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Sun W, Zhu C, Li Y, Wu X, Shi X, Liu W. B cell activation and autoantibody production in autoimmune diseases. Best Pract Res Clin Rheumatol 2024:101936. [PMID: 38326197 DOI: 10.1016/j.berh.2024.101936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
B cells are central players in the immune system, responsible for producing antibodies and modulating immune responses. This review explores the intricate relationship between aberrant B cell activation and the development of autoimmune diseases, emphasizing the essential role of B cells in these conditions. We also summarize B cell receptor signaling and Toll-like receptor signaling in B cell activation, as well as their association with autoimmune diseases, shedding light on the molecular mechanisms behind these associations. Additionally, we explore the clinical observations involving B cell activation and their significance in autoimmune disease management. Various clinical studies related to B cell-targeted therapies are also discussed, offering insights into potential avenues for improving treatment strategies. Overall, this review serves as a resource for researchers and clinicians in the field of immunology and autoimmune diseases, providing a general view of B cell signaling and its role in autoimmunity.
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Affiliation(s)
- Wenbo Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, No. 1, Qinghua Yuan, New Biology Bldg, Haidian District, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China; The First Affiliated Hospital of Anhui Medical University and Institute of Clinical Immunology, Anhui Medical University, Hefei, 230032, China.
| | - Can Zhu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, No. 1, Qinghua Yuan, New Biology Bldg, Haidian District, Beijing, 100084, China.
| | - Yuxin Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, No. 1, Qinghua Yuan, New Biology Bldg, Haidian District, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Xinfeng Wu
- Department of Rheumatology and Immunology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, No. 636, Guanlin Road, 471000, Luoyang, China.
| | - Xiaofei Shi
- Department of Rheumatology and Immunology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, No. 636, Guanlin Road, 471000, Luoyang, China.
| | - Wanli Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Institute for Immunology, China Ministry of Education Key Laboratory of Protein Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, No. 1, Qinghua Yuan, New Biology Bldg, Haidian District, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China; The First Affiliated Hospital of Anhui Medical University and Institute of Clinical Immunology, Anhui Medical University, Hefei, 230032, China.
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2
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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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3
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Jenks SA, Wei C, Bugrovsky R, Hill A, Wang X, Rossi FM, Cashman K, Woodruff MC, Aspey LD, Lim SS, Bao G, Drenkard C, Sanz I. B cell subset composition segments clinically and serologically distinct groups in chronic cutaneous lupus erythematosus. Ann Rheum Dis 2021; 80:1190-1200. [PMID: 34083207 PMCID: PMC8906255 DOI: 10.1136/annrheumdis-2021-220349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/17/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE While the contribution of B-cells to SLE is well established, its role in chronic cutaneous lupus erythematosus (CCLE) remains unclear. Here, we compare B-cell and serum auto-antibody profiles between patients with systemic lupus erythematosus (SLE), CCLE, and overlap conditions. METHODS B-cells were compared by flow cytometry amongst healthy controls, CCLE without systemic lupus (CCLE+/SLE-) and SLE patients with (SLE+/CCLE+) or without CCLE (SLE+/CCLE-). Serum was analyed for autoreactive 9G4+, anti-double-stranded DNA, anti-chromatin and anti-RNA antibodies by ELISA and for anti-RNA binding proteins (RBP) by luciferase immunoprecipitation. RESULTS Patients with CCLE+/SLE- share B-cell abnormalities with SLE including decreased unswitched memory and increased effector B-cells albeit at a lower level than SLE patients. Similarly, both SLE and CCLE+/SLE- patients have elevated 9G4+ IgG autoantibodies despite lower levels of anti-nucleic acid and anti-RBP antibodies in CCLE+/SLE-. CCLE+/SLE- patients could be stratified into those with SLE-like B-cell profiles and a separate group with normal B-cell profiles. The former group was more serologically active and more likely to have disseminated skin lesions. CONCLUSION CCLE displays perturbations in B-cell homeostasis and partial B-cell tolerance breakdown. Our study demonstrates that this entity is immunologically heterogeneous and includes a disease segment whose B-cell compartment resembles SLE and is clinically associated with enhanced serological activity and more extensive skin disease. This picture suggests that SLE-like B-cell changes in primary CCLE may help identify patients at risk for subsequent development of SLE. B-cell profiling in CCLE might also indentify candidates who would benefit from B-cell targeted therapies.
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Affiliation(s)
- Scott A Jenks
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Chungwen Wei
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Regina Bugrovsky
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Aisha Hill
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Xiaoqian Wang
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Francesca M Rossi
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Kevin Cashman
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Laura D Aspey
- Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - S Sam Lim
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gaobin Bao
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Cristina Drenkard
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
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4
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Dörner T, Szelinski F, Lino AC, Lipsky PE. Therapeutic implications of the anergic/postactivated status of B cells in systemic lupus erythematosus. RMD Open 2021; 6:rmdopen-2020-001258. [PMID: 32675278 PMCID: PMC7425190 DOI: 10.1136/rmdopen-2020-001258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/28/2020] [Accepted: 06/12/2020] [Indexed: 12/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterised by numerous abnormalities in B lineage cells, including increased CD27++ plasmablasts/plasma cells, atypical CD27-IgD- B cells with increased CD95, spleen tyrosine kinase (Syk)++, CXCR5- and CXCR5+ subsets and anergic CD11c+Tbet+ age-associated B cells. Most findings, together with preclinical lupus models, support the concept of B cell hyperactivity in SLE. However, it remains largely unknown whether these specific B cell subsets have pathogenic consequences and whether they provide relevant therapeutic targets. Recent findings indicate a global distortion of B cell functional capability, in which the entire repertoire of naïve and memory B cells in SLE exhibits an anergic or postactivated (APA) functional phenotype. The APA status of SLE B cells has some similarities to the functional derangement of lupus T cells. APA B cells are characterised by reduced global cytokine production, diminished B cell receptor (BCR) signalling with decreased Syk and Bruton's tyrosine kinase phosphorylation related to repeated in vivo BCR stimulation as well as hyporesponsiveness to toll-like receptor 9 engagement, but intact CD40 signalling. This APA status was related to constitutive co-localisation of CD22 linked to phosphatase SHP-1 and increased overall protein phosphatase activities. Notably, CD40 co-stimulation could revert this APA status and restore BCR signalling, downregulate protein tyrosine phosphatase transcription and promote B cell proliferation and differentiation. The APA status and their potential rescue by bystander help conveyed through CD40 stimulation not only provides insights into possible mechanisms of escape of autoreactive clones from negative selection but also into novel ways to target B cells therapeutically.
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Affiliation(s)
| | | | - Andreia C Lino
- Department of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Peter E Lipsky
- RILITE Research Institute, Charlottesville, Virginia, USA
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5
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Devaprasad A, Radstake TRDJ, Pandit A. Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies. Front Immunol 2021; 12:669400. [PMID: 34108969 PMCID: PMC8181425 DOI: 10.3389/fimmu.2021.669400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 01/25/2023] Open
Abstract
Objective Development and progression of immune-mediated inflammatory diseases (IMIDs) involve intricate dysregulation of the disease-associated genes (DAGs) and their expressing immune cells. Identifying the crucial disease-associated cells (DACs) in IMIDs has been challenging due to the underlying complex molecular mechanism. Methods Using transcriptome profiles of 40 different immune cells, unsupervised machine learning, and disease-gene networks, we constructed the Disease-gene IMmune cell Expression (DIME) network and identified top DACs and DAGs of 12 phenotypically different IMIDs. We compared the DIME networks of IMIDs to identify common pathways between them. We used the common pathways and publicly available drug-gene network to identify promising drug repurposing targets. Results We found CD4+Treg, CD4+Th1, and NK cells as top DACs in inflammatory arthritis such as ankylosing spondylitis (AS), psoriatic arthritis, and rheumatoid arthritis (RA); neutrophils, granulocytes, and BDCA1+CD14+ cells in systemic lupus erythematosus and systemic scleroderma; ILC2, CD4+Th1, CD4+Treg, and NK cells in the inflammatory bowel diseases (IBDs). We identified lymphoid cells (CD4+Th1, CD4+Treg, and NK) and their associated pathways to be important in HLA-B27 type diseases (psoriasis, AS, and IBDs) and in primary-joint-inflammation-based inflammatory arthritis (AS and RA). Based on the common cellular mechanisms, we identified lifitegrast as a potential drug repurposing candidate for Crohn's disease and other IMIDs. Conclusions Existing methods are inadequate in capturing the intricate involvement of the crucial genes and cell types essential to IMIDs. Our approach identified the key DACs, DAGs, common mechanisms between IMIDs, and proposed potential drug repurposing targets using the DIME network. To extend our method to other diseases, we built the DIME tool (https://bitbucket.org/systemsimmunology/dime/) to help scientists uncover the etiology of complex and rare diseases to further drug development by better-determining drug targets, thereby mitigating the risk of failure in late clinical development.
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Affiliation(s)
- Abhinandan Devaprasad
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Timothy R. D. J. Radstake
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Aridaman Pandit
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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6
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Hart AP, Laufer TM. A review of signaling and transcriptional control in T follicular helper cell differentiation. J Leukoc Biol 2021; 111:173-195. [PMID: 33866600 DOI: 10.1002/jlb.1ri0121-066r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
T follicular helper (Tfh) cells are a critical component of adaptive immunity and assist in optimal Ab-mediated defense. Multiple effector functions of Tfh support germinal center B cell survival, Ab class switching, and plasma cell maturation. In the past 2 decades, the phenotype and functional characteristics of GC Tfh have been clarified allowing for robust studies of the Th subset including activation signals and environmental cues controlling Tfh differentiation and migration during an immune response. A unique, 2-step differentiation process of Tfh has been proposed but the mechanisms underlying transition between unstable Tfh precursors and functional mature Tfh remain elusive. Likewise, newly identified transcriptional regulators of Tfh development have not yet been incorporated into our understanding of how these cells might function in disease. Here, we review the signals and downstream transcription factors that shape Tfh differentiation including what is known about the epigenetic processes that maintain Tfh identity. It is proposed that further evaluation of the stepwise differentiation pattern of Tfh will yield greater insights into how these cells become dysregulated in autoimmunity.
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Affiliation(s)
- Andrew P Hart
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Terri M Laufer
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Rheumatology, Department of Medicine, Corporal Michael C. Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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7
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Tay SH, Celhar T, Fairhurst A. Low-Density Neutrophils in Systemic Lupus Erythematosus. Arthritis Rheumatol 2020; 72:1587-1595. [PMID: 32524751 PMCID: PMC7590095 DOI: 10.1002/art.41395] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
Patients with systemic lupus erythematosus (SLE) display increased numbers of immature neutrophils in the blood, but the exact role of these immature neutrophils is unclear. Neutrophils that sediment within the peripheral blood mononuclear cell fraction after density centrifugation of blood are generally defined as low-density neutrophils (LDNs). Far beyond antimicrobial functions, LDNs are emerging as decision-shapers during innate and adaptive immune responses. Traditionally, neutrophils have been viewed as a homogeneous population. However, the various LDN populations identified in SLE to date are heterogeneously composed of mixed populations of activated mature neutrophils and immature neutrophils at various stages of differentiation. Controversy also surrounds the role of LDNs in SLE in terms of whether they are proinflammatory or polymorphonuclear myeloid-derived suppressor cells. It is clear that LDNs in SLE can secrete increased levels of type I interferon (IFN) and that they contribute to the cycle of inflammation and tissue damage. They readily form neutrophil extracellular traps, exposing modified autoantigens and oxidized mitochondrial DNA, which contribute to autoantibody production and type I IFN signaling, respectively. Importantly, the ability of LDNs in SLE to perform canonical neutrophil functions is polarized, based on mature CD10+ and immature CD10- neutrophils. Although this field is still relatively new, multiomic approaches have advanced our understanding of the diverse origins, phenotype, and function of LDNs in SLE. This review updates the literature on the origin and nature of LDNs, their distinctive features, and their biologic roles in the immunopathogenesis and end-organ damage in SLE.
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Affiliation(s)
- Sen Hee Tay
- National University Hospital Yong Loo Lin School of MedicineInstitute for Molecular and Cellular Biology, Agency for Science, Technology and ResearchSingapore
| | - Teja Celhar
- Singapore Immunology NetworkAgency for Science, Technology and ResearchSingapore
| | - Anna‐Marie Fairhurst
- Institute for Molecular and Cellular BiologyAgency for Science, Technology and ResearchUniversity of Singapore Yong Loo Lin School of MedicineSingapore
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8
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El-Sherbiny YM, Md Yusof MY, Psarras A, Hensor EMA, Kabba KZ, Dutton K, Mohamed AAA, Elewaut D, McGonagle D, Tooze R, Doody G, Wittmann M, Emery P, Vital EM. B Cell Tetherin: A Flow Cytometric Cell-Specific Assay for Response to Type I Interferon Predicts Clinical Features and Flares in Systemic Lupus Erythematosus. Arthritis Rheumatol 2020; 72:769-779. [PMID: 31804007 PMCID: PMC8653884 DOI: 10.1002/art.41187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/03/2019] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Type I interferon (IFN) responses are broadly associated with autoimmune diseases, including systemic lupus erythematosus (SLE). Given the cardinal role of autoantibodies in SLE, this study was undertaken to investigate whether the findings of a B cell-specific IFN assay correlate with SLE activity. METHODS B cells and peripheral blood mononuclear cells (PBMCs) were stimulated with type I IFN and type II IFN. Gene expression was analyzed, and the expression of pathway-related membrane proteins was determined. A flow cytometry assay for tetherin (CD317), an IFN-induced protein ubiquitously expressed on leukocytes, was validated in vitro and then clinically against SLE diagnosis, plasmablast expansion, and the British Isles Lupus Assessment Group (BILAG) 2004 score in a discovery cohort (n = 156 SLE patients, 30 rheumatoid arthritis [RA] patients, and 25 healthy controls). A second, longitudinal validation cohort of 80 SLE patients was also evaluated for flare prediction. RESULTS In vitro, a close cell-specific and dose-response relationship between type I IFN-responsive genes and cell surface tetherin was observed in all immune cell subsets. Tetherin expression on multiple cell subsets was selectively responsive to stimulation with type I IFN compared to types II and III IFNs. In patient samples from the discovery cohort, memory B cell tetherin showed the strongest associations with diagnosis (SLE:healthy control effect size 0.11 [P = 0.003]; SLE:RA effect size 0.17 [P < 0.001]), plasmablast numbers in rituximab-treated patients (R = 0.38, P = 0.047), and BILAG 2004. These associations were equivalent to or stronger than those for IFN score or monocyte tetherin. Memory B cell tetherin was found to be predictive of future clinical flares in the validation cohort (hazard ratio 2.29 [95% confidence interval 1.01-4.64]; P = 0.022). CONCLUSION Our findings indicate that memory B cell surface tetherin, a B cell-specific IFN assay, is associated with SLE diagnosis and disease activity, and predicts flares better than tetherin on other cell subsets or whole blood assays, as determined in an independent validation cohort.
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Affiliation(s)
- Yasser M El-Sherbiny
- University of Leeds, Leeds, UK, Nottingham Trent University School of Science and Technology, Nottingham, UK, and Mansoura University, Mansoura, Egypt
| | - Md Yuzaiful Md Yusof
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Antonios Psarras
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Elizabeth M A Hensor
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Katherine Dutton
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alaa A A Mohamed
- University of Leeds, Leeds, UK, and Assiut University, Assiut, Egypt
| | | | - Dennis McGonagle
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | | | - Miriam Wittmann
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Emery
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Edward M Vital
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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9
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Javier E, Lu X, Kottyan LC. Noncoding Variants as Genetic Contributors to Autoimmune Disease Pathogenesis. J Invest Dermatol 2020; 140:277-278. [PMID: 31980060 DOI: 10.1016/j.jid.2019.07.698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/13/2022]
Abstract
Understanding the functions of disease-associated noncoding variants is essential for understanding the molecular mechanisms driving diseases with a genetic cause and for identifying therapeutic targets. Combined computational and experimental analyses have demonstrated that IRF5 is hyperactivated by a pathogenic allele of TNPO3 through long-distance chromatin looping. This finding identifies a molecular mechanism contributing to the polygenic autoimmune diseases of systemic lupus erythematosus and systemic sclerosis.
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Affiliation(s)
- Ellen Javier
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Molecular and Developmental Biology Graduate Program, University of Cincinnati, Cincinnati, Ohio, USA.
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA
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10
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Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus. Sci Rep 2019; 9:15433. [PMID: 31659207 PMCID: PMC6817816 DOI: 10.1038/s41598-019-51864-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Personalized medicine approaches are increasingly sought for diseases with a heritable component. Systemic lupus erythematosus (SLE) is the prototypic autoimmune disease resulting from loss of immunologic tolerance, but the genetic basis of SLE remains incompletely understood. Genome wide association studies (GWAS) identify regions associated with disease, based on common single nucleotide polymorphisms (SNPs) within them, but these SNPs may simply be markers in linkage disequilibrium with other, causative mutations. Here we use an hierarchical screening approach for prediction and testing of true functional variants within regions identified in GWAS; this involved bioinformatic identification of putative regulatory elements within close proximity to SLE SNPs, screening those regions for potentially causative mutations by high resolution melt analysis, and functional validation using reporter assays. Using this approach, we screened 15 SLE associated loci in 143 SLE patients, identifying 7 new variants including 5 SNPs and 2 insertions. Reporter assays revealed that the 5 SNPs were functional, altering enhancer activity. One novel variant was linked to the relatively well characterized rs9888739 SNP at the ITGAM locus, and may explain some of the SLE heritability at this site. Our study demonstrates that non-coding regulatory elements can contain private sequence variants affecting gene expression, which may explain part of the heritability of SLE.
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11
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Weißenberg SY, Szelinski F, Schrezenmeier E, Stefanski AL, Wiedemann A, Rincon-Arevalo H, Welle A, Jungmann A, Nordström K, Walter J, Imgenberg-Kreuz J, Nordmark G, Rönnblom L, Bachali P, Catalina MD, Grammer AC, Lipsky PE, Lino AC, Dörner T. Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases. Front Immunol 2019; 10:2136. [PMID: 31616406 PMCID: PMC6768969 DOI: 10.3389/fimmu.2019.02136] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022] Open
Abstract
Autoimmune diseases (AID) such as systemic lupus erythematosus (SLE), primary Sjögren's syndrome (pSS), and rheumatoid arthritis (RA) are chronic inflammatory diseases in which abnormalities of B cell function play a central role. Although it is widely accepted that autoimmune B cells are hyperactive in vivo, a full understanding of their functional status in AID has not been delineated. Here, we present a detailed analysis of the functional capabilities of AID B cells and dissect the mechanisms underlying altered B cell function. Upon BCR activation, decreased spleen tyrosine kinase (Syk) and Bruton's tyrosine kinase (Btk) phosphorylation was noted in AID memory B cells combined with constitutive co-localization of CD22 and protein tyrosine phosphatase (PTP) non-receptor type 6 (SHP-1) along with hyporesponsiveness to TLR9 signaling, a Syk-dependent response. Similar BCR hyporesponsiveness was also noted specifically in SLE CD27− B cells together with increased PTP activities and increased transcripts for PTPN2, PTPN11, PTPN22, PTPRC, and PTPRO in SLE B cells. Additional studies revealed that repetitive BCR stimulation of normal B cells can induce BCR hyporesponsiveness and that tissue-resident memory B cells from AID patients also exhibited decreased responsiveness immediately ex vivo, suggesting that the hyporesponsive status can be acquired by repeated exposure to autoantigen(s) in vivo. Functional studies to overcome B cell hyporesponsiveness revealed that CD40 co-stimulation increased BCR signaling, induced proliferation, and downregulated PTP expression (PTPN2, PTPN22, and receptor-type PTPs). The data support the conclusion that hyporesponsiveness of AID and especially SLE B cells results from chronic in vivo stimulation through the BCR without T cell help mediated by CD40–CD154 interaction and is manifested by decreased phosphorylation of BCR-related proximal signaling molecules and increased PTPs. The hyporesponsiveness of AID B cells is similar to a form of functional anergy.
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Affiliation(s)
- Sarah Y Weißenberg
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Franziska Szelinski
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Eva Schrezenmeier
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Ana-Luisa Stefanski
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Annika Wiedemann
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Hector Rincon-Arevalo
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany.,Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Instituto de Investigaciones Médicas, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Anna Welle
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Annemarie Jungmann
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Karl Nordström
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Amrie C Grammer
- RILITE Research Institute, Charlottesville, VA, United States
| | - Peter E Lipsky
- RILITE Research Institute, Charlottesville, VA, United States
| | - Andreia C Lino
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Thomas Dörner
- Department of Rheumatology and Clinical Immunology, Charité University Medicine Berlin, Berlin, Germany.,German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
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12
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Postactivated B cells in systemic lupus erythematosus: update on translational aspects and therapeutic considerations. Curr Opin Rheumatol 2019; 31:175-184. [DOI: 10.1097/bor.0000000000000576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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The potential role of Ets-1 and miR-326 in CD19 +B cells in the pathogenesis of patients with systemic lupus erythematosus. Clin Rheumatol 2018; 38:1031-1038. [PMID: 30456527 DOI: 10.1007/s10067-018-4371-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/09/2018] [Accepted: 11/13/2018] [Indexed: 01/30/2023]
Abstract
OBJECTIVES The aim of this study was to investigate the B cell-associated transcription factors, Ets-1 and microRNA, miR-326 in systemic lupus erythematosus (SLE) patients, and their correlation with the pathogenesis of SLE. METHOD A total of 44 SLE patients and 20 healthy controls were enrolled in this research, all patients fulfilled the American College of Rheumatology classification criteria for SLE. The mRNA expression of Ets-1 and miR-326 in CD19+B cells from SLE patients were examined by qRT-PCR. The percentages of CD19+CD138+plasma cells were analyzed by Flow cytometry. RESULTS We found decreased expression of Ets-1 mRNA in SLE patients compared with the healthy controls ([0.228 (0.145, 0.507)] vs [0.583 (0.452, 0.763)], p = 0.001),while increased expression of miR-326 mRNA in CD19+B cells SLE patients compared with the healthy controls([1.092 (0.457, 2.855)] vs [0.685 (0.274, 0.819)], p = 0.008). The percentage of CD19+CD138+plasma cells in SLE patients was higher than that of healthy controls (0.55 ± 0.21% vs 0.36 ± 0.21%, p = 0.002). Moreover, a negative correlation between expression of Ets-1 mRNA and miR-326 mRNA in CD19+B cells was detected (r = - 0.334, p = 0.027). A significant association between the occurrences of CD19+CD138+plasma cells and the levels of Ets-1 mRNA and miR-326 mRNA was observed (r = - 0.417, p = 0.005 and r = 0.482, p = 0.001, respectively). CONCLUSIONS Our results suggest that miR-326 might promote B cells differentiation by targeting Ets-1, a negative regulator of B cells differentiation and therefore participate in the pathogenesis of SLE.
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14
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Wolf BJ, Ramos PS, Hyer JM, Ramakrishnan V, Gilkeson GS, Hardiman G, Nietert PJ, Kamen DL. An Analytic Approach Using Candidate Gene Selection and Logic Forest to Identify Gene by Environment Interactions (G × E) for Systemic Lupus Erythematosus in African Americans. Genes (Basel) 2018; 9:genes9100496. [PMID: 30326636 PMCID: PMC6211136 DOI: 10.3390/genes9100496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/27/2018] [Accepted: 10/03/2018] [Indexed: 12/17/2022] Open
Abstract
Development and progression of many human diseases, such as systemic lupus erythematosus (SLE), are hypothesized to result from interactions between genetic and environmental factors. Current approaches to identify and evaluate interactions are limited, most often focusing on main effects and two-way interactions. While higher order interactions associated with disease are documented, they are difficult to detect since expanding the search space to all possible interactions of p predictors means evaluating 2p − 1 terms. For example, data with 150 candidate predictors requires considering over 1045 main effects and interactions. In this study, we present an analytical approach involving selection of candidate single nucleotide polymorphisms (SNPs) and environmental and/or clinical factors and use of Logic Forest to identify predictors of disease, including higher order interactions, followed by confirmation of the association between those predictors and interactions identified with disease outcome using logistic regression. We applied this approach to a study investigating whether smoking and/or secondhand smoke exposure interacts with candidate SNPs resulting in elevated risk of SLE. The approach identified both genetic and environmental risk factors, with evidence suggesting potential interactions between exposure to secondhand smoke as a child and genetic variation in the ITGAM gene associated with increased risk of SLE.
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Affiliation(s)
- Bethany J Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Paula S Ramos
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
| | - J Madison Hyer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Viswanathan Ramakrishnan
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Gary S Gilkeson
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
| | - Gary Hardiman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
- Division of Nephrology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
| | - Paul J Nietert
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Department of Medicine, Medical Univeristy of South Carolina, Charleston, SC 29425, USA.
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15
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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] [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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16
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Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nat Genet 2018; 50:699-707. [PMID: 29662164 PMCID: PMC6022759 DOI: 10.1038/s41588-018-0102-3] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/31/2018] [Indexed: 01/10/2023]
Abstract
Explaining the genetics of many diseases is challenging because most associations localize to incompletely characterized regulatory regions. We show that transcription factors (TFs) occupy multiple loci of individual complex genetic disorders using novel computational methods. Application to 213 phenotypes and 1,544 TF binding datasets identifies 2,264 relationships between hundreds of TFs and 94 phenotypes, including AR in prostate cancer and GATA3 in breast cancer. Strikingly, nearly half of the systemic lupus erythematosus risk loci are occupied by the Epstein-Barr virus EBNA2 protein and many co-clustering human TFs, revealing gene-environment interaction. Similar EBNA2-anchored associations exist in multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, juvenile idiopathic arthritis, and celiac disease. Instances of allele-dependent DNA binding and downstream effects on gene expression at plausibly causal variants support genetic mechanisms dependent upon EBNA2. Our results nominate mechanisms that operate across risk loci within disease phenotypes, suggesting new paradigms for disease origins.
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Affiliation(s)
- John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA.
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Avery Maddox
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carmy Forney
- 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
| | - Arthur Lynch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Masashi Yukawa
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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17
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Malkiel S, Barlev AN, Atisha-Fregoso Y, Suurmond J, Diamond B. Plasma Cell Differentiation Pathways in Systemic Lupus Erythematosus. Front Immunol 2018; 9:427. [PMID: 29556239 PMCID: PMC5845388 DOI: 10.3389/fimmu.2018.00427] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/16/2018] [Indexed: 01/20/2023] Open
Abstract
Plasma cells (PCs) are responsible for the production of protective antibodies against infectious agents but they also produce pathogenic antibodies in autoimmune diseases, such as systemic lupus erythematosus (SLE). Traditionally, high affinity IgG autoantibodies are thought to arise through germinal center (GC) responses. However, class switching and somatic hypermutation can occur in extrafollicular (EF) locations, and this pathway has also been implicated in SLE. The pathway from which PCs originate may determine several characteristics, such as PC lifespan and sensitivity to therapeutics. Although both GC and EF responses have been implicated in SLE, we hypothesize that one of these pathways dominates in each individual patient and genetic risk factors may drive this predominance. While it will be important to distinguish polymorphisms that contribute to a GC-driven or EF B cell response to develop targeted treatments, the challenge will be not only to identify the differentiation pathway but the molecular mechanisms involved. In B cells, this task is complicated by the cross-talk between the B cell receptor, toll-like receptors (TLR), and cytokine signaling molecules, which contribute to both GC and EF responses. While risk variants that affect the function of dendritic cells and T follicular helper cells are likely to primarily influence GC responses, it will be important to discover whether some risk variants in the interferon and TLR pathways preferentially influence EF responses. Identifying the pathways of autoreactive PC differentiation in SLE may help us to understand patient heterogeneity and thereby guide precision therapy.
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Affiliation(s)
- Susan Malkiel
- Center of Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Ashley N Barlev
- Center of Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Yemil Atisha-Fregoso
- Center of Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Tecnologico de Monterrey, Monterrey, Mexico
| | - Jolien Suurmond
- Center of Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Betty Diamond
- Center of Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
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18
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Jadot V, Krzesinski JM, Von Frenckell C, Bovy C, Bouquegneau A. [Lupus nephropathy: Insight in new treatments]. Nephrol Ther 2017; 14:1-12. [PMID: 29191575 DOI: 10.1016/j.nephro.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/09/2017] [Accepted: 05/14/2017] [Indexed: 11/16/2022]
Abstract
Systemic lupus erythematosus is a chronic autoimmune disease. Both acquired and innate immune systems are involved in the development of this systemic disease. Lupus nephritis usually is the most serious manifestation of systemic lupus erythematosus, with significant morbidity and mortality. The physiopathological development of the renal involvement of lupus has been increasingly elucidated over the years and various target therapies have recently been developed. After some physiopathological reminders, we discuss the conventional treatment of lupus nephritis as well as the various therapeutic advances, in particular the contribution and the place of the new target therapies in the treatment of the lupus nephritis.
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Affiliation(s)
- Virginie Jadot
- Médecine interne, université de Liège, Avenue d'Hippocrate, CHU Sart-Tilman, 4000 Liège, Belgique
| | - Jean-Marie Krzesinski
- Service de néphrologie-dialyse-transplantation, université de Liège, avenue d'Hippocrate , CHU Sart-Tilman, 4000 Liège, Belgique
| | - Christian Von Frenckell
- Service de rhumatologie, université de Liège, avenue d'Hippocrate, CHU Sart-Tilman, 4000 Liège, Belgique
| | - Christophe Bovy
- Service de néphrologie-dialyse-transplantation, université de Liège, avenue d'Hippocrate , CHU Sart-Tilman, 4000 Liège, Belgique
| | - Antoine Bouquegneau
- Service de néphrologie-dialyse-transplantation, université de Liège, avenue d'Hippocrate , CHU Sart-Tilman, 4000 Liège, Belgique.
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19
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Demirci FY, Wang X, Morris DL, Feingold E, Bernatsky S, Pineau C, Clarke A, Ramsey-Goldman R, Manzi S, Vyse TJ, Kamboh MI. Multiple signals at the extended 8p23 locus are associated with susceptibility to systemic lupus erythematosus. J Med Genet 2017; 54:381-389. [PMID: 28289186 DOI: 10.1136/jmedgenet-2016-104247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/16/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND A major systemic lupus erythematosus (SLE) susceptibility locus lies within a common inversion polymorphism region (encompassing 3.8 - 4.5 Mb) located at 8p23. Initially implicated genes included FAM167A-BLK and XKR6, of which BLK received major attention due to its known role in B-cell biology. Recently, additional SLE risk carried in non-inverted background was also reported. OBJECTIVE AND METHODS In this case -control study, we further investigated the 'extended' 8p23 locus (~ 4 Mb) where we observed multiple SLE signals and assessed these signals for their relation to the inversion affecting this region. The study involved a North American discovery data set (~ 1200 subjects) and a replication data set (> 10 000 subjects) comprising European-descent individuals. RESULTS Meta-analysis of 8p23 SNPs, with p < 0.05 in both data sets, identified 51 genome-wide significant SNPs (p < 5.0 × 10-8). While most of these SNPs were related to previously implicated signals (XKR6-FAM167A-BLK subregion), our results also revealed two 'new' SLE signals, including SGK223-CLDN23-MFHAS1 (6.06 × 10-9 ≤ meta p ≤ 4.88 × 10-8) and CTSB (meta p = 4.87 × 10-8) subregions that are located > 2 Mb upstream and ~ 0.3 Mb downstream from previously reported signals. Functional assessment of relevant SNPs indicated putative cis-effects on the expression of various genes at 8p23. Additional analyses in discovery sample, where the inversion genotypes were inferred, replicated the association of non-inverted status with SLE risk and suggested that a number of SLE risk alleles are predominantly carried in non-inverted background. CONCLUSIONS Our results implicate multiple (known+novel) SLE signals/genes at the extended 8p23 locus, beyond previously reported signals/genes, and suggest that this broad locus contributes to SLE risk through the effects of multiple genes/pathways.
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Affiliation(s)
- F Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Xingbin Wang
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Sasha Bernatsky
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, Canada
| | - Christian Pineau
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, Canada
| | - Ann Clarke
- Division of Rheumatology, Department of Medicine, University of Calgary, Calgary, Canada
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Susan Manzi
- Department of Medicine, Lupus Center of Excellence, Allegheny Health Network, Pittsburgh, USA
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - M I Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
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20
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Microarray to deep sequencing: transcriptome and miRNA profiling to elucidate molecular pathways in systemic lupus erythematosus. Immunol Res 2016; 64:14-24. [PMID: 26188428 DOI: 10.1007/s12026-015-8672-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with diverse clinical manifestations and autoantibody repertoires. The etiology of SLE is multifactorial involving genetic, epigenetic and environmental factors. This complexity leads to poor prognosis, which poses major challenges in the treatment of SLE. Understanding the complex genetic pathways and regulatory mechanisms operative in SLE was feasible by utilizing several highly efficient molecular biological tools during the past few years. In this perspective, DNA microarray technology offered a high-throughput platform in unraveling SLE-associated genes. Additionally, extensive microarray analysis had demonstrated aberrant DNA methylation pattern and differential microRNAs, thus contributing to the knowledge of epigenetic modulators and posttranscriptional regulatory machinery in SLE. It was through the aid of these technologies that interferon signature was identified as an important contributor in SLE pathogenesis along with dysregulation of cytokine-, chemokine- and apoptosis-related genes. The emergence of next-generation sequencing technologies such as RNA sequencing has added new dimensions in understanding the dynamics of the disease processes. Compared with microarrays, deep sequencing has provided higher resolution in gene expression measurement along with identification of different splicing events, noncoding RNAs and novel loci in SLE. The focus, therefore, has now been shifted toward the identification of novel gene loci and their isoforms, and their implication in disease pathogenesis. This advancement in the technology from microarray to deep sequencing has helped in deciphering the molecular pathways involved in pathogenesis of SLE and opens new avenues to develop novel treatment strategies for SLE.
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21
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Pelka K, Shibata T, Miyake K, Latz E. Nucleic acid-sensing TLRs and autoimmunity: novel insights from structural and cell biology. Immunol Rev 2016; 269:60-75. [PMID: 26683145 DOI: 10.1111/imr.12375] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Invasion of pathogenic microorganisms or tissue damage activates innate immune signaling receptors that sample subcellular locations for foreign molecular structures, altered host molecules, or signs of compartment breaches. Upon engagement of innate immune receptors an acute but transient inflammatory response is initiated, aimed at the clearance of pathogens and cellular debris. Among the molecules that are sensed are nucleic acids, which activate several members of the transmembrane Toll-like receptor (TLR) family. Inappropriate recognition of nucleic acids by TLRs can cause inflammatory pathologies and autoimmunity. Here, we review the mechanisms involved in triggering nucleic acid-sensing TLRs and indicate checkpoints that restrict their activation to endolysosomal compartments. These mechanisms are crucial to sample the content of endosomes for nucleic acids in the context of infection or tissue damage, yet prevent accidental activation by host nucleic acids under physiological conditions. Decoding the molecular mechanisms that regulate nucleic acid recognition by TLRs is central to understand pathologies linked to unrestricted nucleic acid sensing and to develop novel therapeutic strategies.
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Affiliation(s)
- Karin Pelka
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
| | - Takuma Shibata
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Kensuke Miyake
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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22
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ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells. Sci Rep 2016; 6:27030. [PMID: 27249108 PMCID: PMC4888756 DOI: 10.1038/srep27030] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/12/2016] [Indexed: 01/16/2023] Open
Abstract
Biobanking is a widespread practice for storing biological samples for future studies ranging from genotyping to RNA analysis. However, methods that probe the status of the epigenome are lacking. Here, the framework for applying the Assay for Transposase Accessible Sequencing (ATAC-seq) to biobanked specimens is described and was used to examine the accessibility landscape of naïve B cells from Systemic Lupus Erythematosus (SLE) patients undergoing disease flares. An SLE specific chromatin accessibility signature was identified. Changes in accessibility occurred at loci surrounding genes involved in B cell activation and contained motifs for transcription factors that regulate B cell activation and differentiation. These data provide evidence for an altered epigenetic programming in SLE B cells and identify loci and transcription factor networks that potentially impact disease. The ability to determine the chromatin accessibility landscape and identify cis-regulatory elements has broad application to studies using biorepositories and offers significant advantages to improve the molecular information obtained from biobanked samples.
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23
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Demirci FY, Wang X, Kelly JA, Morris DL, Barmada MM, Feingold E, Kao AH, Sivils KL, Bernatsky S, Pineau C, Clarke A, Ramsey-Goldman R, Vyse TJ, Gaffney PM, Manzi S, Kamboh MI. Identification of a New Susceptibility Locus for Systemic Lupus Erythematosus on Chromosome 12 in Individuals of European Ancestry. Arthritis Rheumatol 2016; 68:174-83. [PMID: 26316170 PMCID: PMC4747422 DOI: 10.1002/art.39403] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/18/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Genome-wide association studies (GWAS) in individuals of European ancestry identified a number of systemic lupus erythematosus (SLE) susceptibility loci using earlier versions of high-density genotyping platforms. Followup studies on suggestive GWAS regions using larger samples and more markers identified additional SLE loci in subjects of European descent. This multistage study was undertaken to identify novel SLE loci. METHODS In stage 1, we conducted a new GWAS of SLE in a North American case-control sample of subjects of European ancestry (n = 1,166) genotyped on Affymetrix Genome-Wide Human SNP Array 6.0. In stage 2, we further investigated top new suggestive GWAS hits by in silico evaluation and meta-analysis using an additional data set of subjects of European descent (>2,500 individuals), followed by replication of top meta-analysis findings in another data set of subjects of European descent (>10,000 individuals) in stage 3. RESULTS As expected, our GWAS revealed the most significant associations at the major histocompatibility complex locus (6p21), which easily surpassed the genome-wide significance threshold (P < 5 × 10(-8)). Several other SLE signals/loci previously implicated in Caucasians and/or Asians were also confirmed in the stage 1 discovery sample, and the strongest signals were observed at 2q32/STAT4 (P = 3.6 × 10(-7)) and at 8p23/BLK (P = 8.1 × 10(-6)). Stage 2 meta-analyses identified a new genome-wide significant SLE locus at 12q12 (meta P = 3.1 × 10(-8)), which was replicated in stage 3. CONCLUSION Our multistage study identified and replicated a new SLE locus that warrants further followup in additional studies. Publicly available databases suggest that this newly identified SLE signal falls within a functionally relevant genomic region and near biologically important genes.
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MESH Headings
- Adult
- Case-Control Studies
- Casein Kinase II/genetics
- Cell Cycle Proteins/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 6
- Chromosomes, Human, Pair 8
- Computer Simulation
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Genotype
- HLA-DQ alpha-Chains/genetics
- HLA-DQ beta-Chains/genetics
- Humans
- Lupus Erythematosus, Systemic/genetics
- Major Histocompatibility Complex/genetics
- Male
- Middle Aged
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci
- STAT4 Transcription Factor/genetics
- Tenascin/genetics
- Transcriptome
- White People/genetics
- src-Family Kinases/genetics
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Affiliation(s)
- F. Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xingbin Wang
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jennifer A. Kelly
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David L. Morris
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - M. Michael Barmada
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Amy H. Kao
- Lupus Center of Excellence, Department of Medicine, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Kathy L. Sivils
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Sasha Bernatsky
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, QC H3G 1A4, Canada
| | - Christian Pineau
- Division of Rheumatology, Department of Medicine, McGill University, Montreal, QC H3G 1A4, Canada
| | - Ann Clarke
- Division of Rheumatology, Department of Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Timothy J. Vyse
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Patrick M. Gaffney
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Susan Manzi
- Lupus Center of Excellence, Department of Medicine, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - M. Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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24
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B cells biology in systemic lupus erythematosus—from bench to bedside. SCIENCE CHINA-LIFE SCIENCES 2015; 58:1111-25. [DOI: 10.1007/s11427-015-4953-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/09/2015] [Indexed: 12/20/2022]
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25
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Relle M, Weinmann-Menke J, Scorletti E, Cavagna L, Schwarting A. Genetics and novel aspects of therapies in systemic lupus erythematosus. Autoimmun Rev 2015; 14:1005-18. [PMID: 26164648 DOI: 10.1016/j.autrev.2015.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
Abstract
Autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, autoimmune hepatitis and inflammatory bowel disease, have complex pathogeneses and the factors which cause these disorders are not well understood. But all have in common that they arise from a dysfunction of the immune system, interpreting self components as foreign antigens. Systemic lupus erythematosus (SLE) is one of these complex inflammatory disorders that mainly affects women and can lead to inflammation and severe damage of virtually any tissue and organ. Recently, the application of advanced techniques of genome-wide scanning revealed more genetic information about SLE than previously possible. These case-control or family-based studies have provided evidence that SLE susceptibility is based (with a few exceptions) on an individual accumulation of various risk alleles triggered by environmental factors and also help to explain the discrepancies in SLE susceptibility between different populations or ethnicities. Moreover, during the past years new therapies (autologous stem cell transplantation, B cell depletion) and improved conventional treatment options (corticosteroids, traditional and new immune-suppressants like mycophenolate mofetile) changed the perspective in SLE therapeutic approaches. Thus, this article reviews genetic aspects of this autoimmune disease, summarizes clinical aspects of SLE and provides a general overview of conventional and new therapeutic approaches in SLE.
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Affiliation(s)
- Manfred Relle
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Julia Weinmann-Menke
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Eva Scorletti
- Division of Rheumatology, IRCCS Fondazione Policlinico San Matteo, Lombardy, Pavia, Italy
| | - Lorenzo Cavagna
- Division of Rheumatology, IRCCS Fondazione Policlinico San Matteo, Lombardy, Pavia, Italy
| | - Andreas Schwarting
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany; Acura Centre of Rheumatology Rhineland-Palatinate, Bad Kreuznach, Germany.
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26
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Piotrowski P, Wudarski M, Sowińska A, Olesińska M, Jagodziński PP. TNF-308 G/A polymorphism and risk of systemic lupus erythematosus in the Polish population. Mod Rheumatol 2015; 25:719-23. [PMID: 25661739 DOI: 10.3109/14397595.2015.1008778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Numerous studies have been performed with TNF-α-308 G/A (rs1800629) single nuclear polymorphism (SNP) to evaluate the risk of SLE in various ethnicities. However, the significance of TNF-α-308 G/A in both clinical and laboratory studies of the disease remains unclear. METHODS Using a high-resolution melting curve analysis, we assessed the prevalence of TNF-α-308 G/A SNP in SLE patients (n = 262) and controls (n = 528) in a Polish population. We also assessed the contribution of this SNP to various clinical symptoms and the presence of autoantibodies in SLE patients. RESULTS The p-value obtained using a χ(2) test for the trend of TNF-α-308 G/A was statistically significant (ptrend = 0.0297). However, using logistic regression analysis for the presence of the HLA-DRB1*03:01 haplotype, we observed that the TNF-α-308 G/A SNP may be the DRB1*03:01-dependent risk factor of SLE in the Polish population. There was a significant contribution of TNF-α-308 A/A and A/G genotypes to arthritis OR = [2.692 (1.503-4.822, p = 0.0007, pcorr = 0.0119)] as well as renal SLE manifestation OR = [2.632 (1.575-4.397, p = 0.0002, pcorr = 0.0034)]. There was a significant association between TNF-α-308 A/A and A/G genotypes and the presence of anti-Ro antibodies (Ab) OR = 3.375(1.711-6.658, p = 0.0003, pcorr = 0.0051). However, the logistic regression analysis revealed that only renal manifestations and the presence of anti-anti-Ro antibodies remained significant after adjustment to the presence of the HLA-DRB1*03:01 haplotype. CONCLUSION Our studies indicate that the TNF-α-308 G/A polymorphism may be a DRB1*03:01 haplotype-dependent genetic risk factor for SLE. However, this SNP was independently associated with renal manifestations and production of anti-Ro Ab.
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Affiliation(s)
- Piotr Piotrowski
- a Department of Biochemistry and Molecular Biology , Poznań University of Medical Sciences , Poznań , Poland
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27
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Cai X, Qiao Y, Chen Y, Du S, Chen D, Yu S, Liu N, Jiang Y. Expression and Polymorphisms of Lysosome-Associated Protein Transmembrane 5 (LAPTM5) in Patients with Systemic Lupus Erythematosus in a Chinese Population. Biochem Genet 2015; 53:200-10. [PMID: 25998573 DOI: 10.1007/s10528-015-9682-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 05/16/2015] [Indexed: 12/15/2022]
Abstract
Lysosome-associated protein transmembrane 5 (LAPTM5) have been demonstrated a role in the prevention of lymphocyte hyperactivation, and its deficiency is involved in the immunological dysfunction of mouse models. The aim of this study was to detect mRNA expression of LAPTM5 in peripheral blood mononuclear cells (PBMCs) from patients with systemic lupus erythematosus (SLE), and to assess association between LAPTM5 single nucleotide polymorphisms (SNPs) (rs10798801, rs4614309, rs1188348, and rs1188349) and SLE in a Chinese population. Real-time transcription-polymerase chain reaction analysis was used to determine expression of LAPTM5 mRNA in PBMCs from 132 patients with SLE and 62 healthy controls. LAPTM5 mRNA expression decreased in SLE patients (n = 71) compared with healthy controls (n = 58) (p = 3.68 × 10(-5)). The expression of LAPTM5 mRNA in SLE patients with lupus nephritis (LN) (n = 35) was lower than in those without LN (n = 36) (p = 0.004). The expression level of LAPTM5 correlated with serum total protein (r(s) = 0.41, p = 0.027) and negatively correlated with 24-h proteinuria (r(s) = -0.45, p = 0.027). LAPTM5 SNPs (rs10798801, rs4614309, rs1188348, and rs1188349) was also analyzed by restriction fragment length polymorphism (RFLP) in 380 SLE patients and 460 healthy controls. No significant difference in the genotype or allele frequencies for LAPTM5 SNPs was detected in 380 SLE patients and 460 healthy controls (p > 0.05). Substantially low frequency of GGAT haplotype was observed in SLE patients (p < 0.001). It is concluded that insufficient expression of LAPTM5 may take part in the pathogenesis of SLE and contribute to the severity of the disease, and none of LAPTM5 polymorphisms contributes significantly to SLE susceptibility in a Chinese population.
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Affiliation(s)
- Xinze Cai
- Central Laboratory, First Affiliated Hospital of China Medical University, Shenyang, 110001, China
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28
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Abstract
The etiology of systemic lupus erythematosus (SLE) is unknown, but multiple genetic, epigenetic, and environmental risk factors have been implicated. The inheritance of genes alone is not sufficient for developing SLE, suggesting the influence of environmental triggers on disease expression. Despite the tremendous amount of progress in elucidating potential environmental risk factors for SLE, much more needs to be done. An interdisciplinary approach to studies of the causes and, ultimately, prevention of SLE is needed. This article reviews what is understood about the epidemiology of the relationship between environmental exposures and SLE, in addition to emerging areas of study.
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29
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Abstract
Systemic lupus erythematosus (SLE) is a multisystem autoimmune disorder that has a broad spectrum of effects on the majority of organs, including the kidneys. Approximately 40-70% of patients with SLE will develop lupus nephritis. Renal assault during SLE is initiated by genes that breach immune tolerance and promote autoantibody production. These genes might act in concert with other genetic factors that augment innate immune signalling and IFN-I production, which in turn can generate an influx of effector leucocytes, inflammatory mediators and autoantibodies into end organs, such as the kidneys. The presence of cognate antigens in the glomerular matrix, together with intrinsic molecular abnormalities in resident renal cells, might further accentuate disease progression. This Review discusses the genetic insights and molecular mechanisms for key pathogenic contributors in SLE and lupus nephritis. We have categorized the genes identified in human studies of SLE into one of four pathogenic events that lead to lupus nephritis. We selected these categories on the basis of the cell types in which these genes are expressed, and the emerging paradigms of SLE pathogenesis arising from murine models. Deciphering the molecular basis of SLE and/or lupus nephritis in each patient will help physicians to tailor specific therapies.
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30
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Xu Z, Morel L. Contribution of B-1a cells to systemic lupus erythematosus in the NZM2410 mouse model. Ann N Y Acad Sci 2015; 1362:215-23. [PMID: 25728381 DOI: 10.1111/nyas.12607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease of complex etiology in which B cells play a central role. An expanded number of B-1a cells have been consistently associated with murine lupus, and more recently with human SLE. We have identified Cdkn2c, a gene that controls cell cycle progression, as a key regulator of B-1a cell numbers and have associated Cdkn2c deficiency with autoimmune pathology, including the production of autoantibodies and the skewing of CD4(+) T cells toward inflammatory effector functions. We review the genetic studies that have led to these findings, as well as the possible mechanisms by which B-1a cell expansion and Cdkn2c deficiency are related to SLE pathogenesis.
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Affiliation(s)
- Zhiwei Xu
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida
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Akbar N, Nanda S, Belch J, Cohen P, Khan F. An important role for A20-binding inhibitor of nuclear factor-kB-1 (ABIN1) in inflammation-mediated endothelial dysfunction: an in vivo study in ABIN1 (D485N) mice. Arthritis Res Ther 2015; 17:22. [PMID: 25648164 PMCID: PMC4342941 DOI: 10.1186/s13075-015-0543-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 01/23/2015] [Indexed: 01/28/2023] Open
Abstract
Introduction The link between cardiovascular disease (CVD) and patients with chronic inflammation is not clearly understood. We examined a knock-in mouse expressing a poly-ubiquitin-binding-defective mutant of the protein ABIN1 (ABIN1(D485N)), which develops a systemic lupus erythematosus-like autoimmune disease because of the hyperactivation of IκB kinases (IκKs) and mitogen-activated protein kinases (MAPKs). These mice were used to determine the potential role of these signaling pathways in inflammation-mediated CVD development. Methods Laser Doppler imaging in combination with the iontophoresis of vasoactive chemicals were used to assess endothelium-dependent vasodilatation in vivo in ABIN1 (D485N)) mutant defective (n = 29) and wild-type (WT) control (n = 26) mice. Measurements were made at baseline, and animals were subdivided to receive either chow or a proatherogenic diet for 4 weeks, after which, follow-up assessments were made. Paired and unpaired t tests, and ANOVA with post hoc Bonferroni correction were used for statistical significance at P <0.05. Results Endothelium-dependent vasodilatation to acetylcholine was attenuated at 4 weeks in ABIN1(D485N)-chow-fed mice compared with age-matched WT-chow-fed mice (P <0.05). The magnitude of attenuation was similar to that observed in WT-cholesterol-fed animals (versus WT-chow, P <0.01). ABIN1(D485N)-cholesterol-fed mice had the poorest endothelium-dependent responses compared with other groups (P <0.001). ABIN1(D485N)-chow-fed mice had increased plasma interleukin-6 (IL-6) levels (versus WT-chow, P <0.001), and this was further elevated in ABIN1(D485N)-cholesterol-fed mice (versus ABIN1(D485N)-chow; P <0.05). IL-1α was significantly greater in all groups compared with WT-chow (P <0.01). ABIN1(D485N) mice showed significant cardiac hypertrophy (P <0.05). Conclusions The ABIN(D485N) mice display endothelial dysfunction and cardiac hypertrophy, which is possibly mediated through IL-6 and, to a lesser degree, IL-1α. These results suggest that the ABIN1-mediated hyperactivation of IKKs and MAPKs might mediate chronic inflammation and CVD development.
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Affiliation(s)
- Naveed Akbar
- Vascular and Inflammatory Diseases Research Unit, Medical Research Institute, Division of Cardiovascular and Diabetes Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
| | - Sambit Nanda
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK.
| | - Jill Belch
- Vascular and Inflammatory Diseases Research Unit, Medical Research Institute, Division of Cardiovascular and Diabetes Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK.
| | - Faisel Khan
- Vascular and Inflammatory Diseases Research Unit, Medical Research Institute, Division of Cardiovascular and Diabetes Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
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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] [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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Kottyan L, Kelly JA, Harley JB. Genetics of lupus. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Piotrowski P, Lianeri M, Prokop E, Wudarski M, Olesińska M, Jagodziński PP. The FCRL3 -169T>C polymorphism might be associated with some autoantibody presence in patients with SLE in a Polish population. Mod Rheumatol 2014; 24:296-9. [PMID: 24593204 DOI: 10.3109/14397595.2013.854066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES The Fcrl3 -169T>C (rs7528684) polymorphism has been shown to be a risk factor of various autoimmune diseases, including systemic lupus erythematosus (SLE); however, these results are inconsistent between distinct ethnicities. METHODS Using PCR-RFLP we studied the distribution of the FCRL3 -169T>C polymorphism in SLE patients (n = 263) and controls (n = 528) in a sample from the Polish population. RESULTS We found no significant differences of FCRL3 -169T>C genotypes and alleles between patients with SLE and healthy individuals. However, in the dominant model we found a significant association between the FCRL3 -169T>C polymorphism and the presence of anti-Scl-70 antibody (Ab) [OR = 4.747 (95 % CI = 1.639-13.749), p = 0.0011, p corr = 0.0198]. Moreover, in the dominant model we observed a significant contribution of FCRL3 -169T>C to the presence of either anti-La or anti-Scl-70 Abs [OR = 4.378 (95 % CI = 1.793-10.690, p = 0.0003, p corr = 0.0054)]. CONCLUSIONS Our study demonstrated that the FCRL3 -169T>C polymorphism is not a risk factor of SLE in the Polish population, but this polymorphism may contribute to autoantibody production in this disease.
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Affiliation(s)
- Piotr Piotrowski
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences , Poznan , Poland
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Chance, genetics, and the heterogeneity of disease and pathogenesis in systemic lupus erythematosus. Semin Immunopathol 2014; 36:495-517. [PMID: 25102991 DOI: 10.1007/s00281-014-0440-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 06/30/2014] [Indexed: 12/30/2022]
Abstract
Systemic lupus erythematosus (SLE) is a remarkably complex and heterogeneous systemic autoimmune disease. Disease complexity within individuals and heterogeneity among individuals, even genetically identical individuals, is driven by stochastic execution of a complex inherited program. Genome-wide association studies (GWAS) have progressively improved understanding of which genes are most critical to the potential for SLE and provided illuminating insight about the immune mechanisms that are engaged in SLE. What initiates expression of the genetic program to cause SLE within an individual and how that program is initiated remains poorly understood. If we extrapolate from all of the different experimental mouse models for SLE, we can begin to appreciate why SLE is so heterogeneous and consequently why prediction of disease outcome is so difficult. In this review, we critically evaluate extrinsic versus intrinsic cellular functions in the clearance and elimination of cellular debris and how dysfunction in that system may promote autoimmunity to nuclear antigens. We also examine several mouse models genetically prone to SLE either because of natural inheritance or inheritance of induced mutations to illustrate how different immune mechanisms may initiate autoimmunity and affect disease pathogenesis. Finally, we describe the heterogeneity of disease manifestations in SLE and discuss the mechanisms of disease pathogenesis with emphasis on glomerulonephritis. Particular attention is given to discussion of how anti-DNA autoantibody initiates experimental lupus nephritis (LN) in mice.
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Sanz I. Rationale for B cell targeting in SLE. Semin Immunopathol 2014; 36:365-75. [PMID: 24763533 DOI: 10.1007/s00281-014-0430-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 04/01/2014] [Indexed: 01/16/2023]
Abstract
B cells are central pathogenic players in systemic lupus erythematosus and multiple other autoimmune diseases through antibody production as well as antibody independent function. At the same time, B cells are known to play important regulatory functions that may protect against autoimmune manifestations. Yet, the functional role of different B cell populations and their contribution to disease remain to be understood. The advent of agents that specifically target B cells, in particular anti-CD20 and ant-BLyS antibodies, have demonstrated the efficacy of this approach for the treatment of human autoimmunity. The analysis of patients treated with these and other B cell agents provides a unique opportunity to understand the correlates of clinical response and the significance of different B cell subsets. Here, we discuss this information and how it could be used to better understand SLE and improve the rational design of B cell-directed therapies in this disease.
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Affiliation(s)
- Iñaki Sanz
- Division of Rheumatology, Lowance Center for Human Immunology, Georgia Research Alliance Eminent Scholar in Human Immunology, 247 Whitehead Research Bldg. 615 Michael St., Atlanta, GA, 30322, USA,
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Abstract
Genetics unquestionably contributes to systemic lupus erythematosus (SLE) predisposition, progression and outcome. Nevertheless, single-gene defects causing lupus-like phenotypes have been infrequently documented. The majority of the identified genetic SLE risk factors are, therefore, common variants, responsible for a small effect on the global risk. Recently, genome wide association studies led to the identification of a growing number of gene variants associated with SLE susceptibility, particular disease phenotypes, and antibody profiles. Further studies addressed the biological effects of these variants. In addition, the role of epigenetics has recently been revealed. These combined efforts contributed to a better understanding of SLE pathogenesis and to the characterization of clinically relevant pathways. In this review, we describe SLE-associated single-gene defects, common variants, and epigenetic changes. We also discuss the limitations of current methods and the challenges that we still have to face in order to incorporate genomic and epigenomic data into clinical practice.
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Ramos PS, Shaftman SR, Ward RC, Langefeld CD. Genes associated with SLE are targets of recent positive selection. Autoimmune Dis 2014; 2014:203435. [PMID: 24587899 PMCID: PMC3920976 DOI: 10.1155/2014/203435] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/12/2013] [Indexed: 01/03/2023] Open
Abstract
The reasons for the ethnic disparities in the prevalence of systemic lupus erythematosus (SLE) and the relative high frequency of SLE risk alleles in the population are not fully understood. Population genetic factors such as natural selection alter allele frequencies over generations and may help explain the persistence of such common risk variants in the population and the differential risk of SLE. In order to better understand the genetic basis of SLE that might be due to natural selection, a total of 74 genomic regions with compelling evidence for association with SLE were tested for evidence of recent positive selection in the HapMap and HGDP populations, using population differentiation, allele frequency, and haplotype-based tests. Consistent signs of positive selection across different studies and statistical methods were observed at several SLE-associated loci, including PTPN22, TNFSF4, TET3-DGUOK, TNIP1, UHRF1BP1, BLK, and ITGAM genes. This study is the first to evaluate and report that several SLE-associated regions show signs of positive natural selection. These results provide corroborating evidence in support of recent positive selection as one mechanism underlying the elevated population frequency of SLE risk loci and supports future research that integrates signals of natural selection to help identify functional SLE risk alleles.
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Affiliation(s)
- Paula S. Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stephanie R. Shaftman
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ralph C. Ward
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carl D. Langefeld
- Department of Public Health Sciences, Wake Forest School of Medicine and Center for Public Health Genomics, Winston-Salem, NC 27157, USA
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Abstract
Epigenetic mechanisms are proposed to underlie aberrant gene expression in systemic lupus erythematosus (SLE) that results in dysregulation of the immune system and loss of tolerance. Modifications of DNA and histones require substrates derived from diet and intermediary metabolism. DNA and histone methyltransferases depend on S-adenosylmethionine (SAM) as a methyl donor. SAM is generated from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase (MAT), a redox-sensitive enzyme in the SAM cycle. The availability of B vitamins and methionine regulate SAM generation. The DNA of SLE patients is hypomethylated, indicating dysfunction in the SAM cycle and methyltransferase activity. Acetyl-CoA, which is necessary for histone acetylation, is generated from citrate produced in mitochondria. Mitochondria are also responsible for de novo synthesis of flavin adenine dinucleotide (FAD) for histone demethylation. Mitochondrial oxidative phosphorylation is the dominant source of ATP. The depletion of ATP in lupus T cells may affect MAT activity as well as adenosine monophosphate (AMP) activated protein kinase (AMPK), which phosphorylates histones and inhibits mechanistic target of rapamycin (mTOR). In turn, mTOR can modify epigenetic pathways including methylation, demethylation, and histone phosphorylation and mediates enhanced T-cell activation in SLE. Beyond their role in metabolism, mitochondria are the main source of reactive oxygen intermediates (ROI), which activate mTOR and regulate the activity of histone and DNA modifying enzymes. In this review we will focus on the sources of metabolites required for epigenetic regulation and how the flux of the underlying metabolic pathways affects gene expression.
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Affiliation(s)
- Zachary Oaks
- Division of Rheumatology, Departments of Medicine, Microbiology and Immunology, and Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, College of Medicine , Syracuse, NY , USA
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Abstract
Oxidative stress is increased in systemic lupus erythematosus (SLE), and it contributes to immune system dysregulation, abnormal activation and processing of cell-death signals, autoantibody production and fatal comorbidities. Mitochondrial dysfunction in T cells promotes the release of highly diffusible inflammatory lipid hydroperoxides, which spread oxidative stress to other intracellular organelles and through the bloodstream. Oxidative modification of self antigens triggers autoimmunity, and the degree of such modification of serum proteins shows striking correlation with disease activity and organ damage in SLE. In T cells from patients with SLE and animal models of the disease, glutathione, the main intracellular antioxidant, is depleted and serine/threonine-protein kinase mTOR undergoes redox-dependent activation. In turn, reversal of glutathione depletion by application of its amino acid precursor, N-acetylcysteine, improves disease activity in lupus-prone mice; pilot studies in patients with SLE have yielded positive results that warrant further research. Blocking mTOR activation in T cells could conceivably provide a well-tolerated and inexpensive alternative approach to B-cell blockade and traditional immunosuppressive treatments. Nevertheless, compartmentalized oxidative stress in self-reactive T cells, B cells and phagocytic cells might serve to limit autoimmunity and its inhibition could be detrimental. Antioxidant therapy might also be useful in ameliorating damage caused by other treatments. This Review thus seeks to critically evaluate the complexity of oxidative stress and its relevance to the pathogenesis and treatment of SLE.
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Wang S, Wen F, Wiley GB, Kinter MT, Gaffney PM. An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression. PLoS Genet 2013; 9:e1003750. [PMID: 24039598 PMCID: PMC3764111 DOI: 10.1371/journal.pgen.1003750] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/10/2013] [Indexed: 12/22/2022] Open
Abstract
Functional characterization of causal variants present on risk haplotypes identified through genome-wide association studies (GWAS) is a primary objective of human genetics. In this report, we evaluate the function of a pair of tandem polymorphic dinucleotides, 42 kb downstream of the promoter of TNFAIP3, (rs148314165, rs200820567, collectively referred to as TT>A) recently nominated as causal variants responsible for genetic association of systemic lupus erythematosus (SLE) with tumor necrosis factor alpha inducible protein 3 (TNFAIP3). TNFAIP3 encodes the ubiquitin-editing enzyme, A20, a key negative regulator of NF-κB signaling. A20 expression is reduced in subjects carrying the TT>A risk alleles; however, the underlying functional mechanism by which this occurs is unclear. We used a combination of electrophoretic mobility shift assays (EMSA), mass spectrometry (MS), reporter assays, chromatin immunoprecipitation-PCR (ChIP-PCR) and chromosome conformation capture (3C) EBV transformed lymphoblastoid cell lines (LCL) from individuals carrying risk and non-risk TNFAIP3 haplotypes to characterize the effect of TT>A on A20 expression. Our results demonstrate that the TT>A variants reside in an enhancer element that binds NF-κB and SATB1 enabling physical interaction of the enhancer with the TNFAIP3 promoter through long-range DNA looping. Impaired binding of NF-κB to the TT>A risk alleles or knockdown of SATB1 expression by shRNA, inhibits the looping interaction resulting in reduced A20 expression. Together, these data reveal a novel mechanism of TNFAIP3 transcriptional regulation and establish the functional basis by which the TT>A risk variants attenuate A20 expression through inefficient delivery of NF-κB to the TNFAIP3 promoter. These results provide critical functional evidence supporting a direct causal role for TT>A in the genetic predisposition to SLE. A key objective of human genetics is the identification and characterization of variants responsible for association with complex diseases. A pair of single nucleotide polymorphisms (rs148314165, rs200820567) 42 kb downstream from the promoter of TNFAIP3, have been proposed as the variants responsible for association with systemic lupus erythematosus based on comprehensive genetic and bioinformatic analyses. TNFAIP3 encodes for the ubiquitin-editing enzyme, A20, which plays a central role in maintaining immune system homeostasis through restriction of NF-κB signaling. Cells that carry this risk haplotype express low levels of TNFAIP3 compared to cells carrying the nonrisk haplotype. How the risk alleles of rs148314165 and rs200820567 might influence low TNFAIP3 expression is unknown. In this paper, we demonstrate that these variants reside in an enhancer element that binds NF-κB and SATB1 enabling the interaction of the enhancer with the TNFAIP3 promoter through long-range DNA looping. Impaired binding of NF-κB directly to the risk alleles or shRNA-mediated knockdown of SATB1 inhibits interaction of the enhancer with the TNFAIP3 promoter resulting in reduced A20 expression. These results clarify the functional mechanism by which rs148314165 and rs200820567 attenuate A20 expression and support a causal role for these variants in the predisposition to autoimmune disease.
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Affiliation(s)
- Shaofeng Wang
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Feng Wen
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Graham B. Wiley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Michael T. Kinter
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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Abstract
Systemic lupus erythematosus, Sjögren's syndrome, and dermatomyositis are systemic autoimmune diseases that develop after environmental triggering of genetically susceptible individuals. The precise cellular and molecular mechanisms leading to autoimmune disease, and what factors determine which organs are involved, remain poorly understood. Recent insights into genetic susceptibility now make obvious that environmental triggers often act via cellular pathways containing disease-associated polymorphisms. In the breaking of tolerance, the initiating tissue--including dendritic cells--provides a decisive microenvironment that affects immune-cell differentiation, leading to activation of adaptive immunity. Type 1 interferon produced by innate immune cells has a central role in systemic autoimmunity and activates B cells and T cells. In turn, B-cell-derived autoantibodies stimulate dendritic cells to produce type 1 interferon; thus, a positive feedforward loop is formed that includes both the innate and adaptive systems. New treatments could simultaneously and specifically target several such vital pathways in autoimmunity.
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The combination of two Sle2 lupus-susceptibility loci and Cdkn2c deficiency leads to T-cell-mediated pathology in B6.Fas(lpr) mice. Genes Immun 2013; 14:373-9. [PMID: 23698709 PMCID: PMC3752316 DOI: 10.1038/gene.2013.28] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 01/12/2023]
Abstract
The NZM2410 Sle2c1 lupus susceptibility locus is responsible for the expansion of the B1a cell compartment, and for the induction of T-cell induced renal and skin pathology on a CD95-deficient (Fas(lpr)) background. We have previously shown that deficiency in the cyclin-dependent kinase inhibitor p18(INK4c) (p18) was responsible for the B1a cell expansion but was not sufficient to account for the pathology in B6.lpr mice. This study was designed to map the additional Sle2c1 loci responsible for autoimmune pathology when co-expressed with CD95 deficiency. The production, fine-mapping and phenotypic characterization of five recombinant intervals indicated that three interacting subloci were responsive for inducting autoimmune pathogenesis in B6.lpr mice. One of these subloci corresponds most likely to p18 deficiency. Another major locus mapping to a 2-Mb region at the telomeric end of Sle2c1 is necessary to both renal and skin pathology. Finally, a third locus centromeric to p18 enhances the severity of lupus nephritis. These results provide new insights into the genetic interactions leading to systemic lupus erythematosus disease presentation, and represent a major step towards the identification of novel susceptibility genes involved in T-cell-mediated organ damage.
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Piotrowski P, Lianeri M, Prokop E, Wudarski M, Olesińska M, Jagodziński PP. The FCRL3 -169T>C polymorphism might be associated with some autoantibody presence in patients with SLE in a Polish population. Mod Rheumatol 2013. [PMID: 23564408 DOI: 10.1007/s10165-013-0875-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/24/2013] [Indexed: 10/27/2022]
Abstract
OBJECTIVES: The Fcrl3 -169T>C (rs7528684) polymorphism has been shown to be a risk factor of various autoimmune diseases, including systemic lupus erythematosus (SLE); however, these results are inconsistent between distinct ethnicities. METHODS: Using PCR-RFLP we studied the distribution of the FCRL3 -169T>C polymorphism in SLE patients (n = 263) and controls (n = 528) in a sample from the Polish population. RESULTS: We found no significant differences of FCRL3 -169T>C genotypes and alleles between patients with SLE and healthy individuals. However, in the dominant model we found a significant association between the FCRL3 -169T>C polymorphism and the presence of anti-Scl-70 antibody (Ab) [OR = 4.747 (95 % CI = 1.639-13.749), p = 0.0011, p corr = 0.0198]. Moreover, in the dominant model we observed a significant contribution of FCRL3 -169T>C to the presence of either anti-La or anti-Scl-70 Abs [OR = 4.378 (95 % CI = 1.793-10.690, p = 0.0003, p corr = 0.0054)]. CONCLUSIONS: Our study demonstrated that the FCRL3 -169T>C polymorphism is not a risk factor of SLE in the Polish population, but this polymorphism may contribute to autoantibody production in this disease.
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Affiliation(s)
- Piotr Piotrowski
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznan, Poland
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Abstract
Dysregulation of gene expression can cause complex disease phenotypes. MicroRNAs (miRNAs) are well known to fine-tune cellular gene expression to control immune cell development and regulate adaptive and innate immune responses. Discoveries over the past decade have indicated that aberrant expression of miRNAs is associated with the pathogenesis of multiple immunological diseases, including systemic lupus erythematosus (SLE). Indeed, profiling miRNA expression in blood cells, body fluid and target tissues taken from patients with SLE has revealed unique miRNA signatures when compared with healthy individuals or those with other diseases. Moreover, dysregulation of these miRNAs has also been found to be associated with disease activity and major organ involvement. In our opinion, therefore, miRNAs have the potential to act as biomarkers for the diagnosis and assessment of patients with SLE. This Review provides an overview of the novel cellular and molecular mechanisms that seem to underlie the roles of miRNAs in SLE disease processes, as well as the future therapeutic potential of targeting miRNAs in the management of patients with SLE.
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