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Papagiannopoulos OD, Pezoulas VC, Papaloukas C, Fotiadis DI. 3D clustering of gene expression data from systemic autoinflammatory diseases using self-organizing maps (Clust3D). Comput Struct Biotechnol J 2024; 23:2152-2162. [PMID: 38827234 PMCID: PMC11141280 DOI: 10.1016/j.csbj.2024.05.003] [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: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 06/04/2024] Open
Abstract
Background and objective Systemic autoinflammatory diseases (SAIDs) are characterized by widespread inflammation, but for most of them there is a lack of specific biomarkers for accurate diagnosis. Although a number of machine learning algorithms have been used to analyze SAID datasets, aiding in the discovery of novel biomarkers, there is a growing recognition of the importance of SAID timeseries clustering, as it can capture the temporal dynamics of gene expression patterns. Methodology This paper proposes a novel clustering methodology to efficiently associate three-dimensional data. The algorithm utilizes competitive learning to create a self-organizing neural network and adjust neuron positions in time-dependent and high dimensional feature space in order to assign them as clustering centers. The quantitative evaluation of the clustering was based on well-known clustering indices. Furthermore, a differential expression analysis and classification pipeline was employed to assess the capability of the proposed methodology to extract more accurate pathway-specific genes from its clusters. For that, a comparative analysis was also conducted against a heuristic timeseries clustering method. Results The proposed methodology achieved better overall clustering indices scores and classification metrics using genes derived from its clusters. Notable cases include a threefold increase in the Calinski-Harabasz clustering index, a twofold improvement in the Davies-Bouldin clustering index and a ∼ 60 % increase in the classification specificity score. Conclusion A novel clustering methodology was developed and applied on several gene expression timeseries datasets from systemic autoinflammatory diseases, and its ability to efficiently produce well separated clusters compared to existing heuristic methods was demonstrated.
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Affiliation(s)
- Orestis D. Papagiannopoulos
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
| | - Vasileios C. Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
| | - Costas Papaloukas
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
- Dept. of Biological Applications and Technology, University of Ioannina, Ioannina GR45110, Greece
- Institute of Biomedical Research, FORTH (Foundation for Research & Technology), Ioannina GR45110, Greece
| | - Dimitrios I. Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
- Institute of Biomedical Research, FORTH (Foundation for Research & Technology), Ioannina GR45110, Greece
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2
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [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: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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Liu J, Liao X, Li N, Xu Z, Yang W, Zhou H, Liu Y, Zhang Z, Wang G, Hou S. Single‐cell RNA sequencing reveals inflammatory retinal microglia in experimental autoimmune uveitis. MedComm (Beijing) 2024; 5:e534. [PMID: 38585235 PMCID: PMC10999176 DOI: 10.1002/mco2.534] [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: 06/29/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
Autoimmune uveitis (AU) is a kind of immune-mediated disease resulting in irreversible ocular damage and even permanent vision loss. However, the precise mechanism underlying dynamic immune changes contributing to disease initiation and progression of AU remains unclear. Here, we induced an experimental AU (EAU) model with IRBP651-670 and found that day[D]14 was the inflammatory summit with remarking clinical and histopathological manifestations and the activation of retinal microglia exhibited a time-dependent pattern in the EAU course. We conducted single-cell RNA sequencing of retinal immune cells in EAU mice at four time points and found microglia constituting the largest proportion, especially on D14. A novel inflammatory subtype (Cd74high Ccl5high) of retinal microglia was identified at the disease peak that was closely associated with modulating immune responses. In vitro experiments indicated that inflammatory stimuli induced proinflammatory microglia with the upregulation of CD74 and CCL5, and CD74 overexpression in microglia elicited their proinflammatory phenotype via nuclear factor-kappa B signaling that could be attenuated by the treatment of neutralizing CCL5 antibody to a certain extent. In-vivo blockade of Cd74 and Ccl5 effectively alleviated retinal microglial activation and disease phenotype of EAU. Therefore, we propose targeting CD74 and CCL5 of retinal microglia as promising strategies for AU treatment.
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Affiliation(s)
- Jiangyi Liu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Xingyun Liao
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Na Li
- Department of Laboratory MedicineBeijing Tongren HospitalCapital Medical UniversityBeijingChina
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Wang Yang
- Department of KidneyFirst Affiliated HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Hongxiu Zhou
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Yusen Liu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Zhi Zhang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Guoqing Wang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical UniversityChongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye DiseasesChongqing Eye InstituteChongqingChina
- Beijing Institute of OphthalmologyBeijing Tongren Eye CenterBeijing Tongren HospitalCapital Medical UniversityBeijing Ophthalmology and Visual Sciences Key LaboratoryBeijingChina
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Ruan Y, Xu C, Zhang T, Zhu L, Wang H, Wang J, Zhu H, Huang C, Pan M. Single-Cell Profiling Unveils the Inflammatory Heterogeneity within Cutaneous Lesions of Bullous Pemphigoid. J Invest Dermatol 2024:S0022-202X(24)00209-4. [PMID: 38537929 DOI: 10.1016/j.jid.2024.02.029] [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: 11/15/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024]
Abstract
Bullous pemphigoid (BP) is a subepidermal blistering skin disease with a complex pathogenesis involving various immune cells. However, the transcriptional features of these cells remain poorly defined. In this study, we constructed a comprehensive and single-cell resolution atlas of various immune cells within BP skin lesions through integrative single-cell analysis, flow cytometry, and multiplex immunohistochemistry. We observed prominent expansion and transcriptional changes in mast cells, macrophages, basophils, and neutrophils within BP lesions. Mast cells within the lesions adopted an active state and exhibited an elevated capacity for producing proinflammatory mediators. We observed an imbalance of macrophages/dendritic cells within BP lesions. Two macrophage subpopulations (NLRP3+ and C1q+) with distinct transcriptional profiles were identified and upregulated effector programs. T-peripheral helper-like T helper 2 cells were expanded in skin lesions and peripheral blood of patients with BP and were capable of promoting B-cell responses. In addition, we observed clonally expanded granzyme B-positive CD8+ T cells within BP lesions. Chemokine receptor mapping revealed the potential roles of macrophages and mast cells in recruiting pathogenic immune cells and underlying mechanisms within BP lesions. Thus, this study reveals key immune pathogenic features of BP lesions, thereby providing valuable insights for potential therapeutic interventions in this disease.
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Affiliation(s)
- Yue Ruan
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuqiao Xu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyu Zhang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Zhu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailun Wang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingying Wang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiqin Zhu
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanxin Huang
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Biliary Tract Disease Research, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Meng Pan
- Department of Dermatology, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Li T, Xu B, Li W, Cheng X, Tantai W, Zheng H, Zhao L, Li N, Han C. Allosteric inhibitor of SHP2 enhances macrophage endocytosis and bacteria elimination by increasing caveolae activation and protects against bacterial sepsis. Pharmacol Res 2024; 201:107096. [PMID: 38320736 DOI: 10.1016/j.phrs.2024.107096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
The uncontrolled bacterial infection-induced cytokine storm and sequential immunosuppression are commonly observed in septic patients, which indicates that the activation of phagocytic cells and the efficient and timely elimination of bacteria are crucial for combating bacterial infections. However, the role of dysregulated immune cells and their disrupted function in sepsis remains unclear. Here, we found that macrophages exhibited the impaired endocytosis capabilities in sepsis by Single-cell RNA sequencing and bulk RNA sequencing. Caveolae protein Caveolin-1 (Cav-1) of macrophages was inactivated by SHP2 rapidly during Escherichia coli (E.coli) infection. Allosteric inhibitor of SHP2 effectively maintains Cav-1 phosphorylation to enhance macrophage to endocytose and eliminate bacteria. Additionally, TLR4 endocytosis of macrophage was also enhanced upon E.coli infection by SHP099, inducing an increased and rapidly resolved inflammatory response. In vivo, pretreatment or posttreatment with inhibitor of SHP2 significantly reduced the bacterial burden in organs and mortality of mice subjected E.coli infection or CLP-induced sepsis. The cotreatment of inhibitor of SHP2 with an antibiotic conferred complete protection against mortality in mice. Our findings suggest that Cav-1-mediated endocytosis and bacterial elimination may play a critical role in the pathogenesis of sepsis, highlighting inhibitor of SHP2 as a potential therapeutic agent for sepsis.
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Affiliation(s)
- Tianliang Li
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| | - Bing Xu
- School of Anesthesiology, Naval Medical University, Shanghai 200433, China
| | - Wenqian Li
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaotao Cheng
- Suzhou Jizhi Medical Corporation, Jiangsu 215400, China
| | - Wenjing Tantai
- Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai 200433, China
| | - Haiyan Zheng
- Department of Emergency, Dongfang Hospital, Tongji University, Shanghai 200210, China
| | - Liming Zhao
- Department of Emergency, Dongfang Hospital, Tongji University, Shanghai 200210, China.
| | - Nan Li
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China.
| | - Chaofeng Han
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China; Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai 200433, China.
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6
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Yasumizu Y, Takeuchi D, Morimoto R, Takeshima Y, Okuno T, Kinoshita M, Morita T, Kato Y, Wang M, Motooka D, Okuzaki D, Nakamura Y, Mikami N, Arai M, Zhang X, Kumanogoh A, Mochizuki H, Ohkura N, Sakaguchi S. Single-cell transcriptome landscape of circulating CD4 + T cell populations in autoimmune diseases. CELL GENOMICS 2024; 4:100473. [PMID: 38359792 PMCID: PMC10879034 DOI: 10.1016/j.xgen.2023.100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 02/17/2024]
Abstract
CD4+ T cells are key mediators of various autoimmune diseases; however, their role in disease progression remains unclear due to cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations using decomposition-based transcriptome characterization and canonical clustering strategies. This approach identified 12 independent gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell datasets of over 1.8 million peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloging cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.
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Affiliation(s)
- Yoshiaki Yasumizu
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan
| | - Daiki Takeuchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Faculty of Medicine, Osaka University, Osaka, Japan
| | - Reo Morimoto
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yusuke Takeshima
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuhiro Kato
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Min Wang
- Clinical Immunology Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yamami Nakamura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Norihisa Mikami
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Masaya Arai
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Center for Infectious Diseases for Education and Research, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan
| | - Naganari Ohkura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Frontier Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Shimon Sakaguchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Experimental Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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Zhang Y, Deng Y, Jing S, Su G, Li N, Huang Z, Zhang W, Chen Z, Yang P. Proteomic profiling of aqueous humor-derived exosomes in Vogt-Koyanagi-Harada disease and Behcet's uveitis. Clin Immunol 2024; 259:109895. [PMID: 38185270 DOI: 10.1016/j.clim.2024.109895] [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: 09/26/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Vogt-Koyanagi-Harada (VKH) disease and Behcet's uveitis (BU) are the two major vision-threatening uveitis entities. This study performed the first label-free quantitative proteomics on aqueous humor-derived exosomes from 84 patients with VKH or BU to determine their potential roles. Sixty-five differentially expressed proteins (DEPs) and 40 DEPs were detected in the VKH and BU groups, respectively. GO and KEGG analysis showed that DEPs were mainly enriched in the complement-related pathways. The complement C1q subcomponent subunit B (C1QB) was identified as a key exosomal protein, and its expression was significantly increased by western blotting in both diseases. Additionally, the integrated analysis based on the published scRNA-seq data showed that C1QB-containing exosomes were mainly produced by mononuclear macrophages in the anterior segment tissue. Overall, our proteomic profiling highlights that complement-related pathways may be actively involved in the pathogenesis of these two diseases. These pathways may also serve as treatment targets for both diseases.
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Affiliation(s)
- Yinan Zhang
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Yang Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Shixiang Jing
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Na Li
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China
| | - Ziqian Huang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Wanyun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Zhijun Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Peizeng Yang
- Department of Ophthalmology, The First Afliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, Henan Province, PR China; The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, PR China.
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8
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Wang HP, Basisty N, Qu JH, Wang X. Editorial: Multi-omics studies on aging and age-related diseases. Front Cell Dev Biol 2024; 12:1374424. [PMID: 38357003 PMCID: PMC10864650 DOI: 10.3389/fcell.2024.1374424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Affiliation(s)
- He-Ping Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nathan Basisty
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jia-Hua Qu
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Xiaoman Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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9
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Zeng L, Yu G, Yang K, He Q, Hao W, Xiang W, Long Z, Chen H, Tang X, Sun L. Exploring the mechanism of Celastrol in the treatment of rheumatoid arthritis based on systems pharmacology and multi-omics. Sci Rep 2024; 14:1604. [PMID: 38238321 PMCID: PMC10796403 DOI: 10.1038/s41598-023-48248-5] [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: 04/04/2023] [Accepted: 11/23/2023] [Indexed: 01/22/2024] Open
Abstract
To explore the molecular network mechanism of Celastrol in the treatment of rheumatoid arthritis (RA) based on a novel strategy (integrated systems pharmacology, proteomics, transcriptomics and single-cell transcriptomics). Firstly, the potential targets of Celastrol and RA genes were predicted through the database, and the Celastrol-RA targets were obtained by taking the intersection. Then, transcriptomic data and proteomic data of Celastrol treatment of RA were collected. Subsequently, Celastrol-RA targets, differentially expressed genes, and differentially expressed proteins were imported into Metascape for enrichment analysis, and related networks were constructed. Finally, the core targets of Celastrol-RA targets, differentially expressed genes, and differentially expressed proteins were mapped to synoviocytes of RA mice to find potential cell populations for Celastrol therapy. A total of 195 Celastrol-RA targets, 2068 differential genes, 294 differential proteins were obtained. The results of enrichment analysis showed that these targets, genes and proteins were mainly related to extracellular matrix organization, TGF-β signaling pathway, etc. The results of single cell sequencing showed that the main clusters of these targets, genes, and proteins could be mapped to RA synovial cells. For example, Mmp9 was mainly distributed in Hematopoietic cells, especially in Ptprn+fibroblast. The results of molecular docking also suggested that Celastrol could stably combine with molecules predicted by network pharmacology. In conclusion, this study used systems pharmacology, transcriptomics, proteomics, single-cell transcriptomics to reveal that Celastrol may regulate the PI3K/AKT signaling pathway by regulating key targets such as TNF and IL6, and then play an immune regulatory role.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
| | - Ganpeng Yu
- People's Hospital of Ningxiang City, Ningxiang, China
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Qi He
- Department of Rehabilitation Medicine, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wang Xiang
- Department of Rheumatology, The First People's Hospital Changde City, Changde, China
| | - Zhiyong Long
- Department of Rehabilitation Medicine, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Hua Chen
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaojun Tang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China.
| | - Lingyun Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China.
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Anhui, China.
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10
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Guo B, Zhao F, Zhang S. CILP is a potential pan-cancer marker: combined silico study and in vitro analyses. Cancer Gene Ther 2024; 31:119-130. [PMID: 37968343 DOI: 10.1038/s41417-023-00688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
CILP (Cartilage intermediate layer protein), an ECM (extracellular matrix) glycoprotein, is found to be associated with intervertebral disc degeneration, chronic heart failure, obese and cardiac fibrosis. However, there are few reports on the role of CILP in tumors. Thus, in this study, we mainly explored the function of CILP in the occurrence and development of tumors and whether it could be a potential pan-cancer marker. Pan-cancer data in this study were obtained from UCSC Xena. Single-cell data were obtained from GSE152938. ROC (Receiver operating characteristic) curves were used to evaluate the accuracy of CILP in predicting the occurrence of different tumor types. The Kaplan-Meier plots were used to assess the relationship between CILP expression and survival prognosis in different tumor types by COX regression analysis. Pseudotime analysis and cell communication analysis were used to further explore the function of CILP at Single cell level. The human RCC (renal cell carcinoma) cell lines ACHN and 786-O were used for further experimental verification. Bulk RNA-seq showed differences in CILP expression in several tumors. ROC curves showed that 14 tumors have AUC > 0.7. Kaplan-Meier plots indicated that CILP is a risk factor for patients in 3 kinds of tumors. ScRNA-seq (Single cell RNA sequencing) suggested that CILP might influence tumors through fibroblasts and cell-cell communication. Finally, we verified the function of CILP at the cellular level by using RCC cell lines ACHN and 786-O and found that knockdown of CILP could significantly inhibit migration and invasion. This finding supports that CILP could be a risk factor as well as a pan-cancer predictor for patients.
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Affiliation(s)
- Bingjie Guo
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feiran Zhao
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sailong Zhang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, China.
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11
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Yao H, Deng Y, Du G, Wang Y, Tang G. Elevated serum fibrinogen levels in Chinese patients with minor recurrent aphthous stomatitis: An observational study. Exp Dermatol 2024; 33:e14915. [PMID: 37638770 DOI: 10.1111/exd.14915] [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: 02/02/2023] [Revised: 08/01/2023] [Accepted: 08/13/2023] [Indexed: 08/29/2023]
Abstract
Fibrinogen is a protein that reflects systemic inflammation and regulates the immune response to disease. However, there is a scarcity of data on fibrinogen in recurrent aphthous stomatitis (RAS). We aimed to test the hypothesis that fibrinogen is involved in the aetiology of RAS. Between November 2016 and November 2018, we included 109 minor RAS patients and 29 age- and sex-matched controls in a single-center, observational study. Their clinical history and ulcer manifestations led to the diagnosis of minor RAS. The ulcer severity score (USS) was used to assess disease severity, and fibrinogen was also collected. We conducted three analyses: Analysis 1 (comparison of fibrinogen levels between patients and controls), Analysis 2 (comparison of fibrinogen levels between high and low USS patients) and Analysis 3 (comparison of fibrinogen levels between before and after anti-inflammatory treatment in patients). The fibrinogen levels in the 109 minor RAS patients were statistically higher than in the 29 controls (mean [SD], 2.6 [0.5] vs. 2.3 [0.3]; Student's t-test, p < 0.001). However, there were no significant differences in fibrinogen levels among the 43 patients with high USS and the 39 patients with low USS (mean [SD], 2.7 [0.5] vs. 2.6 [0.4]; Student's t-test, p = 0.278). Furthermore, fibrinogen levels were significantly higher before anti-inflammatory treatment in comparison to those after anti-inflammatory treatment in the 35 paired patients (mean [SD], 2.6 [0.4] vs. 2.5 [0.4]; Student's t-test, p = 0.026). Interestingly, fibrinogen levels were significantly higher in the 35 paired patients after anti-inflammatory treatment compared to the 29 control subjects (mean [SD], 2.5 [0.4] vs. 2.3 [0.3]; Student's t-test, p = 0.026]. Fibrinogen may play a role in the aetiology of RAS and may be a drug target for RAS treatment. Clinicians should be alert that high serum fibrinogen levels might be associated with the risk of RAS.
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Affiliation(s)
- Hui Yao
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yiwen Deng
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Guanhuan Du
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yufeng Wang
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Guoyao Tang
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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12
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Kalogeropoulos D, Kanavaros P, Vartholomatos G, Moussa G, Kalogeropoulos C. Cytokines in Immune-mediated "Non-infectious" Uveitis. Klin Monbl Augenheilkd 2023. [PMID: 38134911 DOI: 10.1055/a-2202-8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Uveitis is a significant cause of ocular morbidity and accounts for approximately 5 - 10% of visual impairments worldwide, particularly among the working-age population. Infections are the cause of ~ 50% cases of uveitis, but it has been suggested that infection might also be implicated in the pathogenesis of immune-mediated "non-infectious" uveitis. There is growing evidence that cytokines (i.e., interleukins, interferons, etc.) are key mediators of immune-mediated "non-infectious" uveitis. For example, activation of the interleukin-23/interleukin-17 signalling pathway is involved in immune-mediated "non-infectious" uveitis. Studies in animal models have been important in investigating the role of cytokines in uveitis. Recent studies of clinical samples from patients with uveitis have allowed the measurement of a considerable array of cytokines even from very small sample volumes (e.g., aqueous and vitreous humour). The identification of complex patterns of cytokines may contribute to a better understanding of their potential pathogenetic role in uveitis as well as to an improved diagnostic and therapeutic approach to treat these potentially blinding pathologies. This review provides further insights into the putative pathobiological role of cytokines in immune-mediated "non-infectious" uveitis.
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Affiliation(s)
| | - Panagiotis Kanavaros
- Anatomy-Histology-Embryology, University of Ioannina, Faculty of Medicine, Greece
| | - Georgios Vartholomatos
- Hematology Laboratory, Unit of Molecular Biology, University General Hospital of Ioannina, Greece
| | - George Moussa
- Ophthalmology, Birmingham and Midland Eye Centre, Birmingham, United Kingdom of Great Britain and Northern Ireland
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13
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Beltran JVB, Lin FP, Chang CL, Ko TM. Single-Cell Meta-Analysis of Neutrophil Activation in Kawasaki Disease and Multisystem Inflammatory Syndrome in Children Reveals Potential Shared Immunological Drivers. Circulation 2023; 148:1778-1796. [PMID: 37905415 DOI: 10.1161/circulationaha.123.064734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Kawasaki disease (KD) and multisystem inflammatory syndrome in children (MIS-C) share similar clinical manifestations, including cardiovascular complications, suggesting similar underlying immunopathogenic processes. Aberrant neutrophil activation may play a crucial role in the shared pathologies of KD and MIS-C; however, the associated pathogenic mechanisms and molecular drivers remain unknown. METHODS We performed a single-cell meta-analysis of neutrophil activation with 103 pediatric single-cell transcriptomic peripheral blood mononuclear cell data across 9 cohorts, including healthy controls, KD, MIS-C, compared with dengue virus infection, juvenile idiopathic arthritis, and pediatric celiac disease. We used a series of computational analyses to investigate the shared neutrophil transcriptional programs of KD and MIS-C that are linked to systemic damage and cardiac pathologies, and suggested Food and Drug Administration-approved drugs to consider as KD and MIS-C treatment. RESULTS We meta-analyzed 521 950 high-quality cells. We found that blood signatures associated with risks of cardiovascular events are enriched in neutrophils of KD and MIS-C. We revealed the expansion of CD177+ neutrophils harboring hyperactivated effector functions in both KD and MIS-C, but not in healthy controls or in other viral-, inflammatory-, or immune-related pediatric diseases. KD and MIS-C CD177+ neutrophils had highly similar transcriptomes, marked by conserved signatures and pathways related to molecular damage. We found the induction of a shared neutrophil expression program, potentially regulated by SPI1 (Spi-1 proto-oncogene), which confers enhanced effector functions, especially neutrophil degranulation. CD177 and shared neutrophil expression program expressions were associated with acute stages and attenuated during KD intravenous immunoglobulin treatment and MIS-C recovery. Network analysis identified hub genes that correlated with the high activation of CD177+ neutrophils. Disease-gene association analysis revealed that the KD and MIS-C CD177+ neutrophils' shared expression program was associated with the development of coronary and myocardial disorders. Last, we identified and validated TSPO (translocator protein) and S100A12 (S100 calcium-binding protein A12) as main molecular targets, for which the Food and Drug Administration-approved drugs methotrexate, zaleplon, metronidazole, lorazepam, clonazepam, temazepam, and zolpidem, among others, are primary candidates for drug repurposing. CONCLUSIONS Our findings indicate that CD177+ neutrophils may exert systemic pathological damage contributing to the shared morbidities in KD and MIS-C. We uncovered potential regulatory drivers of CD177+ neutrophil hyperactivation and pathogenicity that may be targeted as a single therapeutic strategy for either KD or MIS-C.
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Affiliation(s)
- Jan Vincent B Beltran
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
| | - Fang-Ping Lin
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
| | - Chaw-Liang Chang
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
- Department of Pediatrics, Cathay General Hospital, Hsinchu, Taiwan (C.-L.C.)
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan (C.-L.C.)
| | - Tai-Ming Ko
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan (T.-M.K.)
- School of Pharmacy, College of Pharmacy, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan (T.-M.K.)
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14
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Verweyen EL, Thakkar K, Dhakal S, Baker E, Chetal K, Schnell D, Canna S, Grom AA, Salomonis N, Schulert GS. Population-level single-cell genomics reveals conserved gene programs in systemic juvenile idiopathic arthritis. J Clin Invest 2023; 133:e166741. [PMID: 37733441 PMCID: PMC10645394 DOI: 10.1172/jci166741] [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: 11/01/2022] [Accepted: 09/19/2023] [Indexed: 09/23/2023] Open
Abstract
Systemic autoimmune and autoinflammatory diseases are characterized by genetic and cellular heterogeneity. While current single-cell genomics methods provide insights into known disease subtypes, these analysis methods do not readily reveal novel cell-type perturbation programs shared among distinct patient subsets. Here, we performed single-cell RNA-Seq of PBMCs of patients with systemic juvenile idiopathic arthritis (SJIA) with diverse clinical manifestations, including macrophage activation syndrome (MAS) and lung disease (LD). We introduced two new computational frameworks called UDON and SATAY-UDON, which define patient subtypes based on their underlying disrupted cellular programs as well as associated biomarkers or clinical features. Among twelve independently identified subtypes, this analysis uncovered what we believe to be a novel complement and interferon activation program identified in SJIA-LD monocytes. Extending these analyses to adult and pediatric lupus patients found new but also shared disease programs with SJIA, including interferon and complement activation. Finally, supervised comparison of these programs in a compiled single-cell pan-immune atlas of over 1,000 healthy donors found a handful of normal healthy donors with evidence of early inflammatory activation in subsets of monocytes and platelets, nominating possible biomarkers for early disease detection. Thus, integrative pan-immune single-cell analysis resolved what we believe to be new conserved gene programs underlying inflammatory disease pathogenesis and associated complications.
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Affiliation(s)
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | | | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Scott Canna
- Children’s Hospital of Philadelphia, Division of Rheumatology, Philadelphia, Pennsylvania, USA
| | - Alexei A. Grom
- Division of Rheumatology and
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Grant S. Schulert
- Division of Rheumatology and
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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15
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Sun P, Cui M, Jing J, Kong F, Wang S, Tang L, Leng J, Chen K. Deciphering the molecular and cellular atlas of immune cells in septic patients with different bacterial infections. J Transl Med 2023; 21:777. [PMID: 37919720 PMCID: PMC10621118 DOI: 10.1186/s12967-023-04631-4] [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: 07/15/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Sepsis is a life-threatening organ dysfunction caused by abnormal immune responses to various, predominantly bacterial, infections. Different bacterial infections lead to substantial variation in disease manifestation and therapeutic strategies. However, the underlying cellular heterogeneity and mechanisms involved remain poorly understood. METHODS Multiple bulk transcriptome datasets from septic patients with 12 types of bacterial infections were integrated to identify signature genes for each infection. Signature genes were mapped onto an integrated large single-cell RNA (scRNA) dataset from septic patients, to identify subsets of cells associated with different sepsis types, and multiple omics datasets were combined to reveal the underlying molecular mechanisms. In addition, an scRNA dataset and spatial transcriptome data were used to identify signaling pathways in sepsis-related cells. Finally, molecular screening, optimization, and de novo design were conducted to identify potential targeted drugs and compounds. RESULTS We elucidated the cellular heterogeneity among septic patients with different bacterial infections. In Escherichia coli (E. coli) sepsis, 19 signature genes involved in epigenetic regulation and metabolism were identified, of which DRAM1 was demonstrated to promote autophagy and glycolysis in response to E. coli infection. DRAM1 upregulation was confirmed in an independent sepsis cohort. Further, we showed that DRAM1 could maintain survival of a pro-inflammatory monocyte subset, C10_ULK1, which induces systemic inflammation by interacting with other cell subsets via resistin and integrin signaling pathways in blood and kidney tissue, respectively. Finally, retapamulin was identified and optimized as a potential drug for treatment of E. coli sepsis targeting the signature gene, DRAM1, and inhibiting E. coli protein synthesis. Several other targeted drugs were also identified in other types of sepsis, including nystatin targeting C1QA in Neisseria sepsis and dalfopristin targeting CTSD in Streptococcus viridans sepsis. CONCLUSION Our study provides a comprehensive overview of the cellular heterogeneity and underlying mechanisms in septic patients with various bacterial infections, providing insights to inform development of stratified targeted therapies for sepsis.
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Affiliation(s)
- Ping Sun
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
- Department of Emergency, Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Mintian Cui
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Fanyu Kong
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Shixi Wang
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Junling Leng
- Department of Emergency, Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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16
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Villanueva-Martin G, Acosta-Herrera M, Carmona EG, Kerick M, Ortego-Centeno N, Callejas-Rubio JL, Mages N, Klages S, Börno S, Timmermann B, Bossini-Castillo L, Martin J. Non-classical circulating monocytes expressing high levels of microsomal prostaglandin E2 synthase-1 tag an aberrant IFN-response in systemic sclerosis. J Autoimmun 2023; 140:103097. [PMID: 37633117 DOI: 10.1016/j.jaut.2023.103097] [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: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
Systemic sclerosis (SSc) is a complex disease that affects the connective tissue, causing fibrosis. SSc patients show altered immune cell composition and activation in the peripheral blood (PB). PB monocytes (Mos) are recruited into tissues where they differentiate into macrophages, which are directly involved in fibrosis. To understand the role of CD14+ PB Mos in SSc, a single-cell transcriptome analysis (scRNA-seq) was conducted on 8 SSc patients and 8 controls. Using unsupervised clustering methods, CD14+ cells were assigned to 11 clusters, which added granularity to the known monocyte subsets: classical (cMos), intermediate (iMos) and non-classical Mos (ncMos) or type 2 dendritic cells. NcMos were significantly overrepresented in SSc patients and showed an active IFN-signature and increased expression levels of PTGES, in addition to monocyte motility and adhesion markers. We identified a SSc-related cluster of IRF7+ STAT1+ iMos with an aberrant IFN-response. Finally, a depletion of M2 polarised cMos in SSc was observed. Our results highlighted the potential of PB Mos as biomarkers for SSc and provided new possibilities for putative drug targets for modulating the innate immune response in SSc.
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Affiliation(s)
- Gonzalo Villanueva-Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Elio G Carmona
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain; Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Jose Luis Callejas-Rubio
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Norbert Mages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Lara Bossini-Castillo
- Department of Genetics and Biotechnology Institute, Biomedical Research Centre (CIBM), University of Granada, 18100, Granada, Spain; Advanced Therapies and Biomedical Technologies (TEC-14), Biosanitary Research Institute Ibs. GRANADA, 18016, Granada, Spain.
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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17
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Tamassia N, Bianchetto-Aguilera F, Gasperini S, Grimaldi A, Montaldo C, Calzetti F, Gardiman E, Signoretto I, Castellucci M, Barnaba V, Tripodi M, Cassatella MA. The slan antigen identifies the prototypical non-classical CD16 +-monocytes in human blood. Front Immunol 2023; 14:1287656. [PMID: 37965335 PMCID: PMC10641684 DOI: 10.3389/fimmu.2023.1287656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction Peripheral monocytes in humans are conventionally divided into classical (CL, CD14++CD16-), intermediate (INT, CD14++CD16+) and non-classical (NC, CD14dim/-CD16++) cells, based on their expression levels of CD14 and CD16. A major fraction of the NC-monocytes has been shown to express the 6-sulfo LacNAc (slan) antigen, but whether these slan+/NC-monocytes represent the prototypical non-classical monocytes or whether they are simply a sub-fraction with identical features as the remainder of NC monocytes is still unclear. Methods We analyzed transcriptome (by bulk and single cell RNA-seq), proteome, cell surface markers and production of discrete cytokines by peripheral slan+/NC- and slan-/NC-monocytes, in comparison to total NC-, CL- and INT- monocytes. Results By bulk RNA-seq and proteomic analysis, we found that slan+/NC-monocytes express higher levels of genes and proteins specific of NC-monocytes than slan-/NC-monocytes do. Unsupervised clustering of scRNA-seq data generated one cluster of NC- and one of INT-monocytes, where all slan+/NC-monocytes were allocated to the NC-monocyte cluster, while slan-/NC-monocytes were found, in part (13.4%), within the INT-monocyte cluster. In addition, total NC- and slan-/NC-monocytes, but not slan+/NC-monocytes, were found by both bulk RNA-seq and scRNA-seq to contain a small percentage of natural killer cells. Conclusion In addition to comparatively characterize total NC-, slan-/NC- and slan+/NC-monocyte transcriptomes and proteomes, our data prove that slan+/NC-, but not slan-/NC-, monocytes are more representative of prototypical NC-monocytes.
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Affiliation(s)
- Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | | | - Sara Gasperini
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Alessio Grimaldi
- Department of Internal Clinical Sciences, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Federica Calzetti
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Elisa Gardiman
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Ilaria Signoretto
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | | | - Vincenzo Barnaba
- Department of Internal Clinical Sciences, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Rome, Italy
| | - Marco Tripodi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Shi W, Ye J, Shi Z, Pan C, Zhang Q, Lin Y, Liang D, Liu Y, Lin X, Zheng Y. Single-cell chromatin accessibility and transcriptomic characterization of Behcet's disease. Commun Biol 2023; 6:1048. [PMID: 37848613 PMCID: PMC10582193 DOI: 10.1038/s42003-023-05420-x] [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: 04/06/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023] Open
Abstract
Behect's disease is a chronic vasculitis characterized by complex multi-organ immune aberrations. However, a comprehensive understanding of the gene-regulatory profile of peripheral autoimmunity and the diverse immune responses across distinct cell types in Behcet's disease (BD) is still lacking. Here, we present a multi-omic single-cell study of 424,817 cells in BD patients and non-BD individuals. This study maps chromatin accessibility and gene expression in the same biological samples, unraveling vast cellular heterogeneity. We identify widespread cell-type-specific, disease-associated active and pro-inflammatory immunity in both transcript and epigenomic aspects. Notably, integrative multi-omic analysis reveals putative TF regulators that might contribute to chromatin accessibility and gene expression in BD. Moreover, we predicted gene-regulatory networks within nominated TF activators, including AP-1, NF-kB, and ETS transcript factor families, which may regulate cellular interaction and govern inflammation. Our study illustrates the epigenetic and transcriptional landscape in BD peripheral blood and expands understanding of potential epigenomic immunopathology in this disease.
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Affiliation(s)
- Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Caineng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
| | - Xianchai Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China.
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, 100085, Beijing, China.
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19
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Hu D, Guan JL. The roles of immune cells in Behçet's disease. Adv Rheumatol 2023; 63:49. [PMID: 37814339 DOI: 10.1186/s42358-023-00328-w] [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: 05/25/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
Behçet's disease (BD) is a systemic vasculitis that can affect multiple systems, including the skin, mucous membranes, joints, eyes, gastrointestinal and nervous. However, the pathogenesis of BD remains unclear, and it is believed that immune-inflammatory reactions play a crucial role in its development. Immune cells are a critical component of this process and contribute to the onset and progression of BD. By regulating the function of these immune cells, effective control over the occurrence and development of BD can be achieved, particularly with regards to monocyte activation and aggregation, macrophage differentiation and polarization, as well as T cell subset differentiation. This review provides a brief overview of immune cells and their role in regulating BD progression, which may serve as a theoretical foundation for preventing and treating this disease.
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Affiliation(s)
- Dan Hu
- Department of Rheumatology and Immunology, Huadong Hospital affiliated with Fudan University, #221 Yan'an West Road, Shanghai, 200040, P.R. China
| | - Jian-Long Guan
- Department of Rheumatology and Immunology, Huadong Hospital affiliated with Fudan University, #221 Yan'an West Road, Shanghai, 200040, P.R. China.
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20
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Kang H, Sun H, Yang Y, Tuong ZK, Shu M, Wei Y, Zhang Y, Yu D, Tao Y. Autoimmune uveitis in Behçet's disease and Vogt-Koyanagi-Harada disease differ in tissue immune infiltration and T cell clonality. Clin Transl Immunology 2023; 12:e1461. [PMID: 37720629 PMCID: PMC10503407 DOI: 10.1002/cti2.1461] [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: 01/06/2023] [Revised: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023] Open
Abstract
Objectives Non-infectious uveitis is often secondary to systemic autoimmune diseases, with Behçet's disease (BD) and Vogt-Koyanagi-Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD can show similar clinical manifestations, but the underlying immunopathogenesis remains unclear. Methods To understand immune landscapes in inflammatory eye tissues, we performed single-cell RNA paired with T cell receptor (TCR) sequencing of immune cell infiltrates in aqueous humour from six patients with BD (N = 3) and VKHD (N = 3) uveitis patients. Results Although T cells strongly infiltrated in both types of autoimmune uveitis, myeloid cells only significantly presented in BD uveitis but not in VKHD uveitis. Conversely, VKHD uveitis but not BD uveitis showed an overwhelming dominance by CD4+ T cells (> 80%) within the T cell population due to expansion of CD4+ T cell clusters with effector memory (Tem) phenotypes. Correspondingly, VKHD uveitis demonstrated a selective expansion of CD4+ T cell clones which were enriched in pro-inflammatory Granzyme H+ CD4+ Tem cluster and showed TCR and Th1 pathway activation. In contrast, BD uveitis showed a preferential expansion of CD8+ T cell clones in pro-inflammatory Granzyme H+ CD8+ Tem cluster, and pathway activation for cytoskeleton remodelling, cellular adhesion and cytotoxicity. Conclusion Single-cell analyses of ocular tissues reveal distinct landscapes of immune cell infiltration and T-cell clonal expansions between VKHD and BD uveitis. Preferential involvements of pro-inflammatory CD4+ Th1 cells in VKHD and cytotoxic CD8+ T cells in BD suggest a difference in disease immunopathogenesis and can guide precision disease management.
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Affiliation(s)
- Hao Kang
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Hongjian Sun
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yang Yang
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zewen K Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Minglei Shu
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yunbo Wei
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yu Zhang
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Di Yu
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
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21
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Shen C, Fang R, Wang J, Wu N, Wang S, Shu T, Dai J, Feng M, Chen X. Visfatin aggravates transverse aortic constriction-induced cardiac remodelling by enhancing macrophage-mediated oxidative stress in mice. J Cell Mol Med 2023; 27:2562-2571. [PMID: 37584247 PMCID: PMC10468652 DOI: 10.1111/jcmm.17854] [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: 03/28/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Previous studies have reported that visfatin can regulate macrophage polarisation, which has been demonstrated to participate in cardiac remodelling. The aims of this study were to investigate whether visfatin participates in transverse aortic constriction (TAC)-induced cardiac remodelling by regulating macrophage polarisation. First, TAC surgery and angiotensin II (Ang II) infusion were used to establish a mouse cardiac remodelling model, visfatin expression was measured, and the results showed that TAC surgery or Ang II infusion increased visfatin expression in the serum and heart in mice, and phenylephrine or hydrogen peroxide promoted the release of visfatin from macrophages in vitro. All these effects were dose-dependently reduced by superoxide dismutase. Second, visfatin was administered to TAC mice to observe the effects of visfatin on cardiac remodelling. We found that visfatin increased the cross-sectional area of cardiomyocytes, aggravated cardiac fibrosis, exacerbated cardiac dysfunction, further regulated macrophage polarisation and aggravated oxidative stress in TAC mice. Finally, macrophages were depleted in TAC mice to investigate whether macrophages mediate the regulatory effect of visfatin on cardiac remodelling, and the results showed that the aggravating effects of visfatin on oxidative stress and cardiac remodelling were abrogated. Our study suggests that visfatin enhances cardiac remodelling by promoting macrophage polarisation and enhancing oxidative stress. Visfatin may be a potential target for the prevention and treatment of clinical cardiac remodelling.
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Affiliation(s)
- Caijie Shen
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Renyuan Fang
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Jian Wang
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Nan Wu
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Shuangsuang Wang
- Department of CardiologyWenling First People's Hospital, The Affiliated Wenling Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Tian Shu
- Zhejiang University School of MedicineHangzhouChina
| | - Jiating Dai
- Health Science Center, Ningbo UniversityNingboChina
| | - Mingjun Feng
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Xiaomin Chen
- Department of Cardiovascular MedicineThe First Affliated Hospital of Ningbo University, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
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Al-Obeidi AF, Nowatzky J. Immunopathogenesis of Behçet's disease. Clin Immunol 2023; 253:109661. [PMID: 37295542 PMCID: PMC10484394 DOI: 10.1016/j.clim.2023.109661] [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: 04/30/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Behçet's disease (BD) is a multi-system inflammatory disorder with vasculitic features. It does not suit any of the current pathogenesis-driven disease classifications well, a unifying concept of its pathogenesis is not unanimously conceivable at present, and its etiology is obscure. Still, evidence from immunogenetic and other studies supports the notion of a complex-polygenic disease with robust innate effector responses, reconstitution of regulatory T cells upon successful treatment, and first clues to the role of an, as of yet, underexplored adaptive immune system and its antigen recognition receptors. Without an attempt to be comprehensive, this review aims to collect and organize impactful parts of this evidence in a way that allows the reader to appreciate the work done and define the efforts needed now. The focus is on literature and notions that drove the field into new directions, whether recent or more remote.
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Affiliation(s)
- Arshed F Al-Obeidi
- New York University Grossman School of Medicine, Department of Medicine, New York, NY, USA
| | - Johannes Nowatzky
- New York University Grossman School of Medicine, Department of Medicine, New York, NY, USA; New York University Grossman School of Medicine, Department of Pathology, USA; New York University Grossman School of Medicine, Department of Medicine, Division of Rheumatology, NYU Langone Ocular Rheumatology Program, New York, NY, USA; New York University Grossman School of Medicine, Department of Medicine, Division of Rheumatology, NYU Langone Center for Behçet's Disease, New York, NY, USA.
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23
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Yi Z, Geng S, Li L. Comparative analyses of monocyte memory dynamics from mice to humans. Inflamm Res 2023; 72:1539-1549. [PMID: 37453943 PMCID: PMC10499745 DOI: 10.1007/s00011-023-01762-8] [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: 04/25/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Innate monocytes can adopt dynamic "memory" states ranging from low-grade inflammation to pathogenic exhaustion, dependent upon signal strength and history of challenges. Low-grade inflammatory monocytes facilitate the pathogenesis of chronic inflammatory diseases, while exhausted monocytes drive the pathogenesis of severe sepsis. Although clinical and basic studies suggest the conservation of key features of exhausted monocytes from human and murine sepsis, systems analyses of monocyte exhaustion among human and murine monocytes are lacking. METHODS We performed cross examination of septic monocytes scRNAseq data recently collected from human sepsis patients as well as experimental septic mice, in reference to monocytes experimentally exhausted in vitro. Furthermore, we performed pseudo-time analyses of in vitro programmed monocytes following prolonged challenges causing either low-grade inflammation or exhaustion. Additional comparative analyses of low-grade inflammatory monocytes were performed with scRNAseq data from selected human patients with chronic low-grade inflammatory diseases. RESULTS Our systems analyses reveal key features of monocyte exhaustion including reduced differentiation, pathogenic inflammation and immune suppression that are highly conserved in human and murine septic monocytes, and captured by in vitro experimental exhaustion. Pseudo-time analyses reveal that monocytes initially transition into a less-differentiated state with proliferative potential. The expansion of proliferative monocytes can be observed not only in experimentally challenged monocytes, but also in tissues of murine sepsis and human septic blood. We observed that monocytes similarly transition into the less-differentiated state when challenged with a subclinical dose endotoxin under chronic inflammatory conditions. Instead of being exhausted, monocytes with prolonged challenges with super-low dose endotoxin bifurcate into the low-grade inflammatory immune-enhancing or the chemotactic/adhesive state, often see in atherosclerosis or auto-immune diseases. CONCLUSIONS Key features of monocyte memory dynamics are identified and conserved in human and murine monocytes, which can be captured by prolonged challenges of innate signals with varying signal strength.
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Affiliation(s)
- Ziyue Yi
- Department of Biological Sciences, Virginia Tech, 149 Life Science 1 Bldg, Blacksburg, VA, 24061-0910, USA
| | - Shuo Geng
- Department of Biological Sciences, Virginia Tech, 149 Life Science 1 Bldg, Blacksburg, VA, 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 149 Life Science 1 Bldg, Blacksburg, VA, 24061-0910, USA.
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Papagiannopoulos OD, Kourou K, Papaloukas C, Karanasiou GS, van de Werken HJG, Mueller YM, Katsikis PD, Herrero-Saboya D, Fotiadis DI. Classification of Inflammation of Unknown Origin patients based on RNA-seq and SomaScan data. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083327 DOI: 10.1109/embc40787.2023.10340537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
A preliminary analysis was conducted on data acquired from RNA sequencing and SomaScan platforms, for the classification of patients with Inflammation of Unknown Origin. To this end, a multimodal data integration approach was designed, by combining the two platforms, in order to assess the potentiality of learning estimators, using the differentially expressed features from the independent profiling experiments of both platforms. The classification framing was the differentiation of Inflammation of Unknown Origin patients against a multitude of Systemic Autoinflammatory disease patients. Separate false discovery rate analyses were performed on each dataset to extract statistically significant features between the two designated sample groups. Genomic analysis managed higher overall classification metrics compared to proteomic analysis, averaging an ~19% increase overall metrics and classifiers, with a ~0.07% increase in standard error. The multimodal data integration approach achieved similar results to the individual platforms' analyses. More specifically, it managed the same classification accuracy, sensitivity, and specificity scores as the best individual analysis, with the simple Logistic Regression estimator.Clinical Relevance- This study highlights the advantage of exploiting RNA sequencing data to identify potential Inflammation of Unknown Origin disease specific biomarkers, even against other Systemic Autoinflammatory diseases. These findings are further emphasized given the non-apparent clinical discrepancy between Inflammation of Unknown Origin and other Systemic Autoinflammatory diseases.
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25
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Constantin AM, Mihu CM, Boşca AB, Melincovici CS, Mărginean MV, Jianu EM, Onofrei MM, Micu CM, Alexandru BC, Sufleţel RT, Moldovan IM, Coneac A, Crintea A, Ştefan RA, Ştefan PA, Djouini A, Şovrea AS. Short histological kaleidoscope - recent findings in histology. Part III. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY = REVUE ROUMAINE DE MORPHOLOGIE ET EMBRYOLOGIE 2023; 64:115-133. [PMID: 37518868 PMCID: PMC10520383 DOI: 10.47162/rjme.64.2.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
The paper provides an overview of the current understanding of different cells' biology (e.g., keratinocytes, Paneth cells, myoepithelial cells, myofibroblasts, chondroclasts, monocytes, atrial cardiomyocytes), including their origin, structure, function, and role in disease pathogenesis, and of the latest findings in the medical literature concerning the brown adipose tissue and the juxtaoral organ of Chievitz.
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Affiliation(s)
- Anne Marie Constantin
- Discipline of Histology, Department of Morphological Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania;
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26
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Banos A, Thomas K, Garantziotis P, Filia A, Malissovas N, Pieta A, Nikolakis D, Panagiotopoulos AG, Chalkia A, Petras D, Bertsias G, Boumpas DT, Vassilopoulos D. The genomic landscape of ANCA-associated vasculitis: Distinct transcriptional signatures, molecular endotypes and comparison with systemic lupus erythematosus. Front Immunol 2023; 14:1072598. [PMID: 37051253 PMCID: PMC10083368 DOI: 10.3389/fimmu.2023.1072598] [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: 10/17/2022] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionAnti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAVs) present with a complex phenotype and are associated with high mortality and multi-organ involvement. We sought to define the transcriptional landscape and molecular endotypes of AAVs and compare it to systemic lupus erythematosus (SLE).MethodsWe performed whole blood mRNA sequencing from 30 patients with AAV (granulomatosis with polyangiitis/GPA and microscopic polyangiitis/MPA) combined with functional enrichment and network analysis for aberrant pathways. Key genes and pathways were validated in an independent cohort of 18 AAV patients. Co-expression network and hierarchical clustering analysis, identified molecular endotypes. Multi-level transcriptional overlap analysis to SLE was based on our published data from 142 patients.ResultsWe report here that “Pan-vasculitis” signature contained 1,982 differentially expressed genes, enriched in leukocyte differentiation, cytokine signaling, type I and type II IFN signaling and aberrant B-T cell immunity. Active disease was characterized by signatures linked to cell cycle checkpoints and metabolism pathways, whereas ANCA-positive patients exhibited a humoral immunity transcriptional fingerprint. Differential expression analysis of GPA and MPA yielded an IFN-g pathway (in addition to a type I IFN) in the former and aberrant expression of genes related to autophagy and mRNA splicing in the latter. Unsupervised molecular taxonomy analysis revealed four endotypes with neutrophil degranulation, aberrant metabolism and B-cell responses as potential mechanistic drivers. Transcriptional perturbations and molecular heterogeneity were more pronounced in SLE. Molecular analysis and data-driven clustering of AAV uncovered distinct transcriptional pathways that could be exploited for targeted therapy.DiscussionWe conclude that transcriptomic analysis of AAV reveals distinct endotypes and molecular pathways that could be targeted for therapy. The AAV transcriptome is more homogenous and less fragmented compared to the SLE which may account for its superior rates of response to therapy.
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Affiliation(s)
- Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Konstantinos Thomas
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Garantziotis
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Department Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nikolaos Malissovas
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Antigone Pieta
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Rheumatology and Clinical Immunology Unit, 4th Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Dimitrios Nikolakis
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Amsterdam Institute for Gastroenterology Endocrinology and Metabolism, Department of Gastroenterology, Academic Medical Center, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology & Immunology Center (ARC), Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection & Immunity, Department of Experimental Immunology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Alexandros G. Panagiotopoulos
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aglaia Chalkia
- Nephrology Department, General Hospital of Athens Ippokrateio, Athens, Greece
| | - Dimitrios Petras
- Nephrology Department, General Hospital of Athens Ippokrateio, Athens, Greece
| | - George Bertsias
- Department of Rheumatology and Clinical Immunology, University Hospital of Heraklion, Medical School, University of Crete, Heraklion, Greece
- Department of Immunity, Institute of Molecular Biology and Biotechnology-Foundation of Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Rheumatology and Clinical Immunology Unit, 4th Department of Internal Medicine, Attikon University Hospital, Athens, Greece
- Joint Academic Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Vassilopoulos
- Clinical Immunology- Rheumatology Unit, 2nd Department of Medicine and Laboratory, General Hospital of Athens Ippokrateio, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Joint Academic Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- *Correspondence: Dimitrios Vassilopoulos,
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Beignon AS, Galeotti C, Menager MM, Schvartz A. Trained immunity as a possible newcomer in autoinflammatory and autoimmune diseases pathophysiology. Front Med (Lausanne) 2023; 9:1085339. [PMID: 36743677 PMCID: PMC9896524 DOI: 10.3389/fmed.2022.1085339] [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: 10/31/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Autoimmune disorders have been well characterized over the years and many pathways-but not all of them-have been found to explain their pathophysiology. Autoinflammatory disorders, on the other hand, are still hiding most of their molecular and cellular mechanisms. During the past few years, a newcomer has challenged the idea that only adaptive immunity could display memory response. Trained immunity is defined by innate immune responses that are faster and stronger to a second stimulus than to the first one, being the same or not. In response to the trained immunity inducer, and through metabolic and epigenetic changes of hematopoietic stem and progenitor cells in the bone marrow that are transmitted to their cellular progeny (peripheral trained immunity), or directly of tissue-resident cells (local innate immunity), innate cells responsiveness and functions upon stimulation are improved in the long-term. Innate immunity can be beneficial, but it could also be detrimental when maladaptive. Here, we discuss how trained immunity could contribute to the physiopathology of autoimmune and autoinflammatory diseases.
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Affiliation(s)
- Anne-Sophie Beignon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases/Infectious Diseases Models and Innovative Technologies (IMVA-HB/IDMIT), U1184, Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Caroline Galeotti
- Department of Pediatric Rheumatology, Reference Center for AutoInflammatory Diseases and Amyloidosis (CEREMAIA), Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, France
| | - Mickael M. Menager
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases/Infectious Diseases Models and Innovative Technologies (IMVA-HB/IDMIT), U1184, Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Adrien Schvartz
- Department of Pediatric Rheumatology, Reference Center for AutoInflammatory Diseases and Amyloidosis (CEREMAIA), Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, France,*Correspondence: Adrien Schvartz,
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Zhang W, Chen Y, Pei H. C1q and central nervous system disorders. Front Immunol 2023; 14:1145649. [PMID: 37033981 PMCID: PMC10076750 DOI: 10.3389/fimmu.2023.1145649] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
C1q is a crucial component of the complement system, which is activated through the classical pathway to perform non-specific immune functions, serving as the first line of defense against pathogens. C1q can also bind to specific receptors to carry out immune and other functions, playing a vital role in maintaining immune homeostasis and normal physiological functions. In the developing central nervous system (CNS), C1q functions in synapse formation and pruning, serving as a key player in the development and homeostasis of neuronal networks in the CNS. C1q has a close relationship with microglia and astrocytes, and under their influence, C1q may contribute to the development of CNS disorders. Furthermore, C1q can also have independent effects on neurological disorders, producing either beneficial or detrimental outcomes. Most of the evidence for these functions comes from animal models, with some also from human specimen studies. C1q is now emerging as a promising target for the treatment of a variety of diseases, and clinical trials are already underway for CNS disorders. This article highlights the role of C1q in CNS diseases, offering new directions for the diagnosis and treatment of these conditions.
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Affiliation(s)
- Wenjie Zhang
- Department of Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of General Practice, Xingyang Sishui Central Health Center, Zhengzhou, China
| | - Yuan Chen
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Pei
- Department of Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Hui Pei,
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Liu Y, Bao D, Meng M, Lu L, Zhu H. The proportion of C1q-high and ISG15-high monocytes in the skin of patients with Behçet disease. Front Pharmacol 2023; 14:1110741. [PMID: 36959847 PMCID: PMC10028182 DOI: 10.3389/fphar.2023.1110741] [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: 11/29/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Behçet disease (BD) is a chronic systemic vasculitis that is clinically characterized by recurrent oral ulcers, genital ulcers, uveitis, and skin lesions. Here, we conducted bulk RNA-seq of skin samples from 4 BD patients and 4 normal controls (NCs). A total of 260 differentially expressed genes (DEGs), including 99 upregulated and 161 downregulated genes, were detected in the skin lesions of BD patients compared to NCs. These DEGs were mainly enriched in the following biological processes: the activation and migration of immune cells, the release of proinflammatory factors, and the IFN-γ signaling pathway. The top upregulated DEGs were CXCL10, CXCL9, FCGR3A, GBP5, GBP4, LILRB2, ADIPOQ, PLIN1, SLC43A2, and MYO1G. Using the deconvolution method CIBERSORT, we analyzed the immune cells subtypes in the skin of BD by integrating the single cell RNA-seq data from PBMC (GSE198616) and bulk RNA-seq data of skin. There was a higher proportion of C1q+ and ISG15 + monocyte subtypes in skin of BD. IHC staining of CD14 and CD16 showed that the monocyte number increased in the skin of BD. IF staining confirmed there was a higher proportion of the C1Q + Mono and ISG15 + Mono subsets in the skin of BD patients. Moreover, we analyzed the average expression level of the top upregulated genes in immune cell types found in PBMC from BD patients and NCs. Almost all the top upregulated genes expressed in monocytes. CXCL10 was specifically expressed in ISG15 + monocyte, and GBP5, GBP4 and IFI44L were expressed more strongly in ISG15 + monocytes. LILRB2 was expressed more strongly in CD16+ monocytes and C1Q + monocytes. In conclusion, our study identified that the IFN-γ pathway was activated in skin of BD and the proportion of C1q+ and ISG15 + monocyte subtype increased in the skin of BD.
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Affiliation(s)
- Yangtengyu Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China
| | - Ding Bao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China
| | - Meng Meng
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, China
| | - Lixia Lu
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, China
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China
- *Correspondence: Honglin Zhu,
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Deng Y, Zhang Y, Cai T, Wang Q, Zhang W, Chen Z, Luo X, Su G, Yang P. Transcriptomic profiling of iris tissue highlights LCK signaling and T cell-mediated immunity in Behcet's uveitis. J Autoimmun 2022; 133:102920. [PMID: 36191467 DOI: 10.1016/j.jaut.2022.102920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 12/13/2022]
Abstract
Uveitis is the most common form of ocular lesions in Behcet's disease, severely affecting visual function. Molecular pathological changes of ocular lesions in patients with Behcet's uveitis (BU) are largely unknown. In this study, we performed the first comprehensive transcriptomic profiling of iris specimens from BU patients and healthy donors to provide an insight into intraocular immunopathogenesis. The mRNA sequencing identified 1633 differentially expressed genes (DEGs) between the BU group and healthy controls. GO functional enrichment analysis on DEGs showed that T cell activation was the most significantly enriched biological process. KEGG analysis of DEGs also revealed several prominently enriched T cell-related pathways, including the T cell receptor signaling pathway, Th17 cell differentiation, and Th1 and Th2 cell differentiation. The lymphocyte-specific protein tyrosine kinase (LCK) was identified as the key hub gene in the protein interaction network of DEGs. Western blot analysis further showed increased expression of active LCK in the BU group, suggesting activation of LCK signaling. Using publicly accessible single-cell RNA-sequencing data of the healthy iris, LCK was found to be expressed in clusters of activated T cells but not in other iris cell clusters, suggesting an overt association between LCK upregulation and T cell-mediated immune dysregulation. Additionally, 16 drugs were predicted to be potential inhibitors of LCK. Overall, these findings not only highlighted the central role of T cell-mediated immunity and previously unreported LCK signaling in intraocular immunopathogenesis but also revealed the potential value of LCK as a new therapeutic target for BU patients.
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Affiliation(s)
- Yang Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Yinan Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, PR China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Tao Cai
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Wanyun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Zhijun Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Xiang Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, PR China.
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Zeng L, Yang K, Zhang T, Zhu X, Hao W, Chen H, Ge J. Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review. J Autoimmun 2022; 133:102919. [PMID: 36242821 DOI: 10.1016/j.jaut.2022.102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/07/2022]
Abstract
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies or sensitized lymphocytes to its own tissues to cause an immune response. Immune disorders caused by autoimmunity can mediate autoimmune diseases. Autoimmune diseases have complicated pathogenesis due to the many types of cells involved, and the mechanism is still unclear. The emergence of single-cell research technology can solve the problem that ordinary transcriptome technology cannot be accurate to cell type. It provides unbiased results through independent analysis of cells in tissues and provides more mRNA information for identifying cell subpopulations, which provides a novel approach to study disruption of immune tolerance and disturbance of pro-inflammatory pathways on a cellular basis. It may fundamentally change the understanding of molecular pathways in the pathogenesis of autoimmune diseases and develop targeted drugs. Single-cell transcriptome sequencing (scRNA-seq) has been widely applied in autoimmune diseases, which provides a powerful tool for demonstrating the cellular heterogeneity of tissues involved in various immune inflammations, identifying pathogenic cell populations, and revealing the mechanism of disease occurrence and development. This review describes the principles of scRNA-seq, introduces common sequencing platforms and practical procedures, and focuses on the progress of scRNA-seq in 41 autoimmune diseases, which include 9 systemic autoimmune diseases and autoinflammatory diseases (rheumatoid arthritis, systemic lupus erythematosus, etc.) and 32 organ-specific autoimmune diseases (5 Skin diseases, 3 Nervous system diseases, 4 Eye diseases, 2 Respiratory system diseases, 2 Circulatory system diseases, 6 Liver, Gallbladder and Pancreas diseases, 2 Gastrointestinal system diseases, 3 Muscle, Bones and joint diseases, 3 Urinary system diseases, 2 Reproductive system diseases). This review also prospects the molecular mechanism targets of autoimmune diseases from the multi-molecular level and multi-dimensional analysis combined with single-cell multi-omics sequencing technology (such as scRNA-seq, Single cell ATAC-seq and single cell immune group library sequencing), which provides a reference for further exploring the pathogenesis and marker screening of autoimmune diseases and autoimmune inflammatory diseases in the future.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Tianqing Zhang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaofei Zhu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China; Hunan Academy of Chinese Medicine, Changsha, China.
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Wu X, Wang Z, Shi J, Yu X, Li C, Liu J, Zhang F, Chen H, Zheng W. Macrophage polarization toward M1 phenotype through NF-κB signaling in patients with Behçet’s disease. Arthritis Res Ther 2022; 24:249. [PMCID: PMC9635113 DOI: 10.1186/s13075-022-02938-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
Background Macrophages are key innate immune cells implicated in the pathogenesis of Behçet’s disease (BD), and macrophage polarization plays a pivotal role in inflammatory response. This study aimed to investigate the role of BD serum on the phenotypes and functions of macrophage polarization. Methods BD or HC serum-treated human monocyte-derived macrophages (HMDMs) were examined M1/M2 phenotypes using flow cytometry and ELISA. The phagocytic capacity of HMDMs and CD4+T cell differentiation facilitated by HMDMs were measured by flow cytometry. Transcriptome analysis of BD and HC serum-stimulated HMDMs was conducted to identify differentially expressed genes. NF-κB signaling was examined using western blot to explore the mechanism of macrophage polarization induced by BD serum. Results BD serum-treated macrophages expressed a higher level of CD86, IL-12, and TNF-α and a lower level of CD163, which were compatible with the M1-like phenotype. Furthermore, BD serum-treated macrophages showed enhanced phagocytic capacity and promoted more Th1 cell differentiation. Sixty-one differentially expressed genes were identified between BD and HC serum-treated macrophages and were enriched in NF-κB signaling. BD serum-treated macrophages showed upregulated p-p65 and downregulated IκBα, and NF-κB inhibitor attenuated BD serum-stimulated M1-like phenotype. Conclusions BD serum promoted macrophage polarization toward a proinflammatory M1-like phenotype through NF-κB signaling and potentially facilitated inflammation in BD. M1 polarized macrophages may be a potential therapeutic target for BD. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02938-z.
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Affiliation(s)
- Xiuhua Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China ,grid.412645.00000 0004 1757 9434Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, 300052 China
| | - Zhimian Wang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Jing Shi
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China ,grid.413087.90000 0004 1755 3939Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
| | - Xin Yu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Chaoran Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Jinjing Liu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Fengchun Zhang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Hua Chen
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
| | - Wenjie Zheng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, 100730 China
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