1
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [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: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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2
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Chen X, Wu Y, Jia S, Zhao M. Fibroblast: A Novel Target for Autoimmune and Inflammatory Skin Diseases Therapeutics. Clin Rev Allergy Immunol 2024:10.1007/s12016-024-08997-1. [PMID: 38940997 DOI: 10.1007/s12016-024-08997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Fibroblasts are crucial components of the skin structure. They were traditionally believed to maintain the skin's structure by producing extracellular matrix and other elements. Recent research illuminated that fibroblasts can respond to external stimuli and exhibit diverse functions, such as the secretion of pro-inflammatory factors, adipogenesis, and antigen presentation, exhibiting remarkable heterogeneity and plasticity. This revelation positions fibroblasts as active contributors to the pathogenesis of skin diseases, challenging the traditional perspective that views fibroblasts solely as structural entities. Based on their diverse functions, fibroblasts can be categorized into six subtypes: pro-inflammatory fibroblasts, myofibroblasts, adipogenic fibroblasts, angiogenic fibroblasts, mesenchymal fibroblasts, and antigen-presenting fibroblasts. Cytokines, metabolism, and epigenetics regulate functional abnormalities in fibroblasts. The dynamic changes fibroblasts exhibit in different diseases and disease states warrant a comprehensive discussion. We focus on dermal fibroblasts' aberrant manifestations and pivotal roles in inflammatory and autoimmune skin diseases, including psoriasis, vitiligo, lupus erythematosus, scleroderma, and atopic dermatitis, and propose targeting aberrantly activated fibroblasts as a potential therapeutic strategy for inflammatory and autoimmune skin diseases.
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Affiliation(s)
- Xiaoyun Chen
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yutong Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Sujie Jia
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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3
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Nishide M, Shimagami H, Kumanogoh A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol 2024:10.1038/s41577-024-01043-3. [PMID: 38914790 DOI: 10.1038/s41577-024-01043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/26/2024]
Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
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Affiliation(s)
- Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hiroshi Shimagami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
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4
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Sol S, Boncimino F, Todorova K, Mandinova A. Unraveling the Functional Heterogeneity of Human Skin at Single-Cell Resolution. Hematol Oncol Clin North Am 2024:S0889-8588(24)00050-9. [PMID: 38839486 DOI: 10.1016/j.hoc.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The skin consists of several cell populations, including epithelial, immune, and stromal cells. Recently, there has been a significant increase in single-cell RNA-sequencing studies, contributing to the development of a consensus Human Skin Cell Atlas. The aim is to understand skin biology better and identify potential therapeutic targets. The present review utilized previously published single-cell RNA-sequencing datasets to explore human skin's cellular and functional heterogeneity. Additionally, it summarizes the functional significance of newly identified cell subpopulations in processes such as wound healing and aging.
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Affiliation(s)
- Stefano Sol
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Fabiana Boncimino
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kristina Todorova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Anna Mandinova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 7 Cambridge Center, MA 02142, USA; Harvard Stem Cell Institute, 7 Divinity Avenue Cambridge, MA 02138, USA.
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5
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Balaji U, Rodríguez-Alcázar J, Balasubramanian P, Smitherman C, Baisch J, Pascual V, Gu J. Ragas: integration and enhanced visualization for single cell subcluster analysis. Bioinformatics 2024; 40:btae366. [PMID: 38867706 PMCID: PMC11209553 DOI: 10.1093/bioinformatics/btae366] [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: 12/26/2023] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
SUMMARY Subcluster analysis is a powerful means to improve clustering and characterization of single cell RNA-Seq data. However, there are no existing tools to systematically integrate results from multiple subclusters, which creates hurdles for accurate data quantification, visualization, and interpretation in downstream analysis. To address this issue, we developed Ragas, an R package that integrates multi-level subclustering objects for streamlined analysis and visualization. A new data structure was implemented to seamlessly connect and assemble miscellaneous single cell analyses from different levels of subclustering, along with several new or enhanced visualization functions. Moreover, a re-projection algorithm was developed to integrate nearest-neighbor graphs from multiple subclusters in order to maximize their separability on the combined cell embeddings, which significantly improved the presentation of rare and homogeneous subpopulations. AVAILABILITY AND IMPLEMENTATION The Ragas package and its documentation can be accessed through https://github.com/jig4003/Ragas and its source code is also available at https://zenodo.org/records/11244921.
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Affiliation(s)
- Uthra Balaji
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Juan Rodríguez-Alcázar
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Preetha Balasubramanian
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Cynthia Smitherman
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Jeanine Baisch
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Virginia Pascual
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
| | - Jinghua Gu
- Drukier Institute for Children’s Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, United States
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6
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Hu Z, Zheng M, Guo Z, Zhou W, Zhou W, Yao N, Zhang G, Lu Q, Zhao M. Single-cell sequencing reveals distinct immune cell features in cutaneous lesions of pemphigus vulgaris and bullous pemphigoid. Clin Immunol 2024; 263:110219. [PMID: 38631594 DOI: 10.1016/j.clim.2024.110219] [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: 01/24/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Bullous pemphigoid (BP) and pemphigus vulgaris (PV) are two common subtypes of autoimmune bullous disease (AIBD). The key role of circulating autoreactive immune cells contributing to skin damage of AIBD has been widely recognized. Nevertheless, the immune characteristics in cutaneous lesions remain unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell VDJ sequencing (scRNA-seq) to generate transcriptional profiles for cells and T/B cell clonetype in skin lesions of BP and PV. We found that the proportions of NK&T, macrophages/ dendritic cells, B cells, and mast cells increased in BP and PV lesions. Then, BP and PV cells constituted over 75% of all myeloid cell subtypes, CD4+ T cell subtypes and CD8+ T cell subtypes. Strikingly, CD8+ Trm was identified to be expanded in PV, and located in the intermediate state of the pseudotime trajectory from CD8+ Tm to CD8+ Tem. Interestingly, CD8+ Tem and CD4+ Treg highly expressed exhaustion-related genes, especially in BP lesions. Moreover, the enhanced cell communication between stromal cells and immune cells like B cells and macrophages/ dendritic cells was also identified in BP and PV lesions. Finally, clone expansion was observed in T cells of BP and PV compared with HC, while CD8+ Trm represented the highest ratio of hyperexpanded TCR clones among all T cell subtypes. Our study generally depicts a large and comprehensive single-cell landscape of cutaneous lesions and highlights immune cell features in BP and PV. This offers potential research targets for further investigation.
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Affiliation(s)
- Zhi Hu
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Meiling Zheng
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Ziyu Guo
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Wenhui Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Wenyu Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Nan Yao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Guiying Zhang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China.
| | - Qianjin Lu
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China.
| | - Ming Zhao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China.
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7
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Zhou Y, Cao T, Li Z, Qiao H, Dang E, Shao S, Wang G. Fibroblasts in immune-mediated inflammatory diseases: The soil of inflammation. Clin Immunol 2024; 258:109849. [PMID: 38008146 DOI: 10.1016/j.clim.2023.109849] [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: 07/09/2023] [Revised: 10/11/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
As one of the most abundant stromal cells, fibroblasts are primarily responsible for the production and remodeling of the extracellular matrix. Traditionally, fibroblasts have been viewed as quiescent cells. However, recent advances in multi-omics technologies have demonstrated that fibroblasts exhibit remarkable functional diversity at the single-cell level. Additionally, fibroblasts are heterogeneous in their origins, tissue locations, and transitions with stromal cells. The dynamic nature of fibroblasts is further underscored by the fact that disease stages can impact their heterogeneity and behavior, particularly in immune-mediated inflammatory diseases such as psoriasis, inflammatory bowel diseases, and rheumatoid arthritis, etc. Fibroblasts can actively contribute to the disease initiation, progression, and relapse by responding to local microenvironmental signals, secreting downstream inflammatory factors, and interacting with immune cells during the pathological process. Here we focus on the development, plasticity, and heterogeneity of fibroblasts in inflammation, emphasizing the need for a developmental and dynamic perspective on fibroblasts.
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Affiliation(s)
- Yifan Zhou
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Tianyu Cao
- Department of Dermatology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhiguo Li
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Hongjiang Qiao
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Erle Dang
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Shuai Shao
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China.
| | - Gang Wang
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China.
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8
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Cai M, Qin Y, Wan A, Jin H, Tang J, Chen Z. COX5A as a potential biomarker for disease activity and organ damage in lupus. Clin Exp Med 2023; 23:4745-4756. [PMID: 37891386 DOI: 10.1007/s10238-023-01215-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: 06/04/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease with limited therapeutic targets or clinical outcome predictors. This study aimed to gain more insights into the underlying immunological pathways and prognostic biomarkers of SLE. Integrated analyses of RNA-seq data from 64 SLE and 62 healthy controls, examining 27 immune cell types to explore the key pathways and driver genes in SLE pathogenesis. Single-cell RNA sequencing data from the skin and kidney were used to determine the association of COX5A expression with organ damage. The associations of COX5A with SLE phenotypes were further evaluated in two independent cohorts, and receiver operating characteristic (ROC) curves were constructed to assess the value of COX5A as a biomarker for disease activity and organ damage in SLE. We found that oxidative phosphorylation (OXPHOS) is the most significantly altered metabolic pathway in SLE, especially in effector T cells. Notably, we identified an OXPHOS-related enzyme, COX5A, whose expression was significantly higher in effector T cells than in naïve T cells and showed associations with disease activity, organ damage, and steroid treatment of SLE. Furthermore, ROC curves showed that COX5A is a robust biomarker for disease activity, kidney involvement, and new-onset skin lesions, with the area under the curve (AUC) values of 0.880, 0.801, and 0.805, respectively. Our results identified the OXPHOS signature as a prominent feature in SLE T cells, and COX5A as a potential candidate biomarker for disease activity and organ damage in SLE.
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Affiliation(s)
- Minglong Cai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yi Qin
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - An Wan
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Huizhi Jin
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Jun Tang
- Department of Dermatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Zhu Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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9
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Wang L, Wang B, Kou E, Du L, Zhu Y. New insight into the role of fibroblasts in the epithelial immune microenvironment in the single-cell era. Front Immunol 2023; 14:1259515. [PMID: 37809065 PMCID: PMC10556469 DOI: 10.3389/fimmu.2023.1259515] [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: 07/16/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
The skin is exposed to environmental challenges and contains heterogeneous cell populations such as epithelial cells, stromal cells, and skin-resident immune cells. As the most abundant type of stromal cells, fibroblasts have been historically considered silent observers in the immune responses of the cutaneous epithelial immune microenvironment (EIME), with little research conducted on their heterogeneity and immune-related functions. Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have overcome the limitations of bulk RNA sequencing and help recognize the functional and spatial heterogeneity of fibroblasts, as well as their crosstalk with other types of cells in the cutaneous EIME. Recently, emerging single-cell sequencing data have demonstrated that fibroblasts notably participate in the immune responses of the EIME and impact the initiation and progression of inflammatory skin diseases. Here, we summarize the latest advances in the role of fibroblasts in the cutaneous EIME of inflammatory skin diseases and discuss the distinct functions and molecular mechanisms of activated fibroblasts in fibrotic skin diseases and non-fibrotic inflammatory skin diseases. This review help unveil the multiple roles of fibroblasts in the cutaneous EIME and offer new promising therapeutic strategies for the management of inflammatory skin diseases by targeting fibroblasts or the fibroblast-centered EIME.
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Affiliation(s)
| | | | | | - Lin Du
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai, China
| | - Yuanjie Zhu
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai, China
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10
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Zhang C, Cai S, Li Y, Xu X, Liu Y, Qiao H, Wong CK, Wu G, Jin H, Gao X. Elevation of Metrnβ and Its Association with Disease Activity in Systemic Lupus Erythematosus. Int J Mol Sci 2023; 24:13607. [PMID: 37686413 PMCID: PMC10563073 DOI: 10.3390/ijms241713607] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an auto-immune disease, the pathogenesis of which remains to be fully addressed. Metrnβ is a novel cytokine involved in the pathogenesis of inflammatory disease, but its regulatory roles in SLE are unclear. We aimed to comprehensively investigate the clinical value of Metrnβ in SLE. A massive elevation of circulating Metrnβ levels was observed in SLE, and patients with an active phase displayed higher Metrnβ concentrations than those with inactive phases. Additionally, we found that Metrnβ expression was positively correlated with clinical indicators of SLE. Longitudinal cytokine and chemokine profiles revealed a disturbed immune response in SLE, with high activity profiles displayed severe pathogenic inflammation, and a positive correlation of the serum Metrnβ with CXCL9, IL10, IL18 and IL1RA was observed as well. Moreover, Metrnβ expressions exhibited an inverse correlation with Treg and B10. Of note, a significant decrease of ILC2 was found in SLE, and there was a negative correlation of Metrnβ with ILC2 as well. Further ROC analysis showed that the area under the curve (AUC) for Metrnβ was 0.8250 (95% CI: 0.7379-0.9121), with a cutoff value of 1131 pg/mL to effectively distinguish SLE patients from healthy controls. Our study herein demonstrated for the first time that Metrnβ values were increased and were immunologically correlated with SLE activity, which could be utilized as an alternative biomarker for the early identification and predicting of the immuno-response of SLE.
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Affiliation(s)
- Chen Zhang
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Shijie Cai
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, China
| | - Ying Li
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Xiaoyan Xu
- Department of Rheumatology, Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Yonghui Liu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Huaiyu Qiao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Chun-Kwok Wong
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, China
| | - Hui Jin
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xun Gao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, China
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11
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Little AJ, Chen PM, Vesely MD, Khan RN, Fiedler J, Garritano J, Maisha FI, McNiff JM, Craft J. HIF-1 regulates pathogenic cytotoxic T cells in lupus skin disease. JCI Insight 2023; 8:e166076. [PMID: 37526979 PMCID: PMC10543720 DOI: 10.1172/jci.insight.166076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
Cutaneous lupus erythematosus (CLE) is a disfiguring autoimmune skin disease characterized by an inflammatory infiltrate rich in T cells, which are strongly implicated in tissue damage. How these cells adapt to the skin environment and promote tissue inflammation and damage is not known. In lupus nephritis, we previously identified an inflammatory gene program in kidney-infiltrating T cells that is dependent on HIF-1, a transcription factor critical for the cellular and developmental response to hypoxia as well as inflammation-associated signals. In our present studies using a mouse model of lupus skin disease, we find that skin-infiltrating CD4+ and CD8+ T cells also express high levels of HIF-1. Skin-infiltrating T cells demonstrated a strong cytotoxic signature at the transcript and protein levels, and HIF-1 inhibition abrogated skin and systemic diseases in association with decreased T cell cytotoxic activity. We also demonstrate in human CLE tissue that the T cell-rich inflammatory infiltrate exhibited increased amounts of HIF-1 and a cytotoxic signature. Granzyme B-expressing T cells were concentrated at sites of skin tissue damage in CLE, suggesting relevance of this pathway to human disease.
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Affiliation(s)
| | - Ping-Min Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei City, Taiwan
| | | | | | | | | | | | - Jennifer M. McNiff
- Department of Dermatology and
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joe Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Internal Medicine (Rheumatology)
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12
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Strobl J, Haniffa M. Functional heterogeneity of human skin-resident memory T cells in health and disease. Immunol Rev 2023; 316:104-119. [PMID: 37144705 PMCID: PMC10952320 DOI: 10.1111/imr.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The human skin is populated by a diverse pool of memory T cells, which can act rapidly in response to pathogens and cancer antigens. Tissue-resident memory T cells (TRM ) have been implicated in range of allergic, autoimmune and inflammatory skin diseases. Clonal expansion of cells with TRM properties is also known to contribute to cutaneous T-cell lymphoma. Here, we review the heterogeneous phenotypes, transcriptional programs, and effector functions of skin TRM . We summarize recent studies on TRM formation, longevity, plasticity, and retrograde migration and contextualize the findings to skin TRM and their role in maintaining skin homeostasis and altered functions in skin disease.
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Affiliation(s)
- Johanna Strobl
- Department of DermatologyMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular MedicineViennaAustria
| | - Muzlifah Haniffa
- Wellcome Sanger InstituteCambridgeUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUK
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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13
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Fenton KA, Pedersen HL. Advanced methods and novel biomarkers in autoimmune diseases ‑ a review of the recent years progress in systemic lupus erythematosus. Front Med (Lausanne) 2023; 10:1183535. [PMID: 37425332 PMCID: PMC10326284 DOI: 10.3389/fmed.2023.1183535] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
There are several autoimmune and rheumatic diseases affecting different organs of the human body. Multiple sclerosis (MS) mainly affects brain, rheumatoid arthritis (RA) mainly affects joints, Type 1 diabetes (T1D) mainly affects pancreas, Sjogren's syndrome (SS) mainly affects salivary glands, while systemic lupus erythematosus (SLE) affects almost every organ of the body. Autoimmune diseases are characterized by production of autoantibodies, activation of immune cells, increased expression of pro-inflammatory cytokines, and activation of type I interferons. Despite improvements in treatments and diagnostic tools, the time it takes for the patients to be diagnosed is too long, and the main treatment for these diseases is still non-specific anti-inflammatory drugs. Thus, there is an urgent need for better biomarkers, as well as tailored, personalized treatment. This review focus on SLE and the organs affected in this disease. We have used the results from various rheumatic and autoimmune diseases and the organs involved with an aim to identify advanced methods and possible biomarkers to be utilized in the diagnosis of SLE, disease monitoring, and response to treatment.
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Affiliation(s)
- Kristin Andreassen Fenton
- UiT The Arctic University of Norway, Tromsø, Norway
- Centre of Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
| | - Hege Lynum Pedersen
- UiT The Arctic University of Norway, Tromsø, Norway
- Centre of Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
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14
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Cheru N, Hafler DA, Sumida TS. Regulatory T cells in peripheral tissue tolerance and diseases. Front Immunol 2023; 14:1154575. [PMID: 37197653 PMCID: PMC10183596 DOI: 10.3389/fimmu.2023.1154575] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
Maintenance of peripheral tolerance by CD4+Foxp3+ regulatory T cells (Tregs) is essential for regulating autoreactive T cells. The loss of function of Foxp3 leads to autoimmune disease in both animals and humans. An example is the rare, X-linked recessive disorder known as IPEX (Immune Dysregulation, Polyendocrinopathy, Enteropathy X-linked) syndrome. In more common human autoimmune diseases, defects in Treg function are accompanied with aberrant effector cytokines such as IFNγ. It has recently become appreciated that Tregs plays an important role in not only maintaining immune homeostasis but also in establishing the tissue microenvironment and homeostasis of non-lymphoid tissues. Tissue resident Tregs show profiles that are unique to their local environments which are composed of both immune and non-immune cells. Core tissue-residence gene signatures are shared across different tissue Tregs and are crucial to homeostatic regulation and maintaining the tissue Treg pool in a steady state. Through interaction with immunocytes and non-immunocytes, tissue Tregs exert a suppressive function via conventional ways involving contact dependent and independent processes. In addition, tissue resident Tregs communicate with other tissue resident cells which allows Tregs to adopt to their local microenvironment. These bidirectional interactions are dependent on the specific tissue environment. Here, we summarize the recent advancements of tissue Treg studies in both human and mice, and discuss the molecular mechanisms that maintain tissue homeostasis and prevent pathogenesis.
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Affiliation(s)
- Nardos Cheru
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - David A. Hafler
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Tomokazu S. Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
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