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Trivioli G, Marquez A, Martorana D, Tesi M, Kronbichler A, Lyons PA, Vaglio A. Genetics of ANCA-associated vasculitis: role in pathogenesis, classification and management. Nat Rev Rheumatol 2022; 18:559-574. [PMID: 36109667 DOI: 10.1038/s41584-022-00819-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 12/15/2022]
Abstract
Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) comprises granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA) and eosinophilic granulomatosis with polyangiitis (EGPA), that share features of pauci-immune small-vessel vasculitis and the positivity of ANCA targeting proteinase-3 (PR3-ANCA) or myeloperoxidase (MPO-ANCA). AAV syndromes are rare, complex diseases and their aetio-pathogenesis is mainly driven by the interaction between environmental and genetic factors. In patients with GPA and MPA, the genetic associations are stronger with ANCA specificity (PR3- versus MPO-ANCA) than with the clinical diagnosis, which, in keeping with the known clinical and prognostic differences between PR3-ANCA-positive and MPO-ANCA-positive patients, supports an ANCA-based re-classification of these disorders. EGPA is also made up of genetically distinct subsets, which can be stratified on ANCA-status (MPO ANCA-positive versus ANCA-negative); these subsets differ in clinical phenotype and possibly in their response to treatment. Interestingly, MPO-ANCA-positive patients with either MPA or EGPA have overlapping genetic determinants, thus strengthening the concept that this EGPA subset is closely related to the other AAV syndromes. The genetics of AAV provides us with essential information to understand its varied phenotype. This Review discusses the main findings of genetic association studies in AAV, their pathogenic implications and their potential effect on classification, management and prognosis.
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Affiliation(s)
- Giorgio Trivioli
- Department of Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | - Ana Marquez
- Institute of Parasitology and Biomedicine "López-Neyra", CSIC, Granada, Spain
| | - Davide Martorana
- Medical Genetics Unit, Department of Diagnostics, University Hospital of Parma, Parma, Italy
- CoreLab Unit, Research Center, University Hospital of Parma, Parma, Italy
| | - Michelangelo Tesi
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | - Andreas Kronbichler
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Vasculitis and Lupus Service, Department of Renal Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Augusto Vaglio
- Department of Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy.
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy.
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Abstract
Two vasculitides, giant cell arteritis (GCA) and Takayasu arteritis (TAK), are recognized as autoimmune and autoinflammatory diseases that manifest exclusively within the aorta and its large branches. In both entities, the age of the affected host is a critical risk factor. TAK manifests during the 2nd-4th decade of life, occurring while the immune system is at its height of performance. GCA is a disease of older individuals, with infrequent cases during the 6th decade and peak incidence during the 8th decade of life. In both vasculitides, macrophages and T cells infiltrate into the adventitia and media of affected vessels, induce granulomatous inflammation, cause vessel wall destruction, and reprogram vascular cells to drive adventitial and neointimal expansion. In GCA, abnormal immunity originates in an aged immune system and evolves within the aged vascular microenvironment. One hallmark of the aging immune system is the preferential loss of CD8+ T cell function. Accordingly, in GCA but not in TAK, CD8+ effector T cells play a negligible role and anti-inflammatory CD8+ T regulatory cells are selectively impaired. Here, we review current evidence of how the process of immunosenescence impacts the risk for GCA and how fundamental differences in the age of the immune system translate into differences in the granulomatous immunopathology of TAK versus GCA.
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Yoshifuji H, Terao C. Roles of cytotoxic lymphocytes and MIC/LILR families in pathophysiology of Takayasu arteritis. Inflamm Regen 2020; 40:9. [PMID: 32514324 PMCID: PMC7265636 DOI: 10.1186/s41232-020-00119-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
Takayasu arteritis (TAK) affects the aorta and its primary branches, mainly in young women. In its advanced stages, it can cause severe complications, such as cerebral infarction, impaired vision, and valvular heart diseases. In the aortic tissue of TAK, there is increased infiltration of cytotoxic lymphocytes, such as natural killer (NK) cells and CD8+T cells, and enhanced expression of accessory molecules, such as major histocompatibility complex (MHC) and MHC class I chain-related gene (MIC) family. Genome-wide association studies on TAK have identified susceptibility genes, such as IL-12p40, MICA, MICB, leukocyte immunoglobulin-like receptor A3 (LILRA3), and LILRB3. Other studies have also shown their involvement in the pathophysiology of TAK. In addition, we reported the importance of NK cells by enhancer enrichment analysis. These results suggest that the gene polymorphisms that potentially upregulate the expression of cytokines and accessory molecules, which contribute to the activation of cytotoxic lymphocytes, are associated with the development of TAK. Based on these results, new molecular targeted therapies look promising.
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Affiliation(s)
- Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.,Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan.,The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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Abstract
PURPOSE OF REVIEW The purpose of this review is to discuss recent observations of epigenetic changes related to the complex pathogenesis of systemic vasculitides and their contribution to the field. RECENT FINDINGS There have been new observations of epigenetic changes in vasculitis and their potential role in disease pathogenesis in antineutrophil cytoplasmic antibody-associated vasculitis, giant-cell arteritis, Kawasaki disease, Behçet's disease, and IgA vasculitis. Some of this recent work has focused on the efficacy of using DNA methylation and miRNA expression as clinical biomarkers for disease activity and how DNA methylation and histone modifications interact to regulate disease-related gene expression. SUMMARY DNA methylation, histone modification, and miRNA expression changes are all fruitful ground for biomarker discovery and therapeutic targets in vasculitis. Current knowledge has provided targeted and suggested effects, but in many cases, has relied upon small cohorts, cosmopolitan cell populations, and limited knowledge of functional interactions. Expanding our knowledge of how these epigenetic mechanisms interact in a disease-specific and cell-specific manner will help to better understand the pathogenesis of systemic vasculitis.
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Ortiz-Fernández L, Carmona FD, López-Mejías R, González-Escribano MF, Lyons PA, Morgan AW, Sawalha AH, Smith KGC, González-Gay MA, Martín J. Cross-phenotype analysis of Immunochip data identifies KDM4C as a relevant locus for the development of systemic vasculitis. Ann Rheum Dis 2018; 77:589-595. [PMID: 29374629 PMCID: PMC5849568 DOI: 10.1136/annrheumdis-2017-212372] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 12/14/2022]
Abstract
OBJETIVE Systemic vasculitides represent a heterogeneous group of rare complex diseases of the blood vessels with a poorly understood aetiology. To investigate the shared genetic component underlying their predisposition, we performed the first cross-phenotype meta-analysis of genetic data from different clinically distinct patterns of vasculitis. METHODS Immunochip genotyping data from 2465 patients diagnosed with giant cell arteritis, Takayasu's arteritis, antineutrophil cytoplasmic antibody-associated vasculitis or IgA vasculitis as well as 4632 unaffected controls were analysed to identify common susceptibility loci for vasculitis development. The possible functional consequences of the associated variants were interrogated using publicly available annotation data. RESULTS The strongest association signal corresponded with an intergenic polymorphism located between HLA-DQB1 and HLA-DQA2 (rs6932517, P=4.16E-14, OR=0.74). This single nucleotide polymorphism is in moderate linkage disequilibrium with the disease-specific human leucocyte antigen (HLA) class II associations of each type of vasculitis and could mark them. Outside the HLA region, we identified the KDM4C gene as a common risk locus for vasculitides (highest peak rs16925200, P=6.23E-07, OR=1.75). This gene encodes a histone demethylase involved in the epigenetic control of gene expression. CONCLUSIONS Through a combined analysis of Immunochip data, we have identified KDM4C as a new risk gene shared between systemic vasculitides, consistent with the increasing evidences of the crucial role that the epigenetic mechanisms have in the development of complex immune-mediated conditions.
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Affiliation(s)
| | - Francisco David Carmona
- Departamento de Genética e Instituto de
Biotecnología, Universidad de Granada, Granada, Spain
| | - Raquel López-Mejías
- Epidemiology, Genetics and Atherosclerosis Research Group on
Systemic Inflammatory Diseases, Rheumatology Division, Hospital Universitario
Marqués de Valdecilla, IDIVAL, Santander, Spain
| | | | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical
Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Ann W Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine,
University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching
Hospitals NHS Trust, Leeds, UK
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine,
University of Michigan, Ann Arbor, Michigan, USA
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge School of Clinical
Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Miguel A González-Gay
- Epidemiology, Genetics and Atherosclerosis Research Group on
Systemic Inflammatory Diseases, Rheumatology Division, Hospital Universitario
Marqués de Valdecilla, IDIVAL, Santander, Spain
- School of Medicine, University of Cantabria, Santander, Spain
| | - Javier Martín
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada,
Spain
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Abstract
The number of peer-reviewed articles published during the 2016 solar year and retrieved using the "autoimmunity" key word remained stable while gaining a minimal edge among the immunology articles. Nonetheless, the quality of the publications has been rising significantly and, importantly, acquisitions have become available through scientific journals dedicated to immunology or autoimmunity. Major discoveries have been made in the fields of systemic lupus erythematosus, rheumatoid arthritis, autoimmunity of the central nervous system, vasculitis, and seronegative spondyloarthrithritides. Selected examples include the role of IL17-related genes and long noncoding RNAs in systemic lupus erythematosus or the effects of anti-pentraxin 3 (PTX3) in the treatment of this paradigmatic autoimmune condition. In the case of rheumatoid arthritis, there have been reports of the role of induced regulatory T cells (iTregs) or fibrocytes and T cell interactions with exciting implications. The large number of studies dealing with neuroimmunology pointed to Th17 cells, CD56(bright) NK cells, and low-level TLR2 ligands as involved in multiple sclerosis, along with a high salt intake or the micriobiome-derived Lipid 654. Lastly, we focused on the rare vasculitides to which numerous studies were devoted and suggested that unsuspected cell populations, including monocytes, mucosal-associated invariant T cells, and innate lymphoid cells, may be crucial to ANCA-associated manifestations. This brief and arbitrary discussion of the findings published in 2016 is representative of a promising background for developments that will enormously impact the work of laboratory scientists and physicians at an exponential rate.
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Affiliation(s)
- Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, via A. Manzoni 56, 20089, Rozzano, Milan, Italy.
- Department of Medical Biotechnologies and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy.
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8
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Xiang Z, Yang Y, Chang C, Lu Q. The epigenetic mechanism for discordance of autoimmunity in monozygotic twins. J Autoimmun 2017; 83:43-50. [PMID: 28412046 DOI: 10.1016/j.jaut.2017.04.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022]
Abstract
Monozygotic twins share an identical DNA sequence but are not truly "identical". In fact, when it comes to health and disease, they may often display some level of phenotypic discordance. The cause of this discordance is often unknown. Epigenetic modifications such as DNA methylation, histone modification, and microRNAs-mediated regulation regulate gene expression and are sensitive to external stimuli. These modifications may be seen to bridge the gap between genetics and the environment. Over the years, the importance of epigenetics as a primary mechanism for the role that the environment plays in defining phenotype has been increasingly appreciated. Mechanisms of epigenetics include DNA methylation, histone modifications and microRNAs. Discordance rates in monozygotic twins vary depending on the specific condition, from 11% in SLE to 64% in psoriasis and 77% in PBC. Other autoimmune diseases in which discordance is found among monozygotic twins has also been studied include type 1 diabetes, multiple sclerosis, rheumatoid arthritis, dermatomyositis and systemic sclerosis. In some cases, the differences in various epigenetic modifications is slight, even though the concordance rate is low, suggesting that epigenetics is not the only factor that needs to be considered. Nonetheless, the study of phenotypic discordance in monozygotic twins may shed light on the pathogenesis of autoimmune diseases and contribute to the development of new methodologies for the diagnosis and treatment of these diseases.
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Affiliation(s)
- Zhongyuan Xiang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yuanqing Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616, United States
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.
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Yang J, Ge H, Poulton CJ, Hogan SL, Hu Y, Jones BE, Henderson CD, McInnis EA, Pendergraft WF, Jennette JC, Falk RJ, Ciavatta DJ. Histone modification signature at myeloperoxidase and proteinase 3 in patients with anti-neutrophil cytoplasmic autoantibody-associated vasculitis. Clin Epigenetics 2016; 8:85. [PMID: 27752292 PMCID: PMC5057507 DOI: 10.1186/s13148-016-0251-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease characterized by destructive vascular inflammation. Two prominent ANCA autoantigens are myeloperoxidase (MPO) and proteinase 3 (PR3), and transcription of MPO and PRTN3, the genes encoding the autoantigens, is associated with disease activity. We investigated whether patients with AAV have alterations in histone modifications, particularly those associated with transcriptional activation, at MPO and PRTN3. RESULTS We identified a network of genes regulating histone modifications that were differentially expressed in AAV patients compared to healthy controls. We focused on four genes (EHMT1 and EHMT2, ING4, and MSL1) and found their expression correlated with expression of MPO and PRTN3. Methylation of histone H3K9, catalyzed by EHMT1 and EHMT2 and associated with gene silencing, was most depleted at MPO and PRTN3 in patients with active disease and the highest MPO and PRTN3 expression. Acetylation of histone H4K16, modified by complexes containing ING4 and MSL1 and associated with gene activation, was most enriched at MPO and PRTN3 in patients with active disease and the highest MPO and PRTN3 expression. Methylation at H3K4, a mark of transcriptional activation, was enriched at MPO and PRTN3 in patients and healthy controls. CONCLUSIONS MPO and PRTN3 in neutrophils of AAV patients with active disease have a distinct pattern of histone modifications, which implicates epigenetic mechanisms in regulating expression of autoantigen genes and suggests that the epigenome may be involved in AAV pathogenesis.
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Affiliation(s)
- Jiajin Yang
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Heng Ge
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Nephrology, The Second Affiliated Hospital, School of Medicine, Xian Jiaotong University, 157 Xiwu Road, Xian, Shaanxi 710004 People's Republic of China
| | - Caroline J Poulton
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan L Hogan
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yichun Hu
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Britta E Jones
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Candace D Henderson
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Elizabeth A McInnis
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - William F Pendergraft
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - J Charles Jennette
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Ronald J Falk
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Dominic J Ciavatta
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Campus Box 7264, Chapel Hill, NC 27599 USA
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Dozmorov MG, Cara LR, Giles CB, Wren JD. GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets. ACTA ACUST UNITED AC 2016; 32:2256-63. [PMID: 27153607 DOI: 10.1093/bioinformatics/btw169] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/23/2016] [Indexed: 01/16/2023]
Abstract
MOTIVATION The growing amount of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opportunities to investigate the functional impact of single nucleotide polymorphisms (SNPs). Yet, given the large number of regulatory datasets, researchers are posed with a challenge of how to efficiently utilize them to interpret the functional impact of SNP sets. RESULTS We developed the GenomeRunner web server to automate systematic statistical analysis of SNP sets within a regulatory context. Besides defining the functional impact of SNP sets, GenomeRunner implements novel regulatory similarity/differential analyses, and cell type-specific regulatory enrichment analysis. Validated against literature- and disease ontology-based approaches, analysis of 39 disease/trait-associated SNP sets demonstrated that the functional impact of SNP sets corresponds to known disease relationships. We identified a group of autoimmune diseases with SNPs distinctly enriched in the enhancers of T helper cell subpopulations, and demonstrated relevant cell type-specificity of the functional impact of other SNP sets. In summary, we show how systematic analysis of genomic data within a regulatory context can help interpreting the functional impact of SNP sets. AVAILABILITY AND IMPLEMENTATION GenomeRunner web server is freely available at http://www.integrativegenomics.org/ CONTACT mikhail.dozmorov@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Lukas R Cara
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Cory B Giles
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jonathan D Wren
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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