have been inconsistent. Methods: We utilized 1,043 CRC cases and their 1,627 unaffected sibling controls obtained from the Colon Cancer Family Registry (C-CFR). Individuals were genotyped for twelve TGFBR1 haplotype tagging SNPs. SNPs associated with CRC risk were validated in 261 CRC cases and 531 controls of African American ancestry and 990 CRC cases and 3,427 controls of Han Chinese ancestry. Validated SNPs were functionally characterized with respect to TGFBR1 expression and TGF-β signaling. Results: The TGFBR1 rs7034462-TT genotype was associated with CRC risk in C-CFR participants (OR 3.80[1.46-9.85]) and African Americans (OR 8.16[2.07-32.08]) (see Table). The TT genotype was associated with stage III and stage IV at diagnosis in C-CFR participants (OR 2.99[1.15-7.81] and OR 9.38[1.54-57.28]) and African Americans (OR 5.89[1.15-30.02] and OR 12.75[1.88-86.33]), respectively. The rs7034462-CT genotype was associated with decreased risk for CRC in African Americans (OR 0.55[0.31-0.99]) and Han Chinese (OR 0.67[0.48-0.95]) (see table). Cells carrying the rs7034462-TT genotype exhibited decreased constitutive TGFBR1 expression, increased SMAD7 expression, and decreased TGF-β signaling. Conclusions: The TGFBR1 rs7034462-T allele has dual, opposite roles with respect to CRC risk. The rare rs7034462-TT genotype is a moderate penetrance genotype associated with risk for CRC and advanced stage disease at diagnosis. In contrast, the common rs7034462-CT genotype is associated with decreased CRC risk. [Table: see text]
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Affiliation(s)
| | - Qinghua Zeng
- University of Alabama at Birmingham, Birmingham, AL
| | | | | | | | | | | | - Steven Gallinger
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Robert W. Haile
- Stanford Cancer Institute, Stanford University, Stanford, CA
| | - John A. Baron
- The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Hong-Tao Zhang
- Soochow University, Suzhou Key Laboratory of Cancer Molecular Genetics, Suzhou, China
| | | | | | | | - Jianfeng Xu
- Wake Forest University, Center for Genomics and Personalized Medicine, Winston-Salem, NC
| | - Kui Zhang
- University of Alabama at Birmingham, Birmingham, AL
| | - Nengjun Yi
- University of Alabama at Birmingham, Birmingham, AL
| | - Boris Pasche
- Wake Forest University Comprehensive Cancer Center, Winston-Salem, NC
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38
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Vaughn SE, Foley C, Lu X, Patel ZH, Zoller EE, Magnusen AF, Williams AH, Ziegler JT, Comeau ME, Marion MC, Glenn SB, Adler A, Shen N, Nath S, Stevens AM, Freedman BI, Tsao BP, Jacob CO, Kamen DL, Brown EE, Gilkeson GS, Alarcón GS, Reveille JD, Anaya JM, James JA, Moser KL, Criswell LA, Vilá LM, Alarcón-Riquelme ME, Petri M, Scofield RH, Kimberly RP, Ramsey-Goldman R, Binjoo Y, Choi J, Bae SC, Boackle SA, Vyse TJ, Guthridge JM, Namjou B, Gaffney PM, Langefeld CD, Kaufman KM, Kelly JA, Harley ITW, Harley JB, Kottyan LC. Lupus risk variants in the PXK locus alter B-cell receptor internalization. Front Genet 2015; 5:450. [PMID: 25620976 PMCID: PMC4288052 DOI: 10.3389/fgene.2014.00450] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/09/2014] [Indexed: 01/17/2023] Open
Abstract
Genome wide association studies have identified variants in PXK that confer risk for humoral autoimmune diseases, including systemic lupus erythematosus (SLE or lupus), rheumatoid arthritis and more recently systemic sclerosis. While PXK is involved in trafficking of epidermal growth factor Receptor (EGFR) in COS-7 cells, mechanisms linking PXK to lupus pathophysiology have remained undefined. In an effort to uncover the mechanism at this locus that increases lupus-risk, we undertook a fine-mapping analysis in a large multi-ancestral study of lupus patients and controls. We define a large (257kb) common haplotype marking a single causal variant that confers lupus risk detected only in European ancestral populations and spans the promoter through the 3′ UTR of PXK. The strongest association was found at rs6445972 with P < 4.62 × 10−10, OR 0.81 (0.75–0.86). Using stepwise logistic regression analysis, we demonstrate that one signal drives the genetic association in the region. Bayesian analysis confirms our results, identifying a 95% credible set consisting of 172 variants spanning 202 kb. Functionally, we found that PXK operates on the B-cell antigen receptor (BCR); we confirmed that PXK influenced the rate of BCR internalization. Furthermore, we demonstrate that individuals carrying the risk haplotype exhibited a decreased rate of BCR internalization, a process known to impact B cell survival and cell fate. Taken together, these data define a new candidate mechanism for the genetic association of variants around PXK with lupus risk and highlight the regulation of intracellular trafficking as a genetically regulated pathway mediating human autoimmunity.
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Affiliation(s)
- Samuel E Vaughn
- Immunology Graduate Program and Medical Scientist Training Program, University of Cincinnati College of Medicine Cincinnati, OH, USA ; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | | | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Zubin H Patel
- Immunology Graduate Program and Medical Scientist Training Program, University of Cincinnati College of Medicine Cincinnati, OH, USA ; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Erin E Zoller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Albert F Magnusen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Adrienne H Williams
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Julie T Ziegler
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Mary E Comeau
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Miranda C Marion
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Stuart B Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Nan Shen
- Immunology Graduate Program and Medical Scientist Training Program, University of Cincinnati College of Medicine Cincinnati, OH, USA ; Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences Shanghai, China
| | - Swapan Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Anne M Stevens
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute Seattle, WA, USA ; Division of Rheumatology, Department of Pediatrics, University of Washington Seattle, WA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles Los Angeles, CA, USA
| | - Chaim O Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California Los Angeles, CA, USA
| | - Diane L Kamen
- Division of Rheumatology, Medical University of South Carolina Charleston, SC, USA
| | - Elizabeth E Brown
- Department of Epidemiology, University of Alabama at Birmingham Birmingham, AL, USA ; Department of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Gary S Gilkeson
- Division of Rheumatology, Medical University of South Carolina Charleston, SC, USA
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston Houston, TX, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Disease Research, Universidad del Rosario Bogota, Colombia
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA ; Department of Medicine, University of Oklahoma Health Sciences Center Oklahoma City, OK, USA
| | - Kathy L Moser
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Lindsey A Criswell
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Research Center, Department of Medicine, University of California, San Francisco San Francisco, CA, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus San Juan, PR, USA
| | - Marta E Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA ; Center for Genomics and Oncological Research, Pfizer-University of Granada-Junta de Andalucia Granada, Spain
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA ; Department of Medicine, University of Oklahoma Health Sciences Center Oklahoma City, OK, USA ; United States Department of Veterans Affairs Medical Center Oklahoma City, OK, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham Birmingham, AL, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
| | - Young Binjoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases Seoul, Korea
| | - Jeongim Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases Seoul, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases Seoul, Korea
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine Aurora, CO, USA
| | - Timothy J Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, King's College London London, UK
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Carl D Langefeld
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine Winston-Salem, NC, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA ; United States Department of Veterans Affairs Medical Center Cincinnati, OH, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation Oklahoma City, OK, USA
| | - Isaac T W Harley
- Immunology Graduate Program and Medical Scientist Training Program, University of Cincinnati College of Medicine Cincinnati, OH, USA ; Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA ; United States Department of Veterans Affairs Medical Center Cincinnati, OH, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA ; United States Department of Veterans Affairs Medical Center Cincinnati, OH, USA
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39
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Martins M, Williams AH, Comeau M, Marion M, Ziegler JT, Freedman BI, Merrill JT, Glenn SB, Kelly JA, Sivils KM, James JA, Guthridge JM, Alarcón-Riquelme ME, Bae SC, Kim JH, Kim D, Anaya JM, Boackle SA, Criswell LA, Kimberly RP, Alarcón GS, Brown EE, Vilá LM, Petri MA, Ramsey-Goldman R, Niewold TB, Tsao BP, Gilkeson GS, Kamen DL, Jacob CO, Stevens AM, Gaffney PM, Harley JB, Langefeld CD, Fesel C. Genetic association of CD247 (CD3ζ) with SLE in a large-scale multiethnic study. Genes Immun 2015; 16:142-50. [PMID: 25569266 DOI: 10.1038/gene.2014.73] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/03/2014] [Accepted: 11/07/2014] [Indexed: 11/09/2022]
Abstract
A classic T-cell phenotype in systemic lupus erythematosus (SLE) is the downregulation and replacement of the CD3ζ chain that alters T-cell receptor signaling. However, genetic associations with SLE in the human CD247 locus that encodes CD3ζ are not well established and require replication in independent cohorts. Our aim was therefore to examine, localize and validate CD247-SLE association in a large multiethnic population. We typed 44 contiguous CD247 single-nucleotide polymorphisms (SNPs) in 8922 SLE patients and 8077 controls from four ethnically distinct populations. The strongest associations were found in the Asian population (11 SNPs in intron 1, 4.99 × 10(-4) < P < 4.15 × 10(-2)), where we further identified a five-marker haplotype (rs12141731-rs2949655-rs16859085-rs12144621-rs858554; G-G-A-G-A; P(hap) = 2.12 × 10(-5)) that exceeded the most associated single SNP rs858554 (minor allele frequency in controls = 13%; P = 4.99 × 10(-4), odds ratio = 1.32) in significance. Imputation and subsequent association analysis showed evidence of association (P < 0.05) at 27 additional SNPs within intron 1. Cross-ethnic meta-analysis, assuming an additive genetic model adjusted for population proportions, showed five SNPs with significant P-values (1.40 × 10(-3) < P< 3.97 × 10(-2)), with one (rs704848) remaining significant after Bonferroni correction (P(meta) = 2.66 × 10(-2)). Our study independently confirms and extends the association of SLE with CD247, which is shared by various autoimmune disorders and supports a common T-cell-mediated mechanism.
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Affiliation(s)
- M Martins
- 1] Instituto de Medicina Molecular, Lisboa, Portugal [2] Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - A H Williams
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - M Comeau
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - M Marion
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - J T Ziegler
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - B I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - J T Merrill
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - S B Glenn
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - J A Kelly
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - K M Sivils
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - J A James
- 1] Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA [2] Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - J M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - M E Alarcón-Riquelme
- 1] Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA [2] Centro de Genómica e Investigaciones Oncológicas (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - S-C Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - J-H Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - D Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - J-M Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogota, Colombia
| | - S A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - L A Criswell
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California, San Francisco, CA, USA
| | - R P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - G S Alarcón
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E E Brown
- Departments of Medicine and Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - L M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - M A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - R Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - T B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - B P Tsao
- Division of Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - G S Gilkeson
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - D L Kamen
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - C O Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - A M Stevens
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute Arthritis Foundation, Seattle, WA, USA
| | - P M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - J B Harley
- 1] Division of Rheumatology and the Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA [2] US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - C D Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - C Fesel
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Kariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, Kimberly RP, Alarcón-Riquelme ME, Jacob CO, Criswell LA, Sivils KL, Langefeld CD, Harley JB, Skol AD, Niewold TB. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun 2014; 16:15-23. [PMID: 25338677 PMCID: PMC4305028 DOI: 10.1038/gene.2014.57] [Citation(s) in RCA: 52] [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: 05/30/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. 40–50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs. low IFN-α in over 1550 SLE cases, including GWAS and replication cohorts. In meta-analysis, the top associations in European ancestry were PRKG1 rs7897633 (PMeta=2.75 × 10−8) and PNP rs1049564 (PMeta=1.24 × 10−7). We also found evidence for cross-ancestral background associations with the ANKRD44 and PLEKHF2 loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic subphenotypes becomes an attractive strategy for genetic discovery in complex disease.
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Affiliation(s)
- S N Kariuki
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Y Ghodke-Puranik
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - J M Dorschner
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - B S Chrabot
- Gwen Knapp Center for Lupus Research, University of Chicago, Chicago, IL, USA
| | - J A Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - B P Tsao
- Department of Medicine, University of California, Los Angeles, CA, USA
| | - R P Kimberly
- Department of Medicine, University of Alabama, Birmingham, AL, USA
| | - M E Alarcón-Riquelme
- 1] Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA [2] GENYO Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - C O Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - L A Criswell
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - K L Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - C D Langefeld
- Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - J B Harley
- Cincinnati Children's Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - A D Skol
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - T B Niewold
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
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Abstract
INTRODUCTION The Fc receptors (FcRs) and their interactions with immunoglobulin and innate immune opsonins, such as C-reactive protein, are key players in humoral and cellular immune responses. As the effector mechanism for some therapeutic monoclonal antibodies, and often a contributor to the pathogenesis and progression of autoimmunity, FcRs are promising targets for treating autoimmune diseases. AREAS COVERED This review discusses the nature of different FcRs and the various mechanisms of their involvement in initiating and modulating immunocyte functions and their biological consequences. It describes a range of current strategies in targeting FcRs and manipulating their interaction with specific ligands, while presenting the pros and cons of these approaches. This review also discusses potential new strategies including regulation of FcR expression and receptor crosstalk. EXPERT OPINION FcRs are appealing targets in the treatment of inflammatory autoimmune diseases. However, there are still knowledge limitations and technical challenges, the most important being a better understanding of the individual roles of each of the FcRs and enhancement of the specificity in targeting particular cell types and specific FcRs.
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Affiliation(s)
- Xinrui Li
- The University of Alabama , SHEL 272, 1825 University Blvd, Birmingham, AL 35294 , USA
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Palmer ND, Ng MCY, Langefeld CD, Divers J, Lea JP, Okusa MD, Kimberly RP, Bowden DW, Freedman BI. Lack of Association of the APOL1 G3 Haplotype in African Americans with ESRD. J Am Soc Nephrol 2014; 26:1021-5. [PMID: 25249559 DOI: 10.1681/asn.2014050444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/05/2014] [Indexed: 01/13/2023] Open
Abstract
Apolipoprotein L1 gene (APOL1) G1 and G2 variants are strongly associated with progressive nondiabetic nephropathy in populations with recent African ancestry. Selection for these variants occurred as a result of protection from human African trypanosomiasis (HAT). Resequencing of this region in 10 genetically and geographically distinct African populations residing in HAT endemic regions identified eight single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium and comprising a novel G3 haplotype. To determine whether the APOL1 G3 haplotype was associated with nephropathy, G1, G2, and G3 SNPs and 70 ancestry informative markers spanning the genome were genotyped in 937 African Americans with nondiabetic ESRD, 965 African Americans with type 2 diabetes-associated ESRD, and 1029 non-nephropathy controls. In analyses adjusting for age, sex, APOL1 G1/G2 risk (recessive), and global African ancestry, the G3 haplotype was not significantly associated with ESRD (P=0.05 for nondiabetic ESRD, P=0.57 for diabetes-associated ESRD, and P=0.27 for all-cause ESRD). We conclude that variation in APOL1 G3 makes a nominal, if any, contribution to ESRD in African Americans; G1 and G2 variants explain the vast majority of nondiabetic nephropathy susceptibility.
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Affiliation(s)
- Nicholette D Palmer
- Departments of Biochemistry, Centers for Genomics and Personalized Medicine Research and Public Health Genomics, and
| | - Maggie C Y Ng
- Centers for Genomics and Personalized Medicine Research and Public Health Genomics, and
| | | | - Jasmin Divers
- Public Health Genomics, and Biostatistical Sciences, and
| | - Janice P Lea
- Division of Renal Medicine, Department of Medicine, Emory School of Medicine, Atlanta, Georgia
| | - Mark D Okusa
- Division of Nephrology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama, Birmingham, Alabama
| | - Donald W Bowden
- Departments of Biochemistry, Centers for Genomics and Personalized Medicine Research and
| | - Barry I Freedman
- Centers for Genomics and Personalized Medicine Research and Public Health Genomics, and Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina; Internal Medicine,
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Kaiser R, Tang LF, Taylor KE, Sterba K, Nititham J, Brown EE, Edberg JC, McGwin G, Alarcón GS, Ramsey-Goldman R, Reveille JD, Vilá LM, Petri M, Rauch J, Miller E, Mesznik K, Kwok PY, Kimberly RP, Salmon JE, Criswell LA. A polymorphism in TLR2 is associated with arterial thrombosis in a multiethnic population of patients with systemic lupus erythematosus. Arthritis Rheumatol 2014; 66:1882-7. [PMID: 24578102 PMCID: PMC4269184 DOI: 10.1002/art.38520] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 02/18/2014] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Thrombosis is a serious complication of systemic lupus erythematosus (SLE). Studies that have investigated the genetics of thrombosis in SLE are limited. We undertook this study to assess the association of previously implicated candidate genes, particularly Toll-like receptor (TLR) genes, with pathogenesis of thrombosis. METHODS We genotyped 3,587 SLE patients from 3 multiethnic populations for 77 single-nucleotide polymorphisms (SNPs) in 10 genes, primarily in TLRs 2, 4, 7, and 9, and we also genotyped 64 ancestry-informative markers (AIMs). We first analyzed association with arterial and venous thrombosis in the combined population via logistic regression, adjusting for top principal components of the AIMs and other covariates. We also subjected an associated SNP, rs893629, to meta-analysis (after stratification by ethnicity and study population) to confirm the association and to test for study population or ethnicity effects. RESULTS In the combined analysis, the SNP rs893629 in the KIAA0922/TLR2 region was significantly associated with arterial thrombosis (logistic P = 6.4 × 10(-5) , false discovery rate P = 0.0044). Two additional SNPs in TLR2 were also suggestive: rs1816702 (logistic P = 0.002) and rs4235232 (logistic P = 0.009). In the meta-analysis by study population, the odds ratio (OR) for arterial thrombosis with rs893629 was 2.44 (95% confidence interval 1.58-3.76), without evidence for heterogeneity (P = 0.78). By ethnicity, the effect was most significant among African Americans (OR 2.42, P = 3.5 × 10(-4) ) and European Americans (OR 3.47, P = 0.024). CONCLUSION TLR2 gene variation is associated with thrombosis in SLE, particularly among African Americans and European Americans. There was no evidence of association among Hispanics, and results in Asian Americans were limited due to insufficient sample size. These results may help elucidate the pathogenesis of this important clinical manifestation.
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Zhao J, Giles BM, Taylor RL, Yette GA, Lough KM, Ng HL, Abraham LJ, Wu H, Kelly JA, Glenn SB, Adler AJ, Williams AH, Comeau ME, Ziegler JT, Marion M, Alarcón-Riquelme ME, Alarcón GS, Anaya JM, Bae SC, Kim D, Lee HS, Criswell LA, Freedman BI, Gilkeson GS, Guthridge JM, Jacob CO, James JA, Kamen DL, Merrill JT, Sivils KM, Niewold TB, Petri MA, Ramsey-Goldman R, Reveille JD, Scofield RH, Stevens AM, Vilá LM, Vyse TJ, Kaufman KM, Harley JB, Langefeld CD, Gaffney PM, Brown EE, Edberg JC, Kimberly RP, Ulgiati D, Tsao BP, Boackle SA. Preferential association of a functional variant in complement receptor 2 with antibodies to double-stranded DNA. Ann Rheum Dis 2014; 75:242-52. [PMID: 25180293 PMCID: PMC4717392 DOI: 10.1136/annrheumdis-2014-205584] [Citation(s) in RCA: 10] [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: 03/18/2014] [Accepted: 08/02/2014] [Indexed: 02/03/2023]
Abstract
Objectives Systemic lupus erythematosus (SLE; OMIM 152700) is characterised by the production of antibodies to nuclear antigens. We previously identified variants in complement receptor 2 (CR2/CD21) that were associated with decreased risk of SLE. This study aimed to identify the causal variant for this association. Methods Genotyped and imputed genetic variants spanning CR2 were assessed for association with SLE in 15 750 case-control subjects from four ancestral groups. Allele-specific functional effects of associated variants were determined using quantitative real-time PCR, quantitative flow cytometry, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP)-PCR. Results The strongest association signal was detected at rs1876453 in intron 1 of CR2 (pmeta=4.2×10−4, OR 0.85), specifically when subjects were stratified based on the presence of dsDNA autoantibodies (case-control pmeta=7.6×10−7, OR 0.71; case-only pmeta=1.9×10−4, OR 0.75). Although allele-specific effects on B cell CR2 mRNA or protein levels were not identified, levels of complement receptor 1 (CR1/CD35) mRNA and protein were significantly higher on B cells of subjects harbouring the minor allele (p=0.0248 and p=0.0006, respectively). The minor allele altered the formation of several DNA protein complexes by EMSA, including one containing CCCTC-binding factor (CTCF), an effect that was confirmed by ChIP-PCR. Conclusions These data suggest that rs1876453 in CR2 has long-range effects on gene regulation that decrease susceptibility to lupus. Since the minor allele at rs1876453 is preferentially associated with reduced risk of the highly specific dsDNA autoantibodies that are present in preclinical, active and severe lupus, understanding its mechanisms will have important therapeutic implications.
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Affiliation(s)
- Jian Zhao
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Brendan M Giles
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rhonda L Taylor
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gabriel A Yette
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kara M Lough
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Han Leng Ng
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia
| | - Lawrence J Abraham
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia
| | - Hui Wu
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Stuart B Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Adam J Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Adrienne H Williams
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Mary E Comeau
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Julie T Ziegler
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Miranda Marion
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Marta E Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain
| | | | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Dam Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Lindsey A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Gary S Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, California, USA
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Diane L Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Joan T Merrill
- Department of Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle A Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - John D Reveille
- Department of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - Anne M Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, USA Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine and Immunology, King's College London, London, UK
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Elizabeth E Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Daniela Ulgiati
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA Denver Veterans Affairs Medical Center, Denver, Colorado, USA
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Dong C, Ptacek TS, Redden DT, Zhang K, Brown EE, Edberg JC, McGwin G, Alarcón GS, Ramsey-Goldman R, Reveille JD, Vilá LM, Petri M, Qin A, Wu J, Kimberly RP. Fcγ receptor IIIa single-nucleotide polymorphisms and haplotypes affect human IgG binding and are associated with lupus nephritis in African Americans. Arthritis Rheumatol 2014; 66:1291-9. [PMID: 24782186 DOI: 10.1002/art.38337] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/19/2013] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To investigate whether the Fcγ receptor IIIa-66L/R/H (FcγRIIIa-66L/R/H) polymorphism influences net effective receptor function and to assess if the FCGR3A combined genotypes formed by FcγRIIIa-66L/R/H and FcγRIIIa-176F/V, as well as copy number variation (CNV), confer risk of developing systemic lupus erythematosus (SLE) and lupus nephritis. METHODS FcγRIIIa variants, expressed on A20 IIA1.6 cells, were used in flow cytometry-based human IgG-binding assays. Using Pyrosequencing methodology, FCGR3A single-nucleotide polymorphism and CNV genotypes were determined in a cohort of 1,728 SLE patients and 2,404 healthy controls. RESULTS The FcγRIIIa-66L/R/H (rs10127939) polymorphism influenced ligand binding capacity in the presence of the FcγRIIIa-176V (rs396991) allele. There was a trend toward an association of the low-binding FcγRIIIa-176F allele with lupus nephritis among African Americans (P = 0.0609) but not among European Americans (P > 0.10). Nephritis among African American patients with SLE was associated with FcγRIIIa low-binding haplotypes containing the 66L/R/H and 176F variants (P = 0.03) and with low-binding genotype combinations (P = 0.002). No association was observed among European American patients with SLE. The distribution of FCGR3A CNV was not significantly different among controls and SLE patients with or without nephritis. CONCLUSION FcγRIIIa-66L/R/H influences ligand binding. The low-binding haplotypes formed by 66L/R/H and 176F confer enhanced risk of lupus nephritis in African Americans. FCGR3A CNVs are not associated with SLE or lupus nephritis in either African Americans or European Americans.
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Affiliation(s)
- Chaoling Dong
- Yangzhou University, Yangzhou, China; University of Alabama at, Birmingham
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Li X, Wu J, Ptacek T, Redden DT, Brown EE, Alarcón GS, Ramsey-Goldman R, Petri MA, Reveille JD, Kaslow RA, Kimberly RP, Edberg JC. Allelic-dependent expression of an activating Fc receptor on B cells enhances humoral immune responses. Sci Transl Med 2014; 5:216ra175. [PMID: 24353158 DOI: 10.1126/scitranslmed.3007097] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
B cells are pivotal regulators of acquired immune responses, and recent work in both experimental murine models and humans has demonstrated that subtle changes in the regulation of B cell function can substantially alter immunological responses. The balance of negative and positive signals in maintaining an appropriate B cell activation threshold is critical in B lymphocyte immune tolerance and autoreactivity. FcγRIIb (CD32B), the only recognized Fcγ receptor on B cells, provides immunoglobulin G (IgG)-mediated negative modulation through a tyrosine-based inhibition motif, which down-regulates B cell receptor-initiated signaling. These properties make FcγRIIb a promising target for antibody-based therapy. We report the discovery of allele-dependent expression of the activating FcγRIIc on B cells. Identical to FcγRIIb in the extracellular domain, FcγRIIc has a tyrosine-based activation motif in its cytoplasmic domain. In both human B cells and B cells from mice transgenic for human FcγRIIc, FcγRIIc expression counterbalances the negative feedback of FcγRIIb and enhances humoral responses to immunization in mice and to BioThrax vaccination in a human anthrax vaccine trial. Moreover, the FCGR2C-ORF allele is associated with the risk of development of autoimmunity in humans. FcγRIIc expression on B cells challenges the prevailing paradigm of unidirectional negative feedback by IgG immune complexes via the inhibitory FcγRIIb, is a previously unrecognized determinant in human antibody/autoantibody responses, and opens the opportunity for more precise personalized use of B cell-targeted antibody-based therapy.
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Affiliation(s)
- Xinrui Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Chung SA, Brown EE, Williams AH, Ramos PS, Berthier CC, Bhangale T, Alarcon-Riquelme ME, Behrens TW, Criswell LA, Graham DC, Demirci FY, Edberg JC, Gaffney PM, Harley JB, Jacob CO, Kamboh MI, Kelly JA, Manzi S, Moser-Sivils KL, Russell LP, Petri M, Tsao BP, Vyse TJ, Zidovetzki R, Kretzler M, Kimberly RP, Freedman BI, Graham RR, Langefeld CD. Lupus nephritis susceptibility loci in women with systemic lupus erythematosus. J Am Soc Nephrol 2014; 25:2859-70. [PMID: 24925725 DOI: 10.1681/asn.2013050446] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [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: 11/03/2022] Open
Abstract
Lupus nephritis is a manifestation of SLE resulting from glomerular immune complex deposition and inflammation. Lupus nephritis demonstrates familial aggregation and accounts for significant morbidity and mortality. We completed a meta-analysis of three genome-wide association studies of SLE to identify lupus nephritis-predisposing loci. Through genotyping and imputation, >1.6 million markers were assessed in 2000 unrelated women of European descent with SLE (588 patients with lupus nephritis and 1412 patients with lupus without nephritis). Tests of association were computed using logistic regression adjusting for population substructure. The strongest evidence for association was observed outside the MHC and included markers localized to 4q11-q13 (PDGFRA, GSX2; P=4.5×10(-7)), 16p12 (SLC5A11; P=5.1×10(-7)), 6p22 (ID4; P=7.4×10(-7)), and 8q24.12 (HAS2, SNTB1; P=1.1×10(-6)). Both HLA-DR2 and HLA-DR3, two well established lupus susceptibility loci, showed evidence of association with lupus nephritis (P=0.06 and P=3.7×10(-5), respectively). Within the class I region, rs9263871 (C6orf15-HCG22) had the strongest evidence of association with lupus nephritis independent of HLA-DR2 and HLA-DR3 (P=8.5×10(-6)). Consistent with a functional role in lupus nephritis, intra-renal mRNA levels of PDGFRA and associated pathway members showed significant enrichment in patients with lupus nephritis (n=32) compared with controls (n=15). Results from this large-scale genome-wide investigation of lupus nephritis provide evidence of multiple biologically relevant lupus nephritis susceptibility loci.
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Affiliation(s)
- Sharon A Chung
- Division of Rheumatology, Rosalind Russell-Ephraim P. Engleman Medical Research Center for Arthritis, University of California, San Francisco, California
| | - Elizabeth E Brown
- Department of Epidemiology, University of Alabama, Birmingham, Alabama; Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Adrienne H Williams
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Celine C Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Marta E Alarcon-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; Human DNA Variability Area, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, Granada, Spain
| | - Timothy W Behrens
- Immunology Tissue Growth and Repair Human Genetics Group, Genentech Inc., South San Francisco, California
| | - Lindsey A Criswell
- Division of Rheumatology, Rosalind Russell-Ephraim P. Engleman Medical Research Center for Arthritis, University of California, San Francisco, California
| | - Deborah Cunninghame Graham
- Divisions of Genetics and Molecular Medicine and Immunology, Infection, and Inflammatory Disease, Kings College, London, United Kingdom
| | - F Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - John B Harley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, California
| | - M Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Susan Manzi
- Department of Medicine, West Penn Allegheny Health System, University of Pittsburgh, Pittsburgh, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Kathy L Moser-Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Laurie P Russell
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California, Los Angeles, California
| | - Tim J Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, Infection, and Inflammatory Disease, Kings College, London, United Kingdom
| | - Raphael Zidovetzki
- Department of Cell Biology and Neuroscience, University of California, Riverside, California; and
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Robert R Graham
- Immunology Tissue Growth and Repair Human Genetics Group, Genentech Inc., South San Francisco, California
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina;
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Armstrong DL, Zidovetzki R, Alarcón-Riquelme ME, Tsao BP, Criswell LA, Kimberly RP, Harley JB, Sivils KL, Vyse TJ, Gaffney PM, Langefeld CD, Jacob CO. GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. Genes Immun 2014; 15:347-54. [PMID: 24871463 PMCID: PMC4156543 DOI: 10.1038/gene.2014.23] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 01/09/2014] [Revised: 03/26/2014] [Accepted: 04/04/2014] [Indexed: 11/16/2022]
Abstract
In a Genome Wide Association Study (GWAS) of individuals of European ancestry afflicted with Systemic Lupus Erythematosus (SLE) the extensive utilization of imputation, stepwise multiple regression, lasso regularization, and increasing study power by utilizing False Discovery Rate (FDR) instead of a Bonferroni multiple test correction enabled us to identify 13 novel non-human leukocyte antigen (HLA) genes and confirmed the association of 4 genes previously reported to be associated. Novel genes associated with SLE susceptibility included two transcription factors (EHF, and MED1), two components of the NFκB pathway (RASSF2 and RNF114), one gene involved in adhesion and endothelial migration (CNTN6), and two genes involved in antigen presentation (BIN1 and SEC61G). In addition, the strongly significant association of multiple single nucleotide polymorphisms (SNPs) in the HLA region was assigned to HLA alleles and serotypes and deconvoluted into four primary signals. The novel SLE-associated genes point to new directions for both the diagnosis and treatment of this debilitating autoimmune disease.
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Affiliation(s)
- D L Armstrong
- 1] The Lupus Genetic Group, Department of Medicine, University of Southern California, Los Angeles, CA, USA [2] Cell Biology and Neuroscience, University of California at Riverside, Riverside, CA, USA
| | - R Zidovetzki
- 1] The Lupus Genetic Group, Department of Medicine, University of Southern California, Los Angeles, CA, USA [2] Cell Biology and Neuroscience, University of California at Riverside, Riverside, CA, USA
| | - M E Alarcón-Riquelme
- 1] Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA [2] Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucia, Granada, Spain
| | - B P Tsao
- Division of Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - L A Criswell
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - R P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J B Harley
- 1] Division of Rheumatology and The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA [2] U.S. Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - K L Sivils
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - T J Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, King's College London, London, UK
| | - P M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - C D Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, NC, USA
| | - C O Jacob
- The Lupus Genetic Group, Department of Medicine, University of Southern California, Los Angeles, CA, USA
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Freedman BI, Langefeld CD, Andringa KK, Croker JA, Williams AH, Garner NE, Birmingham DJ, Hebert LA, Hicks PJ, Segal MS, Edberg JC, Brown EE, Alarcón GS, Costenbader KH, Comeau ME, Criswell LA, Harley JB, James JA, Kamen DL, Lim SS, Merrill JT, Sivils KL, Niewold TB, Patel NM, Petri M, Ramsey-Goldman R, Reveille JD, Salmon JE, Tsao BP, Gibson KL, Byers JR, Vinnikova AK, Lea JP, Julian BA, Kimberly RP. End-stage renal disease in African Americans with lupus nephritis is associated with APOL1. Arthritis Rheumatol 2014; 66:390-6. [PMID: 24504811 DOI: 10.1002/art.38220] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/01/2013] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE) that exhibits familial aggregation and may progress to end-stage renal disease (ESRD). LN is more prevalent among African Americans than among European Americans. This study was undertaken to investigate the hypothesis that the apolipoprotein L1 gene (APOL1) nephropathy risk alleles G1/G2, common in African Americans and rare in European Americans, contribute to the ethnic disparity in risk. METHODS APOL1 G1 and G2 nephropathy alleles were genotyped in 855 African American SLE patients with LN-ESRD (cases) and 534 African American SLE patients without nephropathy (controls) and tested for association under a recessive genetic model, by logistic regression. RESULTS Ninety percent of the SLE patients were female. The mean ± SD age at SLE diagnosis was significantly lower in LN-ESRD cases than in SLE non-nephropathy controls (27.3 ± 10.9 years versus 39.5 ± 12.2 years). The mean ± SD time from SLE diagnosis to development of LN-ESRD in cases was 7.3 ± 7.2 years. The G1/G2 risk alleles were strongly associated with SLE-ESRD, with 25% of cases and 12% of controls having 2 nephropathy alleles (odds ratio [OR] 2.57, recessive model P = 1.49 × 10(-9)), and after adjustment for age, sex, and ancestry admixture (OR 2.72, P = 6.23 × 10(-6)). The age-, sex-, and admixture-adjusted population attributable risk for ESRD among patients with G1/G2 polymorphisms was 0.26, compared to 0.003 among European American patients. The mean time from SLE diagnosis to ESRD development was ∼2 years earlier among individuals with APOL1 risk genotypes (P = 0.01). CONCLUSION APOL1 G1/G2 alleles strongly impact the risk of LN-ESRD in African Americans, as well as the time to progression to ESRD. The high frequency of these alleles in African Americans with near absence in European Americans explains an important proportion of the increased risk of LN-ESRD in African Americans.
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Abstract
Fc receptors play a central role in maintaining the homeostatic balance in the immune system. Our knowledge of the structure and function of these receptors and their naturally occurring polymorphisms, including single nucleotide polymorphisms and/or copy number variations, continues to expand. Through studies of their impact on human biology and clinical phenotype, the contributions of these variants to the pathogenesis, progression, and/or treatment outcome of many diseases that involve immunoglobulin have become evident. They affect susceptibility to bacterial and viral pathogens, constitute as risk factors for IgG or IgE mediated inflammatory diseases, and impact the development of many autoimmune conditions. In this chapter, we will provide an overview of these genetic variations in classical FcγRs, FcRLs, and other Fc receptors, as well as challenges in achieving an accurate and comprehensive understanding of the FcR polymorphisms and genomic architecture.
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Affiliation(s)
- Marc Daeron
- grid.428999.70000000123536535Institut Pasteur, Paris, France
| | - Falk Nimmerjahn
- grid.5330.50000000121073311Department of Biology, Institute of Genetics, University of Erlangen-Nürnberg, Erlangen, Germany
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