201
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He Y, Yu F, Tian Y, Hu Q, Wang B, Wang L, Hu Y, Tao Y, Chen X, Peng M. Single-Cell RNA Sequencing Unravels Distinct Tumor Microenvironment of Different Components of Lung Adenocarcinoma Featured as Mixed Ground-Glass Opacity. Front Immunol 2022; 13:903513. [PMID: 35874770 PMCID: PMC9299373 DOI: 10.3389/fimmu.2022.903513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Lung adenocarcinoma featured as mixed ground-glass opacity (mGGO) doubled its volume half of the time in comparison with that featured as pure ground-glass opacity (pGGO). The mechanisms underlying the heterogeneous appearance of mGGO remain elusive. In this study, we macro-dissected the solid (S) components and ground-glass (GG) components of mGGO and performed single-cell sequencing analyses of six paired components from three mGGO patients. A total of 19,391 single-cell profiles were taken into analysis, and the data of each patient were analyzed independently to obtain a common alteration. Cancer cells and macrophages were the dominant cell types in the S and GG components, respectively. Cancer cells in the S components, which showed relatively malignant phenotypes, were likely to originate from both the GG and S components and monitor the surrounding tumor microenvironment (TME) through an intricate cell interaction network. SPP1hi macrophages were enriched in the S components and showed increased activity of chemoattraction, while macrophages in the GG components displayed an active antimicrobial process with a higher stress-induced state. In addition, the CD47–SIRPA axis was demonstrated to be critical in the maintenance of the GG components. Taken together, our study unraveled the alterations of cell components and transcriptomic features between different components in mGGOs.
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Affiliation(s)
- Yu He
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yi Tian
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Thoracic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qikang Hu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Bin Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan Hu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yongguang Tao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaofeng Chen
- Department of Anaesthesia, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
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202
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Single-Cell Transcriptome Analysis of Radiation Pneumonitis Mice. Antioxidants (Basel) 2022; 11:antiox11081457. [PMID: 35892659 PMCID: PMC9331247 DOI: 10.3390/antiox11081457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Radiation-induced lung injury (RILI), especially radiation pneumonitis (RP), is a common clinical complication associated with thoracic radiotherapy for malignant tumors. However, the specific contributions of each cell subtype to this process are unknown. Here, we provide the single-cell pathology landscape of the RP in a mouse model by unbiased single-cell RNA-seq (scRNA-seq). We found a decline of type 2 alveolar cells in the RP lung tissue, with an expansion of macrophages, especially the Fabp4low and Spp1high subgroup, while Fabp4high macrophages were almost depleted. We observed an elevated expression of multiple mitochondrial genes in the RP group, indicating a type 2 alveolar cell (AT2) response to oxidative stress. We also calculated the enrichment of a cGAS-STING signaling pathway, which may be involved in regulating inflammatory responses and cancer progression in AT2 cells of PR mice. We delineate markers and transcriptional states, identify a type 2 alveolar cell, and uncover fundamental determinants of lung fibrosis and inflammatory response in RP lung tissue of mice.
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203
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Assessment of disease outcome measures in systemic sclerosis. Nat Rev Rheumatol 2022; 18:527-541. [PMID: 35859133 DOI: 10.1038/s41584-022-00803-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 01/08/2023]
Abstract
The assessment of disease activity in systemic sclerosis (SSc) is challenging owing to its heterogeneous manifestations across multiple organ systems, the variable rate of disease progression and regression, and the relative paucity of patients in early-phase therapeutic trials. Despite some recent successes, most clinical trials have failed to show efficacy, underscoring the need for improved outcome measures linked directly to disease pathogenesis, particularly applicable for biomarker studies focused on skin disease. Current outcome measures in SSc-associated interstitial lung disease and SSc skin disease are largely adequate, although advancing imaging technology and the incorporation of skin mRNA biomarkers might provide opportunities for earlier detection of the therapeutic effect. Biomarkers can further inform pathogenesis, enabling early phase trials to act as reverse translational studies through the incorporation of routine high-throughput sequencing.
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204
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Montague B, Summers A, Bhawal R, Anderson ET, Kraus-Malett S, Zhang S, Goggs R. Identifying potential biomarkers and therapeutic targets for dogs with sepsis using metabolomics and lipidomics analyses. PLoS One 2022; 17:e0271137. [PMID: 35802586 PMCID: PMC9269464 DOI: 10.1371/journal.pone.0271137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/23/2022] [Indexed: 11/19/2022] Open
Abstract
Sepsis is a diagnostic and therapeutic challenge and is associated with morbidity and a high risk of death. Metabolomic and lipidomic profiling in sepsis can identify alterations in metabolism and might provide useful insights into the dysregulated host response to infection, but investigations in dogs are limited. We aimed to use untargeted metabolomics and lipidomics to characterize metabolic pathways in dogs with sepsis to identify therapeutic targets and potential diagnostic and prognostic biomarkers. In this prospective observational cohort study, we examined the plasma metabolomes and lipidomes of 20 healthy control dogs and compared them with those of 21 client-owned dogs with sepsis. Patient data including signalment, physical exam findings, clinicopathologic data and clinical outcome were recorded. Metabolites were identified using an untargeted mass spectrometry approach and pathway analysis identified multiple enriched metabolic pathways including pyruvaldehyde degradation; ketone body metabolism; the glucose-alanine cycle; vitamin-K metabolism; arginine and betaine metabolism; the biosynthesis of various amino acid classes including the aromatic amino acids; branched chain amino acids; and metabolism of glutamine/glutamate and the glycerophospholipid phosphatidylethanolamine. Metabolites were identified with high discriminant abilities between groups which could serve as potential biomarkers of sepsis including 13,14-Dihydro-15-keto Prostaglandin A2; 12(13)-DiHOME (12,13-dihydroxy-9Z-octadecenoic acid); and 9-HpODE (9-Hydroxyoctadecadienoic acid). Metabolites with higher abundance in samples from nonsurvivors than survivors included 3-(2-hydroxyethyl) indole, indoxyl sulfate and xanthurenic acid. Untargeted lipidomic profiling revealed multiple sphingomyelin species (SM(d34:0)+H; SM(d36:0)+H; SM(d34:0)+HCOO; and SM(d34:1D3)+HCOO); lysophosphatidylcholine molecules (LPC(18:2)+H) and lipophosphoserine molecules (LPS(20:4)+H) that were discriminating for dogs with sepsis. These biomarkers could aid in the diagnosis of dogs with sepsis, provide prognostic information, or act as potential therapeutic targets.
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Affiliation(s)
- Brett Montague
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - April Summers
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, United States of America
| | - Elizabeth T. Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, United States of America
| | - Sydney Kraus-Malett
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, United States of America
| | - Robert Goggs
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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205
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Kumar A, Elko E, Bruno SR, Mark ZF, Chamberlain N, Mihavics BK, Chandrasekaran R, Walzer J, Ruban M, Gold C, Lam YW, Ghandikota S, Jegga AG, Gomez JL, Janssen-Heininger YM, Anathy V. Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis. Thorax 2022; 77:669-678. [PMID: 34400514 PMCID: PMC8847543 DOI: 10.1136/thoraxjnl-2021-216882] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/29/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND The role of club cells in the pathology of idiopathic pulmonary fibrosis (IPF) is not well understood. Protein disulfide isomerase A3 (PDIA3), an endoplasmic reticulum-based redox chaperone required for the functions of various fibrosis-related proteins; however, the mechanisms of action of PDIA3 in pulmonary fibrosis are not fully elucidated. OBJECTIVES To examine the role of club cells and PDIA3 in the pathology of pulmonary fibrosis and the therapeutic potential of inhibition of PDIA3 in lung fibrosis. METHODS Role of PDIA3 and aberrant club cells in lung fibrosis was studied by analyses of human transcriptome dataset from Lung Genomics Research Consortium, other public resources, the specific deletion or inhibition of PDIA3 in club cells and blocking SPP1 downstream of PDIA3 in mice. RESULTS PDIA3 and club cell secretory protein (SCGB1A1) signatures are upregulated in IPF compared with control patients. PDIA3 or SCGB1A1 increases also correlate with a decrease in lung function in patients with IPF. The bleomycin (BLM) model of lung fibrosis showed increases in PDIA3 in SCGB1A1 cells in the lung parenchyma. Ablation of Pdia3, specifically in SCGB1A1 cells, decreases parenchymal SCGB1A1 cells along with fibrosis in mice. The administration of a PDI inhibitor LOC14 reversed the BLM-induced parenchymal SCGB1A1 cells and fibrosis in mice. Evaluation of PDIA3 partners revealed that SPP1 is a major interactor in fibrosis. Blocking SPP1 attenuated the development of lung fibrosis in mice. CONCLUSIONS Our study reveals a new relationship with distally localised club cells, PDIA3 and SPP1 in lung fibrosis and inhibition of PDIA3 or SPP1 attenuates lung fibrosis.
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Affiliation(s)
- Amit Kumar
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Evan Elko
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Sierra R Bruno
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Zoe F Mark
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Nicolas Chamberlain
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | | | - Ravishankar Chandrasekaran
- Department of Pulmonary, Critical Care Medicine, Larner College of Medicine, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Joseph Walzer
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Mona Ruban
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Clarissa Gold
- Department of Biology & Vermont Biomedical Research Network Proteomics Facility, University of Vermont, Burlington, Vermont, USA
| | - Ying Wai Lam
- Department of Biology & Vermont Biomedical Research Network Proteomics Facility, University of Vermont, Burlington, Vermont, USA
| | - Sudhir Ghandikota
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Computer Science, University of Cincinnati College of Engineering and Applied Science, Cincinnati, Ohio, USA
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Computer Science, University of Cincinnati College of Engineering and Applied Science, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jose L Gomez
- Internal Medicine-Pulmonary, Critical Care and Sleep Section, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Vikas Anathy
- Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
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206
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Li F, Piattini F, Pohlmeier L, Feng Q, Rehrauer H, Kopf M. Monocyte-derived alveolar macrophages autonomously determine severe outcome of respiratory viral infection. Sci Immunol 2022; 7:eabj5761. [PMID: 35776802 DOI: 10.1126/sciimmunol.abj5761] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Various lung insults can result in replacement of resident alveolar macrophages (AM) by bone marrow monocyte-derived (BMo)-AM. However, the dynamics of this process and its long-term consequences for respiratory viral infections remain unclear. Using several mouse models and a marker to unambiguously track fetal monocyte-derived (FeMo)-AM and BMo-AM, we established the kinetics and extent of replenishment and their function to recurrent influenza A virus (IAV) infection. A massive loss of FeMo-AM resulted in rapid replenishment by self-renewal of survivors, followed by the generation of BMo-AM. BMo-AM progressively outcompeted FeMo-AM over several months, and this was due to their increased glycolytic and proliferative capacity. The presence of both naïve and experienced BMo-AM conferred severe pathology to IAV infection, which was associated with a proinflammatory phenotype. Furthermore, upon aging of naïve mice, FeMo-AM were gradually replaced by BMo-AM, which contributed to IAV disease severity in a cell-autonomous manner. Together, our results suggest that the origin rather than training of AM determines long-term function to respiratory viral infection and provide an explanation for the increased severity of infection seen in the elderly.
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Affiliation(s)
- Fengqi Li
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Federica Piattini
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Lea Pohlmeier
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Qian Feng
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Manfred Kopf
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
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207
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Liu X, Zheng N, Liu Y, Zhu B, Hou J, Qian M, Zhang L, Li L, Zeng Y, Chen C, Wang X. Transcriptomic atlas of GNAT family members in pulmonary epithelia under pathological conditions using single-cell and bulk cell sequencing. Clin Transl Med 2022; 12:e841. [PMID: 35858249 PMCID: PMC9299758 DOI: 10.1002/ctm2.841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xuanqi Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Nannan Zheng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China.,Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China
| | - Yifei Liu
- Center of Molecular Diagnosis and therapy, The Second Hospital of Fujian Medical University, Quanzhou, China
| | - Bijun Zhu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Jiayun Hou
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Mengjia Qian
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Linlin Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Liyang Li
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Yiming Zeng
- Quzhou Hospital of Wenzhou Medical University, Quzhou, China
| | - Chengshui Chen
- Quzhou Hospital of Wenzhou Medical University, Quzhou, China
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
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208
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Qin W, Spek CA, Scicluna BP, van der Poll T, Duitman J. Myeloid DNA methyltransferase3b deficiency aggravates pulmonary fibrosis by enhancing profibrotic macrophage activation. Respir Res 2022; 23:162. [PMID: 35725453 PMCID: PMC9210707 DOI: 10.1186/s12931-022-02088-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive and severe disease characterized by excessive matrix deposition in the lungs. Macrophages play crucial roles in maintaining lung homeostasis but are also central in the pathogenesis of lung diseases like pulmonary fibrosis. Especially, macrophage polarization/activation seems to play a crucial role in pathology and epigenetic reprograming is well-known to regulate macrophage polarization. DNA methylation alterations in IPF lungs have been well documented, but the role of DNA methylation in specific cell types, especially macrophages, is poorly defined. METHODS In order to determine the role of DNA methylation in macrophages during pulmonary fibrosis, we subjected macrophage specific DNA methyltransferase (DNMT)3B, which mediates the de novo DNA methylation, deficient mice to the bleomycin-induced pulmonary fibrosis model. Macrophage polarization and fibrotic parameters were evaluated at 21 days after bleomycin administration. Dnmt3b knockout and wild type bone marrow-derived macrophages were stimulated with either interleukin (IL)4 or transforming growth factor beta 1 (TGFB1) in vitro, after which profibrotic gene expression and DNA methylation at the Arg1 promotor were determined. RESULTS We show that DNMT3B deficiency promotes alternative macrophage polarization induced by IL4 and TGFB1 in vitro and also enhances profibrotic macrophage polarization in the alveolar space during pulmonary fibrosis in vivo. Moreover, myeloid specific deletion of DNMT3B promoted the development of experimental pulmonary fibrosis. CONCLUSIONS In summary, these data suggest that myeloid DNMT3B represses fibrotic macrophage polarization and protects against bleomycin induced pulmonary fibrosis.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Room G2-130, 1105AZ, Amsterdam, The Netherlands.
| | - C Arnold Spek
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Room G2-130, 1105AZ, Amsterdam, The Netherlands
| | - Brendon P Scicluna
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Room G2-130, 1105AZ, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Tom van der Poll
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, Room G2-130, 1105AZ, Amsterdam, The Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - JanWillem Duitman
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
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209
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Lee HY, You DJ, Taylor-Just AJ, Linder KE, Atkins HM, Ralph LM, De la Cruz G, Bonner JC. Pulmonary exposure of mice to ammonium perfluoro(2-methyl-3-oxahexanoate) (GenX) suppresses the innate immune response to carbon black nanoparticles and stimulates lung cell proliferation. Inhal Toxicol 2022; 34:244-259. [PMID: 35704474 DOI: 10.1080/08958378.2022.2086651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) have been associated with respiratory diseases in humans, yet the mechanisms through which PFAS cause susceptibility to inhaled agents is unknown. Herein, we investigated the effects of ammonium perfluoro(2-methyl-3-oxahexanoate) (GenX), an emerging PFAS, on the pulmonary immune response of mice to carbon black nanoparticles (CBNP). We hypothesized that pulmonary exposure to GenX would increase susceptibility to CBNP through suppression of innate immunity. METHODS Male C57BL/6 mice were exposed to vehicle, 4 mg/kg CBNP, 10 mg/kg GenX, or CBNP and GenX by oropharyngeal aspiration. Bronchoalveolar lavage fluid (BALF) was collected at 1 and 14 days postexposure for cytokines and total protein. Lung tissue was harvested for histopathology, immunohistochemistry (Ki67 and phosphorylated (p)-STAT3), western blotting (p-STAT3 and p-NF-κB), and qRT-PCR for cytokine mRNAs. RESULTS CBNP increased CXCL-1 and neutrophils in BALF at both time points evaluated. However, GenX/CBNP co-exposure reduced CBNP-induced CXCL-1 and neutrophils in BALF. Moreover, CXCL-1, CXCL-2 and IL-1β mRNAs were increased by CBNP in lung tissue but reduced by GenX. Western blotting showed that CBNP induced p-NF-κB in lung tissue, while the GenX/CBNP co-exposed group displayed decreased p-NF-κB. Furthermore, mice exposed to GenX or GenX/CBNP displayed increased numbers of BALF macrophages undergoing mitosis and increased Ki67 immunostaining. This was correlated with increased p-STAT3 by western blotting and immunohistochemistry in lung tissue from mice co-exposed to GenX/CBNP. CONCLUSIONS Pulmonary exposure to GenX suppressed CBNP-induced innate immune response in the lungs of mice yet promoted the proliferation of macrophages and lung epithelial cells.
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Affiliation(s)
- Ho Young Lee
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dorothy J You
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alexia J Taylor-Just
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Keith E Linder
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Hannah M Atkins
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Lauren M Ralph
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - James C Bonner
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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210
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Justet A, Zhao AY, Kaminski N. From COVID to fibrosis: lessons from single-cell analyses of the human lung. Hum Genomics 2022; 16:20. [PMID: 35698166 PMCID: PMC9189802 DOI: 10.1186/s40246-022-00393-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/26/2022] [Indexed: 01/12/2023] Open
Abstract
The increased resolution of single-cell RNA-sequencing technologies has led to major breakthroughs and improved our understanding of the normal and pathologic conditions of multiple tissues and organs. In the study of parenchymal lung disease, single-cell RNA-sequencing has better delineated known cell populations and identified novel cells and changes in cellular phenotypes and gene expression patterns associated with disease. In this review, we aim to highlight the advances and insights that have been made possible by applying these technologies to two seemingly very different lung diseases: fibrotic interstitial lung diseases, a group of relentlessly progressive lung diseases leading to pulmonary fibrosis, and COVID-19 pneumonia, an acute viral disease with life-threatening complications, including pulmonary fibrosis. We discuss changes in cell populations and gene expression, highlighting potential common features, such as alveolar cell epithelial injury and aberrant repair and monocyte-derived macrophage populations, as well as relevance and implications to mechanisms of disease and future directions.
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Affiliation(s)
- Aurelien Justet
- grid.47100.320000000419368710Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT USA
- grid.460771.30000 0004 1785 9671Service de Pneumologie, Centre de Competences de Maladies Pulmonaires Rares, CHU de Caen UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, GIP CYCERON, Normandie University, 14000 Caen, France
| | - Amy Y. Zhao
- grid.47100.320000000419368710Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT USA
- grid.47100.320000000419368710Yale University School of Medicine, New Haven, CT USA
- grid.47100.320000000419368710Department of Genetics, Yale University School of Medicine, New Haven, CT USA
| | - Naftali Kaminski
- grid.47100.320000000419368710Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT USA
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211
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Wang J, Jiang M, Xiong A, Zhang L, Luo L, Liu Y, Liu S, Ran Q, Wu D, Xiong Y, He X, Leung ELH, Li G. Integrated analysis of single-cell and bulk RNA sequencing reveals pro-fibrotic PLA2G7 high macrophages in pulmonary fibrosis. Pharmacol Res 2022; 182:106286. [PMID: 35662628 DOI: 10.1016/j.phrs.2022.106286] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/09/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
Abstract
Pulmonary fibrosis (PF) is the pathological change of end-stage interstitial lung diseases with high mortality and limited therapeutic options. Lung macrophages have distinct subsets with divergent functions, and play critical roles in the pathogenesis of PF. In this study, integrative analysis of lung single-cell and bulk RNA-seq data from patients with fibrotic hypersensitivity pneumonitis and idiopathic pulmonary fibrosis was utilized to identify particular macrophage subsets during the development of PF. We find a specific macrophage subpopulation highly expressing PLA2G7 in fibrotic lungs. We performed additional single-cell RNA-seq analysis to identify analogous macrophage population in bleomycin (BLM)-induced mouse pulmonary fibrosis models. By in vitro and in vivo experiments, we further reveal the pro-fibrotic role for this PLA2G7high macrophage subset in fibroblast-to-myofibroblast transition (FMT) during pulmonary fibrosis. PLA2G7 promotes FMT via LPC/ATX/LPA/LPA2 axis in macrophages. Moreover, PLA2G7 is regulated by STAT1, and pharmacological inhibition of PLA2G7 by Darapladib ameliorates pulmonary fibrosis in BLM-induced mice. The results of this study support the view that PLA2G7high macrophage subpopulation contributes importantly to the pathogenesis of PF, which provides a potential way for targeted therapy.
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Affiliation(s)
- Junyi Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Taipa, Macao Special Administrative Region of China
| | - Manling Jiang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Taipa, Macao Special Administrative Region of China
| | - Li Luo
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Shengbin Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Qin Ran
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Dehong Wu
- Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Ying Xiong
- Department of Pulmonary and Critical Care Medicine, Sichuan Friendship Hospital, Chengdu, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China.
| | - Elaine Lai-Han Leung
- Faculty of Health Sciences, University of Macau, Taipa, Macao Special Administrative Region of China.
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China.
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212
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Foster PS, Tay HL, Oliver BG. Deficiency in the zinc transporter ZIP8 impairs epithelia renewal and enhances lung fibrosis. J Clin Invest 2022; 132:160595. [PMID: 35642632 PMCID: PMC9151685 DOI: 10.1172/jci160595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although aging and lung injury are linked to the development of idiopathic pulmonary fibrosis (IPF), the underlying pathognomonic processes predisposing to fibrotic lesions remain largely unknown. A deficiency in the ability of type 2 alveolar epithelial cell (AEC2) progenitors to regenerate and repair the epithelia has been proposed as a critical factor. In this issue of the JCI, Liang et al. identify a deficiency in the zinc transporter SLC39A8 (ZIP8) in AEC2s and in the subsequent activation of the sirtuin SIRT1 that predisposes to decreased AEC2 renewal capacity and enhanced lung fibrosis in both IPF and aging lungs. Interestingly, the authors demonstrate the efficacy of modulating dietary zinc levels, suggesting the need for clinical trials to evaluate the therapeutic potential of dietary supplementation and the development of pharmacological modulation of the Zn/ZIP8/SIRT1 axis for treatment.
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Affiliation(s)
- Paul S Foster
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, and Immune Health program, Hunter Medical Research Institute (HMRI), Newcastle, New South Wales, Australia
| | - Hock L Tay
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, and Immune Health program, Hunter Medical Research Institute (HMRI), Newcastle, New South Wales, Australia
| | - Brian G Oliver
- School of Life Sciences, University of Technology Sydney, and the Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
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213
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Carraro G, Stripp BR. Insights gained in the pathology of lung disease through single cell transcriptomics. J Pathol 2022; 257:494-500. [PMID: 35608561 DOI: 10.1002/path.5971] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/17/2022] [Indexed: 11/07/2022]
Abstract
The human lung is a relatively quiescent organ in the normal healthy state but contains stem/progenitor cells that contribute to normal tissue maintenance and either repair or remodeling in response to injury and disease. Maintenance or repair lead to proper restoration of functional lung tissue and maintenance of physiological functions, with remodeling resulting in altered structure and function that is typically associated with disease. Knowledge of cell types contributing to lung tissue maintenance and repair/remodeling have largely relied on mouse models of injury-repair and lineage tracing of local progenitors. Therefore, many of the functional alterations underlying remodeling in human lung disease, have remained poorly defined. However, the advent of advanced genomics approaches to define the molecular phenotype of lung cells at single cell resolution has paved the way for rapid advances in our understanding of cell types present within the normal human lung and changes that accompany disease. Here we summarize recent advances in our understanding of disease-related changes in the molecular phenotype of human lung epithelium that have emerged from single-cell transcriptomic studies. We focus attention on emerging concepts of epithelial transitional states that characterize the pathological remodeling that accompanies chronic lung diseases, including idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, cystic fibrosis, and asthma. Concepts arising from these studies are actively evolving and require corroborative studies to improve our understanding of disease mechanisms. Whenever possible we highlight opportunities for providing a unified nomenclature in this rapidly advancing field of research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianni Carraro
- Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Barry R Stripp
- Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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214
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Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H. Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. JCI Insight 2022; 7:e142984. [PMID: 35420997 PMCID: PMC9220956 DOI: 10.1172/jci.insight.142984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options. The role of the developmental transcription factor Sine oculis homeobox homolog 1 (SIX1) in the pathophysiology of lung fibrosis is not known. IPF lung tissue samples and IPF-derived alveolar type II cells (AT2) showed a significant increase in SIX1 mRNA and protein levels, and the SIX1 transcriptional coactivators EYA1 and EYA2 were elevated. Six1 was also upregulated in bleomycin-treated (BLM-treated) mice and in a model of spontaneous lung fibrosis driven by deletion of Telomeric Repeat Binding Factor 1 (Trf1) in AT2 cells. Conditional deletion of Six1 in AT2 cells prevented or halted BLM-induced lung fibrosis, as measured by a significant reduction in histological burden of fibrosis, reduced fibrotic mediator expression, and improved lung function. These effects were associated with increased macrophage migration inhibitory factor (MIF) in lung epithelial cells in vivo following SIX1 overexpression in BLM-induced fibrosis. A MIF promoter-driven luciferase assay demonstrated direct binding of Six1 to the 5'-TCAGG-3' consensus sequence of the MIF promoter, identifying a likely mechanism of SIX1-driven MIF expression in the pathogenesis of lung fibrosis and providing a potentially novel pathway for targeting in IPF therapy.
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Affiliation(s)
- Cory Wilson
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tinne C.J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Pooja Shivshankar
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Weizen Bi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Scott D. Collum
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Nancy Wareing
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Junsuk Ko
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Ram P. Naikawadi
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Paul J. Wolters
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Pascal Maire
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Soma S.K. Jyothula
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
| | | | - Dewei Ren
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Institute, University of Rochester School of Medicine and Dentistry, KMRB G.9629, Rochester, New York, USA
| | - Howard J. Huang
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Burton F. Dickey
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Heide L. Ford
- Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
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215
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Lu Y, Zhao J, Tian Y, Shao D, Zhang Z, Li S, Li J, Zhang H, Wang W, Jiao P, Ma J. Dichotomous Roles of Men1 in Macrophages and Fibroblasts in Bleomycin-Induced Pulmonary Fibrosis. Int J Mol Sci 2022; 23:ijms23105385. [PMID: 35628193 PMCID: PMC9140697 DOI: 10.3390/ijms23105385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Pulmonary fibrosis therapy is limited by the unclear mechanism of its pathogenesis. C57BL/6 mice were used to construct the pulmonary fibrosis model in this study. The results showed that Men1, which encodes menin protein, was significantly downregulated in bleomycin (BLM)—induced pulmonary fibrosis. Mice were made to overexpress or had Men1 knockdown with adeno-associated virus (AAV) infection and then induced with pulmonary fibrosis. BLM—induced pulmonary fibrosis was attenuated by Men1 overexpression and exacerbated by Men1 knockdown. Further analysis revealed the distinct roles of Men1 in fibroblasts and macrophages. Men1 inhibited fibroblast activation and extracellular matrix (ECM) protein expression while promoting macrophages to be profibrotic (M2) phenotype and enhancing their migration. Accordingly, pyroptosis was potentiated by Men1 in mouse peritoneal macrophages (PMCs) and lung tissues upon BLM stimulation. Furthermore, the expression of profibrotic factor OPN was positively regulated by menin in Raw264.7 cells and lung tissues by binding to the OPN promoter region. Taken together, although Men1 showed antifibrotic properties in BLM—induced pulmonary fibrosis mice, conflictive roles of Men1 were displayed in fibroblasts and macrophages. The profibrotic role of Men1 in macrophages may occur via the regulation of macrophage pyroptosis and OPN expression. This study extends the current pathogenic understanding of pulmonary fibrosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ping Jiao
- Correspondence: (P.J.); (J.M.); Tel.: +86-431-8561-9289 (P.J.); +86-431-8561-9719 (J.M.)
| | - Jie Ma
- Correspondence: (P.J.); (J.M.); Tel.: +86-431-8561-9289 (P.J.); +86-431-8561-9719 (J.M.)
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216
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Liégeois M, Bai Q, Fievez L, Pirottin D, Legrand C, Guiot J, Schleich F, Corhay JL, Louis R, Marichal T, Bureau F. Airway Macrophages Encompass Transcriptionally and Functionally Distinct Subsets Altered by Smoking. Am J Respir Cell Mol Biol 2022; 67:241-252. [PMID: 35522264 PMCID: PMC9348561 DOI: 10.1165/rcmb.2021-0563oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alveolar macrophages (AMs) are functionally important innate cells involved in lung homeostasis and immunity and whose diversity in health and disease is a subject of intense investigations. Yet, it remains unclear to what extent conditions like smoking or chronic obstructive pulmonary disease (COPD) trigger changes in the AM compartment. Here, we aimed to explore heterogeneity of human AMs isolated from healthy nonsmokers, smokers without COPD, and smokers with COPD by analyzing BAL fluid cells by flow cytometry and bulk and single-cell RNA sequencing. We found that subpopulations of BAL fluid CD206+ macrophages could be distinguished based on their degree of autofluorescence in each subject analyzed. CD206+ autofluorescenthigh AMs were identified as classical, self-proliferative AM, whereas autofluorescentlow AMs were expressing both monocyte and classical AM-related genes, supportive of a monocytic origin. Of note, monocyte-derived autofluorescentlow AMs exhibited a functionally distinct immunoregulatory profile, including the ability to secrete the immunosuppressive cytokine IL-10. Interestingly, single-cell RNA-sequencing analyses showed that transcriptionally distinct clusters of classical and monocyte-derived AM were uniquely enriched in smokers with and without COPD as compared with healthy nonsmokers. Of note, such smoking-associated clusters exhibited gene signatures enriched in detoxification, oxidative stress, and proinflammatory responses. Our study independently confirms previous reports supporting that monocyte-derived macrophages coexist with classical AM in the airways of healthy subjects and patients with COPD and identifies smoking-associated changes in the AM compartment that may favor COPD initiation or progression.
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Affiliation(s)
| | - Qiang Bai
- Liege University, 26658, GIGA Institute, Liege, Belgium
| | | | - Dimitri Pirottin
- Liege University, 26658, GIGA Institute, Liege, Belgium.,Liege University, 26658, Faculty of Veterinary Medicine, Liege, Belgium
| | | | - Julien Guiot
- CHU de Liege - Hopital du Sart Tilman, 82316, Pneumology, Liege, Belgium
| | - Florence Schleich
- CHU de Liege - Hopital du Sart Tilman, 82316, Respiratory Medicine, Liege, Belgium
| | | | - Renaud Louis
- University of Liege, Department of Respiratory Diseases, Liege, Belgium
| | - Thomas Marichal
- Liege University, 26658, GIGA Institute, Liege, Belgium.,Liege University, 26658, Veterinary Medicine, Liege, Belgium
| | - Fabrice Bureau
- Liege University, 26658, GIGA Institute, Liege, Belgium;
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217
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Ye L, Liu Y, Zhu X, Duan T, Wang C, Fu X, Song P, Yuan S, Liu H, Sun L, Liu F, Lee K, He JC, Chen A. Digital Spatial Profiling of Individual Glomeruli From Patients With Anti-Neutrophil Cytoplasmic Autoantibody-Associated Glomerulonephritis. Front Immunol 2022; 13:831253. [PMID: 35309370 PMCID: PMC8924137 DOI: 10.3389/fimmu.2022.831253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
We previously showed that the rupture of Bowman’s capsule (BC) promotes the progression of crescentic glomerulonephritis by enhancing the entry of CD8+ T cells into the glomeruli. In the present study, we utilized digital spatial profiling to simultaneously profile the altered abundances of the messenger RNA (mRNA) transcripts and proteins in the glomerular and periglomerular areas of four biopsy samples of anti-neutrophil cytoplasmic autoantibody-associated glomerulonephritis (ANCA-GN) and two biopsy specimens of minimal change disease (MCD) controls. The paraffin-embedded biopsy samples were stained with collagen IV, CD45, and SYTO 13 to distinguish the glomeruli with periglomerular infiltration but intact BC, with focal BC rupture, and with extensive rupture of BC and glomeruli without crescent formation and leukocytic infiltration in ANCA-GN. By assessing multiple discrete glomerular areas, we found that the transcript expression levels of the secreted phosphoprotein-1 and its receptor CD44 were upregulated significantly in the glomeruli with more severe ruptures of BC, and their expression levels correlated positively with the fibrotic markers. We also found that both alternative and classic complement pathways were activated in the glomeruli from patients with ANCA-GN. Furthermore, M1 macrophages were involved mostly in the early stage of BC rupture, while M2 macrophages were involved in the late stage and may contribute to the fibrosis process of the crescents. Finally, loss of glomerular cells in ANCA-GN was likely mediated by apoptosis. Our results show that digital spatial profiling allows the comparative analysis of the mRNA and protein profiles in individual glomeruli affected differently by the disease process and the identification of potential novel mechanisms in ANCA-GN.
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Affiliation(s)
- Lin Ye
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Yu Liu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Xuejing Zhu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Tongyue Duan
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Chang Wang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Xiao Fu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Panai Song
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Shuguang Yuan
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Hong Liu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Lin Sun
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Fuyou Liu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Renal Program, James J. Peters Veterans Affairs Medical Center at Bronx, New York, NY, United States
| | - Anqun Chen
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, Institute of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
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218
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Moshkelgosha S, Duong A, Wilson G, Andrews T, Berra G, Renaud-Picard B, Liu M, Keshavjee S, MacParland S, Yeung J, Martinu T, Juvet S. Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation. J Heart Lung Transplant 2022; 41:1556-1569. [DOI: 10.1016/j.healun.2022.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/27/2022] Open
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219
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Ghosh AJ, Hobbs BD, Yun JH, Saferali A, Moll M, Xu Z, Chase RP, Morrow J, Ziniti J, Sciurba F, Barwick L, Limper AH, Flaherty K, Criner G, Brown KK, Wise R, Martinez FJ, McGoldrick D, Cho MH, DeMeo DL, Silverman EK, Castaldi PJ, Hersh CP. Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Respir Res 2022; 23:97. [PMID: 35449067 PMCID: PMC9026726 DOI: 10.1186/s12931-022-02013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. METHODS We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. RESULTS We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. CONCLUSIONS We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF.
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Affiliation(s)
- Auyon J. Ghosh
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Brian D. Hobbs
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Jeong H. Yun
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Aabida Saferali
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Matthew Moll
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Zhonghui Xu
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Robert P. Chase
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Jarrett Morrow
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - John Ziniti
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Frank Sciurba
- grid.21925.3d0000 0004 1936 9000Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Lucas Barwick
- grid.280434.90000 0004 0459 5494The Emmes Company, Rockville, MD USA
| | - Andrew H. Limper
- grid.66875.3a0000 0004 0459 167XDivision of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN USA
| | - Kevin Flaherty
- grid.214458.e0000000086837370Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Healthy System, Ann Arbor, MI USA
| | - Gerard Criner
- grid.264727.20000 0001 2248 3398Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA USA
| | - Kevin K. Brown
- grid.240341.00000 0004 0396 0728Department of Medicine, National Jewish Health, Denver, CO USA
| | - Robert Wise
- grid.21107.350000 0001 2171 9311Division of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Fernando J. Martinez
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Daniel McGoldrick
- grid.34477.330000000122986657Northwest Genomics Center, University of Washington, Seattle, WA USA
| | - Michael H. Cho
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Dawn L. DeMeo
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Edwin K. Silverman
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Peter J. Castaldi
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Craig P. Hersh
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
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Jakwerth CA, Ordovas-Montanes J, Blank S, Schmidt-Weber CB, Zissler UM. Role of Respiratory Epithelial Cells in Allergic Diseases. Cells 2022; 11:1387. [PMID: 35563693 PMCID: PMC9105716 DOI: 10.3390/cells11091387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
The airway epithelium provides the first line of defense to the surrounding environment. However, dysfunctions of this physical barrier are frequently observed in allergic diseases, which are tightly connected with pro- or anti-inflammatory processes. When the epithelial cells are confronted with allergens or pathogens, specific response mechanisms are set in motion, which in homeostasis, lead to the elimination of the invaders and leave permanent traces on the respiratory epithelium. However, allergens can also cause damage in the sensitized organism, which can be ascribed to the excessive immune reactions. The tight interaction of epithelial cells of the upper and lower airways with local and systemic immune cells can leave an imprint that may mirror the pathophysiology. The interaction with effector T cells, along with the macrophages, play an important role in this response, as reflected in the gene expression profiles (transcriptomes) of the epithelial cells, as well as in the secretory pattern (secretomes). Further, the storage of information from past exposures as memories within discrete cell types may allow a tissue to inform and fundamentally alter its future responses. Recently, several lines of evidence have highlighted the contributions from myeloid cells, lymphoid cells, stromal cells, mast cells, and epithelial cells to the emerging concepts of inflammatory memory and trained immunity.
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Affiliation(s)
- Constanze A. Jakwerth
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Germany, Member of the German Center for Lung Research (DZL), Member of the Immunology and Inflammation Initiative of the Helmholtz Association, 80802 Munich, Germany; (C.A.J.); (S.B.); (C.B.S.-W.)
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA;
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Simon Blank
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Germany, Member of the German Center for Lung Research (DZL), Member of the Immunology and Inflammation Initiative of the Helmholtz Association, 80802 Munich, Germany; (C.A.J.); (S.B.); (C.B.S.-W.)
| | - Carsten B. Schmidt-Weber
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Germany, Member of the German Center for Lung Research (DZL), Member of the Immunology and Inflammation Initiative of the Helmholtz Association, 80802 Munich, Germany; (C.A.J.); (S.B.); (C.B.S.-W.)
| | - Ulrich M. Zissler
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Germany, Member of the German Center for Lung Research (DZL), Member of the Immunology and Inflammation Initiative of the Helmholtz Association, 80802 Munich, Germany; (C.A.J.); (S.B.); (C.B.S.-W.)
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Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs. Viruses 2022; 14:v14040837. [PMID: 35458567 PMCID: PMC9026071 DOI: 10.3390/v14040837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that caused the coronavirus disease 2019 (COVID-19) pandemic. Though previous studies have suggested that SARS-CoV-2 cellular tropism depends on the host-cell-expressed proteins, whether transcriptional regulation controls SARS-CoV-2 tropism factors in human lung cells remains unclear. In this study, we used computational approaches to identify transcription factors (TFs) regulating SARS-CoV-2 tropism for different types of lung cells. We constructed transcriptional regulatory networks (TRNs) controlling SARS-CoV-2 tropism factors for healthy donors and COVID-19 patients using lung single-cell RNA-sequencing (scRNA-seq) data. Through differential network analysis, we found that the altered regulatory role of TFs in the same cell types of healthy and SARS-CoV-2-infected networks may be partially responsible for differential tropism factor expression. In addition, we identified the TFs with high centralities from each cell type and proposed currently available drugs that target these TFs as potential candidates for the treatment of SARS-CoV-2 infection. Altogether, our work provides valuable cell-type-specific TRN models for understanding the transcriptional regulation and gene expression of SARS-CoV-2 tropism factors.
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222
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Single-Cell Landscape of Lungs Reveals Key Role of Neutrophil-Mediated Immunopathology during Lethal SARS-CoV-2 Infection. J Virol 2022; 96:e0003822. [PMID: 35420442 PMCID: PMC9093099 DOI: 10.1128/jvi.00038-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the limitation of human studies with respect to individual difference or the accessibility of fresh tissue samples, how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection results in pathological complications in lung, the main site of infection, is still incompletely understood. Therefore, physiologically relevant animal models under realistic SARS-CoV-2 infection conditions would be helpful to our understanding of dysregulated inflammation response in lung in the context of targeted therapeutics. Here, we characterized the single-cell landscape in lung and spleen upon SARS-CoV-2 infection in an acute severe disease mouse model that replicates human symptoms, including severe lung pathology and lymphopenia. We showed a reduction of lymphocyte populations and an increase of neutrophils in lung and then demonstrated the key role of neutrophil-mediated lung immunopathology in both mice and humans. Under severe conditions, neutrophils recruited by a chemokine-driven positive feedback produced elevated “fatal signature” proinflammatory genes and pathways related to neutrophil activation or releasing of granular content. In addition, we identified a new Cd177high cluster that is undergoing respiratory burst and Stfahigh cluster cells that may dampen antigen presentation upon infection. We also revealed the devastating effect of overactivated neutrophil by showing the highly enriched neutrophil extracellular traps in lung and a dampened B-cell function in either lung or spleen that may be attributed to arginine consumption by neutrophil. The current study helped our understanding of SARS-CoV-2-induced pneumonia and warranted the concept of neutrophil-targeting therapeutics in COVID-19 treatment. IMPORTANCE We demonstrated the single-cell landscape in lung and spleen upon SARS-CoV-2 infection in an acute severe disease mouse model that replicated human symptoms, including severe lung pathology and lymphopenia. Our comprehensive study revealed the key role of neutrophil-mediated lung immunopathology in SARS-CoV-2-induced severe pneumonia, which not only helped our understanding of COVID-19 but also warranted the concept of neutrophil targeting therapeutics in COVID-19 treatment.
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223
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Liang J, Huang G, Liu X, Taghavifar F, Liu N, Wang Y, Deng N, Yao C, Xie T, Kulur V, Dai K, Burman A, Rowan SC, Weigt SS, Belperio J, Stripp B, Parks WC, Jiang D, Noble PW. The ZIP8/SIRT1 axis regulates alveolar progenitor cell renewal in aging and idiopathic pulmonary fibrosis. J Clin Invest 2022; 132:157338. [PMID: 35389887 PMCID: PMC9151700 DOI: 10.1172/jci157338] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractType 2 alveolar epithelial cells (AEC2s) function as progenitor cells in the lung. We have shown previously that failure of AEC2 regeneration results in progressive lung fibrosis in mice and is a cardinal feature of idiopathic pulmonary fibrosis (IPF). In this study, we identified a deficiency of a specific zinc transporter SLC39A8 (ZIP8) in AEC2s from both IPF lungs and lungs of old mice. Loss of ZIP8 expression was associated with impaired renewal capacity of AEC2s and enhanced lung fibrosis. ZIP8 regulation of AEC2 progenitor function was dependent on SIRT1. Replenishment with exogenous zinc and SIRT1 activation promoted self-renewal and differentiation of AEC2s from lung tissues of IPF patients and old mice. Deletion of Zip8 in AEC2s in mice impaired AEC2 renewal, increased susceptibility of the mice to bleomycin injury, and the mice developed spontaneous lung fibrosis. Therapeutic strategies to restore zinc metabolism and appropriate SIRT1 signaling could improve AEC2 progenitor function and mitigate ongoing fibrogenesis.
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Affiliation(s)
- Jiurong Liang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Guanling Huang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Xue Liu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Forough Taghavifar
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Ningshan Liu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Yizhou Wang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Nan Deng
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Changfu Yao
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Ting Xie
- Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Vrishika Kulur
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Kristy Dai
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Ankita Burman
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Simon C Rowan
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - S Samuel Weigt
- Department of Medicine, UCLA, Los Angeles, United States of America
| | - John Belperio
- Department of Medicine, UCLA, Los Angeles, United States of America
| | - Barry Stripp
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - William C Parks
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Dianhua Jiang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
| | - Paul W Noble
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, United States of America
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224
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Extracellular Lipids in the Lung and Their Role in Pulmonary Fibrosis. Cells 2022; 11:cells11071209. [PMID: 35406772 PMCID: PMC8997955 DOI: 10.3390/cells11071209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Lipids are major actors and regulators of physiological processes within the lung. Initial research has described their critical role in tissue homeostasis and in orchestrating cellular communication to allow respiration. Over the past decades, a growing body of research has also emphasized how lipids and their metabolism may be altered, contributing to the development and progression of chronic lung diseases such as pulmonary fibrosis. In this review, we first describe the current working model of the mechanisms of lung fibrogenesis before introducing lipids and their cellular metabolism. We then summarize the evidence of altered lipid homeostasis during pulmonary fibrosis, focusing on their extracellular forms. Finally, we highlight how lipid targeting may open avenues to develop therapeutic options for patients with lung fibrosis.
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225
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Gulhane AV, Chen DL. Overview of positron emission tomography in functional imaging of the lungs for diffuse lung diseases. Br J Radiol 2022; 95:20210824. [PMID: 34752146 PMCID: PMC9153708 DOI: 10.1259/bjr.20210824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Positron emission tomography (PET) is a quantitative molecular imaging modality increasingly used to study pulmonary disease processes and drug effects on those processes. The wide range of drugs and other entities that can be radiolabeled to study molecularly targeted processes is a major strength of PET, thus providing a noninvasive approach for obtaining molecular phenotyping information. The use of PET to monitor disease progression and treatment outcomes in DLD has been limited in clinical practice, with most of such applications occurring in the context of research investigations under clinical trials. Given the high costs and failure rates for lung drug development efforts, molecular imaging lung biomarkers are needed not only to aid these efforts but also to improve clinical characterization of these diseases beyond canonical anatomic classifications based on computed tomography. The purpose of this review article is to provide an overview of PET applications in characterizing lung disease, focusing on novel tracers that are in clinical development for DLD molecular phenotyping, and briefly address considerations for accurately quantifying lung PET signals.
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Affiliation(s)
- Avanti V Gulhane
- Department of Radiology, University of Washington School of Medicine, Seattle, United States
| | - Delphine L Chen
- Department of Radiology, University of Washington School of Medicine, Seattle, United States
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226
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Silva TD, Voisey J, Hopkins P, Apte S, Chambers D, O'Sullivan B. Markers of rejection of a lung allograft: state of the art. Biomark Med 2022; 16:483-498. [PMID: 35315284 DOI: 10.2217/bmm-2021-1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic lung allograft dysfunction (CLAD) affects approximately 50% of all lung transplant recipients by 5 post-operative years and is the leading cause of death in lung transplant recipients. Early CLAD diagnosis or ideally prediction of CLAD is essential to enable early intervention before significant lung injury occurs. New technologies have emerged to facilitate biomarker discovery, including epigenetic modification and single-cell RNA sequencing. This review examines new and existing technologies for biomarker discovery and the current state of research on biomarkers for identifying lung transplant rejection.
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Affiliation(s)
- Tharushi de Silva
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia
| | - Joanne Voisey
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Peter Hopkins
- Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Simon Apte
- Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Daniel Chambers
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
| | - Brendan O'Sullivan
- School of Biomedical Sciences, Centre for Genomics & Personalised Heath, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Queensland Lung Transplant Service, Ground Floor, Clinical Sciences Building, The Prince Charles Hospital, Rode Road, Chermside, 4032, Brisbane, Queensland, Australia.,Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, The University of Queensland, 4032, Brisbane, Queensland, Australia
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227
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RNA Sequencing of Epithelial Cell/Fibroblastic Foci Sandwich in Idiopathic Pulmonary Fibrosis: New Insights on the Signaling Pathway. Int J Mol Sci 2022; 23:ijms23063323. [PMID: 35328744 PMCID: PMC8954546 DOI: 10.3390/ijms23063323] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/27/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by irreversible scarring of the distal lung. IPF is best described by its histopathological pattern of usual interstitial pneumonia (UIP), characterized by spatial heterogeneity with alternating interstitial fibrosis and areas of normal lung, and temporal heterogeneity of fibrosis characterized by scattered fibroblastic foci (FF), dense acellular collagen and honeycomb changes. FF, comprising aggregated fibroblasts/myofibroblasts surrounded by metaplastic epithelial cells (EC), are the cardinal pathological lesion and their presence strongly correlates with disease progression and mortality. We hypothesized that the EC/FF sandwich from patients with UIP/IPF has a distinct molecular signature which could offer new insights into the crosstalk of these two crucial actors in the disease. Laser capture microdissection with RNAseq was used to investigate the transcriptome of the EC/FF sandwich from IPF patients versus controls (primary spontaneous pneumothorax). Differentially expressed gene analysis identified 23 up-regulated genes mainly related to epithelial dysfunction. Gene ontology analysis highlighted the activation of different pathways, mainly related to EC, immune response and programmed cell death. This study provides novel insights into the IPF pathogenetic pathways and suggests that targeting some of these up-regulated pathways (particularly those related to secreto-protein/mucin dysfunction) may be beneficial in IPF. Further studies in a larger number of lung samples, ideally from patients with early and advanced disease, are needed to validate these findings.
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228
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Sklepkiewicz P, Dymek BA, Mlacki M, Koralewski R, Mazur M, Nejman-Gryz P, Korur S, Zagozdzon A, Rymaszewska A, von der Thüsen JH, Siwińska AM, Güner NC, Cheda Ł, Paplinska-Goryca M, Proboszcz M, van den Bosch TPP, Górska K, Golab J, Kamiński RM, Krenke R, Golebiowski A, Dzwonek K, Dobrzanski P. Inhibition of CHIT1 as a novel therapeutic approach in idiopathic pulmonary fibrosis. Eur J Pharmacol 2022; 919:174792. [PMID: 35122869 DOI: 10.1016/j.ejphar.2022.174792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/13/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and eventually fatal lung disease with a complex etiology. Approved drugs, nintedanib and pirfenidone, modify disease progression, but IPF remains incurable and there is an urgent need for new therapies. We identified chitotriosidase (CHIT1) as new driver of fibrosis in IPF and a novel therapeutic target. We demonstrate that CHIT1 activity and expression are significantly increased in serum (3-fold) and induced sputum (4-fold) from IPF patients. In the lungs CHIT1 is expressed in a distinct subpopulation of profibrotic, disease-specific macrophages, which are only present in patients with ILDs and CHIT1 is one of the defining markers of this fibrosis-associated gene cluster. To define CHIT1 role in fibrosis, we used the therapeutic protocol of the bleomycin-induced pulmonary fibrosis mouse model. We demonstrate that in the context of chitinase induction and the macrophage-specific expression of CHIT1, this model recapitulates lung fibrosis in ILDs. Genetic inactivation of Chit1 attenuated bleomycin-induced fibrosis (decreasing the Ashcroft scoring by 28%) and decreased expression of profibrotic factors in lung tissues. Pharmacological inhibition of chitinases by OATD-01 reduced fibrosis and soluble collagen concentration. OATD-01 exhibited anti-fibrotic activity comparable to pirfenidone resulting in the reduction of the Ashcroft score by 32% and 31%, respectively. These studies provide a preclinical proof-of-concept for the antifibrotic effects of OATD-01 and establish CHIT1 as a potential new therapeutic target for IPF.
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Affiliation(s)
| | - Barbara A Dymek
- OncoArendi Therapeutics SA, 02-089, Warsaw, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-097, Warsaw, Poland.
| | | | | | | | - Patrycja Nejman-Gryz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, 02-097, Warsaw, Poland
| | - Serdar Korur
- OncoArendi Therapeutics SA, 02-089, Warsaw, Poland
| | | | | | - Jan H von der Thüsen
- Department of Pathology, Erasmus Medical Center, 3015 GD, Rotterdam, the Netherlands
| | | | | | - Łukasz Cheda
- OncoArendi Therapeutics SA, 02-089, Warsaw, Poland
| | - Magdalena Paplinska-Goryca
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, 02-097, Warsaw, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, 02-097, Warsaw, Poland
| | | | - Katarzyna Górska
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, 02-097, Warsaw, Poland
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, 02-097, Warsaw, Poland
| | | | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, 02-097, Warsaw, Poland
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229
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Liu W, Xiong S, Du J, Song Y, Wang T, Zhang Y, Dong C, Huang Z, He Q, Yu Z, Ma X. Deciphering Key Foreign Body Reaction-Related Transcription Factors and Genes Through Transcriptome Analysis. Front Mol Biosci 2022; 9:843391. [PMID: 35350715 PMCID: PMC8958039 DOI: 10.3389/fmolb.2022.843391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Silicone implants are widely used in the field of plastic surgery for wound repair and cosmetic augmentation. However, molecular mechanisms and signaling pathways underlying the foreign body reaction (FBR) of a host tissue to the silicone require further elucidation. The purpose of this study was to identify key FBR-related transcription factors (TFs) and genes through transcriptome analysis.Methods: We used a rat model with a subcutaneous silicone implant in the scalp and performed high throughput sequencing to determine the transcriptional profiles involved in the FBR. The function was analyzed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-enrichment analysis. A protein-protein interaction (PPI) network of differentially expressed mRNAs (DEmRNAs) was constructed to identify the hub genes and key modules and to determine the regulatory TF-mRNA relationships. In addition, the hub gene and transcript expression levels were determined by Quantitative Reverse Transcription polymerase Chain Reaction (qRT-PCR). Myofibroblasts differentiation and macrophage recruitment were identified by immunofluorescence. The protein expression of MMP9 was detected by immunohistochemistry and Western blot.Results: We identified ten hub genes (Fos, Spp1, Fn1, Ctgf, Tlr2, Itgb2, Itgax, Ccl2, Mmp9, and Serpine1) and 3 TFs (FOS, IRF4, and SPI1) that may be crucial (particularly FOS) for the FBR. Furthermore, we identified multiple differentially expressed genes involved in several important biological processes, including leukocyte migration, cytokine‒ cytokine receptor interaction, phagocytosis, extracellular matrix (ECM) organization, and angiogenesis. We also identified potentially significant signaling pathways, including cytokine‒cytokine receptor interaction, phagosome, ECM‒receptor interaction, complement and coagulation cascades, the IL-17 signaling pathway, and the PI3K‒Akt signaling pathway. In addition, qRT-PCR confirmed the expression patterns of the TFs and hub genes, Western blot and immunohistochemistry validated the expression patterns of MMP9.Conclusion: We generated a comprehensive overview of the gene networks underlying the FBR evoked by silicone implants. Moreover, we identified specific molecular and signaling pathways that may perform key functions in the silicone implant-induced FBR. Our results provide significant insights into the molecular mechanisms underlying silicone-induced FBR and determine novel therapeutic targets to reduce complications related to silicone implantation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhou Yu
- *Correspondence: Zhou Yu, ; Xianjie Ma,
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230
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Hammer Q, Dunst J, Christ W, Picarazzi F, Wendorff M, Momayyezi P, Huhn O, Netskar HK, Maleki KT, García M, Sekine T, Sohlberg E, Azzimato V, Aouadi M, Degenhardt F, Franke A, Spallotta F, Mori M, Michaëlsson J, Björkström NK, Rückert T, Romagnani C, Horowitz A, Klingström J, Ljunggren HG, Malmberg KJ. SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells. Cell Rep 2022; 38:110503. [PMID: 35235832 PMCID: PMC8858686 DOI: 10.1016/j.celrep.2022.110503] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/12/2022] [Accepted: 02/15/2022] [Indexed: 01/08/2023] Open
Abstract
Natural killer (NK) cells are innate immune cells that contribute to host defense against virus infections. NK cells respond to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and are activated in patients with acute coronavirus disease 2019 (COVID-19). However, by which mechanisms NK cells detect SARS-CoV-2-infected cells remains largely unknown. Here, we show that the Non-structural protein 13 of SARS-CoV-2 encodes for a peptide that is presented by human leukocyte antigen E (HLA-E). In contrast with self-peptides, the viral peptide prevents binding of HLA-E to the inhibitory receptor NKG2A, thereby rendering target cells susceptible to NK cell attack. In line with these observations, NKG2A-expressing NK cells are particularly activated in patients with COVID-19 and proficiently limit SARS-CoV-2 replication in infected lung epithelial cells in vitro. Thus, these data suggest that a viral peptide presented by HLA-E abrogates inhibition of NKG2A+ NK cells, resulting in missing self-recognition.
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Affiliation(s)
- Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.
| | - Josefine Dunst
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Wanda Christ
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Pouria Momayyezi
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Oisín Huhn
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Herman K Netskar
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kimia T Maleki
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Marina García
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Takuya Sekine
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Valerio Azzimato
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Myriam Aouadi
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Francesco Spallotta
- Institute for Systems Analysis and Computer Science "A. Ruberti," National Research Council (IASI-CNR), Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum (DRFZ), Institute of the Leibniz Association, Berlin, Germany
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum (DRFZ), Institute of the Leibniz Association, Berlin, Germany; Division of Gastroenterology, Infectiology and Rheumatology, Medical Department I, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Liu J, Gu L, Li W. The Prognostic Value of Integrated Analysis of Inflammation and Hypoxia-Related Genes in Idiopathic Pulmonary Fibrosis. Front Immunol 2022; 13:730186. [PMID: 35309336 PMCID: PMC8929415 DOI: 10.3389/fimmu.2022.730186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Currently, the aetiology and pathogenesis of idiopathic pulmonary fibrosis (IPF) are still largely unclear. Moreover, patients with IPF exhibit a considerable difference in clinical presentation, treatment, and prognosis. Optimal biomarkers or models for IPF prognosis are lacking. Therefore, this study quantified the levels of various hallmarks using a single-sample gene set enrichment analysis algorithm. The hazard ration was calculated using Univariate Cox regression analysis based on the transcriptomic profile of bronchoalveolar lavage cells and clinical survival information. Afterwards, weighted Gene Co-expression Network Analysis was performed to construct a network between gene expression, inflammation response, and hypoxia. Subsequently, univariate Cox, random forest, and multivariate Cox regressions were applied to develop a robust inflammation and hypoxia-related gene signature for predicting clinical outcomes in patients with IPF. Furthermore, a nomogram was constructed to calculate risk assessment. The inflammation response and hypoxia were identified as latent risk factors for patients with IPF. Five genes, including HS3ST1, WFDC2, SPP1, TFPI, and CDC42EP2, were identified that formed the inflammation-hypoxia-related gene signature. Kaplan-Meier plotter showed that the patients with high-risk scores had a worse prognosis than those with low-risk scores in training and validation cohorts. The time-dependent concordance index and the receiver operating characteristic analysis revealed that the risk model could accurately predict the clinical outcome of patients with IPF. Therefore, this study contributes to elucidating the role of inflammation and hypoxia in IPF, which can aid in assessing individual prognosis and personalised treatment decisions.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Liming Gu
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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Single cell transcriptomics in human osteoarthritis synovium and in silico deconvoluted bulk RNA sequencing. Osteoarthritis Cartilage 2022; 30:475-480. [PMID: 34971754 PMCID: PMC10097426 DOI: 10.1016/j.joca.2021.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To reveal the heterogeneity of different cell types of osteoarthritis (OA) synovial tissues at a single-cell resolution, and determine by novel methodology whether bulk-RNA-seq data could be deconvoluted to create in silico scRNA-seq data for synovial tissue analyses. METHODS OA scRNA-seq data (102,077 synoviocytes) were provided by 17 patients undergoing total knee arthroplasty; 9 tissues with matched scRNA-seq and bulk RNA-seq data were used to evaluate six in silico gene deconvolution tools. Predicted and observed cell types and proportions were compared to identify the best deconvolution tool for synovium. RESULTS We identified seven distinct cell types in OA synovial tissues. Gene deconvolution identified three (of six) platforms as suitable for extrapolating cellular gene expression from bulk RNA-seq data. Using paired scRNA-seq and bulk RNA-seq data, an "arthritis" specific signature matrix was created and validated to have a significantly better predictive performance for synoviocytes than a default signature matrix. Use of the machine learning tool, Cell-type Identification By Estimating Relative Subsets of RNA Transcripts x (CIBERSORTx), to analyze rheumatoid arthritis (RA) and OA bulk RNA-seq data yielded proportions of T cells and fibroblasts that were similar to the gold standard observations from RA and OA scRNA-seq data, respectively. CONCLUSION This novel study revealed heterogeneity of synovial cell types in OA and the feasibility of gene deconvolution for synovial tissue.
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Ortega-Peña S, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection? Life (Basel) 2022; 12:341. [PMID: 35330092 PMCID: PMC8954679 DOI: 10.3390/life12030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host's innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.
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Affiliation(s)
- Silvestre Ortega-Peña
- Laboratorio Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación “Luís Guillermo Ibarra Ibarra”, Ciudad de México 14389, Mexico
| | - Sandra Rodríguez-Martínez
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Mario E. Cancino-Diaz
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Juan C. Cancino-Diaz
- Laboratorio de Inmunomicrobiología, Departamento Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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234
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Li H, Qu L, Yang Y, Zhang H, Li X, Zhang X. Single-cell Transcriptomic Architecture Unraveling the Complexity of Tumor Heterogeneity in Distal Cholangiocarcinoma. Cell Mol Gastroenterol Hepatol 2022; 13:1592-1609.e9. [PMID: 35219893 PMCID: PMC9043309 DOI: 10.1016/j.jcmgh.2022.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Distal cholangiocarcinoma (dCCA) are a group of epithelial cell malignancies that occurs at the distal common bile duct, and account for approximately 40% of all cholangiocarcinoma cases. dCCA remains a highly lethal disease as it typically features remarkable cellular heterogeneity. A comprehensive exploration of cellular diversity and the tumor microenvironment is essential to depict the mechanisms driving dCCA progression. METHODS Single-cell RNA sequencing was used here to dissect the heterogeneity landscape and tumor microenvironment composition of human dCCAs. Seven human dCCAs and adjacent normal bile duct samples were included in the current study for single-cell RNA sequencing and subsequent validation approaches. Additionally, the results of the analyses were compared with bulk transcriptomic datasets from extrahepatic cholangiocarcinoma and single-cell RNA data from intrahepatic cholangiocarcinoma. RESULTS We sequenced a total of 49,717 single cells derived from human dCCAs and adjacent tissues, identifying 11 distinct cell types. Malignant cells displayed remarkable inter- and intra-tumor heterogeneity with 5 distinct subsets were defined in tumor samples. The malignant cells displayed variable degree of aneuploidy, which can be classified into low- and high-copy number variation groups based on either amplification or deletion of chr17q12 - chr17q21.2. Additionally, we identified 4 distinct T lymphocytes subsets, of which cytotoxic CD8+ T cells predominated as effectors in tumor tissues, whereas tumor infiltrating FOXP3+ CD4+ regulatory T cells exhibited highly immunosuppressive characteristics. CONCLUSION Our single-cell transcriptomic dataset depicts the inter- and intra-tumor heterogeneity of human dCCAs at the expression level.
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Affiliation(s)
- Hongguang Li
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lingxin Qu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yongheng Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haibin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xuexin Li
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolu Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Xiaolu Zhang, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China. tel: (+86) 17862933917; fax: (+86) 53188565657.
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235
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Tran E, Shi T, Li X, Chowdhury AY, Jiang D, Liu Y, Wang H, Yan C, Wallace WD, Lu R, Ryan AL, Marconett CN, Zhou B, Borok Z, Offringa IA. Development of human alveolar epithelial cell models to study distal lung biology and disease. iScience 2022; 25:103780. [PMID: 35169685 PMCID: PMC8829779 DOI: 10.1016/j.isci.2022.103780] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 10/27/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Many acute and chronic diseases affect the distal lung alveoli. Alveolar epithelial cell (AEC) lines are needed to better model these diseases. We used de-identified human remnant transplant lungs to develop a method to establish AEC lines. The lines grow well in 2-dimensional (2D) culture as epithelial monolayers expressing lung progenitor markers. In 3-dimensional (3D) culture with fibroblasts, Matrigel, and specific media conditions, the cells form alveolar-like organoids expressing mature AEC markers including aquaporin 5 (AQP5), G-protein-coupled receptor class C group 5 member A (GPRC5A), and surface marker HTII280. Single-cell RNA sequencing of an AEC line in 2D versus 3D culture revealed increased cellular heterogeneity and induction of cytokine and lipoprotein signaling in 3D organoids. Our approach yields lung progenitor lines that retain the ability to differentiate along the alveolar cell lineage despite long-term expansion and provides a valuable system to model and study the distal lung in vitro.
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Affiliation(s)
- Evelyn Tran
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Tuo Shi
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Xiuwen Li
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Translational Genomics, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Adnan Y. Chowdhury
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Du Jiang
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Yixin Liu
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Hongjun Wang
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Chunli Yan
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - William D. Wallace
- Department of Pathology, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Rong Lu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Amy L. Ryan
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Beiyun Zhou
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Zea Borok
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
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236
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Simmons DP, Nguyen HN, Gomez-Rivas E, Jeong Y, Jonsson AH, Chen AF, Lange JK, Dyer GS, Blazar P, Earp BE, Coblyn JS, Massarotti EM, Sparks JA, Todd DJ, Rao DA, Kim EY, Brenner MB. SLAMF7 engagement superactivates macrophages in acute and chronic inflammation. Sci Immunol 2022; 7:eabf2846. [PMID: 35148199 PMCID: PMC8991457 DOI: 10.1126/sciimmunol.abf2846] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a superactivated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression and engaging SLAMF7 drove a strong wave of inflammatory cytokine expression. Induction of TNF-α after SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients but also in gut macrophages from patients with active Crohn's disease and in lung macrophages from patients with severe COVID-19. This suggests a central role for SLAMF7 in macrophage superactivation with broad implications in human disease pathology.
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Affiliation(s)
- Daimon P. Simmons
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Hung N. Nguyen
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Emma Gomez-Rivas
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Yunju Jeong
- Harvard Medical School, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - A. Helena Jonsson
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Antonia F. Chen
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Jeffrey K. Lange
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - George S. Dyer
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Philip Blazar
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Brandon E. Earp
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Jonathan S. Coblyn
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Elena M. Massarotti
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jeffrey A. Sparks
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Derrick J. Todd
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | | | - Deepak A. Rao
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Edy Y. Kim
- Harvard Medical School, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Michael B. Brenner
- Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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237
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Zhang B, Zhang Y, Xiong L, Li Y, Zhang Y, Zhao J, Jiang H, Li C, Liu Y, Liu X, Liu H, Ping YF, Zhang QC, Zhang Z, Bian XW, Zhao Y, Hu X. CD127 imprints functional heterogeneity to diversify monocyte responses in inflammatory diseases. J Exp Med 2022; 219:e20211191. [PMID: 35015026 PMCID: PMC8757045 DOI: 10.1084/jem.20211191] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Inflammatory monocytes are key mediators of acute and chronic inflammation; yet, their functional diversity remains obscure. Single-cell transcriptome analyses of human inflammatory monocytes from COVID-19 and rheumatoid arthritis patients revealed a subset of cells positive for CD127, an IL-7 receptor subunit, and such positivity rendered otherwise inert monocytes responsive to IL-7. Active IL-7 signaling engaged epigenetically coupled, STAT5-coordinated transcriptional programs to restrain inflammatory gene expression, resulting in inverse correlation between CD127 expression and inflammatory phenotypes in a seemingly homogeneous monocyte population. In COVID-19 and rheumatoid arthritis, CD127 marked a subset of monocytes/macrophages that retained hypoinflammatory phenotypes within the highly inflammatory tissue environments. Furthermore, generation of an integrated expression atlas revealed unified features of human inflammatory monocytes across different diseases and different tissues, exemplified by those of the CD127high subset. Overall, we phenotypically and molecularly characterized CD127-imprinted functional heterogeneity of human inflammatory monocytes with direct relevance for inflammatory diseases.
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Affiliation(s)
- Bin Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Yuan Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Lei Xiong
- Ministry of Education Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuzhe Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yunliang Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunological Diseases, Beijing, China
| | - Hui Jiang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunological Diseases, Beijing, China
| | - Can Li
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunological Diseases, Beijing, China
| | - Yunqi Liu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Xindong Liu
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Haofei Liu
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yi-Fang Ping
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qiangfeng Cliff Zhang
- Ministry of Education Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xiu-Wu Bian
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yan Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunological Diseases, Beijing, China
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Center for Human Disease Immuno-monitoring, Beijing Friendship Hospital, Beijing, China
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Evren E, Ringqvist E, Doisne JM, Thaller A, Sleiers N, Flavell RA, Di Santo JP, Willinger T. CD116+ fetal precursors migrate to the perinatal lung and give rise to human alveolar macrophages. J Exp Med 2022; 219:212959. [PMID: 35019940 PMCID: PMC8759608 DOI: 10.1084/jem.20210987] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/05/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022] Open
Abstract
Despite their importance in lung health and disease, it remains unknown how human alveolar macrophages develop early in life. Here we define the ontogeny of human alveolar macrophages from embryonic progenitors in vivo, using a humanized mouse model expressing human cytokines (MISTRG mice). We identified alveolar macrophage progenitors in human fetal liver that expressed the GM-CSF receptor CD116 and the transcription factor MYB. Transplantation experiments in MISTRG mice established a precursor-product relationship between CD34-CD116+ fetal liver cells and human alveolar macrophages in vivo. Moreover, we discovered circulating CD116+CD64-CD115+ macrophage precursors that migrated from the liver to the lung. Similar precursors were present in human fetal lung and expressed the chemokine receptor CX3CR1. Fetal CD116+CD64- macrophage precursors had a proliferative gene signature, outcompeted adult precursors in occupying the perinatal alveolar niche, and developed into functional alveolar macrophages. The discovery of the fetal alveolar macrophage progenitor advances our understanding of human macrophage origin and ontogeny.
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Affiliation(s)
- Elza Evren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Ringqvist
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Anna Thaller
- Innate Immunity Unit, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Natalie Sleiers
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Tim Willinger
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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239
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Xu D, Bhattacharyya S, Wang W, Ifergan I, Chiang Wong MYA, Procissi D, Yeldandi A, Bale S, Marangoni RG, Horbinski C, Miller SD, Varga J. PLG nanoparticles target fibroblasts and MARCO+ monocytes to reverse multi-organ fibrosis. JCI Insight 2022; 7:151037. [PMID: 35104243 PMCID: PMC8983146 DOI: 10.1172/jci.insight.151037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Systemic sclerosis (SSc) is a chronic, multisystem orphan disease with a highly variable clinical course, high mortality rate, and a poorly understood complex pathogenesis. We have identified an important role for a subpopulation of monocytes and macrophages characterized by surface expression of the scavenger receptor macrophage receptor with collagenous structure (MARCO) in chronic inflammation and fibrosis in SSc and in preclinical disease models. We show that MARCO+ monocytes and macrophages accumulate in lesional skin and lung in topographic proximity to activated myofibroblasts in patients with SSc and in the bleomycin-induced mouse model of SSc. Short-term treatment of mice with a potentially novel nanoparticle, poly(lactic-co-glycolic) acid (PLG), which is composed of a carboxylated, FDA-approved, biodegradable polymer and modulates activation and trafficking of MARCO+ inflammatory monocytes, markedly attenuated bleomycin-induced skin and lung inflammation and fibrosis. Mechanistically, in isolated cells in culture, PLG nanoparticles inhibited TGF-dependent fibrotic responses in vitro. Thus, MARCO+ monocytes are potent effector cells of skin and lung fibrosis and can be therapeutically targeted in SSc using PLG nanoparticles.
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Affiliation(s)
- Dan Xu
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Swati Bhattacharyya
- Department of Internal Medicine, University of Michigan, Ann Arbor, United States of America
| | - Wenxia Wang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Igal Ifergan
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Ming-Yi Alice Chiang Wong
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Daniele Procissi
- Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Anjana Yeldandi
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Swarna Bale
- Department of Internal Medicine, University of Michigan, Ann Arbor, United States of America
| | - Roberta G Marangoni
- Northwestern Scleroderma Program, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Craig Horbinski
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Stephen D Miller
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - John Varga
- Department of Internal Medicine, University of Michigan, Ann Arbor, United States of America
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240
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Xue D, Tabib T, Morse C, Yang Y, Domsic R, Khanna D, Lafyatis R. Expansion of Fcγ Receptor IIIa-Positive Macrophages, Ficolin 1-Positive Monocyte-Derived Dendritic Cells, and Plasmacytoid Dendritic Cells Associated With Severe Skin Disease in Systemic Sclerosis. Arthritis Rheumatol 2022; 74:329-341. [PMID: 34042322 PMCID: PMC8626521 DOI: 10.1002/art.41813] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 04/07/2021] [Accepted: 05/11/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE In this study, we sought a comprehensive understanding of myeloid cell types driving fibrosis in diffuse cutaneous systemic sclerosis (dcSSc) skin. METHODS We analyzed the transcriptomes of 2,465 myeloid cells from skin biopsy specimens from 12 dcSSc patients and 10 healthy control subjects using single-cell RNA sequencing. Monocyte-derived dendritic cells (mo-DCs) were assessed using immunohistochemical staining and immunofluorescence analyses targeting ficolin-1 (FCN-1). RESULTS A t-distributed stochastic neighbor embedding analysis of single-cell transcriptome data revealed 12 myeloid cell clusters, 9 of which paralleled previously described healthy control macrophage/DC clusters, and 3 of which were dcSSc-specific myeloid cell clusters. One SSc-associated macrophage cluster, highly expressing Fcγ receptor IIIA, was suggested on pseudotime analysis to be derived from normal CCR1+ and MARCO+ macrophages. A second SSc-associated myeloid population highly expressed monocyte markers FCN-1, epiregulin, S100A8, and S100A9, but was closely related to type 2 conventional DCs on pseudotime analysis and identified as mo-DCs. Mo-DCs were associated with more severe skin disease. Proliferating macrophages and plasmacytoid DCs were detected almost exclusively in dcSSc skin, the latter clustering with B cells and apparently derived from lymphoid progenitors. CONCLUSION Transcriptional signatures in these and other myeloid populations indicate innate immune system activation, possibly through Toll-like receptors and highly up-regulated chemokines. However, the appearance and activation of myeloid cells varies between patients, indicating potential differences in the underlying pathogenesis and/or temporal disease activity in dcSSc.
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Affiliation(s)
- Dan Xue
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Tracy Tabib
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yi Yang
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Robyn Domsic
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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241
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Bain CC, MacDonald AS. The impact of the lung environment on macrophage development, activation and function: diversity in the face of adversity. Mucosal Immunol 2022; 15:223-234. [PMID: 35017701 PMCID: PMC8749355 DOI: 10.1038/s41385-021-00480-w] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/04/2021] [Accepted: 12/18/2021] [Indexed: 02/04/2023]
Abstract
The last decade has been somewhat of a renaissance period for the field of macrophage biology. This renewed interest, combined with the advent of new technologies and development of novel model systems to assess different facets of macrophage biology, has led to major advances in our understanding of the diverse roles macrophages play in health, inflammation, infection and repair, and the dominance of tissue environments in influencing all of these areas. Here, we discuss recent developments in our understanding of lung macrophage heterogeneity, ontogeny, metabolism and function in the context of health and disease, and highlight core conceptual advances and key unanswered questions that we believe should be focus of work in the coming years.
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Affiliation(s)
- Calum C Bain
- The University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh Bioquarter, Edinburgh, EH16 4TJ, UK.
| | - Andrew S MacDonald
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, M13 9NT, UK.
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242
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Qian W, Xia S, Yang X, Yu J, Guo B, Lin Z, Wei R, Mao M, Zhang Z, Zhao G, Bai J, Han Q, Wang Z, Luo Q. Complex Involvement of the Extracellular Matrix, Immune Effect, and Lipid Metabolism in the Development of Idiopathic Pulmonary Fibrosis. Front Mol Biosci 2022; 8:800747. [PMID: 35174208 PMCID: PMC8841329 DOI: 10.3389/fmolb.2021.800747] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/06/2021] [Indexed: 01/02/2023] Open
Abstract
Background and objective: Idiopathic pulmonary fibrosis (IPF) is an aggressive fibrotic pulmonary disease with spatially and temporally heterogeneous alveolar lesions. There are no early diagnostic biomarkers, limiting our understanding of IPF pathogenesis. Methods: Lung tissue from surgical lung biopsy of patients with early-stage IPF (n = 7), transplant-stage IPF (n = 2), and healthy controls (n = 6) were subjected to mRNA sequencing and verified by real-time quantitative PCR (RT-qPCR), immunohistochemistry, Western blot, and single-cell RNA sequencing (scRNA-Seq). Results: Three hundred eighty differentially expressed transcripts (DETs) were identified in IPF that were principally involved in extracellular matrix (ECM) remodeling, lipid metabolism, and immune effect. Of these DETs, 21 (DMD, MMP7, POSTN, ECM2, MMP13, FASN, FADS1, SDR16C5, ACAT2, ACSL1, CYP1A1, UGT1A6, CXCL13, CXCL5, CXCL14, IL5RA, TNFRSF19, CSF3R, S100A9, S100A8, and S100A12) were selected and verified by RT-qPCR. Differences in DMD, FASN, and MMP7 were also confirmed at a protein level. Analysis of scRNA-Seq was used to trace their cellular origin to determine which lung cells regulated them. The principal cell sources of DMD were ciliated cells, alveolar type I/II epithelial cells (AT cells), club cells, and alveolar macrophages (AMs); MMP7 derives from AT cells, club cells, and AMs, while FASN originates from AT cells, ciliated cells, and AMs. Conclusion: Our data revealed a comprehensive transcriptional mRNA profile of IPF and demonstrated that ECM remodeling, lipid metabolism, and immune effect were collaboratively involved in the early development of IPF.
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Affiliation(s)
- Weiping Qian
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Shu Xia
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xiaoyun Yang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaying Yu
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bingpeng Guo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhengfang Lin
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Wei
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Mengmeng Mao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ziyi Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Gui Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Junye Bai
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Qian Han
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Zhongfang Wang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Qun Luo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
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243
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White ES, Thomas M, Stowasser S, Tetzlaff K. Challenges for Clinical Drug Development in Pulmonary Fibrosis. Front Pharmacol 2022; 13:823085. [PMID: 35173620 PMCID: PMC8841605 DOI: 10.3389/fphar.2022.823085] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Pulmonary fibrosis is a pathologic process associated with scarring of the lung interstitium. Interstitial lung diseases (ILDs) encompass a large and heterogenous group of disorders, a number of which are characterized by progressive pulmonary fibrosis that leads to respiratory failure and death. Idiopathic pulmonary fibrosis (IPF) has been described as an archetype of progressive fibrosing ILD, and the development of pirfenidone and nintedanib has been a major breakthrough in the treatment of patients with this deadly disease. Both drugs principally target scar-forming fibroblasts and have been shown to significantly slow down the accelerated decline of lung function by approximately 50%. In addition, nintedanib has been approved for patients with other progressive fibrosing ILDs and systemic sclerosis-associated ILD. However, there is still no cure for pulmonary fibrosis and no meaningful improvement of symptoms or quality of life has been shown. Advancement in research, such as the advent of single cell sequencing technology, has identified additional pathologic cell populations beyond the fibroblast which could be targeted for therapeutic purposes. The preclinical and clinical development of novel drug candidates is hampered by profound challenges such as a lack of sensitive clinical outcomes or suitable biomarkers that would provide an early indication of patient benefit. With the availability of these anti-fibrotic treatments, it has become even more difficult to demonstrate added efficacy, in particular in short-term clinical studies. Patient heterogeneity and the paucity of biomarkers of disease activity further complicate clinical development. It is conceivable that future treatment of pulmonary fibrosis will need to embrace more precision in treating the right patient at the right time, explore novel measures of efficacy, and likely combine treatment options.
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Affiliation(s)
- Eric S. White
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, United States
| | - Matthew Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Susanne Stowasser
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Kay Tetzlaff
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
- Department of Sports Medicine, University of Tübingen, Tübingen, Germany
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244
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Characterizing cellular heterogeneity in fibrotic hypersensitivity pneumonitis by single-cell transcriptional analysis. Cell Death Dis 2022; 8:38. [PMID: 35091537 PMCID: PMC8795750 DOI: 10.1038/s41420-022-00831-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022]
Abstract
Fibrotic hypersensitivity pneumonitis (FHP) remains one of fatal interstitial pulmonary disease. Comprehensively dissecting the cellular heterogeneity of FHP paves the way for developing general gene therapeutic solutions for FHP. Here, utilizing an integrated strategy based on scRNA-seq, scTCR-seq, and bulk RNA-seq analysis of FHP profiles, we identified ten major cell types and 19 unique subtypes. FHP exhibited higher features of EMT and inflammation-promoting than normal control. In distinct subsets of lung macrophages in FHP, FN1high, PLA2G7high, and MS4A6Ahigh macrophages with predominant M2 phenotype exhibited higher activity of inflammatory responses and para-inflammation than other macrophages. KRT17high basal-like epithelial cells were significantly increased in FHP, and showed higher ability to induce EMT. We identified roles for ACTA2high, COL1A1high, and PLA2G2Ahigh fibroblasts in FHP, which were significantly related to interstitial fibrosis. NK cells and KLRG1+ effector CD8+ T cells had greater activity in inflammation-promoting. Our results provide a comprehensive portrait of cellular heterogeneity in FHP, and highlight the indispensable role of cell subpopulations in shaping the complexity and heterogeneity of FHP. These subpopulations are potentially key players for FHP pathogenesis.
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245
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Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J 2022; 60:13993003.02057-2021. [PMID: 35086829 PMCID: PMC9386332 DOI: 10.1183/13993003.02057-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions. The discovAIR project contributes to the Human Cell Atlas Lung Biological Network by establishing a first draft of the Human Lung Cell Atlas, advancing our insight into the cellular complexity and spatial organisation of the lung in health and diseasehttps://bit.ly/3zX4cad
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Affiliation(s)
- Malte D Luecken
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Laure-Emmanuelle Zaragozi
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.,These authors made an equal contribution to this manuscript
| | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,These authors made an equal contribution to this manuscript
| | - Lisa Sikkema
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Alexandra B Firsova
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Louis Kümmerle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Janine Schniering
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Christoph H Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Sarah Teichmann
- Wellcome Sanger Institute, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK
| | - Karen van Eunen
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,UMCG Research BV, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Sylvie Leroy
- Département de Pneumologie, Université Côte d'Azur and CHU Nice, FHU-OncoAge, Nice, France
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Maarten van den Berge
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Peter Horváth
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Joachim Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Herbert B Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Pascal Barbry
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Ilya Petoukhov
- A Beta World (former Principal at MIcompany), Amsterdam, the Netherlands
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ian Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Christos Samakovlis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands .,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
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246
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Karolin A, Escher G, Rudloff S, Sidler D. Nephrotoxicity of Calcineurin Inhibitors in Kidney Epithelial Cells is Independent of NFAT Signaling. Front Pharmacol 2022; 12:789080. [PMID: 35140605 PMCID: PMC8819135 DOI: 10.3389/fphar.2021.789080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/29/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Calcineurin inhibitors (CNIs) such as cyclosporine A and tacrolimus are commonly used after renal transplantation to suppress the immune system. In lymphoid cells, cyclosporine A acts via the calcineurin/nuclear factor of activated T-cell (NFAT) axis. In non-lymphoid cells, such as kidney epithelial cells, cyclosporine A induces calcineurin inhibitor toxicity. It is unknown via which off-targets cyclosporine A induces calcineurin inhibitor toxicity in kidney epithelial cells. Methods: To measure a compound’s potential to induce nephrotoxicity, the expression of the surrogate marker Fn14 was measured by flow cytometry. Compounds were tested for their potential to induce Fn14 either chemically or plasmid-mediated. Mice were injected with various compounds, and changes in nephrotoxic gene expression levels of the kidney epithelial cells were then analyzed. Results: Fn14 is specifically upregulated due to calcineurin inhibitor toxicity inducing agents. Inhibition of the NFAT axis showed no increase of the Fn14 expression on the surface of kidney cells. However, inhibition of p38 MAPK, phosphoinositide-3-kinase (PI3K)/Akt, protein kinase C (PKC), and inhibitor of nuclear factor-κB (IκB) kinase (IKK) showed clear induction of Fn14 and increased expressions of nephrotoxic, inflammatory, and fibrotic genes in vitro and in vivo. Conclusions: These findings show that cyclosporine A acts independently of NFAT on kidney epithelial cells. Moreover, inhibition of serine/threonine protein kinases mimics cyclosporine A’s activity on kidney epithelial cells. This mimicking effect indicates that these protein kinases are off-targets of cyclosporine A and damage structural renal cells when inhibited and therefore contributes likely to the development and progression of calcineurin inhibitor toxicity.
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Affiliation(s)
- Andrea Karolin
- Department for Nephrology and Hypertension, University Hospital Insel Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Geneviève Escher
- Department for Nephrology and Hypertension, University Hospital Insel Bern, Bern, Switzerland
| | - Stefan Rudloff
- Department for Nephrology and Hypertension, University Hospital Insel Bern, Bern, Switzerland
| | - Daniel Sidler
- Department for Nephrology and Hypertension, University Hospital Insel Bern, Bern, Switzerland
- *Correspondence: Daniel Sidler,
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247
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Moss BJ, Ryter SW, Rosas IO. Pathogenic Mechanisms Underlying Idiopathic Pulmonary Fibrosis. ANNUAL REVIEW OF PATHOLOGY 2022; 17:515-546. [PMID: 34813355 DOI: 10.1146/annurev-pathol-042320-030240] [Citation(s) in RCA: 210] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogenesis of idiopathic pulmonary fibrosis (IPF) involves a complex interplay of cell types and signaling pathways. Recurrent alveolar epithelial cell (AEC) injury may occur in the context of predisposing factors (e.g., genetic, environmental, epigenetic, immunologic, and gerontologic), leading to metabolic dysfunction, senescence, aberrant epithelial cell activation, and dysregulated epithelial repair. The dysregulated epithelial cell interacts with mesenchymal, immune, and endothelial cells via multiple signaling mechanisms to trigger fibroblast and myofibroblast activation. Recent single-cell RNA sequencing studies of IPF lungs support the epithelial injury model. These studies have uncovered a novel type of AEC with characteristics of an aberrant basal cell, which may disrupt normal epithelial repair and propagate a profibrotic phenotype. Here, we review the pathogenesis of IPF in the context of novel bioinformatics tools as strategies to discover pathways of disease, cell-specific mechanisms, and cell-cell interactions that propagate the profibrotic niche.
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Affiliation(s)
- Benjamin J Moss
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
| | - Stefan W Ryter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
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248
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Mei Q, Liu Z, Zuo H, Yang Z, Qu J. Idiopathic Pulmonary Fibrosis: An Update on Pathogenesis. Front Pharmacol 2022; 12:797292. [PMID: 35126134 PMCID: PMC8807692 DOI: 10.3389/fphar.2021.797292] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, lethal fibrotic lung disease that occurs primarily in middle-aged and elderly adults. It is a major cause of morbidity and mortality. With an increase in life expectancy, the economic burden of IPF is expected to continuously rise in the near future. Although the exact pathophysiological mechanisms underlying IPF remain not known. Significant progress has been made in our understanding of the pathogenesis of this devastating disease in last decade. The current paradigm assumes that IPF results from sustained or repetitive lung epithelial injury and subsequent activation of fibroblasts and myofibroblast differentiation. Persistent myofibroblast phenotype contributes to excessive deposition of the extracellular matrix (ECM) and aberrant lung repair, leading to tissue scar formation, distortion of the alveolar structure, and irreversible loss of lung function. Treatments of patients with IPF by pirfenidone and nintedanib have shown significant reduction of lung function decline and slowing of disease progression in patients with IPF. However, these drugs do not cure the disease. In this review, we discuss recent advances on the pathogenesis of IPF and highlight the development of novel therapeutic strategies against the disease.
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Affiliation(s)
| | | | | | | | - Jing Qu
- *Correspondence: Zhenhua Yang, ; Jing Qu,
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249
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McCormick TS, Hejal RB, Leal LO, Ghannoum MA. GM-CSF: Orchestrating the Pulmonary Response to Infection. Front Pharmacol 2022; 12:735443. [PMID: 35111042 PMCID: PMC8803133 DOI: 10.3389/fphar.2021.735443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
This review summarizes the structure and function of the alveolar unit, comprised of alveolar macrophage and epithelial cell types that work in tandem to respond to infection. Granulocyte-macrophage colony-stimulating factor (GM-CSF) helps to maintain the alveolar epithelium and pulmonary immune system under physiological conditions and plays a critical role in restoring homeostasis under pathologic conditions, including infection. Given the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global spread of coronavirus disease 2019 (COVID-19), with subsequent acute respiratory distress syndrome, understanding basic lung physiology in infectious diseases is especially warranted. This review summarizes clinical and preclinical data for GM-CSF in respiratory infections, and the rationale for sargramostim (yeast-derived recombinant human [rhu] GM-CSF) as adjunctive treatment for COVID-19 and other pulmonary infectious diseases.
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Affiliation(s)
- Thomas S. McCormick
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, United States
| | - Rana B. Hejal
- Medical Intensive Care Unit, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- Pulmonary and Critical Care Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Luis O. Leal
- Partner Therapeutics, Lexington, MA, United States
| | - Mahmoud A. Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, United States
- University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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250
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Sung PS, Kim CM, Cha JH, Park JY, Yu YS, Wang HJ, Kim JK, Bae SH. A Unique Immune-Related Gene Signature Represents Advanced Liver Fibrosis and Reveals Potential Therapeutic Targets. Biomedicines 2022; 10:biomedicines10010180. [PMID: 35052861 PMCID: PMC8774116 DOI: 10.3390/biomedicines10010180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Innate and adaptive immune responses are critically associated with the progression of fibrosis in chronic liver diseases. In this study, we aim to identify a unique immune-related gene signature representing advanced liver fibrosis and to reveal potential therapeutic targets. Seventy-seven snap-frozen liver tissues with various chronic liver diseases at different fibrosis stages (1: n = 12, 2: n = 12, 3: n = 25, 4: n = 28) were subjected to expression analyses. Gene expression analysis was performed using the nCounter PanCancer Immune Profiling Panel (NanoString Technologies, Seattle, WA, USA). Biological meta-analysis was performed using the CBS Probe PINGSTM (CbsBioscience, Daejeon, Korea). Using non-tumor tissues from surgically resected specimens, we identified the immune-related, five-gene signature (CHIT1_FCER1G_OSM_VEGFA_ZAP70) that reliably differentiated patients with low- (F1 and F2) and high-grade fibrosis (F3 and F4; accuracy = 94.8%, specificity = 91.7%, sensitivity = 96.23%). The signature was independent of all pathological and clinical features and was independently associated with high-grade fibrosis using multivariate analysis. Among these genes, the expression of inflammation-associated FCER1G, OSM, VEGFA, and ZAP70 was lower in high-grade fibrosis than in low-grade fibrosis, whereas CHIT1 expression, which is associated with fibrogenic activity of macrophages, was higher in high-grade fibrosis. Meta-analysis revealed that STAT3, a potential druggable target, highly interacts with the five-gene signature. Overall, we identified an immune gene signature that reliably predicts advanced fibrosis in chronic liver disease. This signature revealed potential immune therapeutic targets to ameliorate liver fibrosis.
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Affiliation(s)
- Pil-Soo Sung
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (P.-S.S.); (J.-H.C.)
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Korea
| | - Chang-Min Kim
- CbsBioscience, Inc., Daejeon 34036, Korea; (C.-M.K.); (J.-Y.P.); (Y.-S.Y.)
- Department of Pharmacy, College of Pharmacy, CHA University, Seongnam 13488, Korea;
| | - Jung-Hoon Cha
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (P.-S.S.); (J.-H.C.)
| | - Jin-Young Park
- CbsBioscience, Inc., Daejeon 34036, Korea; (C.-M.K.); (J.-Y.P.); (Y.-S.Y.)
| | - Yun-Suk Yu
- CbsBioscience, Inc., Daejeon 34036, Korea; (C.-M.K.); (J.-Y.P.); (Y.-S.Y.)
| | - Hee-Jung Wang
- Department of Surgery, Inje University Haeundae Paik Hospital, Busan 48108, Korea;
| | - Jin-Kyeoung Kim
- Department of Pharmacy, College of Pharmacy, CHA University, Seongnam 13488, Korea;
| | - Si-Hyun Bae
- The Catholic University Liver Research Center, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (P.-S.S.); (J.-H.C.)
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, Eunpyeong St. Mary’s Hospital, The Catholic University of Korea, Seoul 03383, Korea
- Correspondence: ; Tel.: +82-2-2030-2530; Fax: +82-2-3481-4025
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