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Matsuo M, Tawada C, Tanaka K, Ichiki N, Niwa H, Mizutani Y, Shu E, Iwata H. Oxidative stress and dermatomyositis: Report of d-ROM measurements in 13 cases. Int J Rheum Dis 2024; 27:e14931. [PMID: 37767747 DOI: 10.1111/1756-185x.14931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/25/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Affiliation(s)
- Maho Matsuo
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chisato Tawada
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kayoko Tanaka
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Naohisa Ichiki
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hirofumi Niwa
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoko Mizutani
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - En Shu
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroaki Iwata
- Department of Dermatology, Gifu University Graduate School of Medicine, Gifu, Japan
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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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Wilkinson MGL, Moulding D, McDonnell TCR, Orford M, Wincup C, Ting JYJ, Otto GW, Restuadi R, Kelberman D, Papadopoulou C, Castellano S, Eaton S, Deakin CT, Rosser EC, Wedderburn LR. Role of CD14+ monocyte-derived oxidised mitochondrial DNA in the inflammatory interferon type 1 signature in juvenile dermatomyositis. Ann Rheum Dis 2023; 82:658-669. [PMID: 36564154 PMCID: PMC10176342 DOI: 10.1136/ard-2022-223469] [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: 10/11/2022] [Accepted: 12/01/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES To define the host mechanisms contributing to the pathological interferon (IFN) type 1 signature in Juvenile dermatomyositis (JDM). METHODS RNA-sequencing was performed on CD4+, CD8+, CD14+ and CD19+ cells sorted from pretreatment and on-treatment JDM (pretreatment n=10, on-treatment n=11) and age/sex-matched child healthy-control (CHC n=4) peripheral blood mononuclear cell (PBMC). Mitochondrial morphology and superoxide were assessed by fluorescence microscopy, cellular metabolism by 13C glucose uptake assays, and oxidised mitochondrial DNA (oxmtDNA) content by dot-blot. Healthy-control PBMC and JDM pretreatment PBMC were cultured with IFN-α, oxmtDNA, cGAS-inhibitor, TLR-9 antagonist and/or n-acetyl cysteine (NAC). IFN-stimulated gene (ISGs) expression was measured by qPCR. Total numbers of patient and controls for functional experiments, JDM n=82, total CHC n=35. RESULTS Dysregulated mitochondrial-associated gene expression correlated with increased ISG expression in JDM CD14+ monocytes. Altered mitochondrial-associated gene expression was paralleled by altered mitochondrial biology, including 'megamitochondria', cellular metabolism and a decrease in gene expression of superoxide dismutase (SOD)1. This was associated with enhanced production of oxidised mitochondrial (oxmt)DNA. OxmtDNA induced ISG expression in healthy PBMC, which was blocked by targeting oxidative stress and intracellular nucleic acid sensing pathways. Complementary experiments showed that, under in vitro experimental conditions, targeting these pathways via the antioxidant drug NAC, TLR9 antagonist and to a lesser extent cGAS-inhibitor, suppressed ISG expression in pretreatment JDM PBMC. CONCLUSIONS These results describe a novel pathway where altered mitochondrial biology in JDM CD14+ monocytes lead to oxmtDNA production and stimulates ISG expression. Targeting this pathway has therapeutical potential in JDM and other IFN type 1-driven autoimmune diseases.
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Affiliation(s)
- Meredyth G Ll Wilkinson
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Dale Moulding
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Thomas C R McDonnell
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Michael Orford
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Chris Wincup
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Joanna Y J Ting
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Georg W Otto
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Experimental and Personalised Medicine, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Restuadi Restuadi
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Daniel Kelberman
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Experimental and Personalised Medicine, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Charalampia Papadopoulou
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Rheumatology, Great Ormond Street Hospital NHS Trust, London, UK
| | - Sergi Castellano
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Eaton
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire T Deakin
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Lucy R Wedderburn
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
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4
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Hedberg‐Oldfors C, Lindgren U, Visuttijai K, Lööf D, Roos S, Thomsen C, Oldfors A. Respiratory chain dysfunction in perifascicular muscle fibres in patients with dermatomyositis is associated with mitochondrial DNA depletion. Neuropathol Appl Neurobiol 2022; 48:e12841. [PMID: 35894812 PMCID: PMC9805229 DOI: 10.1111/nan.12841] [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: 04/22/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 01/09/2023]
Abstract
AIMS Patients with dermatomyositis (DM) suffer from reduced aerobic metabolism contributing to impaired muscle function, which has been linked to cytochrome c oxidase (COX) deficiency in muscle tissue. This mitochondrial respiratory chain dysfunction is typically seen in perifascicular regions, which also show the most intense inflammatory reaction along with capillary loss and muscle fibre atrophy. The objective of this study was to investigate the pathobiology of the oxidative phosphorylation deficiency in DM. METHODS Muscle biopsy specimens with perifascicular COX deficiency from five juveniles and seven adults with DM were investigated. We combined immunohistochemical analyses of subunits in the respiratory chain including complex I (subunit NDUFB8), complex II (succinate dehydrogenase, subunit SDHB) and complex IV (COX, subunit MTCO1) with in situ hybridisation, next generation deep sequencing and quantitative polymerase chain reaction (PCR). RESULTS There was a profound deficiency of complexes I and IV in the perifascicular regions with enzyme histochemical COX deficiency, whereas succinate dehydrogenase activity and complex II were preserved. In situ hybridisation of mitochondrial RNA showed depletion of mitochondrial DNA (mtDNA) transcripts in the perifascicular regions. Analysis of mtDNA by next generation deep sequencing and quantitative PCR in affected muscle regions showed an overall reduction of mtDNA copy number particularly in the perifascicular regions. CONCLUSION The respiratory chain dysfunction in DM muscle is associated with mtDNA depletion causing deficiency of complexes I and IV, which are partially encoded by mtDNA, whereas complex II, which is entirely encoded by nuclear DNA, is preserved. The depletion of mtDNA indicates a perturbed replication of mtDNA explaining the muscle pathology and the disturbed aerobic metabolism.
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Affiliation(s)
- Carola Hedberg‐Oldfors
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Ulrika Lindgren
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden,Neuromuscular Center, Department of NeurologySahlgrenska University HospitalGothenburgSweden
| | - Kittichate Visuttijai
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Daniel Lööf
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Sara Roos
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Christer Thomsen
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Anders Oldfors
- Department of Laboratory Medicine, Institute of BiomedicineSahlgrenska Academy at the University of GothenburgGothenburgSweden
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Zhang L, Zhu H, Yang P, Duan X, Wei W, Wu Z, Fang Y, Li Q, Liu S, Shi X, Li H, Wu C, Zhou S, Leng X, Zhao J, Xu D, Wu Q, Tian X, Li M, Zhao Y, Wang Q, Zeng X. Myocardial involvement in idiopathic inflammatory myopathies: a multi-center cross-sectional study in the CRDC-MYO Registry. Clin Rheumatol 2021; 40:4597-4608. [PMID: 34184155 DOI: 10.1007/s10067-021-05828-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES This study aimed to investigate the associated factors of myocardial involvements (MIs) in patients with idiopathic inflammatory myopathies (IIMs). METHODS In this multi-center cross-sectional study, 1946 patients with IIMs were enrolled from Chinese Rheumatism Data Center-Myositis Registry (CRDC-MYO). A total of 108 (5.5%) patients were identified with MIs, including congestive heart failure (n = 67, 62.0%), and severe arrhythmias (n = 61, 56.5%). The other 1838 IIM patients without IMs were set as the control group. Clinical features were collected including age, gender, comorbidities, clinical symptoms, clinical signs of both IIMs and MIs, lab findings including myositis-specific antibodies (MSAs) and myositis-associated antibodies (MAAs), echocardiogram, and radiological exams. Multivariate logistic analysis was used to explore independent associated factors of MIs in patients with IIMs. RESULTS Several independent associated factors were identified in multi-variate logistic regression, including positivity for anti-mitochondrial antibody-subtype 2 (AMA-M2) (OR 5.194, 95% CI 2.509-10.753, P < 0.001), elevation of creatine kinase (CK) (OR 2.611, 95% CI 1.312-5.198, P = 0.006), elevation of C-reactive protein (CRP) (OR 2.150, 95% CI 1.211-3.818, P = 0.001), and pulmonary hypertension (OR 4.165, 95% CI 1.765-9.882, P = 0.009). AMA-M2 and pulmonary hypertension were the most consistent associated factors in the polymyositis subgroup and the dermatomyositis/clinically amyopathic dermatomyositis subgroup. CONCLUSIONS MIs are rare but serious complication of IIMs could lead to congestive heart failure and severe arrhythmias. IIM patients with AMA-M2 positivity, elevation of CK and CRP, and pulmonary hypertension are more likely to develop MI complications. Key Points • This study investigated the independent associated factors for clinically significant myocardial involvements among idiopathic inflammatory myopathies in a large-scale, nation-wide multi-center cross-sectional study.
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Affiliation(s)
- Lixi Zhang
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Huiyi Zhu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Pinting Yang
- Department of Rheumatology, The First Hospital of China Medical University, Shenyang, China
| | - Xinwang Duan
- Department of Rheumatology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Wei
- Department of Rheumatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhenbiao Wu
- Department of Rheumatology, Xijing Hospital of Air Force Military Medical University, Xian, China
| | - Yongfei Fang
- Department of Rheumatology, The Southwest Hospital of Army Medical University, Chongqing, China
| | - Qin Li
- Department of Rheumatology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Shengyun Liu
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofei Shi
- Department of Rheumatology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Hongbin Li
- Department of Rheumatology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Chanyuan Wu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Shuang Zhou
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Xiaomei Leng
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Dong Xu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Qingjun Wu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Xinping Tian
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Mengtao Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yan Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Qian Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
| | - Xiaofeng Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College &Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, No. 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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Ren C, Li M, Zheng Y, Wu F, Du W, Quan R. Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification. PeerJ 2021; 9:e11427. [PMID: 34040897 PMCID: PMC8127958 DOI: 10.7717/peerj.11427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 04/18/2021] [Indexed: 12/13/2022] Open
Abstract
Background The pathogenesis of rheumatoid arthritis (RA) is complex. This study aimed to identify diagnostic biomarkers and transcriptional regulators that underlie RA based on bioinformatics analysis and experimental verification. Material and Methods We applied weighted gene co-expression network analysis (WGCNA) to analyze dataset GSE55457 and obtained the key module most relevant to the RA phenotype. We then conducted gene function annotation, gene set enrichment analysis (GSEA) and immunocytes quantitative analysis (CIBERSORT). Moreover, the intersection of differentially expressed genes (DEGs) and genes within the key module were entered into the STRING database to construct an interaction network and to mine hub genes. We predicted microRNA (miRNA) using a web-based tool (miRDB). Finally, hub genes and vital miRNAs were validated with independent GEO datasets, RT-qPCR and Western blot. Results A total of 367 DEGs were characterized by differential expression analysis. The WGCNA method divided genes into 14 modules, and we focused on the turquoise module containing 845 genes. Gene function annotation and GSEA suggested that immune response and inflammatory signaling pathways are the molecular mechanisms behind RA. Nine hub genes were screened from the network and seven vital regulators were obtained using miRNA prediction. CIBERSORT analysis identified five cell types enriched in RA samples, which were closely related to the expression of hub genes. Through ROC curve and RT-qPCR validation, we confirmed five genes that were specific for RA, including CCL25, CXCL9, CXCL10, CXCL11, and CXCL13. Moreover, we selected a representative gene (CXCL10) for Western blot validation. Vital miRNAs verification showed that only the differences in has-miR-573 and has-miR-34a were statistically significant. Conclusion Our study reveals diagnostic genes and vital microRNAs highly related to RA, which could help improve our understanding of the molecular mechanisms underlying the disorder and provide theoretical support for the future exploration of innovative therapeutic approaches.
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Affiliation(s)
- Conglin Ren
- The Third Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Mingshuang Li
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yang Zheng
- The Third Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Fengqing Wu
- The Third Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Weibin Du
- Department of Orthopedics, Xiaoshan Traditional Chinese Medicine Hospital, Hangzhou, Zhejiang, China
| | - Renfu Quan
- The Third Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.,Department of Orthopedics, Xiaoshan Traditional Chinese Medicine Hospital, Hangzhou, Zhejiang, China
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Nambou K, Nie X, Tong Y, Anakpa M. Weighted gene co-expression network analysis and drug-gene interaction bioinformatics uncover key genes associated with various presentations of malaria infection in African children and major drug candidates. INFECTION GENETICS AND EVOLUTION 2021; 89:104723. [PMID: 33444859 DOI: 10.1016/j.meegid.2021.104723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/06/2023]
Abstract
Malaria is a fatal parasitic disease with unelucidated pathogenetic mechanism. Herein, we aimed to uncover genes associated with different clinical aspects of malaria based on the GSE1124 dataset that is publicly accessible by using WGCNA. We obtained 16 co-expression modules and their correlations with clinical features. Using the MCODE tool, we identified THEM4, STYX, VPS36, LCOR, KIAA1143, EEA1, RAPGEF6, LOC439994, ZBTB33, PTPN22, ESCO1, and KLF3 as hub genes positively associated with Plasmodium falciparum infection (ASPF). These hub genes were involved in the biological processes of endosomal transport, regulation of natural killer cell proliferation, and KEGG pathways of endocytosis and fatty acid elongation. For the purple module negatively correlated with ASPF, we identified 19 hub genes that were involved in the biological processes of positive regulation of cellular protein catabolic process and KEGG pathways of other glycan degradation. For the salmon module positively correlated with severe malaria anemia (SMA), we identified 17 hub genes that were among those driving the biological processes of positive regulation of erythrocyte differentiation. For the brown module positively correlated with cerebral malaria (CM), we identified eight hub genes and these genes participated in phagolysosome assembly and positive regulation of exosomal secretion, and animal mitophagy pathway. For the tan module negatively correlated with CM, we identified four hub genes that were involved in CD8-positive, alpha-beta T cell differentiation and notching signaling pathway. These findings may provide new insights into the pathogenesis of malaria and help define new diagnostic and therapeutic approaches for malaria patients.
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Affiliation(s)
- Komi Nambou
- Shenzhen Nambou1 Biotech Company Limited, West Silicon Valley, No. 5010 Bao'an Avenue, Shenzhen 518000, Guangdong Province, China.
| | - Xiaoling Nie
- Shenzhen Nambou1 Biotech Company Limited, West Silicon Valley, No. 5010 Bao'an Avenue, Shenzhen 518000, Guangdong Province, China
| | - Yin Tong
- Shenzhen Nambou1 Biotech Company Limited, West Silicon Valley, No. 5010 Bao'an Avenue, Shenzhen 518000, Guangdong Province, China
| | - Manawa Anakpa
- Key Laboratory of Trustworthy Distributed Computing and Service, School of Computer Science (National Pilot Software Engineering School), Beijing University of Posts and Telecommunications, Ministry of Education, Beijing 100876, China
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