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Li Q, Jia C, Pan W, Liu H, Tang C, Weber D, Chen K, Long H, Byrne-Steele ML, Han J, He N, Xiao R, Zhao M, Che N, Guo Q, Gui G, Li S, Si H, Guo S, Liu H, Wang G, Zhu G, Yang B, Wang Y, Ding Y, Yang X, Akihiko Y, Lu L, Chang C, Chan V, Lau CS, Qi H, Liu W, Li S, Wu H, Lu Q. Multi-omics study reveals different pathogenesis of the generation of skin lesions in SLE and IDLE patients. J Autoimmun 2024; 146:103203. [PMID: 38643729 DOI: 10.1016/j.jaut.2024.103203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 04/23/2024]
Abstract
Lupus erythematosus (LE) is a heterogeneous, antibody-mediated autoimmune disease. Isolate discoid LE (IDLE) and systematic LE (SLE) are traditionally regarded as the two ends of the spectrum, ranging from skin-limited damage to life-threatening multi-organ involvement. Both belong to LE, but IDLE and SLE differ in appearance of skin lesions, autoantibody panels, pathological changes, treatments, and immunopathogenesis. Is discoid lupus truly a form of LE or is it a completely separate entity? This question has not been fully elucidated. We compared the clinical data of IDLE and SLE from our center, applied multi-omics technology, such as immune repertoire sequencing, high-resolution HLA alleles sequencing and multi-spectrum pathological system to explore cellular and molecular phenotypes in skin and peripheral blood from LE patients. Based on the data from 136 LE patients from 8 hospitals in China, we observed higher damage scores and fewer LE specific autoantibodies in IDLE than SLE patients, more uCDR3 sharing between PBMCs and skin lesion from SLE than IDLE patients, elevated diversity of V-J recombination in IDLE skin lesion and SLE PBMCs, increased SHM frequency and class switch ratio in IDLE skin lesion, decreased SHM frequency but increased class switch ratio in SLE PBMCs, HLA-DRB1*03:01:01:01, HLA-B*58:01:01:01, HLA-C*03:02:02:01, and HLA-DQB1*02:01:01:01 positively associated with SLE patients, and expanded Tfh-like cells with ectopic germinal center structures in IDLE skin lesions. These findings suggest a significant difference in the immunopathogenesis of skin lesions between SLE and IDLE patients. SLE is a B cell-predominate systemic immune disorder, while IDLE appears limited to the skin. Our findings provide novel insights into the pathogenesis of IDLE and other types of LE, which may direct more accurate diagnosis and novel therapeutic strategies.
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Affiliation(s)
- Qianwen Li
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China
| | - Chen Jia
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China
| | - Wenjing Pan
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, Jiangsu, China; iRepertoire Inc., Huntsville, AL, USA
| | - Hongmei Liu
- Hunan University of Technology, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Zhuzhou, Hunan, China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, Jiangsu, China
| | | | - Kaili Chen
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China
| | - Hai Long
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China
| | | | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Nongyue He
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, Jiangsu, China
| | - Rong Xiao
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China
| | - Ming Zhao
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Nan Che
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qing Guo
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510000, China
| | - Guangji Gui
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510000, China
| | - Shanshan Li
- Department of Dermatology, The First Bethune Hospital of Jilin University, Changchun, Jilin, 130000, China
| | - Henan Si
- Department of Dermatology, The First Bethune Hospital of Jilin University, Changchun, Jilin, 130000, China
| | - Shuping Guo
- Department of Dermatology, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030000, China
| | - Hongye Liu
- Department of Dermatology, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030000, China
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, Xi'an, Shaanxi, 710000, China
| | - Guannan Zhu
- Department of Dermatology, Xijing Hospital, Xi'an, Shaanxi, 710000, China
| | - Bin Yang
- Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, 510000, China
| | - Yu Wang
- Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, 510000, China
| | - Yan Ding
- Hainan Provincial Hospital of Skin Disease, Haikou, Hainan, 570100, China
| | - Xianxu Yang
- Hainan Provincial Hospital of Skin Disease, Haikou, Hainan, 570100, China
| | - Yoshimura Akihiko
- Department of Microbiology and Immunology, Keio University School of Medicine 35 Shinanoomachi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, 999077, China
| | - Christopher Chang
- Division of Immunology, Allergy and Rheumatology, Memorial Healthcare System, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Vera Chan
- Division of Rheumatology & Clinical Immunology, Department of Medicine, University of Hong Kong, Hong Kong, China
| | - Chak-Sing Lau
- Division of Rheumatology & Clinical Immunology, Department of Medicine, University of Hong Kong, Hong Kong, China
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wanli Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Song Li
- Hunan University of Technology, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Zhuzhou, Hunan, China.
| | - Haijing Wu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China.
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.
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Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff ME, Whitfield ML. Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. PLoS Comput Biol 2015; 11:e1004005. [PMID: 25569146 PMCID: PMC4288710 DOI: 10.1371/journal.pcbi.1004005] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/27/2014] [Indexed: 12/15/2022] Open
Abstract
Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6-12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk.
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Affiliation(s)
- J. Matthew Mahoney
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Jaclyn Taroni
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Viktor Martyanov
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Tammara A. Wood
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Casey S. Greene
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Patricia A. Pioli
- Department of Obstetrics and Gynecology, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
| | - Monique E. Hinchcliff
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michael L. Whitfield
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America
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