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Liu B, Li A, Liu Y, Zhou X, Xu J, Zuo X, Xue K, Cui Y. Transcobalamin 2 orchestrates monocyte proliferation and TLR4-driven inflammation in systemic lupus erythematosus via folate one-carbon metabolism. Front Immunol 2024; 15:1339680. [PMID: 38881906 PMCID: PMC11176449 DOI: 10.3389/fimmu.2024.1339680] [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: 11/16/2023] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Background SLE is a complex autoimmune disease with deleterious effects on various organs. Accumulating evidence has shown abnormal vitamin B12 and one-carbon flux contribute to immune dysfunction. Transcobalamin II (TCN2) belongs to the vitamin B12-binding protein family responsible for the cellular uptake of vitamin B12. The role of TCN2 in SLE is still unclear. Methods We collected clinical information and blood from 51 patients with SLE and 28 healthy controls. RNA sequencing analysis, qPCR, and western blot confirmed the alteration of TCN2 in disease monocytes. The correlation between TCN2 expression and clinical features and serological abnormalities was analyzed. TCN2 heterozygous knockout THP1 cells were used to explore the effects of TCN2 dysfunction on monocytes. CCK-8 assay and EdU staining were used to detect cell proliferation. ELISA was conducted to assess vitamin B12, glutathione, and cytokines changes. UHPLC-MRM-MS/MS was used to detect changes in the intermediates of the one-carbon cycle. Flow cytometry is used to detect cell cycle, ROS, mitoROS, and CD14 changes. Results Elevated TCN2 in monocytes was correlated positively with disease progression and specific tissue injuries. Using CD14+ monocytes and TCN2 genetically modified THP1 cell lines, we found that the TCN2 was induced by LPS in serum from SLE patients. TCN2 heterozygous knockout inhibited cellular vitamin B12 uptake and one-carbon metabolism, leading to cell proliferation arrest and decreased Toll-like receptor 4 (TLR4)-mediated CCL2 release. Methionine cycle metabolites, s-adenosylmethionine and homocysteine, rescued these effects, whereas folate treatment proved to be ineffective. Folate deficiency also failed to replicate the impact of TCN2 downregulation on THP1 inflammatory response. Conclusion Our study elucidated the unique involvement of TCN2-driven one-carbon flux on SLE-associated monocyte behavior. Increased TCN2 may promote disease progression and tissue damage by enhancing one-carbon flux, fostering monocyte proliferation, and exacerbating TLR4 mediated inflammatory responses. The inhibition of TCN2 may be a promising therapeutic approach to ameliorate SLE.
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Affiliation(s)
- Baoyi Liu
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ang Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Liu
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
- Graduate School, Capital Medical University, Beijing, China
| | - Xinzhu Zhou
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
- Department of Dermatology, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Jingkai Xu
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xianbo Zuo
- Department of Pharmacy, China-Japan Friendship Hospital, Beijing, China
| | - Ke Xue
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
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2
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Bettacchioli E, Chiche L, Chaussabel D, Cornec D, Jourde-Chiche N, Rinchai D. An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity. Database (Oxford) 2024; 2024:baae045. [PMID: 38805754 PMCID: PMC11131423 DOI: 10.1093/database/baae045] [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: 10/02/2023] [Revised: 04/07/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
In the field of complex autoimmune diseases such as systemic lupus erythematosus (SLE), systems immunology approaches have proven invaluable in translational research settings. Large-scale datasets of transcriptome profiling have been collected and made available to the research community in public repositories, but remain poorly accessible and usable by mainstream researchers. Enabling tools and technologies facilitating investigators' interaction with large-scale datasets such as user-friendly web applications could promote data reuse and foster knowledge discovery. Microarray blood transcriptomic data from the LUPUCE cohort (publicly available on Gene Expression Omnibus, GSE49454), which comprised 157 samples from 62 adult SLE patients, were analyzed with the third-generation (BloodGen3) module repertoire framework, which comprises modules and module aggregates. These well-characterized samples corresponded to different levels of disease activity, different types of flares (including biopsy-proven lupus nephritis), different auto-antibody profiles and different levels of interferon signatures. A web application was deployed to present the aggregate-level, module-level and gene-level analysis results from LUPUCE dataset. Users can explore the similarities and heterogeneity of SLE samples, navigate through different levels of analysis, test hypotheses and generate custom fingerprint grids and heatmaps, which may be used in reports or manuscripts. This resource is available via this link: https://immunology-research.shinyapps.io/LUPUCE/. This web application can be employed as a stand-alone resource to explore changes in blood transcript profiles in SLE, and their relation to clinical and immunological parameters, to generate new research hypotheses.
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Affiliation(s)
- Eléonore Bettacchioli
- B Lymphocytes, Autoimmunity and Immunotherapies, UMR 1227, Univ Brest, Inserm, Brest 29200, France
- Brest University Hospital, Brest 29200, France
| | - Laurent Chiche
- Department of Internal Medicine, Hôpital Européen, Marseille 13003, France
| | - Damien Chaussabel
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha 26999, Qatar
- Computational Sciences Department, The Jackson Laboratory, Farmington, CT 06032, USA
| | - Divi Cornec
- B Lymphocytes, Autoimmunity and Immunotherapies, UMR 1227, Univ Brest, Inserm, Brest 29200, France
- Brest University Hospital, Brest 29200, France
| | - Noémie Jourde-Chiche
- Department of Nephrology, AP-HM, Marseille 13003, France
- C2VN, INSERM, INRAE, Aix-Marseille Universite, Marseille 13003, France
| | - Darawan Rinchai
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha 26999, Qatar
- Department of Infectious Diseases, St Jude’s Children Research Hospital, TN, Memphis 38105, USA
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3
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Gómez-Bañuelos E, Goldman DW, Andrade V, Darrah E, Petri M, Andrade F. Uncoupling interferons and the interferon signature explains clinical and transcriptional subsets in SLE. Cell Rep Med 2024; 5:101569. [PMID: 38744279 PMCID: PMC11148857 DOI: 10.1016/j.xcrm.2024.101569] [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: 11/16/2023] [Revised: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Systemic lupus erythematosus (SLE) displays a hallmark interferon (IFN) signature. Yet, clinical trials targeting type I IFN (IFN-I) have shown variable efficacy, and blocking IFN-II failed to treat SLE. Here, we show that IFN type levels in SLE vary significantly across clinical and transcriptional endotypes. Whereas skin involvement correlated with IFN-I alone, systemic features like nephritis associated with co-elevation of IFN-I, IFN-II, and IFN-III, indicating additive IFN effects in severe SLE. Notably, while high IFN-II/-III levels without IFN-I had a limited effect on disease activity, IFN-II was linked to IFN-I-independent transcriptional profiles (e.g., OXPHOS and CD8+GZMH+ cells), and IFN-III enhanced IFN-induced gene expression when co-elevated with IFN-I. Moreover, dysregulated IFNs do not explain the IFN signature in 64% of patients or clinical manifestations including cytopenia, serositis, and anti-phospholipid syndrome, implying IFN-independent endotypes in SLE. This study sheds light on mechanisms underlying SLE heterogeneity and the variable response to IFN-targeted therapies in clinical trials.
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Affiliation(s)
| | - Daniel W Goldman
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Victoria Andrade
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Michelle Petri
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224.
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4
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Wang FQ, Shao L, Dang X, Wang YF, Chen S, Liu Z, Mao Y, Jiang Y, Hou F, Guo X, Li J, Zhang L, Sang Y, Zhao X, Ma R, Zhang K, Zhang Y, Yang J, Wen X, Liu J, Wei W, Zhang C, Li W, Qin X, Lei Y, Feng H, Yang X, She CH, Zhang C, Su H, Chen X, Yang J, Lau YL, Wu Q, Ban B, Song Q, Yang W. Unraveling transcriptomic signatures and dysregulated pathways in systemic lupus erythematosus across disease states. Arthritis Res Ther 2024; 26:99. [PMID: 38741185 DOI: 10.1186/s13075-024-03327-4] [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: 02/17/2024] [Accepted: 04/21/2024] [Indexed: 05/16/2024] Open
Abstract
OBJECTIVES This study aims to elucidate the transcriptomic signatures and dysregulated pathways in patients with Systemic Lupus Erythematosus (SLE), with a particular focus on those persisting during disease remission. METHODS We conducted bulk RNA-sequencing of peripheral blood mononuclear cells (PBMCs) from a well-defined cohort comprising 26 remission patients meeting the Low Lupus Disease Activity State (LLDAS) criteria, 76 patients experiencing disease flares, and 15 healthy controls. To elucidate immune signature changes associated with varying disease states, we performed extensive analyses, including the identification of differentially expressed genes and pathways, as well as the construction of protein-protein interaction networks. RESULTS Several transcriptomic features recovered during remission compared to the active disease state, including down-regulation of plasma and cell cycle signatures, as well as up-regulation of lymphocytes. However, specific innate immune response signatures, such as the interferon (IFN) signature, and gene modules involved in chromatin structure modification, persisted across different disease states. Drug repurposing analysis revealed certain drug classes that can target these persistent signatures, potentially preventing disease relapse. CONCLUSION Our comprehensive transcriptomic study revealed gene expression signatures for SLE in both active and remission states. The discovery of gene expression modules persisting in the remission stage may shed light on the underlying mechanisms of vulnerability to relapse in these patients, providing valuable insights for their treatment.
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Affiliation(s)
- Frank Qingyun Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Li Shao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiao Dang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yong-Fei Wang
- School of Life and Health Sciences, School of Medicine, and Warshel Institute for Computational Biology, The Chinese University of Hong Kong - Shenzhen, Shenzhen, Guangdong, China
| | - Shuxiong Chen
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Zhongyi Liu
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujing Mao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuping Jiang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Fei Hou
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xianghua Guo
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jian Li
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Lili Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuting Sang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xuan Zhao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Ruirui Ma
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Kai Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yanfang Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jing Yang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiwu Wen
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jiong Liu
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Wei Wei
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Chuanpeng Zhang
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Weiyang Li
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiao Qin
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Feng
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xingtian Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Chun Hing She
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Caicai Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Huidong Su
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xinxin Chen
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Qingjun Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Ban
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Qin Song
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
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5
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Ochiai K, Shima H, Tamahara T, Sugie N, Funayama R, Nakayama K, Kurosaki T, Igarashi K. Accelerated plasma-cell differentiation in Bach2-deficient mouse B cells is caused by altered IRF4 functions. EMBO J 2024; 43:1947-1964. [PMID: 38605225 PMCID: PMC11099079 DOI: 10.1038/s44318-024-00077-6] [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: 09/13/2023] [Revised: 02/19/2024] [Accepted: 02/24/2024] [Indexed: 04/13/2024] Open
Abstract
Transcription factors BACH2 and IRF4 are both essential for antibody class-switch recombination (CSR) in activated B lymphocytes, while they oppositely regulate the differentiation of plasma cells (PCs). Here, we investigated how BACH2 and IRF4 interact during CSR and plasma-cell differentiation. We found that BACH2 organizes heterochromatin formation of target gene loci in mouse splenic B cells, including targets of IRF4 activation such as Aicda, an inducer of CSR, and Prdm1, a master plasma-cell regulator. Release of these gene loci from heterochromatin in response to B-cell receptor stimulation was coupled to AKT-mTOR pathway activation. In Bach2-deficient B cells, PC genes' activation depended on IRF4 protein accumulation, without an increase in Irf4 mRNA. Mechanistically, a PU.1-IRF4 heterodimer in activated B cells promoted BACH2 function by inducing gene expression of Bach2 and Pten, a negative regulator of AKT signaling. Elevated AKT activity in Bach2-deficient B cells resulted in IRF4 protein accumulation. Thus, BACH2 and IRF4 mutually modulate the activity of each other, and BACH2 inhibits PC differentiation by both the repression of PC genes and the restriction of IRF4 protein accumulation.
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Toru Tamahara
- Division of Community Oral Health Science, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Sendai, 980-8573, Japan
| | - Nao Sugie
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan
- Laboratory for Lymhocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, 980-8575, Japan.
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6
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Dong C, Guo Y, Chen Z, Li T, Ji J, Sun C, Li J, Cao H, Xia Y, Xue Z, Gu X, Liang Q, Zhao R, Fu T, Ma J, Jiang S, Wu C, Fu Q, Guo G, Bao Y, Guo H, Yang J, Xu M, Zhang X, Sheng Z, Gu Z. Single-Cell Profiling of Bone Marrow B Cells and Early B Cell Developmental Disorders Associated With Systemic Lupus Erythematosus. Arthritis Rheumatol 2024; 76:599-613. [PMID: 37946666 DOI: 10.1002/art.42750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVE The peripheral B cell compartment is heavily disturbed in systemic lupus erythematosus (SLE), but whether B cells develop aberrantly in the bone marrow (BM) is largely unknown. METHODS We performed single-cell RNA/B cell receptor (BCR) sequencing and immune profiling of BM B cells and classified patients with SLE into two groups: early B cell (Pro-B and Pre-B) normal (EBnor) and EB defective/low (EBlo) groups. RESULTS The SLE-EBlo group exhibited more severe disease activity and proinflammatory status, overaction of type I interferon signaling and metabolic pathways within the B cell compartment, and aberrant BCR repertoires compared with the SLE-EBnor group. Moreover, in one patient with SLE who was initially classified in the SLE-EBlo group, early B cell deficiency and associated abnormalities were largely rectified in a second BM sample at the remission phase. CONCLUSION In summary, this study suggests that early B cell loss in BM defines a unique pathological state in a subset of patients with SLE that may play an active role in the dysregulated autoimmune responses.
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Affiliation(s)
- Chen Dong
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Yicheng Guo
- Zukerman Mind Brain Behavior Institute, Columbia University, New York
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York
| | - Zechuan Chen
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Teng Li
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Juan Ji
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Chi Sun
- Department of Geriatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Jing Li
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Haixia Cao
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Yunfei Xia
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Zhonghui Xue
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xixi Gu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qian Liang
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Rui Zhao
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Ting Fu
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiaqiang Ma
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shan Jiang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei Wu
- Department of Rheumatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiong Fu
- Department of Rheumatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Genkai Guo
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Yanfeng Bao
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Hua Guo
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
| | - Junling Yang
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Min Xu
- Research Center of Clinical Medicine, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaoming Zhang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zizhang Sheng
- Zukerman Mind Brain Behavior Institute, Columbia University, New York
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York
| | - Zhifeng Gu
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong University, Nantong, China
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7
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Goto M, Takahashi H, Yoshida R, Itamiya T, Nakano M, Nagafuchi Y, Harada H, Shimizu T, Maeda M, Kubota A, Toda T, Hatano H, Sugimori Y, Kawahata K, Yamamoto K, Shoda H, Ishigaki K, Ota M, Okamura T, Fujio K. Age-associated CD4 + T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity. Sci Immunol 2024; 9:eadk1643. [PMID: 38330141 DOI: 10.1126/sciimmunol.adk1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Aging is a significant risk factor for autoimmunity, and many autoimmune diseases tend to onset during adulthood. We conducted an extensive analysis of CD4+ T cell subsets from 354 patients with autoimmune disease and healthy controls via flow cytometry and bulk RNA sequencing. As a result, we identified a distinct CXCR3midCD4+ effector memory T cell subset that expands with age, which we designated "age-associated T helper (THA) cells." THA cells exhibited both a cytotoxic phenotype and B cell helper functions, and these features were regulated by the transcription factor ZEB2. Consistent with the highly skewed T cell receptor usage of THA cells, gene expression in THA cells from patients with systemic lupus erythematosus reflected disease activity and was affected by treatment with a calcineurin inhibitor. Moreover, analysis of single-cell RNA sequencing data revealed that THA cells infiltrate damaged organs in patients with autoimmune diseases. Together, our characterization of THA cells may facilitate improved understanding of the relationship between aging and autoimmune diseases.
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Affiliation(s)
- Manaka Goto
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroaki Harada
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Meiko Maeda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Akatsuki Kubota
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kimito Kawahata
- Department of Rheumatology and Allergology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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8
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Horisberger A, Griffith A, Keegan J, Arazi A, Pulford J, Murzin E, Howard K, Hancock B, Fava A, Sasaki T, Ghosh T, Inamo J, Beuschel R, Cao Y, Preisinger K, Gutierrez-Arcelus M, Eisenhaure TM, Guthridge J, Hoover PJ, Dall'Era M, Wofsy D, Kamen DL, Kalunian KC, Furie R, Belmont M, Izmirly P, Clancy R, Hildeman D, Woodle ES, Apruzzese W, McMahon MA, Grossman J, Barnas JL, Payan-Schober F, Ishimori M, Weisman M, Kretzler M, Berthier CC, Hodgin JB, Demeke DS, Putterman C, Brenner MB, Anolik JH, Raychaudhuri S, Hacohen N, James JA, Davidson A, Petri MA, Buyon JP, Diamond B, Zhang F, Lederer JA, Rao DA. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.14.575609. [PMID: 38293222 PMCID: PMC10827101 DOI: 10.1101/2024.01.14.575609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.
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9
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Yamamoto K, Ishigaki K, Okada Y. How can genetics analysis allow for early detection of rheumatoid arthritis. Semin Arthritis Rheum 2024; 64S:152323. [PMID: 38151400 DOI: 10.1016/j.semarthrit.2023.152323] [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: 08/25/2023] [Accepted: 09/23/2023] [Indexed: 12/29/2023]
Abstract
Early detection and diagnosis of rheumatoid arthritis (RA) is crucial for initiating appropriate therapy promptly, thereby leading to increase the likelihood of achieving remission and eventual cure. In this article, we will discuss the contribution of genetic information in predicting and detecting RA.
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Affiliation(s)
| | | | - Yukinori Okada
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; The University of Tokyo, Tokyo, Japan; Osaka University, Osaka, Japan
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10
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Huang T, Pi C, Xu X, Feng Y, Zhang J, Gu H, Fang J. Effect of BAFF blockade on the B cell receptor repertoire and transcriptome in a mouse model of systemic lupus erythematosus. Front Immunol 2024; 14:1307392. [PMID: 38264661 PMCID: PMC10803406 DOI: 10.3389/fimmu.2023.1307392] [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: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Anti-B-cell-activating factor (BAFF) therapy effectively depletes B cells and reduces SLE disease activity. This research aimed to evaluate the effect of BAFF blockade on B cell receptor (BCR) repertoire and gene expression. Methods Through next-generation sequencing, we analyzed gene expression and BCR repertoire in MRL/lpr mice that received long-term anti-BAFF therapy. Based on gene expression profiles, we predicted the relative proportion of immune cells using ImmuCellAI-mouse, validating our predictions via flow cytometry and FluoroSpot. Results The loss of BCR repertoire diversity and richness, along with increased clonality and differential frequency distribution of the immunoglobulin heavy chain variable (IGHV) segment gene usage, were observed in BAFF-blockade mice. Meanwhile, the distribution of complementarity-determining region 3 (CDR3) length and CDR3 amino acid usage remained unaffected. BAFF blockade resulted in extensive changes in gene expression, particularly that of genes related to B cells and immunoglobulins. Besides, the tumor necrosis factor (TNF)-α responses and interferon (IFN)-α/γ were downregulated, consistent with the decrease in IFN-γ and TNF-α serum levels following anti-BAFF therapy. In addition, BAFF blockade significantly reduced B cell subpopulations and plasmacytoid dendritic cells, and caused the depletion of antibody-secreting cells. Discussion Our comparative BCR repertoire and transcriptome analyses of MRL/lpr mice subjected to BAFF blockade provide innovative insights into the molecular pathophysiology of SLE.
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Affiliation(s)
- Tao Huang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenyu Pi
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaoqing Xu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yan Feng
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jingming Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hua Gu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jianmin Fang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
- Biomedical Research Center, Tongji University Suzhou Institute, Suzhou, Jiangsu, China
- Department of Neurology, Tongji Hospital, Tongji University, Shanghai, China
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11
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Moriyama M, Noda K, Ito H, Matsushita T, Kurosaka D. Clinical features of newly diagnosed systemic lupus erythematosus after SARS-CoV-2 vaccination. Mod Rheumatol Case Rep 2023; 8:63-68. [PMID: 37348045 DOI: 10.1093/mrcr/rxad036] [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: 04/21/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that causes damage to multiple organs. Various factors, including vaccination, have been associated with SLE development. Vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in 2020, and there are a few reports on the exacerbation of SLE after SARS-CoV-2 vaccination. The influence of SARS-CoV-2 vaccination on SLE development remains unclear. We present the case of a 53-year-old man who developed peritonitis and was subsequently diagnosed with SLE on Day 9 after receiving a third dose of the messenger ribonucleic acid-1273 SARS-CoV-2 vaccine. This case and previous reports have shown that patients who developed SLE after SARS-CoV-2 vaccination are more likely to develop it within 2 weeks of vaccination, especially when they have a higher rate of immunological abnormalities or a family history of autoimmune diseases. Furthermore, these features suggest that type I interferon is involved in the pathogenesis of SLE after SARS-CoV-2 vaccination.
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Affiliation(s)
- Masayori Moriyama
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Kentaro Noda
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Haruyasu Ito
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Takayuki Matsushita
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Daitaro Kurosaka
- Division of Rheumatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
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12
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Ota M, Nakano M, Nagafuchi Y, Kobayashi S, Hatano H, Yoshida R, Akutsu Y, Itamiya T, Ban N, Tsuchida Y, Shoda H, Yamamoto K, Ishigaki K, Okamura T, Fujio K. Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases. Ann Rheum Dis 2023; 82:1455-1463. [PMID: 37468219 DOI: 10.1136/ard-2023-224421] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
OBJECTIVES Despite the involvement of B cells in the pathogenesis of immune-mediated diseases (IMDs), biological mechanisms underlying their function are scarcely understood. To overcome this gap, here we constructed and investigated a large-scale repertoire catalogue of five B cell subsets of patients with IMDs. METHODS We mapped B cell receptor regions from RNA sequencing data of sorted B cell subsets. Our dataset consisted of 595 donors under IMDs and health. We characterised the repertoire features from various aspects, including their association with immune cell transcriptomes and clinical features and their response to belimumab treatment. RESULTS Heavy-chain complementarity-determining region 3 (CDR-H3) length among naïve B cells was shortened among autoimmune diseases. Strong negative correlation between interferon signature strength and CDR-H3 length was observed in naïve B cells and suggested the role for interferon in premature B cell development. VDJ gene usage was skewed especially in plasmablasts and unswitched-memory B cells of patients with systemic lupus erythematosus (SLE). We developed a scoring system to quantify this skewing, and it positively correlated with peripheral helper T cell transcriptomic signatures and negatively correlated with the amount of somatic hyper mutations in plasmablasts, suggesting the association of extrafollicular pathway. Further, this skewing led to high usage of IGHV4-34 gene with 9G4 idiotypes in unswitched-memory B cells, which showed a prominent positive correlation with disease activity in SLE. Gene usage skewing in unswitched-memory B cells was ameliorated after belimumab treatment. CONCLUSIONS Our multimodal repertoire analysis enabled us the system-level understanding of B cell abnormality in diseases.
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Affiliation(s)
- Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Yuko Akutsu
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Nobuhiro Ban
- Research Division, Chugai Pharmaceutical Co Ltd, Yokohama, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
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13
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Leventhal EL, Daamen AR, Grammer AC, Lipsky PE. An interpretable machine learning pipeline based on transcriptomics predicts phenotypes of lupus patients. iScience 2023; 26:108042. [PMID: 37860757 PMCID: PMC10582499 DOI: 10.1016/j.isci.2023.108042] [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: 04/21/2023] [Revised: 07/03/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Machine learning (ML) has the potential to identify subsets of patients with distinct phenotypes from gene expression data. However, phenotype prediction using ML has often relied on identifying important genes without a systems biology context. To address this, we created an interpretable ML approach based on blood transcriptomics to predict phenotype in systemic lupus erythematosus (SLE), a heterogeneous autoimmune disease. We employed a sequential grouped feature importance algorithm to assess the performance of gene sets, including immune and metabolic pathways and cell types, known to be abnormal in SLE in predicting disease activity and organ involvement. Gene sets related to interferon, tumor necrosis factor, the mitoribosome, and T cell activation were the best predictors of phenotype with excellent performance. These results suggest potential relationships between the molecular pathways identified in each model and manifestations of SLE. This ML approach to phenotype prediction can be applied to other diseases and tissues.
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Affiliation(s)
- Emily L. Leventhal
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Andrea R. Daamen
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Amrie C. Grammer
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Peter E. Lipsky
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
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14
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Rector I, Owen KA, Bachali P, Hubbard E, Yazdany J, Dall'era M, Grammer AC, Lipsky PE. Differential regulation of the interferon response in systemic lupus erythematosus distinguishes patients of Asian ancestry. RMD Open 2023; 9:e003475. [PMID: 37709528 PMCID: PMC10503349 DOI: 10.1136/rmdopen-2023-003475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES Type I interferon (IFN) plays a role in the pathogenesis of systemic lupus erythematosus (SLE), but insufficient attention has been directed to the differences in IFN responses between ancestral populations. Here, we explored the expression of the interferon gene signatures (IGSs) in SLE patients of European ancestry (EA) and Asian ancestry (AsA). METHODS We used gene set variation analysis with multiple IGS encompassing the response to both type 1 and type 2 IFN in isolated CD14+ monocytes, CD19+B cells, CD4+T cells and Natural Killer (NK) cells from patients with SLE stratified by self-identified ancestry. The expression of genes upstream of the IGS and influenced by lupus-associated risk alleles was also examined. Lastly, we employed machine learning (ML) models to assess the most important features classifying patients by disease activity. RESULTS AsA patients with SLE exhibited greater enrichment in the IFN core and IFNA2 IGS compared with EA patients in all cell types examined and, in the presence and absence of autoantibodies. Overall, AsA patients with SLE demonstrated higher expression of genes upstream of the IGS than EA counterparts. ML with feature importance analysis indicated that IGS expression in NK cells, anti-dsDNA, complement levels and AsA status contributed to disease activity. CONCLUSIONS AsA patients with SLE exhibited higher IGS than EA patients in all cell types regardless of autoantibody status, with enhanced expression of genetically associated genes upstream of the IGS potentially contributing. AsA, along with the IGS in NK cells, anti-dsDNA and complement, independently influenced SLE disease activity.
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Affiliation(s)
- Ian Rector
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | | | - Prathyusha Bachali
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Erika Hubbard
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Jinoos Yazdany
- Medicine/Rheumatology, University of California, San Francisco, California, USA
| | - Maria Dall'era
- Division of Rheumatology, University of California, San Francisco, California, USA
| | - Amrie C Grammer
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
| | - Peter E Lipsky
- AMPEL Biosolutions LLC and the RILITE Research Institute, Charlottesville, Virginia, USA
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15
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Vinuesa CG, Shen N, Ware T. Genetics of SLE: mechanistic insights from monogenic disease and disease-associated variants. Nat Rev Nephrol 2023; 19:558-572. [PMID: 37438615 DOI: 10.1038/s41581-023-00732-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 07/14/2023]
Abstract
The past few years have provided important insights into the genetic architecture of systemic autoimmunity through aggregation of findings from genome-wide association studies (GWAS) and whole-exome or whole-genome sequencing studies. In the prototypic systemic autoimmune disease systemic lupus erythematosus (SLE), monogenic disease accounts for a small fraction of cases but has been instrumental in the elucidation of disease mechanisms. Defects in the clearance or digestion of extracellular or intracellular DNA or RNA lead to increased sensing of nucleic acids, which can break B cell tolerance and induce the production of type I interferons leading to tissue damage. Current data suggest that multiple GWAS SLE risk alleles act in concert with rare functional variants to promote SLE development. Moreover, introduction of orthologous variant alleles into mice has revealed that pathogenic X-linked dominant and recessive SLE can be caused by novel variants in TLR7 and SAT1, respectively. Such bespoke models of disease help to unravel pathogenic pathways and can be used to test targeted therapies. Cell type-specific expression data revealed that most GWAS SLE risk genes are highly expressed in age-associated B cells (ABCs), which supports the view that ABCs produce lupus autoantibodies and contribute to end-organ damage by persisting in inflamed tissues, including the kidneys. ABCs have thus emerged as key targets of promising precision therapeutics.
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Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- China Australia Centre for Personalized Immunology (CACPI), Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- Center for Autoimmune Genomics and Aetiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Paediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Thuvaraka Ware
- The Francis Crick Institute, London, UK
- University College London, London, UK
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16
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Gómez-Bañuelos E, Goldman DW, Andrade V, Darrah E, Petri M, Andrade F. Uncoupling interferons and the interferon signature explain clinical and transcriptional subsets in SLE. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.28.23294734. [PMID: 37693590 PMCID: PMC10491366 DOI: 10.1101/2023.08.28.23294734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Interferons (IFN) are thought to be key players in systemic lupus erythematosus (SLE). The unique and interactive roles of the different IFN families in SLE pathogenesis, however, remain poorly understood. Using reporter cells engineered to precisely quantify IFN-I, IFN-II and IFN-III activity levels in serum/plasma, we found that while IFNs play essential role in SLE pathogenesis and disease activity, they are only significant in specific subsets of patients. Interestingly, whereas IFN-I is the main IFN that governs disease activity in SLE, clinical subsets are defined by the co-elevation of IFN-II and IFN-III. Thus, increased IFN-I alone was only associated with cutaneous lupus. In contrast, systemic features, such as nephritis, were linked to co-elevation of IFN-I plus IFN-II and IFN-III, implying a synergistic effect of IFNs in severe SLE. Intriguingly, while increased IFN-I levels were strongly associated with IFN-induced gene expression (93.5%), in up to 64% of cases, the IFN signature was not associated with IFN-I. Importantly, neither IFN-II nor IFN-III explained IFN-induced gene expression in patients with normal IFN-I levels, and not every feature in SLE was associated with elevated IFNs, suggesting IFN-independent subsets in SLE. Together, the data suggest that, unlike the IFN signature, direct quantification of bioactive IFNs can identify pathogenic and clinically relevant SLE subsets amenable for precise anti-IFN therapies. Since IFN-I is only elevated in a subset of SLE patients expressing the IFN signature, this study explains the heterogeneous response in clinical trials targeting IFN-I, where patients were selected based on IFN-induced gene expression rather than IFN-I levels.
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Affiliation(s)
- Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
| | - Daniel W. Goldman
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
| | - Victoria Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
| | - Michelle Petri
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224
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17
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Steinmetz TD, Verstappen GM, Suurmond J, Kroese FGM. Targeting plasma cells in systemic autoimmune rheumatic diseases - Promises and pitfalls. Immunol Lett 2023; 260:44-57. [PMID: 37315847 DOI: 10.1016/j.imlet.2023.06.005] [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: 02/03/2023] [Revised: 05/12/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Plasma cells are the antibody secretors of the immune system. Continuous antibody secretion over years can provide long-term immune protection but could also be held responsible for long-lasting autoimmunity in case of self-reactive plasma cells. Systemic autoimmune rheumatic diseases (ARD) affect multiple organ systems and are associated with a plethora of different autoantibodies. Two prototypic systemic ARDs are systemic lupus erythematosus (SLE) and Sjögren's disease (SjD). Both diseases are characterized by B-cell hyperactivity and the production of autoantibodies against nuclear antigens. Analogues to other immune cells, different subsets of plasma cells have been described. Plasma cell subsets are often defined dependent on their current state of maturation, that also depend on the precursor B-cell subset from which they derived. But, a universal definition of plasma cell subsets is not available so far. Furthermore, the ability for long-term survival and effector functions may differ, potentially in a disease-specific manner. Characterization of plasma cell subsets and their specificity in individual patients can help to choose a suitable targeting approach for either a broad or more selective plasma cell depletion. Targeting plasma cells in systemic ARDs is currently challenging because of side effects or varying depletion efficacies in the tissue. Recent developments, however, like antigen-specific targeting and CAR-T-cell therapy might open up major benefits for patients beyond current treatment options.
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Affiliation(s)
- Tobit D Steinmetz
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Gwenny M Verstappen
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolien Suurmond
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frans G M Kroese
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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18
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Zhang X, Zhang J, Pan Z, Zhang Y, Xu X, Sheng Y, Zhu Z, Zhou F, Wen L. Transcriptome sequencing reveals novel molecular features of SLE severity. Front Genet 2023; 14:1121359. [PMID: 37554401 PMCID: PMC10406386 DOI: 10.3389/fgene.2023.1121359] [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: 12/13/2022] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Introduction: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by the production of autoantibodies, immune complex deposition, and tissue/organ damage. In this study, we aimed to identify molecular features and signaling pathways associated with SLE severity using RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), and clinical parameters. Methods: We analyzed transcriptome profiles of 45 SLE patients, grouped into mild (mSLE, SLEDAI ≤ 9) and severe (sSLE, SLEDAI > 9) based on SLE Disease Activity Index (SLEDAI) scores. We also collected clinical data on anti-dsDNA, ANA, ESR, CRP, snRNP, AHA, and anti-Smith antibody status for each patient. Results: By comparing gene expression across groups, we identified 12 differentially expressed genes (DEGs), including 7 upregulated (CEACAM6, UCHL1, ARFGEF3, AMPH, SERPINB10, TACSTD2, and OTX1) and 5 downregulated (SORBS2, TRIM64B, SORCS3, DRAXIN, and PCDHGA10) DEGs in sSLE compared to mSLE. Furthermore, using the CIBERSORT algorithm, we found that Treg cells were significantly decreased in sSLE and negatively correlated with AMPH expression, which was mainly expressed in Treg cells from SLE patients according to public scRNA-seq data (GSE135779). Discussion: Overall, our findings shed light on the molecular mechanisms underlying SLE severity and provide insight into potential therapeutic targets.
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Affiliation(s)
- Xiaojing Zhang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Jiali Zhang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Zhaobing Pan
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Yuxi Zhang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Xiaoqing Xu
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Yujun Sheng
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Zhengwei Zhu
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Fusheng Zhou
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Leilei Wen
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
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19
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Sentis G, Loukogiannaki C, Malissovas N, Nikolopoulos D, Manolakou T, Flouda S, Grigoriou M, Banos A, Boumpas DT, Filia A. A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies. Front Immunol 2023; 14:1203848. [PMID: 37475860 PMCID: PMC10355154 DOI: 10.3389/fimmu.2023.1203848] [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: 04/11/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Objective A blood-based biomarker is needed to assess lupus nephritis (LN) disease activity, minimizing the need for invasive kidney biopsies. Long non-coding RNAs (lncRNAs) are known to regulate gene expression, appear to be stable in human plasma, and can serve as non-invasive biomarkers. Methods Transcriptomic data of whole blood samples from 74 LN patients and 20 healthy subjects (HC) were analyzed to identify differentially expressed (DE) lncRNAs associated with quiescent disease and flares. Weighted gene co-expression network analysis (WGCNA) was performed to uncover lncRNAs with a central role (hub lncRNAs) in regulating key biological processes that drive LN disease activity. The association of hub lncRNAs with disease activity was validated using RT-qPCR on an independent cohort of 15 LN patients and 9 HC. cis- and trans-targets of validated lncRNAs were explored in silico to examine potential mechanisms of their action. Results There were 444 DE lncRNAs associated with quiescent disease and 6 DE lncRNAs associated with flares (FDR <0.05). WGCNA highlighted IFN signaling and B-cell activity/adaptive immunity as the most significant processes contributing to nephritis activity. Four disease-activity-associated lncRNAs, namely, NRIR, KLHDC7B-DT, MIR600HG, and FAM30A, were detected as hub genes and validated in an independent cohort. NRIR and KLHDC7B-DT emerged as potential key regulators of IFN-mediated processes. Network analysis suggests that FAM30A and MIR600HG are likely to play a central role in the regulation of B-cells in LN through cis-regulation effects and a competing endogenous RNA mechanism affecting immunoglobulin gene expression and the IFN-λ pathway. Conclusions The expression of lncRNAs NRIR, KLHDC7B-DT, FAM30A, and MIR600HG were associated with disease activity and could be further explored as blood-based biomarkers and potential liquid biopsy on LN.
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Affiliation(s)
- George Sentis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Catherine Loukogiannaki
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Nikos Malissovas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dionysis Nikolopoulos
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Theodora Manolakou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Sofia Flouda
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Grigoriou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
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20
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Karino K, Kono M, Atsumi T, Kanda M. Reply. Arthritis Rheumatol 2023; 75:1294-1296. [PMID: 36637799 DOI: 10.1002/art.42443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/14/2023]
Affiliation(s)
- Kohei Karino
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Michihito Kono
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Tatsuya Atsumi
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masatoshi Kanda
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
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21
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Nakayamada S, Tanaka Y. Immune Phenotype as a Biomarker for Systemic Lupus Erythematosus. Biomolecules 2023; 13:960. [PMID: 37371540 DOI: 10.3390/biom13060960] [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: 03/31/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The treatment of rheumatoid arthritis was revolutionized with the use of molecular-targeted drugs that target immunoregulatory molecules. The success of treatment with these drugs prompted the development of molecular-targeted drugs for systemic lupus erythematosus. However, systemic lupus erythematosus is a disease with high heterogeneous immune abnormalities, and diverse cells or molecules can be treatment targets. Thus, the identification of subpopulations based on immune abnormalities is essential for the development of effective treatment. One analytical method used to identify subpopulations is the immunophenotyping of peripheral blood samples of patients. This analysis evaluates the validity of target molecules for peripheral blood immune cell subsets, which are expected to be developed as biomarkers for precision medicine in which appropriate treatment targets are set for each subpopulation.
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Affiliation(s)
- Shingo Nakayamada
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahata-nishi-ku, Kitakyushu 807-8555, Fukuoka, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahata-nishi-ku, Kitakyushu 807-8555, Fukuoka, Japan
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22
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Abstract
In this Viewpoint we discuss how experimental medicine applied in the setting of clinical trials can address unmet need in the prototypic autoimmune disease systemic lupus erythematosus (SLE) to improve outcomes for patients.
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Affiliation(s)
| | - Muhammad Shipa
- Department of Rheumatology, University College London, London, UK
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23
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Psarras A, Clarke A. A cellular overview of immunometabolism in systemic lupus erythematosus. OXFORD OPEN IMMUNOLOGY 2023; 4:iqad005. [PMID: 37554724 PMCID: PMC10264559 DOI: 10.1093/oxfimm/iqad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/16/2023] [Accepted: 05/02/2023] [Indexed: 08/10/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease, characterized by a breakdown of immune tolerance and the development of autoantibodies against nucleic self-antigens. Immunometabolism is a rapidly expanding scientific field investigating the metabolic programming of cells of the immune system. During the normal immune response, extensive reprogramming of cellular metabolism occurs, both to generate adenosine triphosphate and facilitate protein synthesis, and also to manage cellular stress. Major pathways upregulated include glycolysis, oxidative phosphorylation, the tricarboxylic acid cycle and the pentose phosphate pathway, among others. Metabolic reprogramming also occurs to aid resolution of inflammation. Immune cells of both patients with SLE and lupus-prone mice are characterized by metabolic abnormalities resulting in an altered functional and inflammatory state. Recent studies have described how metabolic reprogramming occurs in many cell populations in SLE, particularly CD4+ T cells, e.g. favouring a glycolytic profile by overactivation of the mechanistic target of rapamycin pathway. These advances have led to an increased understanding of the metabolic changes affecting the inflammatory profile of T and B cells, monocytes, dendritic cells and neutrophils, and how they contribute to autoimmunity and SLE pathogenesis. In the current review, we aim to summarize recent advances in the field of immunometabolism involved in SLE and how these could potentially lead to new therapeutic strategies in the future.
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Affiliation(s)
- Antonios Psarras
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Alexander Clarke
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
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24
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Liu Q, Deng Y, Liu X, Zheng Y, Li Q, Cai G, Feng Z, Chen X. Transcriptomic analysis of B cells suggests that CD70 and LY9 may be novel features in patients with systemic lupus erythematosus. Heliyon 2023; 9:e15684. [PMID: 37144201 PMCID: PMC10151360 DOI: 10.1016/j.heliyon.2023.e15684] [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: 08/31/2022] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
Dysfunction of B-cell subsets is critical in the development of systemic lupus erythematosus (SLE). There is a great diversity of B-lineage cells, and their features and functions in SLE need to be clarified. In this study, we analyzed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and bulk transcriptomic data of isolated B-cell subsets from patients with SLE and healthy controls (HCs). We preformed scRNA-seq analysis focused on the diversity of B-cell subsets and identified a subset of antigen-presenting B cells in SLE patients that highly expressed ITGAX. A list of marker genes of each B-cell subset in patients with SLE was also identified. Comparison of bulk transcriptomic data of isolated B-cell subpopulations between SLE patients and HCs revealed the upregulated differentially expressed genes (DEGs) for each B-cell subpopulation in SLE. Common genes identified using these two methods were considered to be upregulated marker genes of B cells in SLE. The scRNA-seq data of SLE patients and HCs revealed that CD70 and LY9 were overexpressed in B cells vs. other cell types from SLE patients, and this pattern was validated by RT‒qPCR. Because CD70 is the cellular ligand of CD27, previous studies on CD70 have focused mainly on T cells from SLE patients. LY9 appears to have different functions in mice and humans: its expression is decreased in lupus-prone mice but is increased in T cells and some B-cell subpopulations in SLE patients. Here, we describe the overexpression of two costimulatory molecules, CD70 and LY9, which may be a novel feature of B cells in SLE patients.
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Affiliation(s)
- Qun Liu
- School of Medicine, Nankai University, Tianjin, 300071, China
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China
| | - Yiyao Deng
- Department of Nephrology, Guizhou Provincial People's Hospital, 83, Zhongshan Road, Nanming District, Guiyang, 550002, Guizhou, China
| | - Xiaomin Liu
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China
| | - Ying Zheng
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China
| | - Qinggang Li
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China
| | - Guangyan Cai
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
| | - Zhe Feng
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Corresponding author.
| | - Xiangmei Chen
- School of Medicine, Nankai University, Tianjin, 300071, China
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China
- Corresponding author.
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25
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Zhang C, Han X, Jin Y, Chen X, Gong C, Peng J, Wang Y, Luo X, Yang Z, Zhang Y, Wan W, Liu X, Mao J, Yu H, Li J, Liu L, Sun L, Yang S, An Y, Liu Z, Gao E, Zhu H, Chen Y, Yu X, Zhou Q, Liu Z. Pathogenic Gene Spectrum and Clinical Implication in Chinese Patients with Lupus Nephritis. Clin J Am Soc Nephrol 2023; 18:01277230-990000000-00138. [PMID: 37099456 PMCID: PMC10356117 DOI: 10.2215/cjn.0000000000000185] [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: 11/02/2022] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Lupus nephritis is a rare immunological disorder. Genetic factors are considered important in its causation. We aim to systematically investigate the rare pathogenic gene variants in patients with lupus nephritis. METHODS Whole-exome sequencing was used to screen pathogenic gene variants in 1886 probands with lupus nephritis. Variants were interpreted on the basis of known pathogenic variants or the American College of Medical Genetics and Genomics guidelines and studied by functional analysis, including RNA sequencing, quantitative PCR, cytometric bead array, and Western blotting. RESULTS Mendelian form of lupus nephritis was confirmed in 71 probands, involving 63 variants in 39 pathogenic genes. The detection yield was 4%. The pathogenic genes enriched in nuclear factor kappa-B (NF-κB), type I interferon, phosphatidylinositol-3-kinase/serine/threonine kinase Akt (PI3K/AKT), Ras GTPase/mitogen-activated protein kinase (RAS/MAPK), and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways. Clinical manifestation patterns were diverse among different signaling pathways. More than 50% of the pathogenic gene variants were reported to be associated with lupus or lupus nephritis for the first time. The identified pathogenic gene variants of lupus nephritis overlapped with those of autoinflammatory and immunodeficiency diseases. Inflammatory signatures, such as cytokine levels of IL-6, IL-8, IL-1 β , IFN α , IFN γ , and IP10 in serum and transcriptional levels of interferon-stimulated genes in blood, were significantly higher in patients with pathogenic gene variants compared with controls. The overall survival rate of patients with pathogenic gene variants was lower than those without pathogenic gene variants. CONCLUSIONS A small fraction of patients with lupus nephritis had identifiable pathogenic gene variants, primarily in NF-κB, type I interferon, PI3K/AKT, JAK/STAT, RAS/MAPK, and complement pathways.
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Affiliation(s)
- Changming Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xu Han
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ying Jin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiang Chen
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Cheng Gong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Jiahui Peng
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yusha Wang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaoxin Luo
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Zhaohui Yang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yangyang Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Weiguo Wan
- Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohui Liu
- Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Haiguo Yu
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jingyi Li
- Department of Rheumatology and Immunology, First Affiliated Hospital (Southwest Hospital) of Army Medical University, Chongqing, China
| | - Li Liu
- Children's Hospital of Tianjin University, Tianjin, China
| | - Li Sun
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Sirui Yang
- Department of Pediatric Rheumatology and Allergy, The First Hospital of Jilin University, Changchun, China
| | - Yu An
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhengzhao Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Erzhi Gao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Honghao Zhu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yinghua Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiaomin Yu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Qing Zhou
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
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26
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Fasano S, Milone A, Nicoletti GF, Isenberg DA, Ciccia F. Precision medicine in systemic lupus erythematosus. Nat Rev Rheumatol 2023; 19:331-342. [PMID: 37041269 DOI: 10.1038/s41584-023-00948-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/13/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that has diverse clinical manifestations, ranging from restricted cutaneous involvement to life-threatening systemic organ involvement. The heterogeneity of pathomechanisms that lead to SLE contributes to between-patient variation in clinical phenotype and treatment response. Ongoing efforts to dissect cellular and molecular heterogeneity in SLE could facilitate the future development of stratified treatment recommendations and precision medicine, which is a considerable challenge for SLE. In particular, some genes involved in the clinical heterogeneity of SLE and some phenotype-related loci (STAT4, IRF5, PDGF genes, HAS2, ITGAM and SLC5A11) have an association with clinical features of the disease. An important part is also played by epigenetic varation (in DNA methylation, histone modifications and microRNAs) that influences gene expression and affects cell function without modifying the genome sequence. Immune profiling can help to identify an individual's specific response to a therapy and can potentially predict outcomes, using techniques such as flow cytometry, mass cytometry, transcriptomics, microarray analysis and single-cell RNA sequencing. Furthermore, the identification of novel serum and urinary biomarkers would enable the stratification of patients according to predictions of long-term outcomes and assessments of potential response to therapy.
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Affiliation(s)
- Serena Fasano
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy.
| | - Alessandra Milone
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy
| | - David A Isenberg
- Department of Rheumatology, Division of Medicine, University College London, London, UK
| | - Francesco Ciccia
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy.
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27
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Fujio K. Functional Genome Analysis for Immune Cells Provides Clues for Stratification of Systemic Lupus Erythematosus. Biomolecules 2023; 13:biom13040591. [PMID: 37189338 DOI: 10.3390/biom13040591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is caused by a combination of genetic and environmental factors. Recently, analysis of a functional genome database of genetic polymorphisms and transcriptomic data from various immune cell subsets revealed the importance of the oxidative phosphorylation (OXPHOS) pathway in the pathogenesis of SLE. In particular, activation of the OXPHOS pathway is persistent in inactive SLE, and this activation is associated with organ damage. The finding that hydroxychloroquine (HCQ), which improves the prognosis of SLE, targets toll-like receptor (TLR) signaling upstream of OXPHOS suggests the clinical importance of this pathway. IRF5 and SLC15A4, which are regulated by polymorphisms associated with SLE susceptibility, are functionally associated with OXPHOS as well as blood interferon activity and metabolome. Future analyses of OXPHOS-associated disease-susceptibility polymorphisms, gene expression, and protein function may be useful for risk stratification of SLE.
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28
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Carmona-Rivera C, Kaplan MJ. Low-density granulocytes in systemic autoimmunity and autoinflammation. Immunol Rev 2023; 314:313-325. [PMID: 36305174 PMCID: PMC10050110 DOI: 10.1111/imr.13161] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A body of evidence has re-energized the interest on the role neutrophils in inflammatory and autoimmune conditions. For decades, neutrophils have been considered a homogenous population. Nevertheless, accumulating evidence suggests that neutrophils are more versatile and heterogeneous than initially considered. The notion of neutrophil heterogeneity has been supported by the identification of low-density granulocytes (LDGs) in systemic lupus erythematosus (SLE) and other systemic autoimmune and autoinflammatory conditions. Transcriptomic, epigenetic, proteomic, and functional analyses support that LDGs are a distinct subset of proinflammatory neutrophils implicated in the pathogenesis of SLE and other autoimmune diseases. Importantly, it remains incompletely characterized whether LDGs detected in other inflammatory/autoimmune conditions display the same phenotype that those present in SLE. A shared feature of LDGs across diseases is their association with vascular damage, an important contributor to morbidity and mortality in chronic inflammatory conditions. Additionally, the lack of specific markers to identify LDGs in circulation or in tissue, makes it a challenge to elucidate their role in the pathogenesis of inflammatory and autoimmune conditions. In this review, we aim to examine the evidence on the biology and the putative pathogenic role of LDGs in systemic autoimmune diseases.
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Affiliation(s)
- Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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29
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Tanaka Y. What are the hot topics in Japanese rheumatology? Go above and beyond. RMD Open 2023; 9:rmdopen-2022-002819. [PMID: 36717187 PMCID: PMC9887709 DOI: 10.1136/rmdopen-2022-002819] [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: 12/04/2022] [Accepted: 01/02/2023] [Indexed: 01/31/2023] Open
Abstract
Japanese rheumatology and immunology have contributed to progress in the field and advancement of rheumatology, including postmarketing surveillance, development of IL-6-targeting therapy and concept of drug tapering, have accelerated in the 21st century. The 67th Annual Scientific Meeting of the Japan College of Rheumatology, held on Fukuoka on 24 April 2023-26 April 2023, will go ahead and beyond such an advancement. Profound discussion on future perspectives such as precision medicine, the elucidation of pathology and genome-based drug discovery by multilayered integration with various types of omics information, information on metabolome and proteome of blood metabolites, and database of target proteins and compounds for drug discovery will be discussed.
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Affiliation(s)
- Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Fukuoka, Japan
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30
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Bordon Y. Focusing on the correct gene signatures for SLE. Nat Rev Immunol 2022; 22:595. [PMID: 36068339 DOI: 10.1038/s41577-022-00781-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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