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Hong YK, Hwang DY, Yang CC, Cheng SM, Chen PC, Aala WJ, I-Chen Harn H, Evans ST, Onoufriadis A, Liu SL, Lin YC, Chang YH, Lo TK, Hung KS, Lee YC, Tang MJ, Lu KQ, McGrath JA, Hsu CK. Profibrotic Subsets of SPP1 + Macrophages and POSTN + Fibroblasts Contribute to Fibrotic Scarring in Acne Keloidalis. J Invest Dermatol 2024; 144:1491-1504.e10. [PMID: 38218364 DOI: 10.1016/j.jid.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
Acne keloidalis is a primary scarring alopecia characterized by longstanding inflammation in the scalp causing keloid-like scar formation and hair loss. Histologically, acne keloidalis is characterized by mixed leukocytic infiltrates in the acute stage followed by a granulomatous reaction and extensive fibrosis in the later stages. To further explore its pathogenesis, bulk RNA sequencing, single-cell RNA sequencing, and spatial transcriptomics were applied to occipital scalp biopsy specimens of lesional and adjacent no-lesional skin in patients with clinically active disease. Unbiased clustering revealed 19 distinct cell populations, including 2 notable populations: POSTN+ fibroblasts with enriched extracellular matrix signatures and SPP1+ myeloid cells with an M2 macrophage phenotype. Cell communication analyses indicated that fibroblasts and myeloid cells communicated by SPP1 signaling networks in lesional skin. A reverse transcriptomics in silico approach identified corticosteroids as possessing the capability to reverse the gene expression signatures of SPP1+ myeloid cells and POSTN+ fibroblasts. Intralesional corticosteroid injection greatly reduced SPP1 and POSTN gene expression as well as acne keloidalis disease activity. Spatial transcriptomics and immunofluorescence staining verified microanatomic specificity of SPP1+ myeloid cells and POSTN+ fibroblasts with disease activity. In summary, the communication between POSTN+ fibroblasts and SPP1+ myeloid cells by SPP1 axis may contribute to the pathogenesis of acne keloidalis.
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Affiliation(s)
- Yi-Kai Hong
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Chao-Chun Yang
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Siao Muk Cheng
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wilson Jr Aala
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Spencer T Evans
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Si-Lin Liu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chen Lin
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Han Chang
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Kun Lo
- Department of Dermatology, Tainan Municipal An-Nan Hospital, Tainan, Taiwan
| | - Kuo-Shu Hung
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Chao Lee
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Jer Tang
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kurt Q Lu
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John A McGrath
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, London, United Kingdom
| | - Chao-Kai Hsu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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2
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Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson MS, DeRisi JL, Sperling AI, Shum AK. Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease. ACR Open Rheumatol 2024. [PMID: 38952015 DOI: 10.1002/acr2.11696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/10/2024] [Accepted: 04/26/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVE Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases. Establishing autoimmunity in ILD impacts prognosis and treatment. Patients with ILD are screened for autoimmunity by measuring antinuclear autoantibodies, rheumatoid factors, and other nonspecific tests. However, this approach may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. METHODS We use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct an autoantibody discovery screen of patients with ILD and controls. We screened for novel autoantigen candidates using PhIP-Seq. We next developed a radio-labeled binding assay and validated the leading candidate in 398 patients with ILD recruited from two academic medical centers and 138 blood bank individuals that formed our reference cohort. RESULTS PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among the 17 candidates, we validated CDHR5 and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, patients not previously diagnosed with autoimmunity. Using survival and transplant free-survival data available from one of the two centers, patients with CDHR5 autoantibodies showed worse survival compared with other patients with connective tissue disease ILD. CONCLUSION We used PhIP-Seq to define a novel CDHR5 autoantibody in a subset of select patients with ILD. Our data complement a recent study showing polymorphisms in the CDHR5-IRF7 gene locus strongly associated with titer of anticentromere antibodies in systemic sclerosis, creating a growing body of evidence suggesting a link between CDHR5 and autoimmunity.
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Affiliation(s)
| | | | - Sara E Vazquez
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Tania E Velez
- University of Chicago, Illinois, and University of Virginia, Charlottesville
| | | | | | | | | | | | | | | | - Imre Noth
- University of Virginia, Charlottesville
| | | | | | - Joseph L DeRisi
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Anne I Sperling
- University of Chicago, Illinois, and University of Virginia, Charlottesville
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Song L, Li K, Chen H, Xie L. Cell Cross-Talk in Alveolar Microenvironment: From Lung Injury to Fibrosis. Am J Respir Cell Mol Biol 2024; 71:30-42. [PMID: 38579159 PMCID: PMC11225874 DOI: 10.1165/rcmb.2023-0426tr] [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: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 04/07/2024] Open
Abstract
Alveoli are complex microenvironments composed of various cell types, including epithelial, fibroblast, endothelial, and immune cells, which work together to maintain a delicate balance in the lung environment, ensuring proper growth, development, and an effective response to lung injuries. However, prolonged inflammation or aging can disrupt normal interactions among these cells, leading to impaired repair processes and a substantial decline in lung function. Therefore, it is essential to understand the key mechanisms underlying the interactions among the major cell types within the alveolar microenvironment. We explored the key mechanisms underlying the interactions among the major cell types within the alveolar microenvironment. These interactions occur through the secretion of signaling factors and play crucial roles in the response to injury, repair mechanisms, and the development of fibrosis in the lungs. Specifically, we focused on the regulation of alveolar type 2 cells by fibroblasts, endothelial cells, and macrophages. In addition, we explored the diverse phenotypes of fibroblasts at different stages of life and in response to lung injury, highlighting their impact on matrix production and immune functions. Furthermore, we summarize the various phenotypes of macrophages in lung injury and fibrosis as well as their intricate interplay with other cell types. This interplay can either contribute to the restoration of immune homeostasis in the alveoli or impede the repair process. Through a comprehensive exploration of these cell interactions, we aim to reveal new insights into the molecular mechanisms that drive lung injury toward fibrosis and identify potential targets for therapeutic intervention.
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Affiliation(s)
- Licheng Song
- College of Pulmonary and Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, China; and
| | - Kuan Li
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Huaiyong Chen
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, China; and
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4
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Franzén L, Olsson Lindvall M, Hühn M, Ptasinski V, Setyo L, Keith BP, Collin A, Oag S, Volckaert T, Borde A, Lundeberg J, Lindgren J, Belfield G, Jackson S, Ollerstam A, Stamou M, Ståhl PL, Hornberg JJ. Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nat Genet 2024:10.1038/s41588-024-01819-2. [PMID: 38951642 DOI: 10.1038/s41588-024-01819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/30/2024] [Indexed: 07/03/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. Here we generated spatially resolved transcriptome maps of human IPF (n = 4) and bleomycin-induced mouse pulmonary fibrosis (n = 6) to address these limitations. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by transforming growth factor beta signaling alongside predicted regulators, such as TP53 and APOE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.
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Affiliation(s)
- Lovisa Franzén
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Martina Olsson Lindvall
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael Hühn
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Victoria Ptasinski
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Laura Setyo
- Pathology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Benjamin P Keith
- Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Astrid Collin
- Animal Science and Technology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Steven Oag
- Animal Science and Technology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Volckaert
- Bioscience In Vivo, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Annika Borde
- Bioscience In Vivo, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Julia Lindgren
- Translational Genomics, Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Graham Belfield
- Translational Genomics, Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Sonya Jackson
- Late-Stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Ollerstam
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Marianna Stamou
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Patrik L Ståhl
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Jorrit J Hornberg
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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5
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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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6
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Zhang M, Zhang J, Hu H, Zhou Y, Lin Z, Jing H, Sun B. Multiomic analysis of monocyte-derived alveolar macrophages in idiopathic pulmonary fibrosis. J Transl Med 2024; 22:598. [PMID: 38937806 PMCID: PMC11209973 DOI: 10.1186/s12967-024-05398-y] [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: 01/20/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Monocyte-derived alveolar macrophages (Mo_AMs) are increasingly recognised as potential pathogenic factors for idiopathic pulmonary fibrosis (IPF). While scRNAseq analysis has proven valuable in the transcriptome profiling of Mo_AMs, the integration analysis of multi-omics may provide additional dimensions of understanding of these cellular populations. METHODS We performed multi-omics analysis on 116 scRNAseq, 119 bulkseq and five scATACseq lung tissue samples from IPF. We built a large-scale IPF scRNAseq atlas and conducted the Monocle 2/3 as well as the Cellchat to explore the developmental path and intercellular communication on Mo_AMs. We also reported the difference in metabolisms, tissue repair and phagocytosis between Mo_AMs and tissue-resident alveolar macrophages (TRMs). To determine whether Mo_AMs affected pulmonary function, we projected clinical phenotypes (FVC%pred) from the bulkseq dataset onto the scRNAseq atlas. Finally, we used scATATCseq to uncover the upstream regulatory mechanisms and determine key drivers in Mo_AMs. RESULTS We identified three Mo_AMs clusters and the trajectory analysis further validated the origin of these clusters. Moreover, via the Cellchat analysis, the CXCL12/CXCR4 axis was found to be involved in the molecular basis of reciprocal interactions between Mo_AMs and fibroblasts through the activation of the ERK pathway in Mo_AMs. SPP1_RecMacs (RecMacs, recruited macrophages) were higher in the low-FVC group than in the high-FVC group. Specifically, compared with TRMs, the functions of lipid and energetic metabolism as well as tissue repair were higher in Mo_AMs than TRMs. But, TRMs may have higher level of phagocytosis than TRMs. SPIB (PU.1), JUNB, JUND, BACH2, FOSL2, and SMARCC1 showed stronger association with open chromatin of Mo_AMs than TRMs. Significant upregulated expression and deep chromatin accessibility of APOE were observed in both SPP1_RecMacs and TRMs. CONCLUSION Through trajectory analysis, it was confirmed that SPP1_RecMacs derived from Monocytes. Besides, Mo_AMs may influence FVC% pred and aggravate pulmonary fibrosis through the communication with fibroblasts. Furthermore, distinctive transcriptional regulators between Mo_AMs and TRMs implied that they may depend on different upstream regulatory mechanisms. Overall, this work provides a global overview of how Mo_AMs govern IPF and also helps determine better approaches and intervention therapies.
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Affiliation(s)
- Miaomiao Zhang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Jinghao Zhang
- Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, China
| | - Haisheng Hu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuan Zhou
- Department of Medicine II, Heart Center Bonn, University Hospital Bonn, Bonn, Germany
| | - ZhiWei Lin
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Jing
- Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Guangzhou, 510005, China.
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7
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Yuan DY, McKeague ML, Raghu VK, Schoen RE, Finn OJ, Benos PV. Cellular and transcriptional profiles of peripheral blood mononuclear cells pre-vaccination predict immune response to preventative MUC1 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598031. [PMID: 38948837 PMCID: PMC11212910 DOI: 10.1101/2024.06.14.598031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial ( NCT02134925 ) were conducted in individuals with a history of advanced colonic adenoma to test the safety and immunogenicity of the MUC1 tumor antigen vaccine and its potential to prevent new adenomas. These were the first two trials of a non-viral cancer vaccine administered in the absence of cancer. The vaccine was safe and strongly immunogenic in 43% (NCT007773097) and 25% ( NCT02134925 ) of participants. The lack of response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to some level of suppression previously reported only in cancer. Single-cell RNA-sequencing (scRNA-seq) on banked pre-vaccination peripheral blood mononuclear cells (PBMCs) from 16 immune responders and 16 non-responders identified specific cell types, genes, and pathways of a productive vaccine response. Responders had a significantly higher percentage of CD4+ naive T cells pre-vaccination, but a significantly lower percentage of CD8+ T effector memory (TEM) cells and CD16+ monocytes. Differential gene expression (DGE) and transcription factor inference analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in CD4+ naive T cells, and pathway analysis showed enriched signaling activity in responders. Furthermore, Bayesian network analysis suggested that these genes were mechanistically connected to response. Our analyses identified several immune mechanisms and candidate biomarkers to be further validated as predictors of immune responses to a preventative cancer vaccine that could facilitate selection of individuals likely to benefit from a vaccine or be used to improve vaccine responses.
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8
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Barbosa-Matos C, Borges-Pereira C, Libório-Ramos S, Fernandes R, Oliveira M, Mendes-Frias A, Silvestre R, Osório NS, Bastos HN, Santos RF, Guimarães S, Morais A, Mazzone M, Carvalho A, Cunha C, Costa S. Deregulated immune cell recruitment orchestrated by c-MET impairs pulmonary inflammation and fibrosis. Respir Res 2024; 25:257. [PMID: 38909206 PMCID: PMC11193258 DOI: 10.1186/s12931-024-02884-1] [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: 01/31/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Pulmonary fibrosis (PF) represents the pathologic end stage of several interstitial lung diseases (ILDs) associated with high morbidity and mortality rates. However, current treatments can only delay disease progression rather than provide a cure. The role of inflammation in PF progression is well-established, but new insights into immune regulation are fundamental for developing more efficient therapies. c-MET signaling has been implicated in the migratory capacity and effector functions of immune cells. Nevertheless, the role of this signaling pathway in the context of PF-associated lung diseases remains unexplored. METHODS To determine the influence of c-MET in immune cells in the progression of pulmonary fibrosis, we used a conditional deletion of c-Met in immune cells. To induce pulmonary fibrosis mice were administered with bleomycin (BLM) intratracheally. Over the course of 21 days, mice were assessed for weight change, and after euthanasia at different timepoints, bronchoalveolar lavage fluid cells and lung tissue were assessed for inflammation and fibrosis. Furthermore, c-MET expression was assessed in cryobiopsy sections, bronchoalveolar lavage fluid cells samples and single cell RNA-sequencing dataset from human patients with distinct interstitial lung diseases. RESULTS c-MET expression was induced in lung immune cells, specifically in T cells, interstitial macrophages, and neutrophils, during the inflammatory phase of BLM-induced PF mouse model. Deletion of c-Met in immune cells correlated with earlier weight recovery and improved survival of BLM-treated mice. Moreover, the deletion of c-Met in immune cells was associated with early recruitment of the immune cell populations, normally found to express c-MET, leading to a subsequent attenuation of the cytotoxic and proinflammatory environment. Consequently, the less extensive inflammatory response, possibly coupled with tissue repair, culminated in less exacerbated fibrotic lesions. Furthermore, c-MET expression was up-regulated in lung T cells from patients with fibrosing ILD, suggesting a potential involvement of c-MET in the development of fibrosing disease. CONCLUSIONS These results highlight the critical contribution of c-MET signaling in immune cells to their enhanced uncontrolled recruitment and activation toward a proinflammatory and profibrotic phenotype, leading to the exacerbation of lung injury and consequent development of fibrosis.
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Affiliation(s)
- Catarina Barbosa-Matos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Caroline Borges-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sofia Libório-Ramos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Raquel Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Marcela Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Mendes-Frias
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Hélder N Bastos
- Department of Pneumology, Centro Hospitalar do São João, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita F Santos
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- School of Health Sciences - Polytechnic of Porto, Porto, Portugal
| | - Susana Guimarães
- Department of Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - António Morais
- Department of Pneumology, Centro Hospitalar do São João, Porto, Portugal
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sandra Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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9
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Mannes PZ, Adams TS, Farsijani S, Barnes CE, Latoche JD, Day KE, Nedrow JR, Ahangari F, Kaminski N, Lee JS, Tavakoli S. Noninvasive assessment of the lung inflammation-fibrosis axis by targeted imaging of CMKLR1. SCIENCE ADVANCES 2024; 10:eadm9817. [PMID: 38896611 PMCID: PMC11186491 DOI: 10.1126/sciadv.adm9817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Precision management of fibrotic lung diseases is challenging due to their diverse clinical trajectories and lack of reliable biomarkers for risk stratification and therapeutic monitoring. Here, we validated the accuracy of CMKLR1 as an imaging biomarker of the lung inflammation-fibrosis axis. By analyzing single-cell RNA sequencing datasets, we demonstrated CMKLR1 expression as a transient signature of monocyte-derived macrophages (MDMφ) enriched in patients with idiopathic pulmonary fibrosis (IPF). Consistently, we identified MDMφ as the major driver of the uptake of CMKLR1-targeting peptides in a murine model of bleomycin-induced lung fibrosis. Furthermore, CMKLR1-targeted positron emission tomography in the murine model enabled quantification and spatial mapping of inflamed lung regions infiltrated by CMKLR1-expressing macrophages and emerged as a robust predictor of subsequent lung fibrosis. Last, high CMKLR1 expression by bronchoalveolar lavage cells identified an inflammatory endotype of IPF with poor survival. Our investigation supports the potential of CMKLR1 as an imaging biomarker for endotyping and risk stratification of fibrotic lung diseases.
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Affiliation(s)
- Philip Z. Mannes
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Samaneh Farsijani
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Aging and Population Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Clayton E. Barnes
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph D. Latoche
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kathryn E. Day
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jessie R. Nedrow
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Sina Tavakoli
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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10
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Fransen LFH, Leonard MO. Mononuclear phagocyte sub-types in vitro display diverse transcriptional responses to dust mite exposure. Sci Rep 2024; 14:14187. [PMID: 38902328 PMCID: PMC11189906 DOI: 10.1038/s41598-024-64783-1] [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: 02/02/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
Mononuclear phagocytes (MNP), including macrophages and dendritic cells form an essential component of primary responses to environmental hazards and toxic exposures. This is particularly important in disease conditions such as asthma and allergic airway disease, where many different cell types are present. In this study, we differentiated CD34+ haematopoietic stem cells towards different populations of MNP in an effort to understand how different cell subtypes present in inflammatory disease microenvironments respond to the common allergen house dust mite (HDM). Using single cell mRNA sequencing, we demonstrate that macrophage subtypes MCSPP1+ and MLCMARCO+ display different patterns of gene expression after HDM challenge, noted especially for the chemokines CXCL5, CXCL8, CCL5 and CCL15. MLCCD206Hi alternatively activated macrophages displayed the greatest changes in expression, while neutrophil and monocyte populations did not respond. Further work investigated how pollutant diesel exhaust particles could modify these transcriptional responses and revealed that CXC but not CC type chemokines were further upregulated. Through the use of diesel particles with adsorbed material removed, we suggest that soluble pollutants on these particles are the active constituents responsible for the modifying effects on HDM. This study highlights that environmental exposures may influence tissue responses dependent on which MNP cell type is present, and that these should be considerations when modelling such events in vitro. Understanding the nuanced responsiveness of different immune cell types to allergen and pollutant exposure also contributes to a better understanding of how these exposures influence the development and exacerbation of human disease.
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Affiliation(s)
- Leonie F H Fransen
- Toxicology Department, Radiation, Chemical and Environmental Hazards Directorate, UK Health Security Agency, Harwell Science and Innovation Campus, Harwell, OX11 0RQ, UK
| | - Martin O Leonard
- Toxicology Department, Radiation, Chemical and Environmental Hazards Directorate, UK Health Security Agency, Harwell Science and Innovation Campus, Harwell, OX11 0RQ, UK.
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11
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Zhang H, Yang Y, Cao Y, Guan J. IPF-related new macrophage subpopulations and diagnostic biomarker identification - combine machine learning with single-cell analysis. Respir Res 2024; 25:241. [PMID: 38872139 PMCID: PMC11170785 DOI: 10.1186/s12931-024-02845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic disease of unknown etiology that lacks a specific treatment. In IPF, macrophages play a key regulatory role as a major component of the lung immune system, especially during inflammation and fibrosis. However, our understanding of the cellular heterogeneity and molecular characterization of macrophages in IPF, as well as their relevance in the clinical setting, is relatively limited. In this study, we analyzed in-depth single-cell transcriptome sequencing (scRNA-seq) data from lung tissues of IPF patients, identified macrophage subpopulations in IPF, and probed their molecular characteristics and biological functions. hdWGCNA identified co-expressed gene modules of a subpopulation of IPF-associated macrophages (IPF-MΦ), and probed the IPF-MΦ by a machine-learning approach. hdWGCNA identified a subpopulation of IPF-associated macrophage subpopulations and probed the IPF-MΦ signature gene (IRMG) for its prognostic value, and a prediction model was developed on this basis. In addition, IPF-MΦ was obtained after recluster analysis of macrophages in IPF lung tissues. Coexpressed gene modules of IPF-MΦ were identified by hdWGCNA. Then, a machine learning approach was utilized to reveal the characteristic genes of IPF-MΦ, and a prediction model was built on this basis. In addition, we discovered a type of macrophage unique to IPF lung tissue named ATP5-MΦ. Its characteristic gene encodes a subunit of the mitochondrial ATP synthase complex, which is closely related to oxidative phosphorylation and proton transmembrane transport, suggesting that ATP5-MΦ may have higher ATP synthesis capacity in IPF lung tissue. This study provides new insights into the pathogenesis of IPF and provides a basis for evaluating disease prognosis and predictive medicine in IPF patients.
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Affiliation(s)
- Hao Zhang
- Department of Oncology, The Eighth Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100091, China
- Department of Oncology, The Fifth Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100071, China
| | - Yuwei Yang
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China
- Beijing Key Laboratory of OTIR, Beijing, 100091, China
| | - Yan Cao
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China.
- Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Jingzhi Guan
- Department of Oncology, The Fifth Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100071, China.
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12
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Ke D, Cao M, Ni J, Yuan Y, Deng J, Chen S, Dai X, Zhou H. Macrophage and fibroblast trajectory inference and crosstalk analysis during myocardial infarction using integrated single-cell transcriptomic datasets. J Transl Med 2024; 22:560. [PMID: 38867219 PMCID: PMC11167890 DOI: 10.1186/s12967-024-05353-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Cardiac fibrosis after myocardial infarction (MI) has been considered an important part of cardiac pathological remodeling. Immune cells, especially macrophages, are thought to be involved in the process of fibrosis and constitute a niche with fibroblasts to promote fibrosis. However, the diversity and variability of fibroblasts and macrophages make it difficult to accurately depict interconnections. METHODS We collected and reanalyzed scRNA-seq and snRNA-seq datasets from 12 different studies. Differentiation trajectories of these subpopulations after MI injury were analyzed by using scVelo, PAGA and Slingshot. We used CellphoneDB and NicheNet to infer fibroblast-macrophage interactions. Tissue immunofluorescence staining and in vitro experiments were used to validate our findings. RESULTS We discovered two subsets of ECM-producing fibroblasts, reparative cardiac fibroblasts (RCFs) and matrifibrocytes, which appeared at different times after MI and exhibited different transcriptional profiles. We also observed that CTHRC1+ fibroblasts represent an activated fibroblast in chronic disease states. We identified a macrophage subset expressing the genes signature of SAMs conserved in both human and mouse hearts. Meanwhile, the SPP1hi macrophages were predominantly found in the early stages after MI, and cell communication analysis indicated that SPP1hi macrophage-RCFs interactions are mainly involved in collagen deposition and scar formation. CONCLUSIONS Overall, this study comprehensively analyzed the dynamics of fibroblast and macrophage subsets after MI and identified specific subsets of fibroblasts and macrophages involved in scar formation and collagen deposition.
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Affiliation(s)
- Da Ke
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Mingzhen Cao
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Jian Ni
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Yuan Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Jiangyang Deng
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Si Chen
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Xiujun Dai
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China
| | - Heng Zhou
- Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, People's Republic of China.
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, People's Republic of China.
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13
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Zhao Y, Huang Z, Gao L, Ma H, Chang R. Osteopontin/SPP1: a potential mediator between immune cells and vascular calcification. Front Immunol 2024; 15:1395596. [PMID: 38919629 PMCID: PMC11196619 DOI: 10.3389/fimmu.2024.1395596] [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: 03/04/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Vascular calcification (VC) is considered a common pathological process in various vascular diseases. Accumulating studies have confirmed that VC is involved in the inflammatory response in heart disease, and SPP1+ macrophages play an important role in this process. In VC, studies have focused on the physiological and pathological functions of macrophages, such as pro-inflammatory or anti-inflammatory cytokines and pro-fibrotic vesicles. Additionally, macrophages and activated lymphocytes highly express SPP1 in atherosclerotic plaques, which promote the formation of fatty streaks and plaque development, and SPP1 is also involved in the calcification process of atherosclerotic plaques that results in heart failure, but the crosstalk between SPP1-mediated immune cells and VC has not been adequately addressed. In this review, we summarize the regulatory effect of SPP1 on VC in T cells, macrophages, and dendritic cells in different organs' VC, which could be a potential therapeutic target for VC.
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Affiliation(s)
- Yanli Zhao
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Zujuan Huang
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Limei Gao
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Hongbo Ma
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Rong Chang
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
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14
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Adewale AT, Sharma S, Mouawad J, Nguyen XX, Bradshaw AD, Feghali-Bostwick C. IGF-II Regulates Lysyl Oxidase Propeptide and Mediates its Effects in part via Basic Helix-Loop-Helix E40. Matrix Biol 2024; 132:S0945-053X(24)00078-7. [PMID: 38852924 DOI: 10.1016/j.matbio.2024.06.002] [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: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Pulmonary fibrosis (PF) is a clinically severe and commonly fatal complication of Systemic Sclerosis (SSc). Our group has previously reported profibrotic roles for Insulin-like Growth Factor II (IGF-II) and Lysyl Oxidase (LOX) in SSc-PF. We sought to identify downstream regulatory mediators of IGF-II. In the present work, we show that SSc lung tissues have higher baseline levels of the total (N-glycosylated/unglycosylated) LOX-Propeptide (LOX-PP) than normal lung tissues. LOX-PP-mediated changes were consistent with the extracellular matrix (ECM) deregulation implicated in SSc-PF progression. Furthermore, Tolloid-like 1 (TLL1) and Bone Morphogenetic Protein 1 (BMP1), enzymes that can cleave ProLOX to release LOX-PP, were increased in SSc lung fibrosis and the bleomycin (BLM)-induced murine lung fibrosis model, respectively. In addition, IGF-II regulated the levels of ProLOX, active LOX, LOX-PP, BMP1, and isoforms of TLL1. The Class E Basic Helix-Loop-Helix protein 40 (BHLHE40) transcription factor localized to the nucleus in response to IGF-II. BHLHE40 silencing downregulated TLL1 isoforms and LOX-PP, and restored significant features of ECM deregulation triggered by IGF-II. Our findings indicate that IGF-II, BHLHE40, and LOX-PP may serve as targets of therapeutic intervention to halt SSc-PF progression.
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Affiliation(s)
- Adegboyega Timothy Adewale
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Shailza Sharma
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
| | - Joe Mouawad
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Xinh-Xinh Nguyen
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Amy D Bradshaw
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carol Feghali-Bostwick
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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15
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Lin JH, Liu CC, Liu CY, Hsu TW, Yeh YC, How CK, Hsu HS, Hung SC. Selenite selectively kills lung fibroblasts to treat bleomycin-induced pulmonary fibrosis. Redox Biol 2024; 72:103148. [PMID: 38603946 PMCID: PMC11017345 DOI: 10.1016/j.redox.2024.103148] [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: 12/28/2023] [Revised: 02/01/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Interstitial lung disease (ILD) treatment is a critical unmet need. Selenium is an essential trace element for human life and an antioxidant that activates glutathione, but the gap between its necessity and its toxicity is small and requires special attention. Whether selenium can be used in the treatment of ILD remains unclear. METHODS We investigated the prophylactic and therapeutic effects of selenite, a selenium derivative, in ILD using a murine model of bleomycin-induced idiopathic pulmonary fibrosis (IPF). We further elucidated the underlying mechanism using in vitro cell models and examined their relevance in human tissue specimens. The therapeutic effect of selenite in bleomycin-administered mice was assessed by respiratory function and histochemical changes. Selenite-induced apoptosis and reactive oxygen species (ROS) production in murine lung fibroblasts were measured. RESULTS Selenite, administered 1 day (inflammation phase) or 8 days (fibrotic phase) after bleomycin, prevented and treated deterioration of lung function and pulmonary fibrosis in mice. Mechanistically, selenite inhibited the proliferation and induced apoptosis of murine lung fibroblasts after bleomycin treatment both in vitro and in vivo. In addition, selenite upregulated glutathione reductase (GR) and thioredoxin reductase (TrxR) in murine lung fibroblasts, but not in lung epithelial cells, upon bleomycin treatment. GR and TrxR inhibition eliminates the therapeutic effects of selenite. Furthermore, we found that GR and TrxR were upregulated in the human lung fibroblasts of IPF patient samples. CONCLUSIONS Selenite induces ROS production and apoptosis in murine lung fibroblasts through GR and TrxR upregulation, thereby providing a therapeutic effect in bleomycin-induced IPF.
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Affiliation(s)
- Jiun-Han Lin
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chen-Chi Liu
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Traumatology, Emergency Department, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Chao-Yu Liu
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Thoracic Surgery, Department of Surgery, Far-Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Tien-Wei Hsu
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Chen Yeh
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chorng-Kuang How
- Division of Traumatology, Emergency Department, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Han-Shui Hsu
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Shih-Chieh Hung
- Drug Development Center, Institute of Translational Medicine and New Drug Development, School of Medicine, Taiwan; College of Life Sciences, China Medical University, Taichung, Taiwan; Integrative Stem Cell Center, Department of Orthopedics, China Medical University Hospital, Taichung, Taiwan.
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16
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Huang G, Geng Y, Kulur V, Liu N, Liu X, Taghavifar F, Liang J, Noble PW, Jiang D. Arrestin beta 1 Regulates Alveolar Progenitor Renewal and Lung Fibrosis. JOURNAL OF RESPIRATORY BIOLOGY AND TRANSLATIONAL MEDICINE 2024; 1:10006. [PMID: 38736470 PMCID: PMC11087074 DOI: 10.35534/jrbtm.2024.10006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
The molecular mechanisms that regulate progressive pulmonary fibrosis remain poorly understood. Type 2 alveolar epithelial cells (AEC2s) function as adult stem cells in the lung. We previously showed that there is a loss of AEC2s and a failure of AEC2 renewal in the lungs of idiopathic pulmonary fibrosis (IPF) patients. We also reported that beta-arrestins are the key regulators of fibroblast invasion, and beta-arrestin 1 and 2 deficient mice exhibit decreased mortality, decreased matrix deposition, and increased lung function in bleomycin-induced lung fibrosis. However, the role of beta-arrestins in AEC2 regeneration is unclear. In this study, we investigated the role and mechanism of Arrestin beta 1 (ARRB1) in AEC2 renewal and in lung fibrosis. We used conventional deletion as well as cell type-specific deletion of ARRB1 in mice and found that Arrb1 deficiency in fibroblasts protects mice from lung fibrosis, and the knockout mice exhibit enhanced AEC2 regeneration in vivo, suggesting a role of fibroblast-derived ARRB1 in AEC2 renewal. We further found that Arrb1-deficient fibroblasts promotes AEC2 renewal in 3D organoid assays. Mechanistically, we found that CCL7 is among the top downregulated cytokines in Arrb1 deficient fibroblasts and CCL7 inhibits AEC2 regeneration in 3D organoid experiments. Therefore, fibroblast ARRB1 mediates AEC2 renewal, possibly by releasing chemokine CCL7, leading to fibrosis in the lung.
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Affiliation(s)
- Guanling Huang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Current Address: GH, Sanofi, 500 Kendall Street, Cambridge, MA 02142, USA
| | - Yan Geng
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Current Address: YG, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, China
| | - Vrishika Kulur
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ningshan Liu
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xue Liu
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Forough Taghavifar
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jiurong Liang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W. Noble
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dianhua Jiang
- Division of Pulmonary, Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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17
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Sun G, Zhou Y, Han X, Che X, Yu S, Song D, Ma F, Huang L. Potential marker genes for chronic obstructive pulmonary disease revealed based on single-cell sequencing and Mendelian randomization analysis. Aging (Albany NY) 2024; 16:8922-8943. [PMID: 38787375 PMCID: PMC11164476 DOI: 10.18632/aging.205849] [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: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Progress is being made in the prevention and treatment of chronic obstructive pulmonary disease (COPD), but it is still unsatisfactory. With the development of genetic technology, validated genetic information can better explain COPD. OBJECTIVE The study utilized scRNA-seq and Mendelian randomization analysis of eQTLs to identify crucial genes and potential mechanistic pathways underlying COPD pathogenesis. MEHODS Single-cell sequencing data were used to identify marker genes for immune cells in the COPD process. Data on eQTLs for immune cell marker genes were obtained from the eQTLGen consortium. To estimate the causal effect of marker genes on COPD, we selected an independent cohort (ukb-b-16751) derived from the UK Biobank database for two-sample Mendelian randomization analysis. Subsequently, we performed immune infiltration analysis, gene set enrichment analysis (GSEA), and co-expression network analysis on the key genes. RESULTS The 154 immune cell-associated marker genes identified were mainly involved in pathways such as vacuolar cleavage, positive regulation of immune response and regulation of cell activation. Mendelian randomization analysis screened four pairs of marker genes (GZMH, COTL1, CSTA and CD14) were causally associated with COPD. These four key genes were significantly associated with immune cells. In addition, we have identified potential transcription factors associated with these key genes using the Cistrome database, thus contributing to a deeper understanding of the regulatory network of these gene expressions. CONCLUSIONS This eQTLs Mendelian randomization study identified four key genes (GZMH, COTL1, CSTA, and CD14) causally associated with COPD, providing new insights for prevention and treatment of COPD.
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Affiliation(s)
- Gang Sun
- General Hospital of Northern Theater Command, Shenyang 110000, Liaoning, China
| | - Yun Zhou
- East China Normal University Wuhu Affiliated Hospital (The Second People’s Hospital of Wuhu City), Wuhu 241000, Anhui, China
| | - Xiaoxiao Han
- The Second People's Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei 230022, Anhui China
| | - Xiangqian Che
- General Hospital of Northern Theater Command, Shenyang 110000, Liaoning, China
| | - Shuo Yu
- The Second People's Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei 230022, Anhui China
| | - Di Song
- General Hospital of Northern Theater Command, Shenyang 110000, Liaoning, China
| | - Feifei Ma
- General Hospital of Northern Theater Command, Shenyang 110000, Liaoning, China
| | - Lewei Huang
- General Hospital of Northern Theater Command, Shenyang 110000, Liaoning, China
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18
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Zhang X, Xiao Y, Hu B, Li Y, Zhang S, Tian J, Wang S, Tao Z, Zeng X, Liu NN, Li B, Liu S. Multi-omics analysis of human tendon adhesion reveals that ACKR1-regulated macrophage migration is involved in regeneration. Bone Res 2024; 12:27. [PMID: 38714649 PMCID: PMC11076548 DOI: 10.1038/s41413-024-00324-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: 10/20/2023] [Revised: 01/09/2024] [Accepted: 02/19/2024] [Indexed: 05/10/2024] Open
Abstract
Tendon adhesion is a common complication after tendon injury with the development of accumulated fibrotic tissues without effective anti-fibrotic therapies, resulting in severe disability. Macrophages are widely recognized as a fibrotic trigger during peritendinous adhesion formation. However, different clusters of macrophages have various functions and receive multiple regulation, which are both still unknown. In our current study, multi-omics analysis including single-cell RNA sequencing and proteomics was performed on both human and mouse tendon adhesion tissue at different stages after tendon injury. The transcriptomes of over 74 000 human single cells were profiled. As results, we found that SPP1+ macrophages, RGCC+ endothelial cells, ACKR1+ endothelial cells and ADAM12+ fibroblasts participated in tendon adhesion formation. Interestingly, despite specific fibrotic clusters in tendon adhesion, FOLR2+ macrophages were identified as an antifibrotic cluster by in vitro experiments using human cells. Furthermore, ACKR1 was verified to regulate FOLR2+ macrophages migration at the injured peritendinous site by transplantation of bone marrow from Lysm-Cre;R26RtdTomato mice to lethally irradiated Ackr1-/- mice (Ackr1-/- chimeras; deficient in ACKR1) and control mice (WT chimeras). Compared with WT chimeras, the decline of FOLR2+ macrophages was also observed, indicating that ACKR1 was specifically involved in FOLR2+ macrophages migration. Taken together, our study not only characterized the fibrosis microenvironment landscape of tendon adhesion by multi-omics analysis, but also uncovered a novel antifibrotic cluster of macrophages and their origin. These results provide potential therapeutic targets against human tendon adhesion.
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Affiliation(s)
- Xinshu Zhang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China
| | - Yao Xiao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China
| | - Bo Hu
- Section of Spine Surgery, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, PR China
| | - Yanhao Li
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China
| | - Shaoyang Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200241, PR China
| | - Jian Tian
- Department of Orthopaedics, Wuxi Ninth People's Hospital Affiliated to Soochow University, Wuxi, 214062, PR China
| | - Shuo Wang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China
| | - Zaijin Tao
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China
| | - Xinqi Zeng
- Department of Orthopaedics, Wuxi Ninth People's Hospital Affiliated to Soochow University, Wuxi, 214062, PR China
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Baojie Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200241, PR China.
| | - Shen Liu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Rd, Shanghai, 200233, PR China.
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Wong IG, Stark J, Ya V, Moye AL, Vazquez AB, Dang SM, Shehaj A, Rouhani MJ, Bronson R, Janes SM, Rowbotham SP, Paschini M, Franklin RA, Kim CF. Airway injury induces alveolar epithelial and mesenchymal responses mediated by macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587596. [PMID: 38617297 PMCID: PMC11014629 DOI: 10.1101/2024.04.02.587596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Acute injury in the airways or the lung activates local progenitors and stimulates changes in cell-cell interactions to restore homeostasis, but it is not appreciated how more distant niches are impacted. We utilized mouse models of airway-specific epithelial injury to examine secondary tissue-wide alveolar, immune, and mesenchymal responses. Single-cell transcriptomics and in vivo validation revealed transient, tissue-wide proliferation of alveolar type 2 (AT2) progenitor cells after club cell-specific ablation. The AT2 cell proliferative response was reliant on alveolar macrophages (AMs) via upregulation of Spp1 which encodes the secreted factor Osteopontin. A previously uncharacterized mesenchymal population we termed Mesenchymal Airway/Adventitial Niche Cell 2 (MANC2) also exhibited dynamic changes in abundance and a pro-fibrotic transcriptional signature after club cell ablation in an AM-dependent manner. Overall, these results demonstrate that acute airway damage can trigger distal lung responses including altered cell-cell interactions that may contribute to potential vulnerabilities for further dysregulation and disease.
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Zhu J, Jiang Q, Gao S, Xia Q, Zhang H, Liu B, Zhao R, Jiang H, Li X, Xu A, Zhou H, Xu Z, Yang C. IL20Rb aggravates pulmonary fibrosis through enhancing bone marrow derived profibrotic macrophage activation. Pharmacol Res 2024; 203:107178. [PMID: 38583686 DOI: 10.1016/j.phrs.2024.107178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is one of the most fatal chronic interstitial lung diseases with unknown pathogenesis, current treatments cannot truly reverse the progression of the disease. Pulmonary macrophages, especially bone marrow derived pro-fibrotic macrophages, secrete multiple kinds of profibrotic mediators (SPP1, CD206, CD163, IL-10, CCL18…), thus further promote myofibroblast activation and fibrosis procession. IL20Rb is a cell-surface receptor that belongs to IL-20 family. The role of IL20Rb in macrophage activation and pulmonary fibrosis remains unclear. In this study, we established a bleomycin-induced pulmonary fibrosis model, used IL4/13-inducing THP1 cells to induce profibrotic macrophage (M2-like phenotype) polarization models. We found that IL20Rb is upregulated in the progression of pulmonary fibrosis, and its absence can alleviate the progression of pulmonary fibrosis. In addition, we demonstrated that IL20Rb promote the activation of bone marrow derived profibrotic macrophages by regulating the Jak2/Stat3 and Pi3k/Akt signaling pathways. In terms of therapeutic strategy, we used IL20Rb neutralizing antibodies for animal administration, which was found to alleviate the progression of IPF. Our results suggest that IL20Rb plays a profibrotic role by promoting profibrotic macrophage polarization, and IL20Rb may become a potential therapeutic target for IPF. Neutralizing antibodies against IL20Rb may become a potential drug for the clinical treatment of IPF.
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Affiliation(s)
- Jingyan Zhu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China
| | - Qiuyan Jiang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China
| | - Shaoyan Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China
| | - Qin Xia
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China
| | - Huizhe Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China
| | - Bowen Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China
| | - Ruixi Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China
| | - Haixia Jiang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China
| | - Xiaohe Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China
| | - Aiguo Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| | - Honggang Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China.
| | - Zuojun Xu
- Department of Respiratory and Critical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300000, China; High-throughput Molecular Drug Screening Centre, Tianjin International Joint Academy of Biomedicine, Tianjin 300070, China.
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21
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Bhattacharyya A, Khan R, Lee JY, Tassew G, Oskouian B, Allende ML, Proia RL, Yin X, Ortega JG, Bhattacharya M, Saba JD. Gene therapy with AAV9-SGPL1 in an animal model of lung fibrosis. J Pathol 2024; 263:22-31. [PMID: 38332723 PMCID: PMC10987276 DOI: 10.1002/path.6256] [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: 08/10/2023] [Revised: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease of the lung that leads rapidly to respiratory failure. Novel approaches to treatment are urgently needed. The bioactive lipid sphingosine-1-phosphate (S1P) is increased in IPF lungs and promotes proinflammatory and profibrotic TGF-β signaling. Hence, decreasing lung S1P represents a potential therapeutic strategy for IPF. S1P is degraded by the intracellular enzyme S1P lyase (SPL). Here we find that a knock-in mouse with a missense SPL mutation mimicking human disease resulted in reduced SPL activity, increased S1P, increased TGF-β signaling, increased lung fibrosis, and higher mortality after injury compared to wild type (WT). We then tested adeno-associated virus 9 (AAV9)-mediated overexpression of human SGPL1 (AAV-SPL) in mice as a therapeutic modality. Intravenous treatment with AAV-SPL augmented lung SPL activity, attenuated S1P levels within the lungs, and decreased injury-induced fibrosis compared to controls treated with saline or only AAV. We confirmed that AAV-SPL treatment led to higher expression of SPL in the epithelial and fibroblast compartments during bleomycin-induced lung injury. Additionally, AAV-SPL decreased expression of the profibrotic cytokines TNFα and IL1β as well as markers of fibroblast activation, such as fibronectin (Fn1), Tgfb1, Acta2, and collagen genes in the lung. Taken together, our results provide proof of concept for the use of AAV-SPL as a therapeutic strategy for the treatment of IPF. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Aritra Bhattacharyya
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ranjha Khan
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Joanna Y. Lee
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Gizachew Tassew
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Babak Oskouian
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Maria L. Allende
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard L. Proia
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xiaoyang Yin
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Javier G. Ortega
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mallar Bhattacharya
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Julie D. Saba
- Department of Pediatrics, University of California, San Francisco, CA, USA
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22
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Pervizaj-Oruqaj L, Ferrero MR, Matt U, Herold S. The guardians of pulmonary harmony: alveolar macrophages orchestrating the symphony of lung inflammation and tissue homeostasis. Eur Respir Rev 2024; 33:230263. [PMID: 38811033 PMCID: PMC11134199 DOI: 10.1183/16000617.0263-2023] [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: 12/20/2023] [Accepted: 03/20/2024] [Indexed: 05/31/2024] Open
Abstract
Recent breakthroughs in single-cell sequencing, advancements in cellular and tissue imaging techniques, innovations in cell lineage tracing, and insights into the epigenome collectively illuminate the enigmatic landscape of alveolar macrophages in the lung under homeostasis and disease conditions. Our current knowledge reveals the cellular and functional diversity of alveolar macrophages within the respiratory system, emphasising their remarkable adaptability. By synthesising insights from classical cell and developmental biology studies, we provide a comprehensive perspective on alveolar macrophage functional plasticity. This includes an examination of their ontology-related features, their role in maintaining tissue homeostasis under steady-state conditions and the distinct contribution of bone marrow-derived macrophages (BMDMs) in promoting tissue regeneration and restoring respiratory system homeostasis in response to injuries. Elucidating the signalling pathways within inflammatory conditions, the impact of various triggers on tissue-resident alveolar macrophages (TR-AMs), as well as the recruitment and polarisation of macrophages originating from the bone marrow, presents an opportunity to propose innovative therapeutic approaches aimed at modulating the equilibrium between phenotypes to induce programmes associated with a pro-regenerative or homeostasis phenotype of BMDMs or TR-AMs. This, in turn, can lead to the amelioration of disease outcomes and the attenuation of detrimental inflammation. This review comprehensively addresses the pivotal role of macrophages in the orchestration of inflammation and resolution phases after lung injury, as well as ageing-related shifts and the influence of clonal haematopoiesis of indeterminate potential mutations on alveolar macrophages, exploring altered signalling pathways and transcriptional profiles, with implications for respiratory homeostasis.
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Affiliation(s)
- Learta Pervizaj-Oruqaj
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, University Hospital Giessen, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen, Germany
| | - Maximiliano Ruben Ferrero
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, University Hospital Giessen, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen, Germany
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), Buenos Aires, Argentina
| | - Ulrich Matt
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, University Hospital Giessen, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, University Hospital Giessen, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen, Germany
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23
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Lin S, Lin R, Zhu P, Sun X, Qiu C, Zhang B, He Y, Xu Q, Zhang H. Neutrophil extracellular traps promoting fibroblast activation and aggravating limb ischemia through Wnt5a pathway. Am J Cancer Res 2024; 14:1866-1879. [PMID: 38726275 PMCID: PMC11076237 DOI: 10.62347/sqoc7984] [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: 03/03/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
Although the formation of NETs contributes to cancer cell invasion and distant metastasis, its role in the pathological progression of limb ischemia remains unknown. This study investigated the functional significance of NETs in cell-cell crosstalk during limb ischemia. The changes of cell subsets in lower limb ischemia samples were detected by single-cell RNA sequencing. The expression of neutrophil extracellular traps (NETs) related markers in lower limb ischemia samples was detected by immunohistochemistry and Western blotting. The signaling pathway of NETs activation in fibroblasts was verified by immunofluorescence, PCR and Western blotting. Through single-cell RNA sequencing (scRNA-seq), we identified 9 distinct cell clusters, with significantly upregulated activation levels in fibroblasts and neutrophils and phenotypic transformation of smooth muscle cells (SMCs) into a proliferative state in ischemic tissue. At the same time, the interaction between fibroblasts and smooth muscle cells was significantly enhanced in ischemic tissue. NETs levels rise and fibroblast activation is induced in ischemic conditions. Mechanistically, activated fibroblasts promote smooth muscle cell proliferation through the Wnt5a pathway. In ischemic mice, inhibition of Wnt5a mitigated vascular remodeling and subsequent ischemia. These findings highlighting the role of cell-cell crosstalk in ischemia and vascular remodeling. We found that the NETs-initiated fibroblast-SMC interaction is a critical regulator of limb ischemia via Wnt5a pathway, a potential therapeutic target for the treatment.
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Affiliation(s)
- Shigang Lin
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Ruoran Lin
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Pengwei Zhu
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Xiaotong Sun
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Chenyang Qiu
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Bohuan Zhang
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Yangyan He
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Qingbo Xu
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Hongkun Zhang
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
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24
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Xiao Z, Nian Z, Zhang M, Liu Z, Zhang P, Zhang Z. Single-cell and bulk RNA-sequencing reveal SPP1 and CXCL12 as cell-to-cell communication markers to predict prognosis in lung adenocarcinoma. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38622884 DOI: 10.1002/tox.24297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
Lung adenocarcinoma (LUAD) generally presents as an immunosuppressive microenvironment. The characteristics of cell-to-cell communication in the LUAD microenvironment has been unclear. In this study, the LUAD bulk RNA-seq data and single-cell RNA-seq data were retrieved from public dataset. Differential expression genes (DEGs) between LUAD tumor and adjacent non-tumor tissues were calculated by limma algorithm, and then detected by PPI, KEGG, and GO analysis. Cell-cell interactions were explored using the single-cell RNA-seq data. Finally, the first 15 CytoHubba genes were used to establish related pathways and these pathways were used to characterize the immune-related ligands and their receptors in LUAD. Our analyses showed that monocytes or macrophages interact with tissue stem cells and NK cells via SPP1 signaling pathway and tissue stem cells interact with T and B cells via CXCL signaling pathway in different states. Hub genes of SPP1 participated in SPP1 signaling pathway, which was negatively correlated with CD4+ T cell and CD8+ T cell. The expression of SPP1 in LUAD tumor tissues was negatively correlated with the prognosis. While CXCL12 participated in CXCL signaling pathway, which was positively correlated with CD4+ T cell and CD8+ T cell. The role of CXCL12 in LUAD tumor tissues exhibits an opposite effect to that of SPP1. This study reveals that tumor-associated monocytes or macrophages may affect tumor progression. Moreover, the SPP1 and CXCL12 may be the critic genes of cell-to-cell communication in LUAD, and targeting these pathways may provide a new molecular mechanism for the treatment of LUAD.
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Affiliation(s)
- Zengtuan Xiao
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Zhe Nian
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Mengzhe Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Zuo Liu
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Pengpeng Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
| | - Zhenfa Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, China
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25
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Cheng D, Lian W, Wang T, Xi S, Jia X, Li Z, Xiong H, Wang Y, Sun W, Zhou S, Peng L, Han L, Liu Y, Ni C. The interplay of Cxcl10 +/Mmp14 + monocytes and Ccl3 + neutrophils proactively mediates silica-induced pulmonary fibrosis. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133713. [PMID: 38335607 DOI: 10.1016/j.jhazmat.2024.133713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
As a fatal occupational disease with limited therapeutic options, molecular mechanisms underpinning silicosis are still undefined. Herein, single-cell RNA sequencing of the lung tissue of silicosis mice identified two monocyte subsets, which were characterized by Cxcl10 and Mmp14 and enriched in fibrotic mouse lungs. Both Cxcl10+ and Mmp14+ monocyte subsets exhibited activation of inflammatory marker genes and positive regulation of cytokine production. Another fibrosis-unique neutrophil population characterized by Ccl3 appeared to be related to the pro-fibrotic process, specifically the "inflammatory response". Meanwhile, the proportion of monocytes and neutrophils was significantly higher in the serum of silicosis patients and slices of lung tissue from patients with silicosis further validated the over-expression of Cxcl10 and Mmp14 in monocytes, also Ccl3 in neutrophils, respectively. Mechanically, receptor-ligand interaction analysis identified the crosstalk of Cxcl10+/Mmp14+ monocytes with Ccl3+ neutrophils promoting fibrogenesis via coupling of HBEGF-CD44 and CSF1-CSF1R. In vivo, administration of clodronate liposomes, Cxcl10 or Mmp14 siRNA-loaded liposomes, Ccl3 receptor antagonist BX471, CD44 or CSF1R neutralizing antibodies significantly alleviated silica-induced lung fibrosis. Collectively, these results demonstrate that the newly defined Cxcl10+/Mmp14+ monocytes and Ccl3+ neutrophils participate in the silicosis process and highlight anti-receptor-ligand pair treatment as a potentially effective therapeutic strategy in managing silicosis.
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Affiliation(s)
- Demin Cheng
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Wenxiu Lian
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ting Wang
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210000, China
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Xinying Jia
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ziwei Li
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Haojie Xiong
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yue Wang
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Wenqing Sun
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Siyun Zhou
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lan Peng
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lei Han
- Institute of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210028, China
| | - Yi Liu
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Gusu School, Nanjing Medical University, Nanjing 211166, China.
| | - Chunhui Ni
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Public Health, Kangda College of Nanjing Medical University, Lianyungang 320700, China.
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Gong P, Ding Y, Li W, Yang J, Su X, Tian R, Zhou Y, Wang T, Jiang J, Liu R, Fang J, Feng C, Shao C, Shi Y, Li P. Neutrophil-Driven M2-Like Macrophages Are Critical for Skin Fibrosis in a Systemic Sclerosis Model. J Invest Dermatol 2024:S0022-202X(24)00274-4. [PMID: 38580106 DOI: 10.1016/j.jid.2024.03.031] [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: 04/28/2023] [Revised: 01/04/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024]
Abstract
Systemic sclerosis (SSc) is a challenging autoimmune disease characterized by progressive fibrosis affecting the skin and internal organs. Despite the known infiltration of macrophages and neutrophils, their precise contributions to SSc pathogenesis remain elusive. In this study, we elucidated that CD206hiMHCIIlo M2-like macrophages constitute the predominant pathogenic immune cell population in the fibrotic skin of a bleomycin-induced SSc mouse model. These cells emerged as pivotal contributors to the profibrotic response by orchestrating the production of TGF-β1 through a MerTK signaling-dependent manner. Notably, we observed that neutrophil infiltration was a prerequisite for accumulation of M2-like macrophages. Strategies such as neutrophil depletion or inhibition of CXCR1/2 were proven effective in reducing M2-like macrophages, subsequently mitigating SSc progression. Detailed investigations revealed that in fibrotic skin, neutrophil-released neutrophil extracellular traps were responsible for the differentiation of M2-like macrophages. Our findings illuminate the significant involvement of the neutrophil-macrophage-fibrosis axis in SSc pathogenesis, offering critical information for the development of potential therapeutic strategies.
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Affiliation(s)
- Pixia Gong
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China; Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yayun Ding
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Wen Li
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Jie Yang
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Xiao Su
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Ruifeng Tian
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yipeng Zhou
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Tingting Wang
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Junjie Jiang
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Rui Liu
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Jiankai Fang
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Chao Feng
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Changshun Shao
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yufang Shi
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China.
| | - Peishan Li
- The First Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, China.
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27
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Hu W, Xu Y. Transcriptomics in idiopathic pulmonary fibrosis unveiled: a new perspective from differentially expressed genes to therapeutic targets. Front Immunol 2024; 15:1375171. [PMID: 38566986 PMCID: PMC10985171 DOI: 10.3389/fimmu.2024.1375171] [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: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Background The underlying molecular pathways of idiopathic pulmonary fibrosis (IPF), a progressive lung condition with a high death rate, are still mostly unknown. By using microarray datasets, this study aims to identify new genetic targets for IPF and provide light on the genetic factors that contribute to the development of IPF. Method We conducted a comprehensive analysis of three independent IPF datasets from the Gene Expression Omnibus (GEO) database, employing R software for data handling and normalization. Our evaluation of the relationships between differentially expressed genes (DEGs) and IPF included differential expression analysis, expression quantitative trait loci (eQTL) analysis, and Mendelian Randomization(MR) analyses. Additionally, we used Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to explore the functional roles and pathways of these genes. Finally, we validated the results obtained for the target genes. Results We identified 486 highly expressed genes and 468 lowly expressed genes that play important roles in IPF. MR analysis identified six significantly co-expressed genes associated with IPF, specifically C12orf75, SPP1, ZG16B, LIN7A, PPP1R14A, and TLR2. These genes participate in essential biological processes and pathways, including macrophage activation and neural system regulation. Additionally, CIBERSORT analysis indicated a unique immune cell distribution in IPF, emphasized the significance of immunological processes in the disease. The MR analysis was consistent with the results of the analysis of variance in the validation cohort, which strengthens the reliability of our MR findings. Conclusion Our findings provide new insights into the molecular basis of IPF and highlight the promise of therapeutic interventions. They emphasize the potential of targeting specific molecular pathways for the treatment of IPF, laying the foundation for further research and clinical work.
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Affiliation(s)
- Wenzhong Hu
- Guang’anmen Hospital South Campus, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yun Xu
- People's Hospital of Beijing Daxing District, Capital Medical University, Beijing, China
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28
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Zhou BW, Liu HM, Xu F, Jia XH. The role of macrophage polarization and cellular crosstalk in the pulmonary fibrotic microenvironment: a review. Cell Commun Signal 2024; 22:172. [PMID: 38461312 PMCID: PMC10924385 DOI: 10.1186/s12964-024-01557-2] [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: 12/28/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024] Open
Abstract
Pulmonary fibrosis (PF) is a progressive interstitial inflammatory disease with a high mortality rate. Patients with PF commonly experience a chronic dry cough and progressive dyspnoea for years without effective mitigation. The pathogenesis of PF is believed to be associated with dysfunctional macrophage polarization, fibroblast proliferation, and the loss of epithelial cells. Thus, it is of great importance and necessity to explore the interactions among macrophages, fibroblasts, and alveolar epithelial cells in lung fibrosis, as well as in the pro-fibrotic microenvironment. In this review, we discuss the latest studies that have investigated macrophage polarization and activation of non-immune cells in the context of PF pathogenesis and progression. Next, we discuss how profibrotic cellular crosstalk is promoted in the PF microenvironment by multiple cytokines, chemokines, and signalling pathways. And finally, we discuss the potential mechanisms of fibrogenesis development and efficient therapeutic strategies for the disease. Herein, we provide a comprehensive summary of the vital role of macrophage polarization in PF and its profibrotic crosstalk with fibroblasts and alveolar epithelial cells and suggest potential treatment strategies to target their cellular communication in the microenvironment.
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Affiliation(s)
- Bo-Wen Zhou
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Hua-Man Liu
- Department of General Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Fei Xu
- Department of Pneumology and Critical Care Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Xin-Hua Jia
- Department of Pneumology and Critical Care Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China.
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29
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Li C, Feng X, Li S, He X, Luo Z, Cheng X, Yao J, Xiao J, Wang X, Wen D, Liu D, Li Y, Zhou H, Ma L, Lin T, Cai X, Lin Y, Guo L, Yang M. Tetrahedral DNA loaded siCCR2 restrains M1 macrophage polarization to ameliorate pulmonary fibrosis in chemoradiation-induced murine model. Mol Ther 2024; 32:766-782. [PMID: 38273656 PMCID: PMC10928155 DOI: 10.1016/j.ymthe.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/05/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lethal disease in the absence of demonstrated efficacy for preventing progression. Although macrophage-mediated alveolitis is determined to participate in myofibrotic transition during disease development, the paradigm of continuous macrophage polarization is still under-explored due to lack of proper animal models. Here, by integrating 2.5 U/kg intratracheal Bleomycin administration and 10 Gy thorax irradiation at day 7, we generated a murine model with continuous alveolitis-mediated fibrosis, which mimics most of the clinical features of our involved IPF patients. In combination with data from scRNA-seq of patients and a murine IPF model, a decisive role of CCL2/CCR2 axis in driving M1 macrophage polarization was revealed, and M1 macrophage was further confirmed to boost alveolitis in leading myofibroblast activation. Multiple sticky-end tetrahedral framework nucleic acids conjunct with quadruple ccr2-siRNA (FNA-siCCR2) was synthesized in targeting M1 macrophages. FNA-siCCR2 successfully blocked macrophage accumulation in pulmonary parenchyma of the IPF murine model, thus preventing myofibroblast activation and leading to the disease remitting. Overall, our studies lay the groundwork to develop a novel IPF murine model, reveal M1 macrophages as potential therapeutic targets, and establish new treatment strategy by using FNA-siCCR2, which are highly relevant to clinical scenarios and translational research in the field of IPF.
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Affiliation(s)
- Chen Li
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Xiaorong Feng
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xing He
- School of Clinical Medicine, Chengdu Medical College, Chengdu 610500, China
| | - Zeli Luo
- Department of Pulmonary and Critical Care Medicine, Wenjiang Hospital of Sichuan Provincial People's, Chengdu 611138, China
| | - Xia Cheng
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Jie Yao
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Jie Xiao
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Xiaofei Wang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dingke Wen
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Duanya Liu
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Yanfei Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Hong Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610056, China
| | - Lu Ma
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tongyu Lin
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; College of Biomedical Engineering, Sichuan University, Chengdu 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; College of Biomedical Engineering, Sichuan University, Chengdu 610041, China.
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.
| | - Mu Yang
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China.
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30
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Liu W, Li W, Zhao Z. Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients. Mol Cancer Res 2024; 22:240-253. [PMID: 38063850 PMCID: PMC10922768 DOI: 10.1158/1541-7786.mcr-23-0692] [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: 08/27/2023] [Revised: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Coronavirus disease 2019 (COVID-19) and cancer are major health threats, and individuals may develop both simultaneously. Recent studies have indicated that patients with cancer are particularly vulnerable to COVID-19, but the molecular mechanisms underlying the associations remain poorly understood. To address this knowledge gap, we collected single-cell RNA-sequencing data from COVID-19, lung adenocarcinoma, small cell lung carcinoma patients, and normal lungs to perform an integrated analysis. We characterized altered cell populations, gene expression, and dysregulated intercellular communication in diseases. Our analysis identified pathologic conditions shared by COVID-19 and lung cancer, including upregulated TMPRSS2 expression in epithelial cells, stronger inflammatory responses mediated by macrophages, increased T-cell response suppression, and elevated fibrosis risk by pathologic fibroblasts. These pre-existing conditions in patients with lung cancer may lead to more severe inflammation, fibrosis, and weakened adaptive immune response upon COVID-19 infection. Our findings revealed potential molecular mechanisms driving an increased COVID-19 risk in patients with lung cancer and suggested preventive and therapeutic targets for COVID-19 in this population. IMPLICATIONS Our work reveals the potential molecular mechanisms contributing to the vulnerability to COVID-19 in patients with lung cancer.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenbo Li
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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31
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Simkin J, Aloysius A, Adam M, Safaee F, Donahue RR, Biswas S, Lakhani Z, Gensel JC, Thybert D, Potter S, Seifert AW. Tissue-resident macrophages specifically express Lactotransferrin and Vegfc during ear pinna regeneration in spiny mice. Dev Cell 2024; 59:496-516.e6. [PMID: 38228141 PMCID: PMC10922778 DOI: 10.1016/j.devcel.2023.12.017] [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: 01/17/2022] [Revised: 05/30/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
The details of how macrophages control different healing trajectories (regeneration vs. scar formation) remain poorly defined. Spiny mice (Acomys spp.) can regenerate external ear pinnae tissue, whereas lab mice (Mus musculus) form scar tissue in response to an identical injury. Here, we used this dual species system to dissect macrophage phenotypes between healing modes. We identified secreted factors from activated Acomys macrophages that induce a pro-regenerative phenotype in fibroblasts from both species. Transcriptional profiling of Acomys macrophages and subsequent in vitro tests identified VEGFC, PDGFA, and Lactotransferrin (LTF) as potential pro-regenerative modulators. Examining macrophages in vivo, we found that Acomys-resident macrophages secreted VEGFC and LTF, whereas Mus macrophages do not. Lastly, we demonstrate the requirement for VEGFC during regeneration and find that interrupting lymphangiogenesis delays blastema and new tissue formation. Together, our results demonstrate that cell-autonomous mechanisms govern how macrophages react to the same stimuli to differentially produce factors that facilitate regeneration.
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Affiliation(s)
- Jennifer Simkin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Department of Orthopaedic Surgery, LSU Health-New Orleans, New Orleans, LA 70112, USA.
| | - Ajoy Aloysius
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mike Adam
- Department of Pediatrics, University of Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - Fatemeh Safaee
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Renée R Donahue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Shishir Biswas
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Zohaib Lakhani
- Department of Orthopaedic Surgery, LSU Health-New Orleans, New Orleans, LA 70112, USA
| | - John C Gensel
- Department of Physiology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA
| | - David Thybert
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Steven Potter
- Department of Pediatrics, University of Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA.
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32
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Podolsky MJ, Kheyfets B, Pandey M, Beigh AH, Yang CD, Lizama CO, Datta R, Lin LL, Wang Z, Wolters PJ, McManus MT, Qi L, Atabai K. Genome-wide screens identify SEL1L as an intracellular rheostat controlling collagen turnover. Nat Commun 2024; 15:1531. [PMID: 38378719 PMCID: PMC10879544 DOI: 10.1038/s41467-024-45817-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, here we execute unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discover a mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism appears to be dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of this protein. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus, we describe cell-autonomous, rheostatic collagen clearance as an important pathway of tissue homeostasis.
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Affiliation(s)
- Michael J Podolsky
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Benjamin Kheyfets
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Monika Pandey
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Afaq H Beigh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher D Yang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Carlos O Lizama
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Ritwik Datta
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Liangguang L Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhihong Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology and UCSF Diabetes Center, University of California, San Francisco, CA, USA
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kamran Atabai
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Lung Biology Center, University of California, San Francisco, CA, USA.
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Montesi SB, Gomez CR, Beers M, Brown R, Chattopadhyay I, Flaherty KR, Garcia CK, Gomperts B, Hariri LP, Hogaboam CM, Jenkins RG, Kaminski N, Kim GHJ, Königshoff M, Kolb M, Kotton DN, Kropski JA, Lasky J, Magin CM, Maher TM, McCormick M, Moore BB, Nickerson-Nutter C, Oldham J, Podolanczuk AJ, Raghu G, Rosas I, Rowe SM, Schmidt WT, Schwartz D, Shore JE, Spino C, Craig JM, Martinez FJ. Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report. Am J Respir Crit Care Med 2024; 209:362-373. [PMID: 38113442 PMCID: PMC10878386 DOI: 10.1164/rccm.202307-1154ws] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023] Open
Abstract
Despite progress in elucidation of disease mechanisms, identification of risk factors, biomarker discovery, and the approval of two medications to slow lung function decline in idiopathic pulmonary fibrosis and one medication to slow lung function decline in progressive pulmonary fibrosis, pulmonary fibrosis remains a disease with a high morbidity and mortality. In recognition of the need to catalyze ongoing advances and collaboration in the field of pulmonary fibrosis, the NHLBI, the Three Lakes Foundation, and the Pulmonary Fibrosis Foundation hosted the Pulmonary Fibrosis Stakeholder Summit on November 8-9, 2022. This workshop was held virtually and was organized into three topic areas: 1) novel models and research tools to better study pulmonary fibrosis and uncover new therapies, 2) early disease risk factors and methods to improve diagnosis, and 3) innovative approaches toward clinical trial design for pulmonary fibrosis. In this workshop report, we summarize the content of the presentations and discussions, enumerating research opportunities for advancing our understanding of the pathogenesis, treatment, and outcomes of pulmonary fibrosis.
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Affiliation(s)
| | - Christian R. Gomez
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Beers
- Pulmonary and Critical Care Division, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert Brown
- Program in Neurotherapeutics, University of Massachusetts Chan Medical School, Worchester, Massachusetts
| | | | | | - Christine Kim Garcia
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York
| | | | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine and
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Cory M. Hogaboam
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Grace Hyun J. Kim
- Center for Computer Vision and Imaging Biomarkers, Department of Radiological Sciences, David Geffen School of Medicine, and
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
| | - Melanie Königshoff
- Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Martin Kolb
- Division of Respirology, McMaster University, Hamilton, Ontario, Canada
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, Massachusetts
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph Lasky
- Pulmonary Fibrosis Foundation, Chicago, Illinois
- Department of Medicine, Tulane University, New Orleans, Louisiana
| | - Chelsea M. Magin
- Department of Bioengineering
- Department of Pediatrics
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, and
| | - Toby M. Maher
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | | | | | - Anna J. Podolanczuk
- Division of Pulmonary and Critical Care, Weill Cornell Medical College, New York, New York
| | - Ganesh Raghu
- Division of Pulmonary, Sleep and Critical Care Medicine, University of Washington, Seattle, Washington
| | - Ivan Rosas
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, Texas; and
| | - Steven M. Rowe
- Department of Medicine and
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - David Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - J. Matthew Craig
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care, Weill Cornell Medical College, New York, New York
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Li B, Li X, Yang Q, Jiang Y, Zhang Q, Zhang J, Cui W, Xu F. Overexpression of SPP1 is a prognostic indicator of immune infiltration in lung adenocarcinoma. Aging (Albany NY) 2024; 16:2953-2977. [PMID: 38329443 PMCID: PMC10911343 DOI: 10.18632/aging.205526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVE The extracellular phosphoprotein, secreted phosphoprotein 1 (SPP1), plays a crucial role in various tumors and regulating the immune system. This study aimed to evaluate its prognostic value and relationship to immune infiltration in lung adenocarcinoma (LUAD). METHODS In the TCGA and GEO datasets, the information on clinic and transcriptome analysis of SPP1 in non-small-cell lung cancer (NSCLC) was examined accordingly. The association of SPP1 expression with overall survival and clinicopathologic characteristics was investigated by univariate and multivariate analysis. CancerSEA database was utilized to investigate the role of SPP1 at the cellular level by single-cell analysis. Additionally, the CIBERSORT algorithm was utilized to assess the correlation among the immune cells that infiltrated. RESULTS NSCLC tissues exhibited a notable rise in SPP1 expression compared with that of normal tissues. Furthermore, the overexpression of SPP1 was substantially associated with clinicopathological features and unfavorable survival outcomes in individuals with LUAD, whereas no such correlation was observed in lung squamous cell carcinoma. Immune cells that infiltrate tumors and their corresponding genes were associated with SPP1 expression levels in LUAD. CONCLUSIONS SPP1 is a reliable indicator for assessing LUAD immune infiltration status and prognosis. With this approach, SPP1 can help earlier LUAD diagnosis and act as a possible immunotherapy target.
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Affiliation(s)
- Binbin Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Xue Li
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Qingfeng Yang
- Department of Pneumology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Yiyang Jiang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Qianwen Zhang
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Jingtao Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Wenqiang Cui
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Fei Xu
- Department of Pneumology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 168] [Impact Index Per Article: 168.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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36
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Chen Y, Li Z, Ji G, Wang S, Mo C, Ding B. Lung regeneration: diverse cell types and the therapeutic potential. MedComm (Beijing) 2024; 5:e494. [PMID: 38405059 PMCID: PMC10885188 DOI: 10.1002/mco2.494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Lung tissue has a certain regenerative ability and triggers repair procedures after injury. Under controllable conditions, lung tissue can restore normal structure and function. Disruptions in this process can lead to respiratory system failure and even death, causing substantial medical burden. The main types of respiratory diseases are chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and acute respiratory distress syndrome (ARDS). Multiple cells, such as lung epithelial cells, endothelial cells, fibroblasts, and immune cells, are involved in regulating the repair process after lung injury. Although the mechanism that regulates the process of lung repair has not been fully elucidated, clinical trials targeting different cells and signaling pathways have achieved some therapeutic effects in different respiratory diseases. In this review, we provide an overview of the cell type involved in the process of lung regeneration and repair, research models, and summarize molecular mechanisms involved in the regulation of lung regeneration and fibrosis. Moreover, we discuss the current clinical trials of stem cell therapy and pharmacological strategies for COPD, IPF, and ARDS treatment. This review provides a reference for further research on the molecular and cellular mechanisms of lung regeneration, drug development, and clinical trials.
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Affiliation(s)
- Yutian Chen
- The Department of Endovascular SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan UniversityChengduChina
| | - Zhen Li
- The Department of Endovascular SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Gaili Ji
- Department of GynecologyThe Third Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Shaochi Wang
- Department of Translational MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan UniversityChengduChina
| | - Bi‐Sen Ding
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan UniversityChengduChina
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Jia Q, Ouyang Y, Yang Y, Yao S, Chen X, Hu Z. Osteopontin: A Novel Therapeutic Target for Respiratory Diseases. Lung 2024; 202:25-39. [PMID: 38060060 DOI: 10.1007/s00408-023-00665-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Osteopontin (OPN) is a multifunctional phosphorylated protein that is involved in physiological and pathological events. Emerging evidence suggests that OPN also plays a critical role in the pathogenesis of respiratory diseases. OPN can be produced and secreted by various cell types in lungs and overexpression of OPN has been found in acute lung injury/acute respiratory distress syndrome (ALI/ARDS), pulmonary hypertension (PH), pulmonary fibrosis diseases, lung cancer, lung infection, chronic obstructive pulmonary disease (COPD), and asthma. OPN exerts diverse effects on the inflammatory response, immune cell activation, fibrosis and tissue remodeling, and tumorigenesis of these respiratory diseases, and genetic and pharmacological moudulation of OPN exerts therapeutic effects in the treatment of respiratory diseases. In this review, we summarize the recent evidence of multifaceted roles and underlying mechanisms of OPN in these respiratory diseases, and targeting OPN appears to be a potential therapeutic intervention for these diseases.
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Affiliation(s)
- Qi Jia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China
| | - Yeling Ouyang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China
| | - Yiyi Yang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China
| | - Shanglong Yao
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China
| | - Zhiqiang Hu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Key Laboratory of Anesthesiology and Resuscitation, Huazhong University of Science and Technology, Ministry of Education, Wuhan, 430022, China.
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Creyns B, MacKenzie B, Sa Y, Coelho AL, Christensen D, Parimon T, Windsor B, Hogaboam CM. Caveolin scaffolding domain (CSD) peptide LTI-2355 modulates the phagocytic and synthetic activity of lung derived myeloid cells in Idiopathic Pulmonary Fibrosis (IPF) and Post-acute sequelae of COVID-fibrosis (PASC-F). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.01.569608. [PMID: 38654821 PMCID: PMC11037873 DOI: 10.1101/2023.12.01.569608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Rationale The role of the innate immune system in Idiopathic Pulmonary Fibrosis (IPF) remains poorly understood. However, a functional myeloid compartment is required to remove dying cells and cellular debris, and to mediate innate immune responses against pathogens. Aberrant macrophage activity has been described in patients with Post-acute sequelae of COVID fibrosis (PASC-F). Therefore, we examined the functional and synthetic properties of myeloid cells isolated from normal donor lung and lung explant tissue from both IPF and PASC-F patients and explored the effect of LTI-2355, a Caveolin Scaffolding Domain (CSD) peptide, on these cells. Methods & Results CD45 + myeloid cells isolated from lung explant tissue from IPF and PASC-F patients exhibited an impaired capacity to clear autologous dead cells and cellular debris. Uptake of pathogen-coated bioparticles was impaired in myeloid cells from both fibrotic patient groups independent of type of pathogen highlighting a cell intrinsic functional impairment. LTI-2355 improved the phagocytic activity of both IPF and PASC-F myeloid cells, and this improvement was paired with decreased pro-inflammatory and pro-fibrotic synthetic activity. LTI-2355 was also shown to primarily target CD206-expressing IPF and PASC-F myeloid cells. Conclusions Primary myeloid cells from IPF and PASC-F patients exhibit dysfunctional phagocytic and synthetic properties that are reversed by LTI-2355. Thus, these studies highlight an additional mechanism of action of a CSD peptide in the treatment of IPF and progressive fibrotic lung disease.
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M. S. Barron A, Fabre T, De S. Distinct fibroblast functions associated with fibrotic and immune-mediated inflammatory diseases and their implications for therapeutic development. F1000Res 2024; 13:54. [PMID: 38681509 PMCID: PMC11053351 DOI: 10.12688/f1000research.143472.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/28/2023] [Indexed: 05/01/2024] Open
Abstract
Fibroblasts are ubiquitous cells that can adopt many functional states. As tissue-resident sentinels, they respond to acute damage signals and shape the earliest events in fibrotic and immune-mediated inflammatory diseases. Upon sensing an insult, fibroblasts produce chemokines and growth factors to organize and support the response. Depending on the size and composition of the resulting infiltrate, these activated fibroblasts may also begin to contract or relax thus changing local stiffness within the tissue. These early events likely contribute to the divergent clinical manifestations of fibrotic and immune-mediated inflammatory diseases. Further, distinct changes to the cellular composition and signaling dialogue in these diseases drive progressive fibroblasts specialization. In fibrotic diseases, fibroblasts support the survival, activation and differentiation of myeloid cells, granulocytes and innate lymphocytes, and produce most of the pathogenic extracellular matrix proteins. Whereas, in immune-mediated inflammatory diseases, sequential accumulation of dendritic cells, T cells and B cells programs fibroblasts to support local, destructive adaptive immune responses. Fibroblast specialization has clear implications for the development of effective induction and maintenance therapies for patients with these clinically distinct diseases.
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Affiliation(s)
- Alexander M. S. Barron
- Inflammation & Immunology Research Unit, Pfizer, Inc., Cambridge, Massachusetts, 02139, USA
| | - Thomas Fabre
- Inflammation & Immunology Research Unit, Pfizer, Inc., Cambridge, Massachusetts, 02139, USA
| | - Saurav De
- Inflammation & Immunology Research Unit, Pfizer, Inc., Cambridge, Massachusetts, 02139, USA
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40
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Choi S, Lee J, Kim S, Lee YW, Kim GC, Hong SM, An SH, Noh H, Kim KE, On D, Lee SG, Jang HJ, Kim SH, Kim J, Seo JS, Kim JJ, Park IH, Oh J, Kim DJ, Yoon JH, Seok SH, Lee YJ, Kim SY, Kim YB, Hwang JY, Lee HJ, Kim HB, Park JW, Yun JW, Shin JS, Seo JY, Nam KT, Choi KS, Kwon HK, Lee HY, Kim JK, Seong JK. A longitudinal molecular and cellular lung atlas of lethal SARS-CoV-2 infection in K18-hACE2 transgenic mice. EBioMedicine 2024; 99:104932. [PMID: 38118400 PMCID: PMC10772566 DOI: 10.1016/j.ebiom.2023.104932] [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: 11/18/2022] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to approximately 500 million cases and 6 million deaths worldwide. Previous investigations into the pathophysiology of SARS-CoV-2 primarily focused on peripheral blood mononuclear cells from patients, lacking detailed mechanistic insights into the virus's impact on inflamed tissue. Existing animal models, such as hamster and ferret, do not faithfully replicate the severe SARS-CoV-2 infection seen in patients, underscoring the need for more relevant animal system-based research. METHODS In this study, we employed single-cell RNA sequencing (scRNA-seq) with lung tissues from K18-hACE2 transgenic (TG) mice during SARS-CoV-2 infection. This approach allowed for a comprehensive examination of the molecular and cellular responses to the virus in lung tissue. FINDINGS Upon SARS-CoV-2 infection, K18-hACE2 TG mice exhibited severe lung pathologies, including acute pneumonia, alveolar collapse, and immune cell infiltration. Through scRNA-seq, we identified 36 different types of cells dynamically orchestrating SARS-CoV-2-induced pathologies. Notably, SPP1+ macrophages in the myeloid compartment emerged as key drivers of severe lung inflammation and fibrosis in K18-hACE2 TG mice. Dynamic receptor-ligand interactions, involving various cell types such as immunological and bronchial cells, defined an enhanced TGFβ signaling pathway linked to delayed tissue regeneration, severe lung injury, and fibrotic processes. INTERPRETATION Our study provides a comprehensive understanding of SARS-CoV-2 pathogenesis in lung tissue, surpassing previous limitations in investigating inflamed tissues. The identified SPP1+ macrophages and the dysregulated TGFβ signaling pathway offer potential targets for therapeutic intervention. Insights from this research may contribute to the development of innovative diagnostics and therapies for COVID-19. FUNDING This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020M3A9I2109027, 2021R1A2C2004501).
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Affiliation(s)
- Seunghoon Choi
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Jusung Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Suhyeon Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; BIO-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Youn Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Gi-Cheon Kim
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seung-Min Hong
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Se-Hee An
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuna Noh
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyung Eun Kim
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Dain On
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Gyu Lee
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Sung-Hee Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jiseon Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Seon Seo
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeong Jin Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - In Ho Park
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jooyeon Oh
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Da-Jung Kim
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jong-Hwi Yoon
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sang-Hyuk Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Yu Jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Seo Yeon Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Young Been Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam 23620, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 23620, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Jun-Won Yun
- Laboratory of Veterinary Toxicology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeon-Soo Shin
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jun-Young Seo
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ki Taek Nam
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea.
| | - Ho-Keun Kwon
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea; Department of Nuclear Medicine, Seoul National University, College of Medicine, Seoul 03080, South Korea.
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; BIO-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea.
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Bahudhanapati H, Tan J, Apel RM, Seeliger B, Schupp J, Li X, Sullivan DI, Sembrat J, Rojas M, Tabib T, Valenzi E, Lafyatis R, Mitash N, Hernandez Pineda R, Jawale C, Peroumal D, Biswas P, Tedrow J, Adams T, Kaminski N, Wuyts WA, McDyer JF, Gibson KF, Alder JK, Königshoff M, Zhang Y, Nouraie M, Prasse A, Kass DJ. Increased expression of CXCL6 in secretory cells drives fibroblast collagen synthesis and is associated with increased mortality in idiopathic pulmonary fibrosis. Eur Respir J 2024; 63:2300088. [PMID: 37918852 DOI: 10.1183/13993003.00088-2023] [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: 01/14/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
Abstract
RATIONALE Recent data suggest that the localisation of airway epithelial cells in the distal lung in idiopathic pulmonary fibrosis (IPF) may drive pathology. We set out to discover whether chemokines expressed in these ectopic airway epithelial cells may contribute to the pathogenesis of IPF. METHODS We analysed whole lung and single-cell transcriptomic data obtained from patients with IPF. In addition, we measured chemokine levels in blood, bronchoalveolar lavage (BAL) of IPF patients and air-liquid interface cultures. We employed ex vivo donor and IPF lung fibroblasts and an animal model of pulmonary fibrosis to test the effects of chemokine signalling on fibroblast function. RESULTS By analysis of whole-lung transcriptomics, protein and BAL, we discovered that CXCL6 (a member of the interleukin-8 family) was increased in patients with IPF. Elevated CXCL6 levels in the BAL of two cohorts of patients with IPF were associated with poor survival (hazard ratio of death or progression 1.89, 95% CI 1.16-3.08; n=179, p=0.01). By immunostaining and single-cell RNA sequencing, CXCL6 was detected in secretory cells. Administration of mCXCL5 (LIX, murine CXCL6 homologue) to mice increased collagen synthesis with and without bleomycin. CXCL6 increased collagen I levels in donor and IPF fibroblasts 4.4-fold and 1.7-fold, respectively. Both silencing of and chemical inhibition of CXCR1/2 blocked the effects of CXCL6 on collagen, while overexpression of CXCR2 increased collagen I levels 4.5-fold in IPF fibroblasts. CONCLUSIONS CXCL6 is expressed in ectopic airway epithelial cells. Elevated levels of CXCL6 are associated with IPF mortality. CXCL6-driven collagen synthesis represents a functional consequence of ectopic localisation of airway epithelial cells in IPF.
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Affiliation(s)
- Harinath Bahudhanapati
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
| | - Jiangning Tan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
| | - Rosa Marie Apel
- Fraunhofer ITEM, Hannover, Germany
- DZL BREATH, Hannover, Germany
| | - Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
| | - Jonas Schupp
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
| | - Xiaoyun Li
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel I Sullivan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Sembrat
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Pulmonary, Critical Care and Sleep Medicine, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleanor Valenzi
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nilay Mitash
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ricardo Hernandez Pineda
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chetan Jawale
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Partha Biswas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Tedrow
- Norman Regional Health System, Norman, OK, USA
| | - Taylor Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wim A Wuyts
- Unit for Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - John F McDyer
- Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kevin F Gibson
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Melanie Königshoff
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yingze Zhang
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mehdi Nouraie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Antje Prasse
- Fraunhofer ITEM, Hannover, Germany
- DZL BREATH, Hannover, Germany
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Centre for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover, Hannover, Germany
- Denotes equal contribution
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Denotes equal contribution
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Zhan W, Luo W, Zhang Y, Xiang K, Chen X, Shen S, Huang C, Xu T, Ding W, Chen Y, Lin M, Pan X, Lai K. Sputum Transcriptomics Reveals FCN1+ Macrophage Activation in Mild Eosinophilic Asthma Compared to Non-Asthmatic Eosinophilic Bronchitis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2024; 16:55-70. [PMID: 38262391 PMCID: PMC10823142 DOI: 10.4168/aair.2024.16.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/08/2023] [Accepted: 08/05/2023] [Indexed: 01/25/2024]
Abstract
PURPOSE Eosinophilic asthma (EA) and non-asthmatic eosinophilic bronchitis (EB) share similar eosinophilic airway inflammation. Unlike EA, EB did not present airway hyperresponsiveness or airflow obstruction. We aimed to compare the mechanism underlying the different manifestations between EA and EB via sputum transcriptomics analysis. METHODS Induced-sputum cells from newly physician-diagnosed EA, EB patients, and healthy controls (HCs) were collected for RNA sequencing. RESULTS Bulk RNA sequencing was performed using sputum cells from patients with EA (n = 18), EB (n = 15) and HCs (n = 28). Principal component analysis revealed similar gene expression patterns in EA and EB. The most differentially expressed genes in EB compared with HC were also shared by EA, including IL4, IL5 IL13, CLC, CPA3, and DNASE1L3. However, gene set enrichment analysis showed that the signatures regulating macrophage activation were enriched in EA compared to EB. Sputum cells were profiled using single-cell RNA sequencing. FABP4+ macrophages, SPP1+ macrophages, FCN1+ macrophages, dendritic cells, T cells, B cells, mast cells, and epithelial cells were identified based on gene expression profiling. Analysis of cell-cell communication revealed that interactions between FCN1+ macrophages and other cells were higher in EA than in EB. A wealth of transforming growth factor beta (TGF-β) and vascular endothelial growth factor (VEGF) interactions between FCN1+ macrophages and other cells have been shown in EA. The gene expression levels of EREG, TGFBI, and VEGFA in FCN1+ macrophages of EA were significantly higher than those of EB. Furthermore, signatures associated with the response to TGF-β, cellular response to VEGF stimulus and developmental cell growth were enriched in FCN1+ macrophages of EA compared to those of EB. CONCLUSIONS FCN1+ macrophage activation associated with airway remodeling processes was upregulated in EA compared to that in EB, which may contribute to airway hyperresponsiveness and airflow obstruction.
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Affiliation(s)
- Wenzhi Zhan
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Luo
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yulong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Keheng Xiang
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaomei Chen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuirong Shen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuqing Huang
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tingting Xu
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenbin Ding
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuehan Chen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mingtong Lin
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Kefang Lai
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell 2023; 186:5876-5891.e20. [PMID: 38134877 DOI: 10.1016/j.cell.2023.11.026] [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: 05/01/2023] [Revised: 08/24/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023]
Abstract
Harmonizing cell types across the single-cell community and assembling them into a common framework is central to building a standardized Human Cell Atlas. Here, we present CellHint, a predictive clustering tree-based tool to resolve cell-type differences in annotation resolution and technical biases across datasets. CellHint accurately quantifies cell-cell transcriptomic similarities and places cell types into a relationship graph that hierarchically defines shared and unique cell subtypes. Application to multiple immune datasets recapitulates expert-curated annotations. CellHint also reveals underexplored relationships between healthy and diseased lung cell states in eight diseases. Furthermore, we present a workflow for fast cross-dataset integration guided by harmonized cell types and cell hierarchy, which uncovers underappreciated cell types in adult human hippocampus. Finally, we apply CellHint to 12 tissues from 38 datasets, providing a deeply curated cross-tissue database with ∼3.7 million cells and various machine learning models for automatic cell annotation across human tissues.
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Affiliation(s)
- Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simone Webb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Laura Jardine
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Benjamin J Stewart
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
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Hou J, Yang Y, Han X. Machine Learning and Single-Cell Analysis Identify Molecular Features of IPF-Associated Fibroblast Subtypes and Their Implications on IPF Prognosis. Int J Mol Sci 2023; 25:94. [PMID: 38203265 PMCID: PMC10778894 DOI: 10.3390/ijms25010094] [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: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease of unknown cause, and the involvement of fibroblasts in its pathogenesis is well recognized. However, a comprehensive understanding of fibroblasts' heterogeneity, their molecular characteristics, and their clinical relevance in IPF is lacking. In this study, we aimed to systematically classify fibroblast populations, uncover the molecular and biological features of fibroblast subtypes in fibrotic lung tissue, and establish an IPF-associated, fibroblast-related predictive model for IPF. Herein, a meticulous analysis of scRNA-seq data obtained from lung tissues of both normal and IPF patients was conducted to identify fibroblast subpopulations in fibrotic lung tissues. In addition, hdWGCNA was utilized to identify co-expressed gene modules associated with IPF-related fibroblasts. Furthermore, we explored the prognostic utility of signature genes for these IPF-related fibroblast subtypes using a machine learning-based approach. Two predominant fibroblast subpopulations, termed IPF-related fibroblasts, were identified in fibrotic lung tissues. Additionally, we identified co-expressed gene modules that are closely associated with IPF-fibroblasts by utilizing hdWGCNA. We identified gene signatures that hold promise as prognostic markers in IPF. Moreover, we constructed a predictive model specifically focused on IPF-fibroblasts which can be utilized to assess disease prognosis in IPF patients. These findings have the potential to improve disease prediction and facilitate targeted interventions for patients with IPF.
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Affiliation(s)
- Jiwei Hou
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | | | - Xin Han
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China;
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Zou Y, Tan X, Yuan G, Tang Y, Wang Y, Yang C, Luo S, Wu Z, Yao K. SPP1 is associated with adverse prognosis and predicts immunotherapy efficacy in penile cancer. Hum Genomics 2023; 17:116. [PMID: 38111044 PMCID: PMC10729401 DOI: 10.1186/s40246-023-00558-5] [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: 06/15/2023] [Accepted: 11/22/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The effect of SPP1 in squamous cell carcinoma of the penis (PSCC) remained unknown. We attempted to clarify the function of the SPP1 gene in PSCC. METHOD Eight paired penile cancer specimens (including penile cancer tissue, paracancerous tissue, and positive lymph node tissue) subjected to whole transcriptome sequencing were analysed to identify differentially expressed genes. We used immunohistochemistry to detect the expression of SPP1 protein and immune cell related proteins in penile cancer tissue. Then, we performed weighted gene coexpression network analysis (WGCNA) to identify the genes related to SPP1 in penile cancer tissue and positive lymph node tissue. Based on the GSE57955 dataset, the CIBERSORT and ssGSEA algorithms were carried out to investigate the immune environment of PSCC. GSVA analysis was conducted to identify the signaling pathways related to SPP1 subgroups. Enzyme-linked immunosorbent assay (ELISA) method was adopted to detect SPP1 level in the serum of 60 patients with penile cancer. RESULTS Differential analysis indicated that SPP1 was the most differentially upregulated gene in both penile cancer tissues and positive lymph node tissues. Survival analysis suggested that the prognosis of the low-SPP1 group was significantly poorer than that of the high-SPP1 group. Subsequently, immune-related bioinformatics showed that SPP1 was significantly associated with B cells, CD8 + T cells, CD4 + T cells, macrophages, helper T cells, neutrophils and dendritic cells. The immunohistochemical results showed that the high-SPP1 group was characterized by relatively high expression of CD16 and relatively low expression of CD4. GSVA analysis indicated that high-SPP1 group was significantly associated with immune-related pathways such as PD-L1 expression and the PD-1 checkpoint pathway in cancer and the TNF signaling pathway. ELISA demonstrated that the serum level of SPP1 in patients with positive lymph node metastasis of penile cancer was significantly higher than that in patients with negative lymph node metastasis of penile cancer. CONCLUSION Our study shows that the SPP1 gene might be an effective biomarker for predicting the prognosis and the efficacy of immunotherapy in PSCC patients.
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Affiliation(s)
- Yuantao Zou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Xingliang Tan
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Gangjun Yuan
- Department of Urology Oncological Surgery, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yi Tang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Yanjun Wang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Cong Yang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Sihao Luo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China
| | - Zhiming Wu
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China.
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China.
| | - Kai Yao
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in Southern China, Guangzhou, 510060, China.
- Collaborative Innovation Center of Cancer Medicine, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China.
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Vannan A, Lyu R, Williams AL, Negretti NM, Mee ED, Hirsh J, Hirsh S, Nichols DS, Calvi CL, Taylor CJ, Polosukhin VV, Serezani APM, McCall AS, Gokey JJ, Shim H, Ware LB, Bacchetta MJ, Shaver CM, Blackwell TS, Walia R, Sucre JMS, Kropski JA, McCarthy DJ, Banovich NE. Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571954. [PMID: 38168317 PMCID: PMC10760144 DOI: 10.1101/2023.12.15.571954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell-types, established the cellular and molecular basis of classical PF histopathologic disease features, and identified a diversity of distinct molecularly-defined spatial niches in control and PF lungs. Using machine-learning and trajectory analysis methods to segment and rank airspaces on a gradient from normal to most severely remodeled, we identified a sequence of compositional and molecular changes that associate with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially-resolved characterization of the cellular and molecular programs of PF and control lungs, provide new insights into the heterogeneous pathobiology of PF, and establish analytical approaches which should be broadly applicable to other imaging-based spatial transcriptomic studies.
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Affiliation(s)
- Annika Vannan
- Translational Genomics Research Institute, Phoenix, AZ
| | - Ruqian Lyu
- St. Vincent’s Institute of Medical Research, Fitzroy, VIC, AUS
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
| | | | - Nicholas M. Negretti
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan D. Mee
- Translational Genomics Research Institute, Phoenix, AZ
| | - Joseph Hirsh
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Samuel Hirsh
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David S. Nichols
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carla L. Calvi
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chase J. Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vasiliy. V. Polosukhin
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ana PM Serezani
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - A. Scott McCall
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jason J. Gokey
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Heejung Shim
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew J. Bacchetta
- Department of Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Department of Veterans Affairs Medical Center, Nashville, TN
| | - Rajat Walia
- Department of Thoracic Disease and Transplantation, Norton Thoracic Institute, Phoenix, AZ, USA
| | - Jennifer MS Sucre
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Department of Veterans Affairs Medical Center, Nashville, TN
| | - Davis J McCarthy
- St. Vincent’s Institute of Medical Research, Fitzroy, VIC, AUS
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
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Herrera-De La Mata S, Ramírez-Suástegui C, Mistry H, Castañeda-Castro FE, Kyyaly MA, Simon H, Liang S, Lau L, Barber C, Mondal M, Zhang H, Arshad SH, Kurukulaaratchy RJ, Vijayanand P, Seumois G. Cytotoxic CD4 + tissue-resident memory T cells are associated with asthma severity. MED 2023; 4:875-897.e8. [PMID: 37865091 PMCID: PMC10964988 DOI: 10.1016/j.medj.2023.09.003] [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: 01/03/2023] [Revised: 07/02/2023] [Accepted: 09/18/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Patients with severe uncontrolled asthma represent a distinct endotype with persistent airway inflammation and remodeling that is refractory to corticosteroid treatment. CD4+ TH2 cells play a central role in orchestrating asthma pathogenesis, and biologic therapies targeting their cytokine pathways have had promising outcomes. However, not all patients respond well to such treatment, and their effects are not always durable nor reverse airway remodeling. This observation raises the possibility that other CD4+ T cell subsets and their effector molecules may drive airway inflammation and remodeling. METHODS We performed single-cell transcriptome analysis of >50,000 airway CD4+ T cells isolated from bronchoalveolar lavage samples from 30 patients with mild and severe asthma. FINDINGS We observed striking heterogeneity in the nature of CD4+ T cells present in asthmatics' airways, with tissue-resident memory T (TRM) cells making a dominant contribution. Notably, in severe asthmatics, a subset of CD4+ TRM cells (CD103-expressing) was significantly increased, comprising nearly 65% of all CD4+ T cells in the airways of male patients with severe asthma when compared to mild asthma (13%). This subset was enriched for transcripts linked to T cell receptor activation (HLA-DRB1, HLA-DPA1) and cytotoxicity (GZMB, GZMA) and, following stimulation, expressed high levels of transcripts encoding for pro-inflammatory non-TH2 cytokines (CCL3, CCL4, CCL5, TNF, LIGHT) that could fuel persistent airway inflammation and remodeling. CONCLUSIONS Our findings indicate the need to look beyond the traditional T2 model of severe asthma to better understand the heterogeneity of this disease. FUNDING This research was funded by the NIH.
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Affiliation(s)
| | | | - Heena Mistry
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton Foundation Trust, Southampton SO16 6YD, UK; The David Hide Asthma and Allergy Research Centre, St. Mary's Hospital, Newport PO30 5TG, Isle of Wight, UK
| | | | - Mohammad A Kyyaly
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; The David Hide Asthma and Allergy Research Centre, St. Mary's Hospital, Newport PO30 5TG, Isle of Wight, UK
| | - Hayley Simon
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Shu Liang
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Laurie Lau
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton Foundation Trust, Southampton SO16 6YD, UK
| | - Clair Barber
- National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton Foundation Trust, Southampton SO16 6YD, UK
| | | | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton Foundation Trust, Southampton SO16 6YD, UK; The David Hide Asthma and Allergy Research Centre, St. Mary's Hospital, Newport PO30 5TG, Isle of Wight, UK
| | - Ramesh J Kurukulaaratchy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton Foundation Trust, Southampton SO16 6YD, UK; The David Hide Asthma and Allergy Research Centre, St. Mary's Hospital, Newport PO30 5TG, Isle of Wight, UK.
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis. Sci Transl Med 2023; 15:eadh0908. [PMID: 38055803 DOI: 10.1126/scitranslmed.adh0908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT-staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type-specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.
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Affiliation(s)
- Niklas J Lang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Janine Gote-Schniering
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Rheumatology and Immunology, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Lung Precision Medicine Program, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Diana Porras-Gonzalez
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lin Yang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Laurens J De Sadeleer
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - R Christoph Jentzsch
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Vladimir A Shitov
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Shuhong Zhou
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Ahmed Agami
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Christoph H Mayr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Baharak Hooshiar Kashani
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Yuexin Chen
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lukas Heumos
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Jeanine C Pestoni
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Eszter Sarolta Molnar
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | | | | | | | - Melanie Wögrath
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Michael Gerckens
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Mareike Lehmann
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), 35043 Marburg, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Rudolf Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Jürgen Behr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - Mircea-Gabriel Stoleriu
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Malte D Luecken
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
- Department of Mathematics, Technische Universität München, 85748 Garching bei München, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
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49
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Tang Z, Xia Z, Wang X, Liu Y. The critical role of osteopontin (OPN) in fibrotic diseases. Cytokine Growth Factor Rev 2023; 74:86-99. [PMID: 37648616 DOI: 10.1016/j.cytogfr.2023.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Fibrosis is a pathological condition characterized by the excessive deposition of extracellular matrix components in tissues and organs, leading to progressive architectural remodelling and contributing to the development of various diseases. Osteopontin (OPN), a highly phosphorylated glycoprotein, has been increasingly recognized for its involvement in the progression of tissue fibrosis. This review provides a comprehensive overview of the genetic and protein structure of OPN and focuses on our current understanding of the role of OPN in the development of fibrosis in the lungs and other tissues. Additionally, special attention is given to the potential of OPN as a biomarker and a novel therapeutic target in the treatment of fibrosis.
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Affiliation(s)
- Ziyi Tang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zijing Xia
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiangpeng Wang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100000, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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50
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Yang G, Yang Y, Liu Y, Liu X. Regulation of alveolar macrophage death in pulmonary fibrosis: a review. Apoptosis 2023; 28:1505-1519. [PMID: 37707713 PMCID: PMC10618387 DOI: 10.1007/s10495-023-01888-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/15/2023]
Abstract
Pulmonary fibrosis (PF) is a disease in which excessive extracellular matrix (ECM) accumulation occurs in pulmonary mesenchyme, which induces the destruction of alveolar structures and poor prognosis. Macrophage death is responsible for ECM accumulation after alveolar epithelial injury in PF. Depending on the local micro-environments, macrophages can be polarized to either classically activated (M1) or alternatively activated (M2) macrophage phenotypes. In general, M1 macrophages can promote inflammation and sterilization, stop the continuous damage process and prevent excessive repair, while M2 macrophages are anti-inflammatory and promote tissue repair, and excessive M2 macrophage activity may inhibit the absorption and degradation of ECM. Emerging evidence has revealed that death forms such as pyroptosis mediated by inflammasome affect polarization direction and ultimately lead to the development of PF. Pharmacological manipulation of macrophages death signals may serve as a logical therapeutic strategy for PF. This review will focus on the current state of knowledge regarding the regulation and underlying mechanisms of macrophages and their mediators in the influence of macrophage death on the development of PF. We expect to provide help in developing effective therapeutic strategies in clinical settings.
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Affiliation(s)
- Ganghao Yang
- Department of Respiratory and Critical Medicine, University of Electronic Science and Technology of China Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences and Sichuan People's Hospital, Chengdu, Sichuan, China
| | - Yang Yang
- Department of Respiratory and Critical Medicine, University of Electronic Science and Technology of China Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences and Sichuan People's Hospital, Chengdu, Sichuan, China
| | - Yiping Liu
- Department of Respiratory and Critical Medicine, University of Electronic Science and Technology of China Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences and Sichuan People's Hospital, Chengdu, Sichuan, China
| | - Xiaoshu Liu
- Department of Respiratory and Critical Medicine, University of Electronic Science and Technology of China Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences and Sichuan People's Hospital, Chengdu, Sichuan, China.
- Department of Respiratory and Critical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuai Fu Yuan Street, Dong Cheng District, Beijing, 100730, China.
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