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Fukasawa T, Yoshizaki-Ogawa A, Enomoto A, Yamashita T, Miyagawa K, Sato S, Yoshizaki A. Single cell analysis in systemic sclerosis - A systematic review. Immunol Med 2024; 47:118-129. [PMID: 38818750 DOI: 10.1080/25785826.2024.2360690] [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: 12/08/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
In recent years, rapid advances in research methods have made single cell analysis possible. Systemic sclerosis (SSc), a disease characterized by the triad of immune abnormalities, fibrosis, and vasculopathy, has also been the subject of various analyses. To summarize the results of single cell analysis in SSc accumulated to date and to deepen our understanding of SSc. Four databases were used to perform a database search on 23rd June 2023. Assessed Grading of Recommendations Assessment, Development and Evaluation certainty of evidence were performed according to PRISMA guidelines. The analysis was completed on July 2023. 17 studies with 358 SSc patients were included. Three studies used PBMCs, six used skin, nine used lung with SSc-interstitial lung diseases (ILDs), and one used lung with SSc-pulmonary arterial hypertension (PAH). The cells studied included immune cells such as T cells, natural killer cells, monocytes, macrophages, and dendritic cells, as well as endothelial cells, fibroblasts, keratinocytes, alveolar type I cells, basal epithelial cells, smooth muscle cells, mesothelial cells, etc. This systematic review revealed the results of single cell analysis, suggesting that PBMCs, skin, SSc-ILD, and SSc-PAH show activation and dysfunction of cells associated with immune-abnormalities, fibrosis, and vasculopathy, respectively.
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Affiliation(s)
- Takemichi Fukasawa
- Department of Dermatology, Systemic sclerosis center, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Cannabinoid Research, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Asako Yoshizaki-Ogawa
- Department of Dermatology, Systemic sclerosis center, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Enomoto
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takashi Yamashita
- Department of Dermatology, Systemic sclerosis center, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, Systemic sclerosis center, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, Systemic sclerosis center, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Cannabinoid Research, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Tang Y, Zhuo D, Yu Y, Pu W, Ma Y, Zhang Y, Huang Y, Zhang Q, Tang K, Meng C, Yang D, Bai L, He D, Jin L, Zou H, Xu H, Zhu Q, Wang J, Chen Y, Liu J. Single-cell RNA sequencing reveals the CRTAC1 + population actively contributes to the pathogenesis of spinal ligament degeneration by SPP1 + macrophage. Aging Cell 2024:e14320. [PMID: 39158018 DOI: 10.1111/acel.14320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/12/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024] Open
Abstract
Degenerative spinal stenosis is a chronic disease that affects the spinal ligaments and associated bones, resulting in back pain and disorders of the limbs among the elderly population. There are few preventive strategies for such ligament degeneration. We here aimed to establish a comprehensive transcriptomic atlas of ligament tissues to identify high-priority targets for pharmaceutical treatment of ligament degeneration. Here, single-cell RNA sequencing was performed on six degenerative ligaments and three traumatic ligaments to understand tissue heterogeneity. After stringent quality control, high-quality data were obtained from 32,014 cells. Distinct cell clusters comprising stromal and immune cells were identified in ligament tissues. Among them, we noted that collagen degradation associated with CTHRC1+ fibroblast-like cells and calcification linked to CRTAC1+ chondrocyte-like cells were key features of ligament degeneration. SCENIC analysis and further experiments identified ATF3 as a key transcription factor regulating the pathogenesis of CRTAC1+ chondrocyte-like cells. Typically, immune cells infiltrate localized organs, causing tissue damage. In our study, myeloid cells were found to be inflammatory-activated, and SPP1+ macrophages were notably enriched in degenerative ligaments. Further exploration via CellChat analysis demonstrated a robust interaction between SPP1+ macrophages and CRTAC1+ chondrocyte-like cells. Activated by SPP1, ATF3 propels the CRTAC1/MGP/CLU axis, fostering ligament calcification. Our unique resource provides novel insights into possible mechanisms underlying ligament degeneration, the target cell types, and molecules that are expected to mitigate degenerative spinal ligament. We also highlight the role of immune regulation in ligament degeneration and calcification, enhancing our understanding of this disease.
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Affiliation(s)
- Yulong Tang
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Dachun Zhuo
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Yuexin Yu
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Weilin Pu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China
| | - Yuting Zhang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Yan Huang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Qing Zhang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Kunhai Tang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Chen Meng
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Di Yang
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Lu Bai
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Dongyi He
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China
| | - Hejian Zou
- Division of Rheumatology, Huashan Hospital, and Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Huji Xu
- Department of Rheumatology and Immunology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Qi Zhu
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China
- Division of Rheumatology, Huashan Hospital, and Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Yuanyuan Chen
- Orthopedic Department, Shanghai Sixth People's Hospital, Shanghai Jiaotong University Affiliated, Shanghai, China
- Orthopaedic Department, People's Hospital of Shigatse City, Shigatse, China
| | - Jing Liu
- Shanghai Key Laboratory of Vascular Lesions and Remodeling, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
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Shen S, Hu M, Peng Y, Zheng Y, Zhang R. Research Progress in pathogenesis of connective tissue disease-associated interstitial lung disease from the perspective of pulmonary cells. Autoimmun Rev 2024; 23:103600. [PMID: 39151642 DOI: 10.1016/j.autrev.2024.103600] [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: 04/14/2024] [Revised: 07/16/2024] [Accepted: 08/10/2024] [Indexed: 08/19/2024]
Abstract
The lungs are a principal factor in the increased morbidity and mortality observed in patients with Connective Tissue Disease (CTD), frequently presenting as CTD-associated Interstitial Lung Disease (ILD). Currently, there is a lack of comprehensive descriptions of the pulmonary cells implicated in the development of CTD-ILD. This review leverages the Human Lung Cell Atlas (HLCA) and spatial multi-omics atlases to discuss the advancements in research on the pathogenesis of CTD-ILD from a pulmonary cell perspective. This facilitates a more precise localization of disease sites and a more systematic consideration of disease progression, supporting further mechanistic studies and targeted therapies.
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Affiliation(s)
- Shuyi Shen
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Ming Hu
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Yi Peng
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Yi Zheng
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Rong Zhang
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning, China.
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Zhou Y, Tabib T, Huang M, Yuan K, Kim Y, Morse C, Sembrat J, Valenzi E, Lafyatis R. Molecular Changes Implicate Angiogenesis and Arterial Remodeling in Systemic Sclerosis-Associated and Idiopathic Pulmonary Hypertension. Arterioscler Thromb Vasc Biol 2024; 44:e210-e225. [PMID: 38841857 PMCID: PMC11269037 DOI: 10.1161/atvbaha.123.320005] [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: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Pulmonary hypertension (PH) is a common complication of systemic sclerosis (SSc) and a leading cause of mortality among patients with this disease. PH can also occur as an idiopathic condition (idiopathic pulmonary arterial hypertension). Investigation of transcriptomic alterations in vascular populations is critical to elucidating cellular mechanisms underlying pathobiology of SSc-associated and idiopathic PH. METHODS We analyzed single-cell RNA sequencing profiles of endothelial and perivascular mesenchymal populations from explanted lung tissue of patients with SSc-associated PH (n=16), idiopathic pulmonary arterial hypertension (n=3), and healthy controls (n=15). Findings were validated by immunofluorescence staining of explanted human lung tissue. RESULTS Three disease-associated endothelial populations emerged. Two angiogenic endothelial cell (EC) subtypes markedly expanded in SSc-associated PH lungs: tip ECs expressing canonical tip markers PGF and APLN and phalanx ECs expressing genes associated with vascular development, endothelial barrier integrity, and Notch signaling. Gene regulatory network analysis suggested enrichment of Smad1 (SMAD family member 1) and PPAR-γ (peroxisome proliferator-activated receptor-γ) regulon activities in these 2 populations, respectively. Mapping of potential ligand-receptor interactions highlighted Notch, apelin-APJ (apelin receptor), and angiopoietin-Tie (tyrosine kinase with immunoglobulin-like and EGF-like domains 1) signaling pathways between angiogenic ECs and perivascular cells. Transitional cells, expressing both endothelial and pericyte/smooth muscle cell markers, provided evidence for the presence of endothelial-to-mesenchymal transition. Transcriptional programs associated with arterial endothelial dysfunction implicated VEGF-A (vascular endothelial growth factor-A), TGF-β1 (transforming growth factor beta-1), angiotensin, and TNFSF12 (tumor necrosis factor ligand superfamily member 12)/TWEAK (TNF-related weak inducer of apoptosis) in the injury/remodeling phenotype of PH arterial ECs. CONCLUSIONS These data provide high-resolution insights into the complexity and plasticity of the pulmonary endothelium in SSc-associated PH and idiopathic pulmonary arterial hypertension and provide direct molecular insights into soluble mediators and transcription factors driving PH vasculopathy.
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Affiliation(s)
- Yuechen Zhou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
- School of Medicine, Tsinghua University; Beijing 100084, China
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Ke Yuan
- Division of Pulmonary Medicine, Boston Children’s Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Yunhye Kim
- Division of Pulmonary Medicine, Boston Children’s Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
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Lee SC, Huang CH, Oyang YJ, Huang HC, Juan HF. Macrophages as determinants and regulators of systemic sclerosis-related interstitial lung disease. J Transl Med 2024; 22:600. [PMID: 38937794 PMCID: PMC11212242 DOI: 10.1186/s12967-024-05403-4] [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: 05/06/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Interstitial lung disease (ILD) is the primary cause of mortality in systemic sclerosis (SSc), an autoimmune disease characterized by tissue fibrosis. SSc-related ILD (SSc-ILD) occurs more frequently in females aged 30-55 years, whereas idiopathic pulmonary fibrosis (IPF) is more prevalent in males aged 60-75 years. SSc-ILD occurs earlier than IPF and progresses rapidly. FCN1, FABP4, and SPP1 macrophages are involved in the pathogenesis of lung fibrosis; SPP1 macrophages demonstrate upregulated expression in both SSc-ILD and IPF. To identify the differences between SSc-ILD and IPF using single-cell analysis, clarify their distinct pathogeneses, and propose directions for prevention and treatment. METHODS We performed single-cell RNA sequencing on NCBI Gene Expression Omnibus (GEO) databases GSE159354 and GSE212109, and analyzed lung tissue samples across healthy controls, IPF, and SSc-ILD. The primary measures were the filtered genes integrated with batch correction and annotated cell types for distinguishing patients with SSc-ILD from healthy controls. We proposed an SSc-ILD pathogenesis using cell-cell interaction inferences, and predicted transcription factors regulating target genes using SCENIC. Drug target prediction of the TF gene was performed using Drug Bank Online. RESULTS A subset of macrophages activates the MAPK signaling pathway under oxidative stress. Owing to the lack of inhibitory feedback from ANNEXIN and the autoimmune characteristics, this leads to an earlier onset of lung fibrosis compared to IPF. During initial lung injury, fibroblasts begin to activate the IL6 pathway under the influence of SPP1 alveolar macrophages, but IL6 appears unrelated to other inflammatory and immune cells. This may explain why tocilizumab (an anti-IL6-receptor antibody) only preserves lung function in patients with early SSc-ILD. Finally, we identified BCLAF1 and NFE2L2 as influencers of MAPK activation in macrophages. Metformin downregulates NFE2L2 and could serve as a repurposed drug candidate. CONCLUSIONS SPP1 alveolar macrophages play a role in the profibrotic activity of IPF and SSc-ILD. However, SSc-ILD is influenced by autoimmunity and oxidative stress, leading to the continuous activation of MAPK in macrophages. This may result in an earlier onset of lung fibrosis than in IPF. Such differences could serve as potential research directions for early prevention and treatment.
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Affiliation(s)
- Shih-Ching Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
- Division of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan
| | - Chen-Hao Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Yen-Jen Oyang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Hsueh-Fen Juan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan.
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan.
- Center for Computational and Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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Xu L, Chen Y, Liu L, Hu X, He C, Zhou Y, Ding X, Luo M, Yan J, Liu Q, Li H, Lai D, Zou Z. Tumor-associated macrophage subtypes on cancer immunity along with prognostic analysis and SPP1-mediated interactions between tumor cells and macrophages. PLoS Genet 2024; 20:e1011235. [PMID: 38648200 PMCID: PMC11034676 DOI: 10.1371/journal.pgen.1011235] [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: 09/27/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Tumor-associated macrophages (TAM) subtypes have been shown to impact cancer prognosis and resistance to immunotherapy. However, there is still a lack of systematic investigation into their molecular characteristics and clinical relevance in different cancer types. Single-cell RNA sequencing data from three different tumor types were used to cluster and type macrophages. Functional analysis and communication of TAM subpopulations were performed by Gene Ontology-Biological Process and CellChat respectively. Differential expression of characteristic genes in subpopulations was calculated using zscore as well as edgeR and Wilcoxon rank sum tests, and subsequently gene enrichment analysis of characteristic genes and anti-PD-1 resistance was performed by the REACTOME database. We revealed the heterogeneity of TAM, and identified eleven subtypes and their impact on prognosis. These subtypes expressed different molecular functions respectively, such as being involved in T cell activation, apoptosis and differentiation, or regulating viral bioprocesses or responses to viruses. The SPP1 pathway was identified as a critical mediator of communication between TAM subpopulations, as well as between TAM and epithelial cells. Macrophages with high expression of SPP1 resulted in poorer survival. By in vitro study, we showed SPP1 mediated the interactions between TAM clusters and between TAM and tumor cells. SPP1 promoted the tumor-promoting ability of TAM, and increased PDL1 expression and stemness of tumor cells. Inhibition of SPP1 attenuated N-cadherin and β-catenin expression and the activation of AKT and STAT3 pathway in tumor cells. Additionally, we found that several subpopulations could decrease the sensitivity of anti-PD-1 therapy in melanoma. SPP1 signal was a critical pathway of communication between macrophage subtypes. Some specific macrophage subtypes were associated with immunotherapy resistance and prognosis in some cancer types.
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Affiliation(s)
- Liu Xu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingling Liu
- Department of Hematology, The Third Affiliated Hospital of Sun Yat-sen University & Sun Yat-sen Institute of Hematology, Guangzhou, China
| | - Xinyu Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Chengsi He
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yuan Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Xinyi Ding
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Minhua Luo
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Jiajing Yan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hongsheng Li
- Department of Breast Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Dongming Lai
- Shenshan Medical Center and Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhengzhi Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
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Wang Y, Chen S, Bao S, Yao L, Wen Z, Xu L, Chen X, Guo S, Pang H, Zhou Y, Zhou P. Deciphering the fibrotic process: mechanism of chronic radiation skin injury fibrosis. Front Immunol 2024; 15:1338922. [PMID: 38426100 PMCID: PMC10902513 DOI: 10.3389/fimmu.2024.1338922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
This review explores the mechanisms of chronic radiation-induced skin injury fibrosis, focusing on the transition from acute radiation damage to a chronic fibrotic state. It reviewed the cellular and molecular responses of the skin to radiation, highlighting the role of myofibroblasts and the significant impact of Transforming Growth Factor-beta (TGF-β) in promoting fibroblast-to-myofibroblast transformation. The review delves into the epigenetic regulation of fibrotic gene expression, the contribution of extracellular matrix proteins to the fibrotic microenvironment, and the regulation of the immune system in the context of fibrosis. Additionally, it discusses the potential of biomaterials and artificial intelligence in medical research to advance the understanding and treatment of radiation-induced skin fibrosis, suggesting future directions involving bioinformatics and personalized therapeutic strategies to enhance patient quality of life.
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Affiliation(s)
- Yiren Wang
- School of Nursing, Southwest Medical University, Luzhou, China
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
| | - Shouying Chen
- School of Nursing, Southwest Medical University, Luzhou, China
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
| | - Shuilan Bao
- School of Nursing, Southwest Medical University, Luzhou, China
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
| | - Li Yao
- School of Nursing, Southwest Medical University, Luzhou, China
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
| | - Zhongjian Wen
- School of Nursing, Southwest Medical University, Luzhou, China
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
| | - Lixia Xu
- School of Nursing, Southwest Medical University, Luzhou, China
| | - Xiaoman Chen
- School of Nursing, Southwest Medical University, Luzhou, China
| | - Shengmin Guo
- Department of Nursing, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Haowen Pang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yun Zhou
- School of Medical Information and Engineering, Southwest Medical University, Luzhou, China
| | - Ping Zhou
- Wound Healing Basic Research and Clinical Application Key Laboratory of Luzhou, Southwest Medical University, Luzhou, China
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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8
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Huang X, Song C, Zhang G, Li Y, Zhao Y, Zhang Q, Zhang Y, Fan S, Zhao J, Xie L, Li C. scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse. Nucleic Acids Res 2024; 52:D293-D303. [PMID: 37889053 PMCID: PMC10767939 DOI: 10.1093/nar/gkad885] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF-target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF-target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.
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Affiliation(s)
- Xuemei Huang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Chao Song
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Guorui Zhang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ye Li
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yu Zhao
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Qinyi Zhang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yuexin Zhang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Shifan Fan
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jun Zhao
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Liyuan Xie
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Chunquan Li
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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9
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Qiu Y, Feng X, Liu C, Shi Y, Xu L, You H, Wang L, Lv C, Wang F, Tan W. Proteomic profiling identifies SPP1 associated with rapidly progressive interstitial lung disease in anti-MDA5-positive dermatomyositis. Arthritis Res Ther 2024; 26:9. [PMID: 38167532 PMCID: PMC10759429 DOI: 10.1186/s13075-023-03243-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Anti-melanoma differentiation-associated gene five antibody positive (MDA5+) dermatomyositis (DM) is significantly associated with rapidly progressive interstitial lung disease (RP-ILD). Early detection of RP-ILD remains a major challenge. This study aims to identify and validate prognostic factors for RP-ILD in MDA5+ DM patients. METHODS Plasma samples from 20 MDA5+ DM patients and 10 healthy controls (HC) were collected for proteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The proteins of interest were validated in independent samples (20 HC, 20 MDA5+ DM with RP-ILD, and 20 non-RP-ILD patients) with enzyme-linked immunosorbent assay (ELISA). RESULTS A total of 413 differentially expressed proteins (DEPs) were detected between the MDA5+ DM patients and HC. When comparing DEPs between RP-ILD and non-RP-ILD patients, 79 proteins were changed in RP-ILD patients, implicating acute inflammatory response, coagulation, and complement cascades. Six candidate biomarkers were confirmed with ELISA. Secreted phosphoprotein 1 (SPP1), serum amyloid A1 (SAA1), and Kininogen 1 (KNG1) concentrations were significantly elevated in RP-ILD patients than those in non-RP-ILD patients and HC. In the different clinical subgroups, SPP1 was particularly elevated in the high-risk RP-ILD subgroup of MDA5+ DM. CONCLUSION This study provides novel insights into the pathogenesis of RP-ILD development in MDA5+ DM and suggests the plasma protein SPP1 could serve as a potential blood biomarker for RP-ILD early warning.
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Affiliation(s)
- Yulu Qiu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Xiaoke Feng
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Integrated Traditional Chinese and Western Medicine Institute of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chang Liu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Yumeng Shi
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Lingxiao Xu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Hanxiao You
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Lei Wang
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Chengyin Lv
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Fang Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
| | - Wenfeng Tan
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
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10
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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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11
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Amati F, Bongiovanni G, Tonutti A, Motta F, Stainer A, Mangiameli G, Aliberti S, Selmi C, De Santis M. Treatable Traits in Systemic Sclerosis. Clin Rev Allergy Immunol 2023; 65:251-276. [PMID: 37603199 DOI: 10.1007/s12016-023-08969-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/22/2023]
Abstract
Systemic sclerosis (SSc) is a chronic systemic disease within the spectrum of connective tissue diseases, specifically characterized by vascular abnormalities and inflammatory and fibrotic involvement of the skin and internal organs resulting in high morbidity and mortality. The clinical phenotype of SSc is heterogeneous, and serum autoantibodies together with the extent of skin involvement have a predictive value in the risk stratification. Current recommendations include an organ-based management according to the predominant involvement with only limited individual factors included in the treatment algorithm. Similar to what has been proposed for other chronic diseases, we hypothesize that a "treatable trait" approach based on relevant phenotypes and endotypes could address the unmet needs in SSc stratification and treatment to maximize the outcomes. We provide herein a comprehensive review and a critical discussion of the literature regarding potential treatable traits in SSc, focusing on established and candidate biomarkers, with the purpose of setting the bases for a precision medicine-based approach. The discussion, structured based on the organ involvement, allows to conjugate the pathogenetic mechanisms of tissue injury with the proposed predictors, particularly autoantibodies and other serum biomarkers. Ultimately, we are convinced that precision medicine is the ideal guide to manage a complex condition such as SSc for which available treatments are largely unsatisfactory.
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Affiliation(s)
- Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Gabriele Bongiovanni
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Antonio Tonutti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Francesca Motta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anna Stainer
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Giuseppe Mangiameli
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.
| | - Maria De Santis
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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12
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Bondonese A, Craig A, Fan L, Valenzi E, Bain W, Lafyatis R, Sembrat J, Chen K, Snyder ME. Impact of enzymatic digestion on single cell suspension yield from peripheral human lung tissue. Cytometry A 2023; 103:777-785. [PMID: 37449375 PMCID: PMC10592386 DOI: 10.1002/cyto.a.24777] [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: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
An increasing number of translational investigations of lung biology rely on analyzing single cell suspensions obtained from human lungs. To obtain these single cell suspensions, human lungs from biopsies or research-consented organ donors must be subjected to mechanical and enzymatic digestion prior to analysis with either flow cytometry or single cell RNA sequencing. A variety of enzymes have been used to perform tissue digestion, each with potential limitations. To better understand the limitations of each enzymatic digestion protocol and to establish a framework for comparing studies across protocols, we performed five commonly published protocols in parallel from identical samples obtained from 6 human lungs. Following mechanical (gentleMACS™) and enzymatic digestion, we quantified cell count and viability using a Nexcelom Cellometer and determined cell phenotype using multiparameter spectral flow cytometry (Cytek™ Aurora). We found that all protocols were superior in cellular yield and viability when compared to mechanical digestion alone. Protocols high in dispase cleaved immune markers CD4, CD8, CD69, and CD103 and contributed to an increased monocyte to macrophage yield. Similarly, dispase led to a differential epithelial cell yield, with increased TSPN8+ and ITGA6+ epithelial cells and reduced CD66e+ cells. When compared to collagenase D, collagenase P protocols yielded increased AT1 and AT2 cells and decreased endothelial cells. These results provide a framework for selecting an enzymatic digestion protocol best suited to the scientific question and allow for comparison of studies using different protocols.
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Affiliation(s)
| | - Andrew Craig
- Department of Medicine, University of Pittsburgh
| | - Li Fan
- Department of Medicine, University of Pittsburgh
| | | | - William Bain
- Department of Medicine, University of Pittsburgh
| | | | - John Sembrat
- Department of Medicine, University of Pittsburgh
| | - Kong Chen
- Department of Medicine, University of Pittsburgh
| | - Mark E. Snyder
- Department of Medicine, University of Pittsburgh
- Department of Immunology, University of Pittsburgh
- Starzl Transplantation Institute
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13
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Liao Y, Wang R, Wen F. Diagnostic and prognostic value of secreted phosphoprotein 1 for idiopathic pulmonary fibrosis: a systematic review and meta-analysis. Biomarkers 2023; 28:87-96. [PMID: 36377416 DOI: 10.1080/1354750x.2022.2148744] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BackgroundThere is an increasing number of studies on the diagnostic and prognostic biomarkers associated with IPF. The purpose of this study was to explore the diagnostic and prognostic value of secreted phosphoprotein 1 (SPP1) in IPF.MethodsUsing five database, appropriate studies were included. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and 95% confidence intervals (CIs) were calculated. Pooled hazard ratios (HRs) and 95% CIs related to prognosis were calculated.ResultsThirteen studies were included in the meta-analyses. The pooled sensitivity, specificity, PLR, NLR and DOR were 0.84 (95% CI 0.72-0.91), 0.89 (95% CI 0.83-0.94), 7.94 (95% CI 4.63-13.62), 0.18 (95% CI 0.10-0.33), 43.08 (95% CI 15.88-116.84) for SPP1 in the differential diagnosis of IPF and healthy people. The pooled sensitivity, specificity, PLR, NLR and DOR were 0.97 (95% CI 0.57-1.00), 0.93 (95% CI 0.73-0.98), 13.87 (95% CI 3.26-58.99), 0.03 (95% CI 0-0.68), 446.91 (95% CI 21.02-9504.41) for SPP1 to differentiate IPF and lung cancer patients. High SPP1 expression predicts poor prognosis for IPF patients (HR= 1.42, 95% CI = 1.27 and 1.58, P < 0.001).ConclusionsSPP1 is a potential diagnostic and prognostic biomarker for IPF patients.
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Affiliation(s)
- Yi Liao
- Laboratory of Pulmonary Disease, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China school of Medicine, Sichuan University, Chengdu, China
| | - Ran Wang
- Laboratory of Pulmonary Disease, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China school of Medicine, Sichuan University, Chengdu, China
| | - Fuqiang Wen
- Laboratory of Pulmonary Disease, and Department of Respiratory and Critical Care Medicine, West China Hospital, West China school of Medicine, Sichuan University, Chengdu, China
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14
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Fang D, Chen B, Lescoat A, Khanna D, Mu R. Immune cell dysregulation as a mediator of fibrosis in systemic sclerosis. Nat Rev Rheumatol 2022; 18:683-693. [DOI: 10.1038/s41584-022-00864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2022] [Indexed: 11/11/2022]
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