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Kerns S, Owen KA, Schwalbe D, Grammer AC, Lipsky PE. Examination of the shared genetic architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel lupus risk loci. Hum Genet 2024; 143:703-719. [PMID: 38609570 DOI: 10.1007/s00439-024-02672-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease with heterogeneous manifestations, including neurological and psychiatric symptoms. Genetic association studies in SLE have been hampered by insufficient sample size and limited power compared to many other diseases. Multiple Sclerosis (MS) is a chronic relapsing autoimmune disease of the central nervous system (CNS) that also manifests neurological and immunological features. Here, we identify a method of leveraging large-scale genome wide association studies (GWAS) in MS to identify novel genetic risk loci in SLE. Statistical genetic comparison methods including linkage disequilibrium score regression (LDSC) and cross-phenotype association analysis (CPASSOC) to identify genetic overlap in disease pathophysiology, traditional 2-sample and novel PPI-based mendelian randomization to identify causal associations and Bayesian colocalization were applied to association studies conducted in MS to facilitate discovery in the smaller, more limited datasets available for SLE. Pathway analysis using SNP-to-gene mapping identified biological networks composed of molecular pathways with causal implications for CNS disease in SLE specifically, as well as pathways likely causal of both pathologies, providing key insights for therapeutic selection.
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Affiliation(s)
- Sophia Kerns
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA.
- The RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Dana Schwalbe
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
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2
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Pisetsky DS. Unique Interplay Between Antinuclear Antibodies and Nuclear Molecules in the Pathogenesis of Systemic Lupus Erythematosus. Arthritis Rheumatol 2024. [PMID: 38622070 DOI: 10.1002/art.42863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that primarily affects young women and causes a wide range of inflammatory manifestations. The hallmark of SLE is the production of antibodies to components of the cell nucleus (antinuclear antibodies [ANAs]). These antibodies can bind to DNA, RNA, and protein complexes with nucleic acids. Among ANAs, antibodies to DNA (anti-DNA) are markers for classification and disease activity, waxing and waning disease activity in many patients. In the blood, anti-DNA antibodies can bind to DNA to form immune complexes with two distinct roles in pathogenesis: (1) renal deposition to provoke nephritis and (2) stimulation of cytokine production following uptake into innate immune cells and interaction with internal nucleic acid sensors. These sensors are part of an internal host defense system in the cell cytoplasm that can respond to DNA from infecting organisms; during cell stress, DNA from nuclear and mitochondrial sources can also trigger these sensors. The formation of immune complexes requires a source of extracellular DNA in an immunologically accessible form. As shown in in vivo and in vitro systems, extracellular DNA can emerge from dead and dying cells in both a free and a particulate form. Neutrophils undergoing the process of NETosis can release DNA in mesh-like structures called neutrophil extracellular traps. In SLE, therefore, the combination of ANAs and immunologically active DNA can create new structures that can promote inflammation throughout the body as well as drive organ inflammation and damage.
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Affiliation(s)
- David S Pisetsky
- Duke University Medical Center and Durham Veterans Administration Medical Center, Durham, North Carolina
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3
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Singh MK, Rallabandi HR, Zhou XJ, Qi YY, Zhao ZZ, Gan T, Zhang H, Looger LL, Nath SK. KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homoeostasis. Ann Rheum Dis 2024:ard-2023-224953. [PMID: 38373841 DOI: 10.1136/ard-2023-224953] [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: 09/01/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024]
Abstract
OBJECTIVE A recent genome-wide association study linked KLF2 as a novel Asian-specific locus for systemic lupus erythematosus (SLE) susceptibility. However, the underlying causal functional variant(s), cognate target gene(s) and genetic mechanisms associated with SLE risk are unknown. METHODS We used bioinformatics to prioritise likely functional variants and validated the best candidate with diverse experimental techniques, including genome editing. Gene expression was compared between healthy controls (HCs) and patients with SLE with or without lupus nephritis (LN+, LN-). RESULTS Through bioinformatics and expression quantitative trait locus analyses, we prioritised rs4808485 in active chromatin, predicted to modulate KLF2 expression. Luciferase reporter assays and chromatin immunoprecipitation-qPCR demonstrated differential allele-specific enhancer activity and binding of active histone marks (H3K27ac, H3K4me3 and H3K4me1), Pol II, CTCF, P300 and the transcription factor PARP1. Chromosome conformation capture-qPCR revealed long-range chromatin interactions between rs4808485 and the KLF2 promoter. These were directly validated by CRISPR-based genetic and epigenetic editing in Jurkat and lymphoblastoid cells. Deleting the rs4808485 enhancer in Jurkat (KO) cells disrupted NLRP3 inflammasome machinery by reducing KLF2 and increasing CASPASE1, IL-1β and GSDMD levels. Knockout cells also exhibited higher proliferation and cell-cycle progression than wild type. RNA-seq validated interplay between KLF2 and inflammasome machinery in HC, LN+ and LN-. CONCLUSIONS We demonstrate how rs4808485 modulates the inflammasome and cellular homoeostasis through regulating KLF2 expression. This establishes mechanistic connections between rs4808485 and SLE susceptibility.
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Affiliation(s)
- Manish Kumar Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Harikrishna Reddy Rallabandi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Xu-Jie Zhou
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Yuan-Yuan Qi
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhan-Zheng Zhao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ting Gan
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Hong Zhang
- Renal Division, Peking University Institute of Nephrology, Peking University First Hospital, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Loren L Looger
- Howard Hughes Medical Institute, Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
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Parodis I, Lanata C, Nikolopoulos D, Blazer A, Yazdany J. Reframing health disparities in SLE: A critical reassessment of racial and ethnic differences in lupus disease outcomes. Best Pract Res Clin Rheumatol 2023:101894. [PMID: 38057256 DOI: 10.1016/j.berh.2023.101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Health disparities in the prevalence and outcomes of systemic lupus erythematosus (SLE) are well documented across racial and ethnic groups. Similar to other chronic diseases, differences in disease severity among individuals with SLE are likely influenced by both genetic predisposition and multiple social determinants of health. However, research in SLE that jointly examines the genetic and environmental contributions to the disease course is limited, resulting in an incomplete understanding of the biologic and social mechanisms that underly health disparities. While research on health disparities can reveal inequalities and inform resource allocation to improve outcomes, research that relies on racial and ethnic categories to describe diverse groups of people can pose challenges. Additionally, results from research comparing outcomes across socially constructed groups without considering other contributing factors can be misleading. We herein comprehensively examine existing literature on health disparities in SLE, including both clinical studies that examine the relationship between self-reported race and ethnicity and disease outcomes and studies that explore the relationships between genomics and lupus outcomes. Having surveyed this body of research, we propose a framework for research examining health disparities in SLE, including ways to mitigate bias in future studies.
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Affiliation(s)
- Ioannis Parodis
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden; Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Cristina Lanata
- Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dionysis Nikolopoulos
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Ashira Blazer
- Division of Rheumatology, Department of Medicine, Hospital for Special, Surgery, New York, NY, USA
| | - Jinoos Yazdany
- Division of Rheumatology, University of California, San Francisco, USA
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5
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Singh MK, Maiti GP, Reddy-Rallabandi H, Fazel-Najafabadi M, Looger LL, Nath SK. A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility. FRONTIERS IN LUPUS 2023; 1:1244670. [PMID: 38317862 PMCID: PMC10843804 DOI: 10.3389/flupu.2023.1244670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
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Affiliation(s)
- Manish Kumar Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | - Guru Prashad Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | | | - Mehdi Fazel-Najafabadi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | - Loren L. Looger
- Howard Hughes Medical Institute, Department of Neurosciences, University of California San Diego, La Jolla CA, USA
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
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6
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Singh MK, Maiti GP, Reddy-Rallabandi H, Fazel-Najafabadi M, Looger LL, Nath SK. A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551056. [PMID: 37546883 PMCID: PMC10402135 DOI: 10.1101/2023.07.28.551056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4 . Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1 , and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
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Rector I, Owen KA, Bachali P, Hubbard E, Yazdany J, Dall'era M, Grammer AC, Lipsky PE. Differential regulation of the interferon response in systemic lupus erythematosus distinguishes patients of Asian ancestry. RMD Open 2023; 9:e003475. [PMID: 37709528 PMCID: PMC10503349 DOI: 10.1136/rmdopen-2023-003475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES Type I interferon (IFN) plays a role in the pathogenesis of systemic lupus erythematosus (SLE), but insufficient attention has been directed to the differences in IFN responses between ancestral populations. Here, we explored the expression of the interferon gene signatures (IGSs) in SLE patients of European ancestry (EA) and Asian ancestry (AsA). METHODS We used gene set variation analysis with multiple IGS encompassing the response to both type 1 and type 2 IFN in isolated CD14+ monocytes, CD19+B cells, CD4+T cells and Natural Killer (NK) cells from patients with SLE stratified by self-identified ancestry. The expression of genes upstream of the IGS and influenced by lupus-associated risk alleles was also examined. Lastly, we employed machine learning (ML) models to assess the most important features classifying patients by disease activity. RESULTS AsA patients with SLE exhibited greater enrichment in the IFN core and IFNA2 IGS compared with EA patients in all cell types examined and, in the presence and absence of autoantibodies. Overall, AsA patients with SLE demonstrated higher expression of genes upstream of the IGS than EA counterparts. ML with feature importance analysis indicated that IGS expression in NK cells, anti-dsDNA, complement levels and AsA status contributed to disease activity. CONCLUSIONS AsA patients with SLE exhibited higher IGS than EA patients in all cell types regardless of autoantibody status, with enhanced expression of genetically associated genes upstream of the IGS potentially contributing. AsA, along with the IGS in NK cells, anti-dsDNA and complement, independently influenced SLE disease activity.
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Affiliation(s)
- Ian Rector
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | | | - Prathyusha Bachali
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Erika Hubbard
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Jinoos Yazdany
- Medicine/Rheumatology, University of California, San Francisco, California, USA
| | - Maria Dall'era
- Division of Rheumatology, University of California, San Francisco, California, USA
| | - Amrie C Grammer
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Peter E Lipsky
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
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8
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Gatto M, Depascale R, Stefanski AL, Schrezenmeier E, Dörner T. Translational implications of newly characterized pathogenic pathways in systemic lupus erythematosus. Best Pract Res Clin Rheumatol 2023:101864. [PMID: 37625930 DOI: 10.1016/j.berh.2023.101864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Improved characterization of relevant pathogenic pathways in systemic lupus erythematosus (SLE) has been further delineated over the last decades. This led to the development of targeted treatments including belimumab and anifrolumab, which recently became available in clinics. Therapeutic targets in SLE encompass interferon (IFN) signaling, B-T costimulation including immune checkpoints, and increasing modalities of B lineage targeting, such as chimeric antigen receptor (CAR) T cells directed against CD19 or sequential anti-B cell targeting. Patient profiling based on characterization of underlying molecular abnormalities, often performed through comprehensive omics analyses, has recently been shown to better predict patients' treatment responses and also holds promise to unravel key molecular mechanisms driving SLE. SLE carries two key signatures, namely the IFN and B lineage/plasma cell signatures. Recent advances in SLE treatments clearly indicate that targeting innate and adaptive immunity is successful in such a complex autoimmune disease. Although those signatures may interact at the molecular level and provide the basis for the first selective treatments in SLE, it remains to be clarified whether these distinct treatments show different treatment responses among certain patient subsets. In fact, notwithstanding the remarkable amount of novel clues for innovative SLE treatment, harmonization of big data within tailored treatment strategies will be instrumental to better understand and treat this challenging autoimmune disorder. This review will provide an overview of recent improvements in SLE pathogenesis, related insights by analyses of big data and machine learning as well as technical improvements in conducting clinical trials with the ultimate goal that translational research results in improved patient outcomes.
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Affiliation(s)
- Mariele Gatto
- Unit of Rheumatology, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Roberto Depascale
- Unit of Rheumatology, Department of Medicine, University of Padova, Padova, Italy
| | - Ana Luisa Stefanski
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Eva Schrezenmeier
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany; Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Dörner
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany; Department of Rheumatology and Clinical Immunology - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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9
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Crow MK. Pathogenesis of systemic lupus erythematosus: risks, mechanisms and therapeutic targets. Ann Rheum Dis 2023; 82:999-1014. [PMID: 36792346 DOI: 10.1136/ard-2022-223741] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Research elucidating the pathogenesis of systemic lupus erythematosus (SLE) has defined two critical families of mediators, type I interferon (IFN-I) and autoantibodies targeting nucleic acids and nucleic acid-binding proteins, as fundamental contributors to the disease. On the fertile background of significant genetic risk, a triggering stimulus, perhaps microbial, induces IFN-I, autoantibody production or most likely both. When innate and adaptive immune system cells are engaged and collaborate in the autoimmune response, clinical SLE can develop. This review describes recent data from genetic analyses of patients with SLE, along with current studies of innate and adaptive immune function that contribute to sustained IFN-I pathway activation, immune activation and autoantibody production, generation of inflammatory mediators and tissue damage. The goal of these studies is to understand disease mechanisms, identify therapeutic targets and stimulate development of therapeutics that can achieve improved outcomes for patients.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York, USA
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10
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Touil H, Mounts K, De Jager PL. Differential impact of environmental factors on systemic and localized autoimmunity. Front Immunol 2023; 14:1147447. [PMID: 37283765 PMCID: PMC10239830 DOI: 10.3389/fimmu.2023.1147447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
The influence of environmental factors on the development of autoimmune disease is being broadly investigated to better understand the multifactorial nature of autoimmune pathogenesis and to identify potential areas of intervention. Areas of particular interest include the influence of lifestyle, nutrition, and vitamin deficiencies on autoimmunity and chronic inflammation. In this review, we discuss how particular lifestyles and dietary patterns may contribute to or modulate autoimmunity. We explored this concept through a spectrum of several autoimmune diseases including Multiple Sclerosis (MS), Systemic Lupus Erythematosus (SLE) and Alopecia Areata (AA) affecting the central nervous system, whole body, and the hair follicles, respectively. A clear commonality between the autoimmune conditions of interest here is low Vitamin D, a well-researched hormone in the context of autoimmunity with pleiotropic immunomodulatory and anti-inflammatory effects. While low levels are often correlated with disease activity and progression in MS and AA, the relationship is less clear in SLE. Despite strong associations with autoimmunity, we lack conclusive evidence which elucidates its role in contributing to pathogenesis or simply as a result of chronic inflammation. In a similar vein, other vitamins impacting the development and course of these diseases are explored in this review, and overall diet and lifestyle. Recent work exploring the effects of dietary interventions on MS showed that a balanced diet was linked to improvement in clinical parameters, comorbid conditions, and overall quality of life for patients. In patients with MS, SLE and AA, certain diets and supplements are linked to lower incidence and improved symptoms. Conversely, obesity during adolescence was linked with higher incidence of MS while in SLE it was associated with organ damage. Autoimmunity is thought to emerge from the complex interplay between environmental factors and genetic background. Although the scope of this review focuses on environmental factors, it is imperative to elaborate the interaction between genetic susceptibility and environment due to the multifactorial origin of these disease. Here, we offer a comprehensive review about the influence of recent environmental and lifestyle factors on these autoimmune diseases and potential translation into therapeutic interventions.
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Affiliation(s)
- Hanane Touil
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Kristin Mounts
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Philip Lawrence De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
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Abstract
Autoimmune diseases are a diverse group of conditions characterized by aberrant B cell and T cell reactivity to normal constituents of the host. These diseases occur widely and affect individuals of all ages, especially women. Among these diseases, the most prominent immunological manifestation is the production of autoantibodies, which provide valuable biomarkers for diagnosis, classification and disease activity. Although T cells have a key role in pathogenesis, they are technically more difficult to assay. In general, autoimmune disease results from an interplay between a genetic predisposition and environmental factors. Genetic predisposition to autoimmunity is complex and can involve multiple genes that regulate the function of immune cell populations. Less frequently, autoimmunity can result from single-gene mutations that affect key regulatory pathways. Infection seems to be a common trigger for autoimmune disease, although the microbiota can also influence pathogenesis. As shown in seminal studies, patients may express autoantibodies many years before the appearance of clinical or laboratory signs of disease - a period called pre-clinical autoimmunity. Monitoring autoantibody expression in at-risk populations may therefore enable early detection and the initiation of therapy to prevent or attenuate tissue damage. Autoimmunity may not be static, however, and remission can be achieved by some patients treated with current agents.
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Affiliation(s)
- David S Pisetsky
- Duke University Medical Center, Medical Research Service, Durham Veterans Administration Medical Center, Durham, NC, USA.
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12
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Mok CC, Teng YKO, Saxena R, Tanaka Y. Treatment of lupus nephritis: consensus, evidence and perspectives. Nat Rev Rheumatol 2023; 19:227-238. [PMID: 36864291 DOI: 10.1038/s41584-023-00925-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2023] [Indexed: 03/04/2023]
Abstract
Despite the continuing development of immunomodulatory agents and supportive care, the prognosis associated with lupus nephritis (LN) has not improved substantially in the past decade, with end-stage kidney disease still developing in 5-30% of patients within 10 years of LN diagnosis. Moreover, inter-ethnic variation in the tolerance of, clinical response to and level of evidence regarding various therapeutic regimens for LN has led to variation in treatment prioritization in different international recommendations. Modalities that better preserve kidney function and reduce the toxicities of concomitant glucocorticoids are unmet needs in the development of therapeutics for LN. In addition to the conventional recommended therapies for LN, there are newly approved treatments as well as investigational drugs in the pipeline, including the newer generation calcineurin inhibitors and biologic agents. In view of the heterogeneity of LN in terms of clinical presentation and prognosis, the choice of therapies depends on a number of clinical considerations. Molecular profiling, gene-signature fingerprints and urine proteomic panels might enhance the accuracy of patient stratification for treatment personalization in the future.
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Affiliation(s)
- Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, Hong Kong, China.
| | - Y K Onno Teng
- Center of Expertise for Lupus-, Vasculitis- and Complement-mediated systemic diseases, Department of Internal Medicine, Section of Nephrology, Leiden University Medical Center, Leiden, Netherlands
| | - Ramesh Saxena
- Department of Internal Medicine, Division of Nephrology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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13
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Owen KA, Bell KA, Price A, Bachali P, Ainsworth H, Marion MC, Howard TD, Langefeld CD, Shen N, Yazdany J, Dall'era M, Grammer AC, Lipsky PE. Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry. Sci Rep 2023; 13:5339. [PMID: 37005464 PMCID: PMC10067935 DOI: 10.1038/s41598-023-32569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of Asian-Ancestry (AsA) disproportionately experience more severe SLE compared to individuals of European-Ancestry (EA), including increased renal involvement and tissue damage. However, the mechanisms underlying elevated severity in the AsA population remain unclear. Here, we utilized available gene expression data and genotype data based on all non-HLA SNP associations in EA and AsA SLE patients detected using the Immunochip genotyping array. We identified 2778 ancestry-specific and 327 trans-ancestry SLE-risk polymorphisms. Genetic associations were examined using connectivity mapping and gene signatures based on predicted biological pathways and were used to interrogate gene expression datasets. SLE-associated pathways in AsA patients included elevated oxidative stress, altered metabolism and mitochondrial dysfunction, whereas SLE-associated pathways in EA patients included a robust interferon response (type I and II) related to enhanced cytosolic nucleic acid sensing and signaling. An independent dataset derived from summary genome-wide association data in an AsA cohort was interrogated and identified similar molecular pathways. Finally, gene expression data from AsA SLE patients corroborated the molecular pathways predicted by SNP associations. Identifying ancestry-related molecular pathways predicted by genetic SLE risk may help to disentangle the population differences in clinical severity that impact AsA and EA individuals with SLE.
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Affiliation(s)
- Katherine A Owen
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Kristy A Bell
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Andrew Price
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Prathyusha Bachali
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Hannah Ainsworth
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Miranda C Marion
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Timothy D Howard
- Department of Biochemistry, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinoos Yazdany
- University of California San Francisco, San Francisco, CA, 94117, USA
| | - Maria Dall'era
- University of California San Francisco, San Francisco, CA, 94117, USA
| | - Amrie C Grammer
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
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14
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Sun X, Liu Z, Li Z, Zeng Z, Peng W, Zhu J, Zhao J, Zhu C, Zeng C, Stearrett N, Crandall KA, Bachali P, Grammer AC, Lipsky PE. Abnormalities in intron retention characterize patients with systemic lupus erythematosus. Sci Rep 2023; 13:5141. [PMID: 36991079 PMCID: PMC10060252 DOI: 10.1038/s41598-023-31890-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Regulation of intron retention (IR), a form of alternative splicing, is a newly recognized checkpoint in gene expression. Since there are numerous abnormalities in gene expression in the prototypic autoimmune disease systemic lupus erythematosus (SLE), we sought to determine whether IR was intact in patients with this disease. We, therefore, studied global gene expression and IR patterns of lymphocytes in SLE patients. We analyzed RNA-seq data from peripheral blood T cell samples from 14 patients suffering from systemic lupus erythematosus (SLE) and 4 healthy controls and a second, independent data set of RNA-seq data from B cells from16 SLE patients and 4 healthy controls. We identified intron retention levels from 26,372 well annotated genes as well as differential gene expression and tested for differences between cases and controls using unbiased hierarchical clustering and principal component analysis. We followed with gene-disease enrichment analysis and gene-ontology enrichment analysis. Finally, we then tested for significant differences in intron retention between cases and controls both globally and with respect to specific genes. Overall decreased IR was found in T cells from one cohort and B cells from another cohort of patients with SLE and was associated with increased expression of numerous genes, including those encoding spliceosome components. Different introns within the same gene displayed both up- and down-regulated retention profiles indicating a complex regulatory mechanism. These results indicate that decreased IR in immune cells is characteristic of patients with active SLE and may contribute to the abnormal expression of specific genes in this autoimmune disease.
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Affiliation(s)
- Xiaoqian Sun
- Computer Science Department, George Washington University, Washington, DC, 20052, USA
| | - Zhichao Liu
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Zongzhu Li
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Zhouhao Zeng
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Weiqun Peng
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Jun Zhu
- Mokobio Biotechnology R&D Center, 1445 Research Blvd, Suite 150, Rockville, MD, 20850, USA
| | - Joel Zhao
- Walt Whitman High School, Bethesda, MD, 20817, USA
| | | | - Chen Zeng
- Physics Department, George Washington University, Washington, DC, 20052, USA.
| | - Nathaniel Stearrett
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
| | - Prathyusha Bachali
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA.
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15
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Kain J, Owen KA, Marion MC, Langefeld CD, Grammer AC, Lipsky PE. Mendelian randomization and pathway analysis demonstrate shared genetic associations between lupus and coronary artery disease. Cell Rep Med 2022; 3:100805. [PMID: 36334592 PMCID: PMC9729823 DOI: 10.1016/j.xcrm.2022.100805] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Coronary artery disease (CAD) is a leading cause of death in patients with systemic lupus erythematosus (SLE). Despite clinical evidence supporting an association between SLE and CAD, pleiotropy-adjusted genetic association studies are limited and focus on only a few common risk loci. Here, we identify a net positive causal estimate of SLE-associated non-HLA SNPs on CAD by traditional Mendelian randomization (MR) approaches. Pathway analysis using SNP-to-gene mapping followed by unsupervised clustering based on protein-protein interactions (PPIs) identifies biological networks composed of positive and negative causal sets of genes. In addition, we confirm the casual effects of specific SNP-to-gene modules on CAD using only SNP mapping to each PPI-defined functional gene set as instrumental variables. This PPI-based MR approach elucidates various molecular pathways with causal implications between SLE and CAD and identifies biological pathways likely causative of both pathologies, revealing known and novel therapeutic interventions for managing CAD in SLE.
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Affiliation(s)
- Jessica Kain
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA.
| | - Miranda C Marion
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
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16
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Yin X, Kim K, Suetsugu H, Bang SY, Wen L, Koido M, Ha E, Liu L, Sakamoto Y, Jo S, Leng RX, Otomo N, Kwon YC, Sheng Y, Sugano N, Hwang MY, Li W, Mukai M, Yoon K, Cai M, Ishigaki K, Chung WT, Huang H, Takahashi D, Lee SS, Wang M, Karino K, Shim SC, Zheng X, Miyamura T, Kang YM, Ye D, Nakamura J, Suh CH, Tang Y, Motomura G, Park YB, Ding H, Kuroda T, Choe JY, Li C, Niiro H, Park Y, Shen C, Miyamoto T, Ahn GY, Fei W, Takeuchi T, Shin JM, Li K, Kawaguchi Y, Lee YK, Wang YF, Amano K, Park DJ, Yang W, Tada Y, Lau YL, Yamaji K, Zhu Z, Shimizu M, Atsumi T, Suzuki A, Sumida T, Okada Y, Matsuda K, Matsuo K, Kochi Y, Yamamoto K, Ohmura K, Kim TH, Yang S, Yamamoto T, Kim BJ, Shen N, Ikegawa S, Lee HS, Zhang X, Terao C, Cui Y, Bae SC. Biological insights into systemic lupus erythematosus through an immune cell-specific transcriptome-wide association study. Ann Rheum Dis 2022; 81:1273-1280. [PMID: 35609976 PMCID: PMC9380500 DOI: 10.1136/annrheumdis-2022-222345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/11/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Genome-wide association studies (GWAS) have identified >100 risk loci for systemic lupus erythematosus (SLE), but the disease genes at most loci remain unclear, hampering translation of these genetic discoveries. We aimed to prioritise genes underlying the 110 SLE loci that were identified in the latest East Asian GWAS meta-analysis. METHODS We built gene expression predictive models in blood B cells, CD4+ and CD8+ T cells, monocytes, natural killer cells and peripheral blood cells of 105 Japanese individuals. We performed a transcriptome-wide association study (TWAS) using data from the latest genome-wide association meta-analysis of 208 370 East Asians and searched for candidate genes using TWAS and three data-driven computational approaches. RESULTS TWAS identified 171 genes for SLE (p<1.0×10-5); 114 (66.7%) showed significance only in a single cell type; 127 (74.3%) were in SLE GWAS loci. TWAS identified a strong association between CD83 and SLE (p<7.7×10-8). Meta-analysis of genetic associations in the existing 208 370 East Asian and additional 1498 cases and 3330 controls found a novel single-variant association at rs72836542 (OR=1.11, p=4.5×10-9) around CD83. For the 110 SLE loci, we identified 276 gene candidates, including 104 genes at recently-identified SLE novel loci. We demonstrated in vitro that putative causal variant rs61759532 exhibited an allele-specific regulatory effect on ACAP1, and that presence of the SLE risk allele decreased ACAP1 expression. CONCLUSIONS Cell-level TWAS in six types of immune cells complemented SLE gene discovery and guided the identification of novel genetic associations. The gene findings shed biological insights into SLE genetic associations.
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Affiliation(s)
- Xianyong Yin
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, People's Republic of China
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, People's Republic of China
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Human Phenome Institute, Fudan University, Shanghai, People's Republic of China
| | - Kwangwoo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Hiroyuki Suetsugu
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Leilei Wen
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eunji Ha
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Lu Liu
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Yuma Sakamoto
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Koga Hospital 21, Kurume, Japan
| | - Sungsin Jo
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, People's Republic of China
| | - Nao Otomo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Young-Chang Kwon
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Yujun Sheng
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Nobuhiko Sugano
- Department of Orthopaedic Medical Engineering, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Weiran Li
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Masaya Mukai
- Department of Rheumatology & Clinical Immunology, Sapporo City General Hospital, Hokkaido, Japan
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Minglong Cai
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Won Tae Chung
- Department of Internal Medicine, Dong-A University Hospital, Busan, South Korea
| | - He Huang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Daisuke Takahashi
- Department of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Shin-Seok Lee
- Division of Rheumatology, Department of Internal Medicine, Chonnam National University Medical School and Hospital, Gwangju, South Korea
| | - Mengwei Wang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Kohei Karino
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Seung-Cheol Shim
- Division of Rheumatology, Department of Internal Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Xiaodong Zheng
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Tomoya Miyamura
- Department of Internal Medicine and Rheumatology, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Young Mo Kang
- Division of Rheumatology, Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Dongqing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, People's Republic of China
| | - Junichi Nakamura
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Goro Motomura
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Takeshi Kuroda
- Niigata University Health Administration Center, Niigata, Japan
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, South Korea
| | - Chengxu Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Hiroaki Niiro
- Department of Medical Education, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Youngho Park
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Changbing Shen
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, People's Republic of China
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ga-Young Ahn
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Wenmin Fei
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Jung-Min Shin
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Keke Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Yasushi Kawaguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yeon-Kyung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Koichi Amano
- Department of Rheumatology & Clinical Immunology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Dae Jin Park
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Yoshifumi Tada
- Department of Rheumatology, Faculty of Medicine, Saga University, Saga, Japan
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Ken Yamaji
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Zhengwei Zhu
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Masato Shimizu
- Hokkaido Medical Center for Rheumatic Diseases, Sapporo, Japan
| | - Takashi Atsumi
- Department of Orthopaedic Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Takayuki Sumida
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Sen Yang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
| | - Takuaki Yamamoto
- Department of Orthopaedic Surgery, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine (SJTUSM), Shanghai, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
| | - Xuejun Zhang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, People's Republic of China
- Key Lab of Dermatology, Ministry of Education (Anhui Medical University), Hefei, Anhui, People's Republic of China
- Department of Dermatology, Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research, Seoul, South Korea
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17
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Ullah S, Haroon M, Hashmi F, Tayyab Z, Javed S. A Prospective Follow-Up Study on the Disease Course and Predictors of Poor Outcomes in a Random Population-Based Cohort of Newly Diagnosed Lupus Patients. Cureus 2022; 14:e27430. [PMID: 36051712 PMCID: PMC9420196 DOI: 10.7759/cureus.27430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2022] [Indexed: 11/05/2022] Open
Abstract
Background and objective Systemic lupus erythematosus (SLE) is one of the most devastating systemic autoimmune connective tissue diseases. There is a paucity of prospective data on Pakistani SLE patients, and in this prospective study, we aimed to investigate the disease course, clinical outcomes, and the predictors of poor outcomes in a random population-based cohort of newly diagnosed SLE patients (diagnosed within the last one year). Methods This was a prospective observational study carried out in the rheumatology department of the Fatima Memorial Hospital, Lahore. Lupus patients are regularly reviewed in our dedicated lupus clinic every one to three months. For the purpose of this study, a focus group of newly diagnosed patients (diagnosed within the last one year) attending our lupus clinic was identified and prospectively followed up for 12 months. A wide range of demographical and clinical parameters was recorded. The association of clinical variables with the progressive disease was determined using univariate and multivariate logistic regressions. Results Prospective data of 89 newly diagnosed SLE patients regularly attending our dedicated lupus clinic were reviewed. During the study period, (January 2021 through January 2022), these patients had multiple visits overall - median: five, minimum: three, and maximum: nine visits [interquartile range (IQR) 4-7]. All 89 patients had completed one year of follow-up. Of note, 46% of the cohort was noted to have an ongoing active disease during the majority of visits in the study period. On multiple logistic regression analysis, there was a significant association between ongoing active disease ("progressors") and low education status [odds ratio (OR): 2.81, 95% confidence interval (CI): 1.01-7.76, p=0.046], stress at home (OR: 5.8, 95% CI: 2.13-15.8, p=0.001), and hematologic manifestations (OR: 3.0, 95% CI: 1.08-8.32, p=0.03). Conclusions Almost half of our cohort of lupus patients demonstrated active disease manifestations throughout the one-year prospective follow-up, and these were found to be associated with low education status, stress at home, and hematological manifestations.
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18
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Choi MY, Costenbader KH. Understanding the Concept of Pre-Clinical Autoimmunity: Prediction and Prevention of Systemic Lupus Erythematosus: Identifying Risk Factors and Developing Strategies Against Disease Development. Front Immunol 2022; 13:890522. [PMID: 35720390 PMCID: PMC9203849 DOI: 10.3389/fimmu.2022.890522] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/04/2022] [Indexed: 12/27/2022] Open
Abstract
There is growing evidence that preceding the diagnosis or classification of systemic lupus erythematosus (SLE), patients undergo a preclinical phase of disease where markers of inflammation and autoimmunity are already present. Not surprisingly then, even though SLE management has improved over the years, many patients will already have irreversible disease-related organ damage by time they have been diagnosed with SLE. By gaining a greater understanding of the pathogenesis of preclinical SLE, we can potentially identify patients earlier in the disease course who are at-risk of transitioning to full-blown SLE and implement preventative strategies. In this review, we discuss the current state of knowledge of SLE preclinical pathogenesis and propose a screening and preventative strategy that involves the use of promising biomarkers of early disease, modification of lifestyle and environmental risk factors, and initiation of preventative therapies, as examined in other autoimmune diseases such as rheumatoid arthritis and type 1 diabetes.
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Affiliation(s)
- May Y Choi
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Department of Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, McCaig Institute for Bone and Joint Health, Calgary, AB, Canada
| | - Karen H Costenbader
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
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19
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Garantziotis P, Nikolakis D, Doumas S, Frangou E, Sentis G, Filia A, Fanouriakis A, Bertsias G, Boumpas DT. Molecular Taxonomy of Systemic Lupus Erythematosus Through Data-Driven Patient Stratification: Molecular Endotypes and Cluster-Tailored Drugs. Front Immunol 2022; 13:860726. [PMID: 35615355 PMCID: PMC9125979 DOI: 10.3389/fimmu.2022.860726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Treatment of Systemic Lupus Erythematosus (SLE) is characterized by a largely empirical approach and relative paucity of novel compound development. We sought to stratify SLE patients based on their molecular phenotype and identify putative therapeutic compounds for each molecular fingerprint. Methods By the use of whole blood RNA-seq data from 120 SLE patients, and in a data-driven, clinically unbiased manner, we established modules of commonly regulated genes (molecular endotypes) and re-stratified patients through hierarchical clustering. Disease activity and severity were assessed using SLEDAI-2K and Lupus Severity Index, respectively. Through an in silico drug prediction pipeline, we investigated drugs currently in use, tested in lupus clinical trials, and listed in the iLINCS prediction databases, for their ability to reverse the gene expression signatures in each molecular endotype. Drug repurposing analysis was also performed to identify perturbagens that counteract group-specific SLE signatures. Results Molecular taxonomy identified five lupus endotypes, each characterized by a unique gene module enrichment pattern. Neutrophilic signature group consisted primarily of patients with active lupus nephritis, while the B-cell expression group included patients with constitutional features. Patients with moderate severity and serologic activity exhibited a signature enriched for metabolic processes. Mild disease was distributed in two groups, exhibiting enhanced basic cellular functions, myelopoiesis, and autophagy. Bortezomib was predicted to reverse disturbances in the "neutrophilic" cluster, azathioprine and ixazomib in the "B-cell" cluster, and fostamatinib in the "metabolic" patient subgroup. Conclusion The clinical spectrum of SLE encompasses distinct molecular endotypes, each defined by unique pathophysiologic aberrancies potentially reversible by distinct compounds.
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Affiliation(s)
- Panagiotis Garantziotis
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Dimitrios Nikolakis
- Department of Gastroenterology, Academic Medical Center, Amsterdam Institute for Gastroenterology Endocrinology and Metabolism Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Rheumatology and Immunology Center (ARC), Academic Medical Center, Amsterdam, Netherlands.,Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Stavros Doumas
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Department of Medicine, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Eleni Frangou
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Department of Nephrology, Limassol General Hospital, Limassol, Cyprus
| | - George Sentis
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Antonis Fanouriakis
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Rheumatology Unit, First Department of Propaedeutic and Internal Medicine, National Kapodistrian University of Athens Medical School, Athens, Greece.,4th Department of Internal Medicine, "Attikon" University Hospital, Athens, Greece.,Joint Rheumatology Program, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Bertsias
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete School of Medicine, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Dimitrios T Boumpas
- Laboratory of Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,4th Department of Internal Medicine, "Attikon" University Hospital, Athens, Greece.,Joint Rheumatology Program, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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20
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Anaparti V, Wiens D, O'Neil LJ, Hubbard E, Robl R, Smolik I, Hitchon C, Lipsky PE, El-Gabalawy H. Utility of Baseline Transcriptomic Analysis of Rheumatoid Arthritis Synovium as an Indicator for Long-Term Clinical Outcomes. Front Med (Lausanne) 2022; 9:823244. [PMID: 35592852 PMCID: PMC9110862 DOI: 10.3389/fmed.2022.823244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/28/2022] [Indexed: 11/18/2022] Open
Abstract
Objective: Rheumatoid arthritis is a chronic inflammatory autoimmune disease that can lead to synovial damage, persistent joint pain, and functional disability. Our objective was to evaluate baseline synovial transcriptome from early inflammatory arthritis patients (EIA) and identify pretreatment biomarkers that could potentially provide insights into long-term functional outcomes of rheumatoid arthritis (RA). Methods Synovial biopsies from clinically inflamed knee joints were procured from either 17 EIA patients before initiation of disease modifying anti-rheumatic drug (DMARD) therapy (DMARD-naïve EIA) using the minimally invasive closed needle biopsy technique or advanced RA patients undergoing arthroplasty. Affymetrix Human Genome U133 Plus 2 microarray platform was used to profile the synovial transcriptome. The cohort was followed clinically for a median of 12.3 years, and patient data was collected at each visit. Short-term and long-term clinical outcomes were determined by assessing RA-associated clinical parameters Statistical adjustments were made to account for asynchronous clinical visits and duration of follow up. Results Based on the transcriptomic analysis, we identified 5 differentially expressed genes (DEGs), including matrix metalloproteinase (MMP)-1 (fibroblast collagenase) and MMP-3 (stromelysin-1) in DMARD-naïve EIA patients, relative to advanced RA patients (q < 0.05). Dichotomous expression of MMP-1 and MMP-3 mRNA and protein was confirmed by qPCR and immunohistochemistry respectively, based on which DMARD-naïve EIA subjects were classified as MMP-high or MMP-low. Hierarchical clustering of transcriptomic data identified 947 DEGs between MMP-high and MMP-low cohorts. Co-expression and IPA analysis of DEGs in the MMP-high cohort showed an enrichment of genes that participated in metabolic or biochemical functions and intracellular immune signaling were regulated through NF-κB and β-catenin complexes and correlated with markers of systemic inflammation. Analysis of short-term clinical outcomes in MMP-high cohort showed a significant reduction in the DAS-CRP scores relative to baseline (P <0.001), whereas area under the curve analyses of modified HAQ (mHAQ) scores correlated negatively with baseline MMP-1 (R = −0.59, P = 0.03). Further, longitudinal mHAQ scores, number of swollen joints, number of DMARDs and median follow-up duration appeared to be higher in MMP-low cohort. Conclusion Overall, our results indicate that the gene expression profiling of synovial biopsies obtained at the DMARD-naive stage in patients with EIA categorizes them into subsets with varying degrees of inflammation and can predict the future of long-term clinical outcome.
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Affiliation(s)
- Vidyanand Anaparti
- Manitoba Center of Proteomics and Systems Biology, Winnipeg, MB, Canada.,Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Dana Wiens
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Liam J O'Neil
- Manitoba Center of Proteomics and Systems Biology, Winnipeg, MB, Canada.,Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Erika Hubbard
- Ampel BioSolutions LLC, Charlottesville, VA, United States
| | - Robert Robl
- Ampel BioSolutions LLC, Charlottesville, VA, United States
| | - Irene Smolik
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Carol Hitchon
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Peter E Lipsky
- Ampel BioSolutions LLC, Charlottesville, VA, United States
| | - Hani El-Gabalawy
- Manitoba Center of Proteomics and Systems Biology, Winnipeg, MB, Canada.,Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
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21
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Wang P, Xiang K, Xu YY, He YS, Hu YQ, Ni J, Pan HF. Genetically Predicted Circulating Omega-3 Fatty Acids Levels Are Causally Associated With Increased Risk for Systemic Lupus Erythematosus. Front Nutr 2022; 9:783338. [PMID: 35223943 PMCID: PMC8864316 DOI: 10.3389/fnut.2022.783338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/06/2022] [Indexed: 11/22/2022] Open
Abstract
Background Accumulating evidence has demonstrated the associations of omega-3 or omega-6 polyunsaturated fatty acids (PUFAs) with the disease activity and inflammatory mediators of systemic lupus erythematosus (SLE), but the evidence of causal links of omega-3 or omega-6 PUFAs on the risk for SLE remains inconclusive. Objectives This study was conducted to evaluate the causal relationships between omega-3/omega-6 PUFAs and SLE by performing the Mendelian randomization (MR) analysis. Methods Genome-wide significant single-nucleotide polymorphisms (SNPs) were obtained from genome-wide association studies (GWASs) of circulating omega-3/omega-6 levels (n = up to 13,544) and GWAS meta-analyses of SLE (n = 14,267), respectively. The bidirectional two-sample MR (TSMR) analysis was conducted to infer the causality. Results The inverse-variance weighted (IVW) method revealed that genetically determined per SD increase in omega-3 levels were causally associated with an increased risk for SLE (odds ratios [ORs] = 1.49, 95% CI: 1.07, 2.08, p = 0.021), but no causal effect of omega-6 on the risk SLE was observed (IVW OR = 1.06, 95% CI: 0.72, 1.57, p = 0.759). In addition, there were no significantly causal associations in genetic predisposition to SLE with the changes of omega-3 and omega-6 levels, respectively (IVW beta for omega-3: 0.007, 95% CI: −0.006, 0.022, p = 0.299; IVW beta for omega-6: −0.008, 95% CI: −0.023, 0.006, p = 0.255). Conclusion The present study revealed the possible causal role of omega-3 on increasing the risk for SLE, it could be the potential implications for dietary recommendations.
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Affiliation(s)
- Peng Wang
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Kun Xiang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Yuan-Yuan Xu
- Department of Outpatient Wound Care Center, 901 Hospital of Joint Logistics Support Force of People Liberation Army, Hefei, China
| | - Yi-Sheng He
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Yu-Qian Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Jing Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- Jing Ni
| | - Hai-Feng Pan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- *Correspondence: Hai-Feng Pan ;
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22
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Ghodke-Puranik Y, Jin Z, Zimmerman KD, Ainsworth HC, Fan W, Jensen MA, Dorschner JM, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Langefeld CD, Niewold TB. Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes. Arthritis Res Ther 2021; 23:290. [PMID: 34847931 PMCID: PMC8630910 DOI: 10.1186/s13075-021-02660-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background We performed expression quantitative trait locus (eQTL) analysis in single classical (CL) and non-classical (NCL) monocytes from patients with systemic lupus erythematosus (SLE) to quantify the impact of well-established genetic risk alleles on transcription at single-cell resolution. Methods Single-cell gene expression was quantified using qPCR in purified monocyte subpopulations (CD14++CD16− CL and CD14dimCD16+ NCL) from SLE patients. Novel analysis methods were used to control for the within-person correlations observed, and eQTLs were compared between cell types and risk alleles. Results The SLE-risk alleles demonstrated significantly more eQTLs in NCLs as compared to CLs (p = 0.0004). There were 18 eQTLs exclusive to NCL cells, 5 eQTLs exclusive to CL cells, and only one shared eQTL, supporting large differences in the impact of the risk alleles between these monocyte subsets. The SPP1 and TNFAIP3 loci were associated with the greatest number of transcripts. Patterns of shared influence in which different SNPs impacted the same transcript also differed between monocyte subsets, with greater evidence for synergy in NCL cells. IRF1 expression demonstrated an on/off pattern, in which expression was zero in all of the monocytes studied from some individuals, and this pattern was associated with a number of SLE risk alleles. We observed corroborating evidence of this IRF1 expression pattern in public data sets. Conclusions We document multiple SLE-risk allele eQTLs in single monocytes which differ greatly between CL and NCL subsets. These data support the importance of the SPP1 and TNFAIP3 risk variants and the IRF1 transcript in SLE patient monocyte function. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02660-2.
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Affiliation(s)
- Yogita Ghodke-Puranik
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Ave, New York, NY, 10016, USA
| | - Zhongbo Jin
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science and Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Hannah C Ainsworth
- Department of Biostatistics and Data Science and Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wei Fan
- Department of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mark A Jensen
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Ave, New York, NY, 10016, USA
| | - Jessica M Dorschner
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Danielle M Vsetecka
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Shreyasee Amin
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Ashima Makol
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | - Thomas Osborn
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Kevin Moder
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Vaidehi Chowdhary
- Division of Rheumatology, Allergy and Immunology, Yale University School of Medicine, New Haven, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science and Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Ave, New York, NY, 10016, USA.
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23
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Owen KA, Grammer AC, Lipsky PE. Deconvoluting the heterogeneity of SLE: The contribution of ancestry. J Allergy Clin Immunol 2021; 149:12-23. [PMID: 34857396 DOI: 10.1016/j.jaci.2021.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Systemic lupus erythematosus (SLE) is a multiorgan autoimmune disorder with a prominent genetic component. Evidence has shown that individuals of non-European ancestry experience the disease more severely, exhibiting an increased incidence of cardiovascular disease, renal involvement, and tissue damage compared with European ancestry populations. Furthermore, there seems to be variability in the response of individuals within different ancestral groups to standard medications, including cyclophosphamide, mycophenolate, rituximab, and belimumab. Although the widespread application of candidate gene, Immunochip, and genome-wide association studies has contributed to our understanding of the link between genetic variation (typically single nucleotide polymorphisms) and SLE, despite decades of research it is still unclear why ancestry remains a key determinant of poorer outcome in non-European-ancestry patients with SLE. Here, we will discuss the impact of ancestry on SLE disease burden in patients from diverse backgrounds and highlight how research efforts using novel bioinformatic and pathway-based approaches have begun to disentangle the complex genetic architecture linking ancestry to SLE susceptibility. Finally, we will illustrate how genomic and gene expression analyses can be combined to help identify novel molecular pathways and drug candidates that might uniquely impact SLE among different ancestral populations.
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24
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Yavuz S, Lipsky PE. Current Status of the Evaluation and Management of Lupus Patients and Future Prospects. Front Med (Lausanne) 2021; 8:682544. [PMID: 34124113 PMCID: PMC8193052 DOI: 10.3389/fmed.2021.682544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/27/2021] [Indexed: 12/24/2022] Open
Abstract
The vastly diverse nature of systemic lupus erythematosus (SLE) poses great challenges to clinicians and patients, as well as to research and drug development efforts. Precise management of lupus patients would be advanced by the ability to identify specific abnormalities operative in individual patients at the time of encounter with the clinician. Advances in new technologies and bioinformatics have greatly improved the understanding of the pathophysiology of SLE. Recent research has focused on the discovery and classification of sensitive and specific markers that could aid early accurate diagnosis, better monitoring of disease and identification of appropriate therapy choices based on specific dysregulated molecular pathways. Here, we summarize some of the advances and discuss the challenges in moving toward precise patient-centric management modalities in SLE.
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Affiliation(s)
- Sule Yavuz
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Peter E Lipsky
- Ampel BioSolutions and Re-Imagine Lupus Investigation, Treatment and Education Research Institute, Charlottesville, VA, United States
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