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Veldkamp SR, van Wijk F, van Royen-Kerkhof A, Jansen MH. Personalised medicine in juvenile dermatomyositis: From novel insights in disease mechanisms to changes in clinical practice. Best Pract Res Clin Rheumatol 2024:101976. [PMID: 39174374 DOI: 10.1016/j.berh.2024.101976] [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: 04/26/2024] [Revised: 06/12/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
Juvenile dermatomyositis is characterized by childhood-onset chronic inflammation of the muscles and skin, with potential involvement of other organs. Patients are at risk for long-term morbidity due to insufficient disease control and steroid-related toxicity. Personalised treatment is challenged by a lack of validated tools that can reliably predict treatment response and monitor ongoing (subclinical) inflammation, and by a lack of evidence regarding the best choice of medication for individual patients. A better understanding of the involved disease mechanisms could reveal potential biomarkers and novel therapeutic targets. In this review, we highlight the most relevant immune and non-immune mechanisms, elucidating the effects of interferon overexpression on tissue alongside the interplay between the interferon signature, mitochondrial function, and immune cells. We review mechanism-based biomarkers that are promising for clinical implementation, and the latest advances in targeted therapy development. Finally, we discuss key steps needed for translating these discoveries into clinical practice.
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Affiliation(s)
- Saskia R Veldkamp
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Femke van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Annet van Royen-Kerkhof
- Department of Pediatric Immunology and Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marc Ha Jansen
- Department of Pediatric Immunology and Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.
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2
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Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J. Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics. JCI Insight 2024; 9:e176963. [PMID: 38743491 PMCID: PMC11383589 DOI: 10.1172/jci.insight.176963] [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: 11/07/2023] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Juvenile dermatomyositis (JDM) is one of several childhood-onset autoimmune disorders characterized by a type I IFN response and autoantibodies. Treatment options are limited due to an incomplete understanding of how the disease emerges from dysregulated cell states across the immune system. We therefore investigated the blood of patients with JDM at different stages of disease activity using single-cell transcriptomics paired with surface protein expression. By immunophenotyping peripheral blood mononuclear cells, we observed skewing of the B cell compartment toward an immature naive state as a hallmark of JDM at diagnosis. Furthermore, we find that these changes in B cells are paralleled by T cell signatures suggestive of Th2-mediated inflammation that persist despite disease quiescence. We applied network analysis to reveal that hyperactivation of the type I IFN response in all immune populations is coordinated with previously masked cell states including dysfunctional protein processing in CD4+ T cells and regulation of cell death programming in NK cells, CD8+ T cells, and γδ T cells. Together, these findings unveil the coordinated immune dysregulation underpinning JDM and provide insight into strategies for restoring balance in immune function.
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Affiliation(s)
- Gabrielle Rabadam
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, and
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, California, USA
| | - Camilla Wibrand
- Aarhus University, Aarhus, Denmark
- Division of Pediatric Rheumatology, Department of Pediatrics
| | | | - George C Hartoularos
- Graduate Program in Biological and Medical Informatics
- Division of Rheumatology, Department of Medicine
- Institute for Human Genetics
| | - Yang Sun
- Division of Rheumatology, Department of Medicine
| | - Chioma Madubata
- Division of Pediatric Rheumatology, Department of Pediatrics
- CoLabs
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine
- Institute for Human Genetics
- Department of Epidemiology and Biostatistics, and
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Susan Kim
- Division of Pediatric Rheumatology, Department of Pediatrics
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Jessica Neely
- Division of Pediatric Rheumatology, Department of Pediatrics
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3
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Ward JM, Ambatipudi M, O'Hanlon TP, Smith MA, de Los Reyes M, Schiffenbauer A, Rahman S, Zerrouki K, Miller FW, Sanjuan MA, Li JL, Casey KA, Rider LG. Shared and Distinctive Transcriptomic and Proteomic Pathways in Adult and Juvenile Dermatomyositis. Arthritis Rheumatol 2023; 75:2014-2026. [PMID: 37229703 PMCID: PMC10615891 DOI: 10.1002/art.42615] [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: 11/19/2022] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
OBJECTIVE Transcript and protein expression were interrogated to examine gene locus and pathway regulation in the peripheral blood of active adult dermatomyositis (DM) and juvenile DM patients receiving immunosuppressive therapies. METHODS Expression data from 14 DM and 12 juvenile DM patients were compared to matched healthy controls. Regulatory effects at the transcript and protein level were analyzed by multi-enrichment analysis for assessment of affected pathways within DM and juvenile DM. RESULTS Expression of 1,124 gene loci were significantly altered at the transcript or protein levels across DM or juvenile DM, with 70 genes shared. A subset of interferon-stimulated genes was elevated, including CXCL10, ISG15, OAS1, CLEC4A, and STAT1. Innate immune markers specific to neutrophil granules and neutrophil extracellular traps were up-regulated in both DM and juvenile DM, including BPI, CTSG, ELANE, LTF, MPO, and MMP8. Pathway analysis revealed up-regulation of PI3K/AKT, ERK, and p38 MAPK signaling, whose central components were broadly up-regulated in DM, while peripheral upstream and downstream components were differentially regulated in both DM and juvenile DM. Up-regulated components shared by DM and juvenile DM included cytokine:receptor pairs LGALS9:HAVCR2, LTF/NAMPT/S100A8/HSPA1A:TLR4, CSF2:CSF2RA, EPO:EPOR, FGF2/FGF8:FGFR, several Bcl-2 components, and numerous glycolytic enzymes. Pathways unique to DM included sirtuin signaling, aryl hydrocarbon receptor signaling, protein ubiquitination, and granzyme B signaling. CONCLUSION The combination of proteomics and transcript expression by multi-enrichment analysis broadened the identification of up- and down-regulated pathways among active DM and juvenile DM patients. These pathways, particularly those which feed into PI3K/AKT and MAPK signaling and neutrophil degranulation, may be potential therapeutic targets.
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Affiliation(s)
- James M Ward
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Mythri Ambatipudi
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | - Terrance P O'Hanlon
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | | | | | - Adam Schiffenbauer
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | - Saifur Rahman
- BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | | | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | | | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Kerry A Casey
- BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
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4
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Papadopoulou C, Chew C, Wilkinson MGL, McCann L, Wedderburn LR. Juvenile idiopathic inflammatory myositis: an update on pathophysiology and clinical care. Nat Rev Rheumatol 2023; 19:343-362. [PMID: 37188756 PMCID: PMC10184643 DOI: 10.1038/s41584-023-00967-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
The childhood-onset or juvenile idiopathic inflammatory myopathies (JIIMs) are a heterogenous group of rare and serious autoimmune diseases of children and young people that predominantly affect the muscles and skin but can also involve other organs, including the lungs, gut, joints, heart and central nervous system. Different myositis-specific autoantibodies have been identified that are associated with different muscle biopsy features, as well as with different clinical characteristics, prognoses and treatment responses. Thus, myositis-specific autoantibodies can be used to subset JIIMs into sub-phenotypes; some of these sub-phenotypes parallel disease seen in adults, whereas others are distinct from adult-onset idiopathic inflammatory myopathies. Although treatments and management have much improved over the past decade, evidence is still lacking for many of the current treatments and few validated prognostic biomarkers are available with which to predict response to treatment, comorbidities (such as calcinosis) or outcome. Emerging data on the pathogenesis of the JIIMs are leading to proposals for new trials and tools for monitoring disease.
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Affiliation(s)
- Charalampia Papadopoulou
- Department of Paediatric Rheumatology, Great Ormond Street Hospital for Children NHS Foundation Trust (GOSH), London, UK
- Rare Diseases Theme NIHR Biomedical Research Centre at GOSH, London, UK
| | - Christine Chew
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Meredyth G Ll Wilkinson
- Rare Diseases Theme NIHR Biomedical Research Centre at GOSH, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, London, UK
- Infection Immunity and Inflammation Research and Teaching Department, UCL GOS Institute of Child Health, London, UK
| | - Liza McCann
- Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Lucy R Wedderburn
- Department of Paediatric Rheumatology, Great Ormond Street Hospital for Children NHS Foundation Trust (GOSH), London, UK.
- Rare Diseases Theme NIHR Biomedical Research Centre at GOSH, London, UK.
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, London, UK.
- Infection Immunity and Inflammation Research and Teaching Department, UCL GOS Institute of Child Health, London, UK.
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5
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Chen X, Lian D, Zeng H. Single-cell profiling of peripheral blood and muscle cells reveals inflammatory features of juvenile dermatomyositis. Front Cell Dev Biol 2023; 11:1166017. [PMID: 37152289 PMCID: PMC10157079 DOI: 10.3389/fcell.2023.1166017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Juvenile dermatomyositis (JDM) is a rare yet serious childhood systemic autoimmune condition that primarily causes skin rashes and inflammatory myopathy of the proximal muscles. Although the associated immune response involves the innate and adaptive arms, a detailed analysis of the pertinent immune cells remains to be performed. This study aims to investigate the dynamic changes of cell type, cell composition and transcriptional profiles in peripheral blood and muscle tissues, and in order to clarify the involvement of immune cells in the pathogenesis of JDM and provide a theoretical reference for JDM. Methods: Single-cell RNA sequencing combined with bioinformatic analyses were used to investigate the dynamic changes in cell composition and transcriptional profiles. Results: Analysis of 45,859 cells revealed nine and seven distinct cell subsets in the peripheral blood and muscle tissues respectively. IFITM2+ and CYP4F3+ monocytes were largely produced, and CD74+ smooth muscle cells (SMCs) and CCL19+ fibroblasts were identified as inflammatory-related cell subtypes in JDM patients, exhibiting patient-specific cell population heterogeneity.The dynamic gene expression patterns presented an enhanced type I interferon response in peripheral blood monocytes and T-cells, and SMCs and fibroblasts in muscle of untreated JDM patients. EGR1 and IRF7 may play central roles in the inflammation in both CD74+ SMCs and CCL19+ fibroblasts. Moreover, inflammatory-related monocytes could regulate T-cells, and the interaction between immune cells and SMCs or fibroblasts in muscle was enhanced under the inflammatory state. Conclusions: Immune dysregulation is one of the key pathogenic factors of JDM, and type I interferon responses are significantly enhanced in peripheral blood Monos and T cells as well as SMCs and fibroblasts. EGR1 and IRF7 may play central roles in the inflammation and are considered as potential therapeutic targets for JDM.
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Affiliation(s)
- Xiangyuan Chen
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Dongsheng Lian
- Department Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Huasong Zeng
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Huasong Zeng,
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6
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Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. Front Immunol 2022; 13:902232. [PMID: 35799782 PMCID: PMC9254730 DOI: 10.3389/fimmu.2022.902232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/04/2022] [Indexed: 02/01/2023] Open
Abstract
Juvenile dermatomyositis (JDM) is a rare autoimmune condition with insufficient biomarkers and treatments, in part, due to incomplete knowledge of the cell types mediating disease. We investigated immunophenotypes and cell-specific genes associated with disease activity using multiplexed RNA and protein single-cell sequencing applied to PBMCs from 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months post-treatment and 4 subjects with inactive disease on treatment. Analysis of 55,564 cells revealed separate clustering of TN-JDM cells within monocyte, NK, CD8+ effector T and naïve B populations. The proportion of CD16+ monocytes was reduced in TN-JDM, and naïve B cells and CD4+ Tregs were expanded. Cell-type differential gene expression analysis and hierarchical clustering identified a pan-cell-type IFN gene signature over-expressed in TN-JDM in all cell types and correlated with disease activity most strongly in cytotoxic cell types. TN-JDM CD16+ monocytes expressed the highest IFN gene score and were highly skewed toward an inflammatory and antigen-presenting phenotype at both the transcriptomic and proteomic levels. A transitional B cell population with a distinct transcriptomic signature was expanded in TN-JDM and characterized by higher CD24 and CD5 proteins and less CD39, an immunoregulatory protein. This data provides new insights into JDM immune dysregulation at cellular resolution and serves as a novel resource for myositis investigators.
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Affiliation(s)
- Jessica Neely
- Division of Pediatric Rheumatology, Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - George Hartoularos
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, United States
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Daniel Bunis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - David Lee
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Susan Kim
- Division of Pediatric Rheumatology, Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Chun Jimmie Ye
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, United States
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
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7
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Abstract
PURPOSE OF REVIEW This review provides updates regarding the role of interferon (IFN) in juvenile dermatomyositis (JDM), including comparison to interferonopathies and therapeutic implications. RECENT FINDINGS Transcriptomic and protein-based studies in different tissues and peripheral IFN-α assessment have demonstrated the importance of the dysregulated IFN pathway in JDM. Additional studies have validated IFN-regulated gene and protein expression correlation with disease activity in blood and muscle, with potential to predict flares. Type I and II IFN both are dysregulated in peripheral blood and muscle, with more type I IFN in skin. Muscle studies connects hypoxia to IFN production and IFN to vascular dysfunction and muscle atrophy. JDM overlaps with interferonopathy phenotype and IFN signature. There are multiple case reports and case series noting decreased IFN markers and clinical improvement in refractory JDM with Janus kinase (JAK) inhibitors. SUMMARY Studies confirm IFN, particularly type I and II IFN, is an important part of JDM pathogenesis by the level of dysregulation and correlation with disease activity, as well as IFN recapitulating key JDM muscle pathology. Smaller studies indicate there may be differences by myositis-specific autoantibody group, but validation is needed. JAK inhibitors are a promising therapy as they can inhibit IFN signaling, but further study is needed regarding which patients will benefit, dosing, and safety monitoring.
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Affiliation(s)
- Hanna Kim
- Juvenile Myositis Pathogenesis and Therapeutics Unit, National Institute of Arthritis Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
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8
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Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Front Immunol 2021; 12:638066. [PMID: 34177888 PMCID: PMC8223752 DOI: 10.3389/fimmu.2021.638066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/17/2021] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need to identify biomarkers for diagnosis and disease activity monitoring in rheumatoid arthritis (RA). We leveraged publicly available microarray gene expression data in the NCBI GEO database for whole blood (N=1,885) and synovial (N=284) tissues from RA patients and healthy controls. We developed a robust machine learning feature selection pipeline with validation on five independent datasets culminating in 13 genes: TNFAIP6, S100A8, TNFSF10, DRAM1, LY96, QPCT, KYNU, ENTPD1, CLIC1, ATP6V0E1, HSP90AB1, NCL and CIRBP which define the RA score and demonstrate its clinical utility: the score tracks the disease activity DAS28 (p = 7e-9), distinguishes osteoarthritis (OA) from RA (OR 0.57, p = 8e-10) and polyJIA from healthy controls (OR 1.15, p = 2e-4) and monitors treatment effect in RA (p = 2e-4). Finally, the immunoblotting analysis of six proteins on an independent cohort confirmed two proteins, TNFAIP6/TSG6 and HSP90AB1/HSP90.
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Affiliation(s)
- Dmitry Rychkov
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Jessica Neely
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
| | - Steven Yu
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, United States
| | - Noah Perlmutter
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Joanne Nititham
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Alexander Carvidi
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Melissa Krueger
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Andrew Gross
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Institute for Human Genetics (IHG), University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Judith F. Ashouri
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
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9
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Yang H, Liu D, Zhao C, Feng B, Lu W, Yang X, Xu M, Zhou W, Jing H, Yang J. Mendelian randomization integrating GWAS and eQTL data revealed genes pleiotropically associated with major depressive disorder. Transl Psychiatry 2021; 11:225. [PMID: 33866329 PMCID: PMC8053199 DOI: 10.1038/s41398-021-01348-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 01/21/2023] Open
Abstract
Previous genome-wide association studies (GWAS) have identified potential genetic variants associated with the risk of major depressive disorder (MDD), but the underlying biological interpretation remains largely unknown. We aimed to prioritize genes that were pleiotropically or potentially causally associated with MDD. We applied the summary data-based Mendelian randomization (SMR) method integrating GWAS and gene expression quantitative trait loci (eQTL) data in 13 brain regions to identify genes that were pleiotropically associated with MDD. In addition, we repeated the analysis by using the meta-analyzed version of the eQTL summary data in the brain (brain-eMeta). We identified multiple significant genes across different brain regions that may be involved in the pathogenesis of MDD. The prime-specific gene BTN3A2 (corresponding probe: ENSG00000186470.9) was the top hit showing pleiotropic association with MDD in 9 of the 13 brain regions and in brain-eMeta, after correction for multiple testing. Many of the identified genes are located in the human major histocompatibility complex (MHC) region on chromosome 6 and are mainly involved in the immune response. Our SMR analysis indicated that multiple genes showed pleiotropic association with MDD across the brain regions. These findings provided important leads to a better understanding of the mechanism of MDD and revealed potential therapeutic targets for the prevention and effective treatment of MDD.
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Affiliation(s)
- Huarong Yang
- grid.452244.1Department of Neurology, The Second Affiliated Hospital of Guizhou Medical University, Kaili, Guizhou China
| | - Di Liu
- grid.24696.3f0000 0004 0369 153XBeijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Chuntao Zhao
- grid.239573.90000 0000 9025 8099Brain Tumor Center, Cancer & Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Bowen Feng
- grid.267455.70000 0004 1936 9596Odette School of Business, University of Windsor, Windsor, ON Canada
| | - Wenjin Lu
- grid.83440.3b0000000121901201Department of Mathematics, University College London, London, UK
| | - Xiaohan Yang
- grid.24696.3f0000 0004 0369 153XDepartment of Health Management and Policy, School of Public Health, Capital Medical University, Beijing, China
| | - Minglu Xu
- grid.24696.3f0000 0004 0369 153XDepartment of Health Management and Policy, School of Public Health, Capital Medical University, Beijing, China
| | - Weizhu Zhou
- grid.415680.e0000 0000 9549 5392Department of Epidemiology and Health Statistics, School of Public Health, Shenyang Medical College, Shenyang, China
| | - Huiquan Jing
- Department of Health Management and Policy, School of Public Health, Capital Medical University, Beijing, China.
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA. .,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
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10
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Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. Commun Biol 2021; 4:419. [PMID: 33772100 PMCID: PMC7997983 DOI: 10.1038/s42003-021-01932-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis. Megremis, Walker at al. identify immunogenic epitopes in dermatomyositis patients. They identify antibodies recognizing a wider diversity of microbial antigens including poxviruses, and autoantibodies recognizing a large portion of the human proteome. Shared epitope homology between viral and human proteins suggests that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.
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Lim N, Tesar S, Belmadani M, Poirier-Morency G, Mancarci BO, Sicherman J, Jacobson M, Leong J, Tan P, Pavlidis P. Curation of over 10 000 transcriptomic studies to enable data reuse. Database (Oxford) 2021; 2021:6143045. [PMID: 33599246 PMCID: PMC7904053 DOI: 10.1093/database/baab006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 01/07/2023]
Abstract
Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html.
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Affiliation(s)
- Nathaniel Lim
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Stepan Tesar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Manuel Belmadani
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Burak Ogan Mancarci
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Jordan Sicherman
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Justin Leong
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Patrick Tan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
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Turnier JL, Kahlenberg JM. The Role of Cutaneous Type I IFNs in Autoimmune and Autoinflammatory Diseases. THE JOURNAL OF IMMUNOLOGY 2020; 205:2941-2950. [PMID: 33229366 DOI: 10.4049/jimmunol.2000596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/18/2020] [Indexed: 01/31/2023]
Abstract
IFNs are well known as mediators of the antimicrobial response but also serve as important immunomodulatory cytokines in autoimmune and autoinflammatory diseases. An increasingly critical role for IFNs in evolution of skin inflammation in these patients has been recognized. IFNs are produced not only by infiltrating immune but also resident skin cells, with increased baseline IFN production priming for inflammatory cell activation, immune response amplification, and development of skin lesions. The IFN response differs by cell type and host factors and may be modified by other inflammatory pathway activation specific to individual diseases, leading to differing clinical phenotypes. Understanding the contribution of IFNs to skin and systemic disease pathogenesis is key to development of new therapeutics and improved patient outcomes. In this review, we summarize the immunomodulatory role of IFNs in skin, with a focus on type I, and provide insight into IFN dysregulation in autoimmune and autoinflammatory diseases.
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Affiliation(s)
- Jessica L Turnier
- Department of Pediatrics, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109; and
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109
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Aljabban J, Syed S, Syed S, Rohr M, Weisleder N, McElhanon KE, Hasan L, Safeer L, Hoffman K, Aljabban N, Mukhtar M, Adapa N, Allarakhia Z, Panahiazar M, Neuhaus I, Kim S, Hadley D, Jarjour W. Investigating genetic drivers of dermatomyositis pathogenesis using meta-analysis. Heliyon 2020; 6:e04866. [PMID: 33015383 PMCID: PMC7522761 DOI: 10.1016/j.heliyon.2020.e04866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/17/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
AIMS Dermatomyositis (DM) is a progressive, idiopathic inflammatory myopathy with poorly understood pathogenesis. A hallmark of DM is an increased risk for developing breast, ovarian, and lung cancer. Since autoantibodies against anti-TIF-1-γ, a member of the tripartite motif (TRIM) proteins, has a strong association with malignancy, we examined expression of the TRIM gene family to identify pathways that may be contributing to DM pathogenesis. MATERIALS AND METHODS We employed the Search Tag Analyze Resource for GEO platform to search the NCBI Gene Expression Omnibus to elucidate TRIM family gene expression as well as oncogenic drivers in DM pathology. We conducted meta-analysis of the data from human skin (60 DM vs 34 healthy) and muscle (71 DM vs 22 healthy). KEY FINDINGS We identified genes involved in innate immunity, antigen presentation, metabolism, and other cellular processes as facilitators of DM disease activity and confirmed previous observations regarding the presence of a robust interferon signature. Moreover, analysis of DM muscle samples revealed upregulation of TRIM14, TRIM22, TRIM25, TRIM27, and TRIM38. Likewise, analysis of DM skin samples showed upregulation of TRIM5, TRIM6, TRIM 14, TRIM21, TRIM34, and TRIM38 and downregulation of TRIM73. Additionally, we noted upregulation of oncogenes IGLC1, IFI44, POSTN, MYC, NPM1, and IDO1 and related this change to interferon signaling. While the clinical data associated with genetic data that was analyzed did not contain clinical data regarding malignancy in these cohorts, the observed genetic changes may be associated with homeostatic and signaling changes that relate to the increased risk in malignancy in DM. SIGNIFICANCE Our results implicate previously unknown genes as potential drivers of DM pathology and suggest certain TRIM family members may have disease-specific roles with potential diagnostic and therapeutic implications.
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Affiliation(s)
- Jihad Aljabban
- University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Saad Syed
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharjeel Syed
- University of Chicago Medical Center, Chicago, IL, USA
| | - Michael Rohr
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Noah Weisleder
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Laith Hasan
- Tulane School of Medicine, New Orleans, LA, USA
| | | | - Kalyn Hoffman
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Mohamed Mukhtar
- Michigan State University College of Human Medicine, Lansing, MI, USA
| | | | - Zahir Allarakhia
- The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Isaac Neuhaus
- University of California San Francisco, San Francisco, CA, USA
| | - Susan Kim
- University of California San Francisco, San Francisco, CA, USA
| | - Dexter Hadley
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Wael Jarjour
- The Ohio State University College of Medicine, Columbus, OH, USA
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