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Soul J, Carlsson E, Hofmann SR, Russ S, Hawkes J, Schulze F, Sergon M, Pablik J, Abraham S, Hedrich CM. Tissue gene expression profiles and communication networks inform candidate blood biomarker identification in psoriasis and atopic dermatitis. Clin Immunol 2024; 265:110283. [PMID: 38880200 DOI: 10.1016/j.clim.2024.110283] [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: 02/18/2024] [Revised: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Overlapping clinical and pathomechanistic features can complicate the diagnosis and treatment of inflammatory skin diseases, including psoriasis and atopic dermatitis (AD). Spatial transcriptomics allows the identification of disease- and cell-specific molecular signatures that may advance biomarker development and future treatments. This study identified transcriptional signatures in keratinocytes and sub-basal CD4+ and CD8+ T lymphocytes from patients with psoriasis and AD. In silico prediction of ligand:receptor interactions delivered key signalling pathways (interferon, effector T cells, stroma cell and matrix biology, neuronal development, etc.). Targeted validation of selected transcripts, including CCL22, RELB, and JUND, in peripheral blood T cells suggests the chosen approach as a promising tool also in other inflammatory diseases. Psoriasis and AD are characterized by transcriptional dysregulation in T cells and keratinocytes that may be targeted therapeutically. Spatial transcriptomics is a valuable tool in the search for molecular signatures that can be used as biomarkers and/or therapeutic targets.
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Affiliation(s)
- J Soul
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - E Carlsson
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - S R Hofmann
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - S Russ
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - J Hawkes
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - F Schulze
- Department of Pediatrics, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - M Sergon
- Institut of Pathology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - J Pablik
- Institut of Pathology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - S Abraham
- Department of Dermatology, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - C M Hedrich
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, United Kingdom.
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Zhang H, Zhang Z, Fan K, Chen H, Guo Y, Mo X. Decoding the genetic landscape of juvenile dermatomyositis: insights from phosphorylation-associated single nucleotide polymorphisms. Immunogenetics 2024:10.1007/s00251-024-01350-y. [PMID: 39085621 DOI: 10.1007/s00251-024-01350-y] [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: 03/22/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
Genome-wide association studies (GWASs) have identified genetic susceptibility loci associated with juvenile dermatomyositis (JDM). Single nucleotide polymorphisms related to phosphorylation (phosSNPs) are critical nonsynonymous mutations exerting substantial influence on gene expression regulation. The aim of this study was to identify JDM susceptibility genes in the GWAS loci by the use of phosSNPs. We explored quantitative trait loci (QTLs) among the phosSNPs associated with JDM using data from eQTL (bulk tissues and single-cell) and pQTL studies. For gene expression and protein levels significantly influenced by JDM-associated phosSNPs, we assessed their associations with JDM through MR analyses. Additionally, we conducted differential expression gene analyses, incorporating single-cell transcriptomic profiling of 6 JDM cases and 11 juvenile controls (99,396 cells). We identified 31 phosSNPs situated in the 6p21 locus that were associated with JDM. Half of these phosSNPs showed effects on gene expression in various cells and circulating protein levels. In MR analyses, we established associations between the expression levels of pivotal JDM-associated genes, including MICB, C4A, HLA-DRB1, HLA-DRB5, and PSMB9, in skin, muscle, or blood cells and circulating levels of C4A, with JDM. Utilizing single-cell eQTL data, we identified a total of 276 association signals across 14 distinct immune cell types for 28 phosSNPs. Further insights were gained through single-cell differential expression analysis, revealing differential expression of PSMB9, HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1, and HLA-DRB1 in immune cells. The present study pinpointed phosSNPs within susceptibility genes for JDM and unraveled the intricate relationships among these SNPs, gene expression levels, and JDM.
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Affiliation(s)
- Huan Zhang
- Department of Epidemiology, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China
| | - Zhentao Zhang
- Department of Epidemiology, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China
- Center for Genetic Epidemiology and Genomics, MOE Key Laboratory of Geriatric Diseases and Immunology, School of Public Health, Suzhou Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Kedi Fan
- Department of Epidemiology, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China
- Center for Genetic Epidemiology and Genomics, MOE Key Laboratory of Geriatric Diseases and Immunology, School of Public Health, Suzhou Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Hongru Chen
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Yufan Guo
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu, 215000, People's Republic of China.
| | - Xingbo Mo
- Department of Epidemiology, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China.
- Center for Genetic Epidemiology and Genomics, MOE Key Laboratory of Geriatric Diseases and Immunology, School of Public Health, Suzhou Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China.
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Shan X, Wu S, Chen X, Ge Y. Janus kinase inhibition (JAKi) therapy in refractory anti-synthetase syndrome: A retrospective cohort study. Semin Arthritis Rheum 2024; 68:152474. [PMID: 38857549 DOI: 10.1016/j.semarthrit.2024.152474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024]
Abstract
OBJECTIVES To evaluate the efficacy and safety of Janus kinase inhibitors (JAKi) in the treatment of refractory anti-synthetase syndrome (ASS) in real-world clinical settings. METHODS The medical records of all refractory ASS patients who were treated with JAKi from October 2020 to June 2023 were retrospectively reviewed. RESULTS Twenty patients were included, and all (100 %) patients had interstitial lung disease (ILD). After treatment with JAKi, 14 (70 %) of the refractory ASS patients showed significant improvement in clinical manifestations, including arthritis (56.3 % vs. 6.3 %, p = 0.002), rash (77.8 % vs. 27.8 %, p = 0.012), shortness of breath (55.6 % vs. 16.7 %, p = 0.039), cough (61.1 % vs. 11.1 %, p = 0.012). Improvement was noted for myalgia (50 % vs. 11.1 %, p = 0.016) and muscular weakness (61.1 % vs. 11.1 %, p = 0.012), while creatine kinase (CK) levels, which were abnormally elevated in five patients prior treatment, were significantly lowered (1096 ± 1042.98 IU/L vs. 199.2 ± 144.66 IU/L, p = 0.043). A decrease in levels of inflammatory markers, including erythrocyte sedimentation rate (ESR) (p = 0.001) and C-reactive protein (CRP) (p = 0.023) was observed in the patients. In ASS-ILD, the CT score reduced (188.75 ± 69.67 vs. 156.35 ± 74.62, p = 0.001). Furthermore, the glucocorticoid dose significantly reduced (21.42 ± 13.26 mg vs. 11.32 ± 8.59 mg; p = 0.001). CONCLUSIONS JAKi were effective in most refractory ASS patients as evidenced by improved skin rash, myositis, and ILD. However, larger prospective controlled studies are required to evaluate its efficacy.
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Affiliation(s)
- Xueyan Shan
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100032, PR China; Beijing University of Chinese Medicine, Beijing 100029, PR China
| | - Shiyu Wu
- Peking University China-Japan Friendship school of clinical medicine, Beijing, PR China
| | - Xixia Chen
- Peking University China-Japan Friendship school of clinical medicine, Beijing, PR China
| | - Yongpeng Ge
- Department of Rheumatology, The Key Laboratory of Myositis, China-Japan Friendship Hospital, Beijing 100029, PR China.
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Zhong X, Shang J, Zhang R, Zhang X, Yu L, Niu H, Duan X. Explore the shared molecular mechanism between dermatomyositis and nasopharyngeal cancer by bioinformatic analysis. PLoS One 2024; 19:e0296034. [PMID: 38753689 PMCID: PMC11098312 DOI: 10.1371/journal.pone.0296034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/04/2023] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Dermatomyositis (DM) is prone to nasopharyngeal carcinoma (NPC), but the mechanism is unclear. This study aimed to explore the potential pathogenesis of DM and NPC. METHODS The datasets GSE46239, GSE142807, GSE12452, and GSE53819 were downloaded from the GEO dataset. The disease co-expression module was obtained by R-package WGCNA. We built PPI networks for the key modules. ClueGO was used to analyze functional enrichment for the key modules. DEG analysis was performed with the R-package "limma". R-package "pROC" was applied to assess the diagnostic performance of hub genes. MiRNA-mRNA networks were constructed using MiRTarBase and miRWalk databases. RESULTS The key modules that positively correlated with NPC and DM were found. Its intersecting genes were enriched in the negative regulation of viral gene replication pathway. Similarly, overlapping down-regulated DEGs in DM and NPC were also enriched in negatively regulated viral gene replication. Finally, we identified 10 hub genes that primarily regulate viral biological processes and type I interferon responses. Four key genes (GBP1, IFIH1, IFIT3, BST2) showed strong diagnostic performance, with AUC>0.8. In both DM and NPC, the expression of key genes was correlated with macrophage infiltration level. Based on hub genes' miRNA-mRNA network, hsa-miR-146a plays a vital role in DM-associated NPC. CONCLUSIONS Our research discovered pivot genes between DM and NPC. Viral gene replication and response to type I interferon may be the crucial bridge between DM and NPC. By regulating hub genes, MiR-146a will provide new strategies for diagnosis and treatment in DM complicated by NPC patients. For individuals with persistent viral replication in DM, screening for nasopharyngeal cancer is necessary.
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Affiliation(s)
- Xiuqin Zhong
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jingjing Shang
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Rongwei Zhang
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiuling Zhang
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Le Yu
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Haitao Niu
- School of Medicine, Key Laboratory of Viral Pathogenesis & Infection Prevention and Control, Guangzhou Key Laboratory of Germ-free Animals and Microbiota Application, Jinan University, Guangzhou, China
| | - Xinwang Duan
- Department of rheumatology and immunology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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Vinci M, Vitello GA, Greco D, Treccarichi S, Ragalmuto A, Musumeci A, Fallea A, Federico C, Calì F, Saccone S, Elia M. Next Generation Sequencing and Electromyography Reveal the Involvement of the P2RX6 Gene in Myopathy. Curr Issues Mol Biol 2024; 46:1150-1163. [PMID: 38392191 PMCID: PMC10887510 DOI: 10.3390/cimb46020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Ion channelopathies result from impaired ion channel protein function, due to mutations affecting ion transport across cell membranes. Over 40 diseases, including neuropathy, pain, migraine, epilepsy, and ataxia, are associated with ion channelopathies, impacting electrically excitable tissues and significantly affecting skeletal muscle. Gene mutations affecting transmembrane ionic flow are strongly linked to skeletal muscle disorders, particularly myopathies, disrupting muscle excitability and contraction. Electromyography (EMG) analysis performed on a patient who complained of weakness and fatigue revealed the presence of primary muscular damage, suggesting an early-stage myopathy. Whole exome sequencing (WES) did not detect potentially causative variants in known myopathy-associated genes but revealed a novel homozygous deletion of the P2RX6 gene likely disrupting protein function. The P2RX6 gene, predominantly expressed in skeletal muscle, is an ATP-gated ion channel receptor belonging to the purinergic receptors (P2RX) family. In addition, STRING pathways suggested a correlation with more proteins having a plausible role in myopathy. No previous studies have reported the implication of this gene in myopathy. Further studies are needed on patients with a defective ion channel pathway, and the use of in vitro functional assays in suppressing P2RX6 gene expression will be required to validate its functional role.
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Affiliation(s)
| | | | | | | | | | | | | | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | | | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
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Patrikiou E, Liaskos C, Bogdanos DP. On the role of anti-cN1A antibodies in sporadic inclusion body myositis and beyond: a challenging task full of surprises. Reumatologia 2024; 61:411-413. [PMID: 38322102 PMCID: PMC10839911 DOI: 10.5114/reum/177075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 02/08/2024] Open
Affiliation(s)
- Eleni Patrikiou
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University General Hospital of Larissa, Thessaly, Greece
| | - Christos Liaskos
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, University General Hospital of Larissa, Thessaly, Greece
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Ghirardello A, Franco C, Gatto M. Recent findings in idiopathic inflammatory myopathies with potential diagnostic and therapeutic implications. Curr Opin Rheumatol 2023; 35:371-373. [PMID: 37755404 DOI: 10.1097/bor.0000000000000964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Affiliation(s)
- Anna Ghirardello
- Unit of Rheumatology, Department of Medicine, University of Padua
| | - Chiara Franco
- Unit of Rheumatology, Department of Medicine, University of Padua
| | - Mariele Gatto
- Unit of Rheumatology, Department of Medicine, University of Padua
- Unit of Rheumatology, Department of Clinical and Biologic Sciences, University of Turin, Italy
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Zhang Z, Tao W, Cheng D, Qin M, Fu J, Liu D. Deciphering the crosstalk of immune dysregulation between COVID-19 and idiopathic inflammatory myopathy. Front Immunol 2023; 14:1197493. [PMID: 37638007 PMCID: PMC10449257 DOI: 10.3389/fimmu.2023.1197493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Background The coronavirus disease (COVID-19) pandemic is a serious threat to public health worldwide. Growing evidence reveals that there are certain links between COVID-19 and autoimmune diseases; in particular, COVID-19 and idiopathic inflammatory myopathies (IIM) have been observed to be clinically comorbid. Hence, this study aimed to elucidate the molecular mechanisms of COVID-19 and IIM from a genomic perspective. Methods We obtained transcriptome data of patients with COVID-19 and IIM separately from the GEO database and identified common differentially expressed genes (DEGs) by intersection. We then performed functional enrichment, PPI, machine learning, gene expression regulatory network, and immune infiltration analyses of co-expressed genes. Results A total of 91 common genes were identified between COVID-19 and IIM. Functional enrichment analysis revealed that these genes were mainly involved in immune dysregulation, response to external stimuli, and MAPK signaling pathways. The MCODE algorithm recognized two densely linked clusters in the common genes, which were related to inflammatory factors and interferon signaling. Subsequently, three key genes (CDKN1A, IFI27, and STAB1) were screened using machine learning to predict the occurrence of COVID-19 related IIM. These key genes exhibited excellent diagnostic performance in both training and validation cohorts. Moreover, we created TF-gene and miRNA-gene networks to reveal the regulation of key genes. Finally, we estimated the relationship between key genes and immune cell infiltration, of which IFI27 was positively associated with M1 macrophages. Conclusion Our work revealed common molecular mechanisms, core genes, potential targets, and therapeutic approaches for COVID-19 and IIM from a genomic perspective. This provides new ideas for the diagnosis and treatment of COVID-19 related IIM in the future.
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Affiliation(s)
- Zhao Zhang
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Weidong Tao
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Debin Cheng
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Marong Qin
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Jun Fu
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Dong Liu
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
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Tokareva K, Reid P, Yang V, Liew D, Peterson AC, Baraff A, Giles J, Singh N. JAK inhibitors and black box warnings: what is the future for JAK inhibitors? Expert Rev Clin Immunol 2023; 19:1385-1397. [PMID: 37596779 PMCID: PMC10615860 DOI: 10.1080/1744666x.2023.2249237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION Janus kinase inhibitors (JAKi) have dramatically improved the treatment of various autoimmune and myeloproliferative disorders. Recently, concern has arisen regarding their safety in patients with rheumatoid arthritis. AREAS COVERED Here, we provide a comprehensive summary of the major current and emerging JAKi and their indications, address recent studies on comparative safety, and provide insight into their future and use. We emphasize that the application of the research findings on a case-by-case basis should consider a patient's age, comorbidities, disease for which JAKi is being considered, disease activity, the JAKi target(s), alternate treatment options available for the patient, and the planned duration of JAKi. EXPERT OPINION Rheumatologists are used to prescribing therapies in which a risk-to-benefit assessment is required as well as to screening and monitoring the safety of medications. Thus, rheumatologists are already practiced in applying specific criteria to effectively screen and monitor patients who are candidates for JAKi therapy. Ongoing research will help to clarify any mechanisms underlying differential safety signals between JAK and other therapies, what the balance between risk and efficacy is, who the susceptible subpopulations are, and whether safety signals are shared between different JAKis and across indications.
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Affiliation(s)
- Kate Tokareva
- Medical Student, University of Washington, Seattle, WA, USA
| | - Pankti Reid
- Division of Rheumatology and Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, University of Chicago Biological Sciences Division, Chicago, Illinois, USA
| | - Victor Yang
- Department of Rheumatology, Austin Health, Melbourne, Victoria, Australia
| | - David Liew
- Department of Rheumatology, Austin Health, Melbourne, Victoria, Australia
- Department of Clinical Pharmacology and Therapeutics, Austin Health, Melbourne, Victoria, Australia
| | | | - Aaron Baraff
- VA Puget Sound Healthcare System, Seattle, WA, USA
| | - Jon Giles
- Columbia University, New York, NY, USA
| | - Namrata Singh
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
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