1
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Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault MP, Perlman H, Balch WE, Chandel NS, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Nunes Amaral LA. Aging is associated with a systemic length-associated transcriptome imbalance. Nat Aging 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA.
| | - Rogan A Grant
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Sophia S Liu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Michael Schwake
- Department of Neurology, Northwestern University, Evanston, IL, USA
- Faculty of Chemistry, University of Bielefeld, Bielefeld, Germany
| | - Marie-Pier Tetreault
- Division of Gastroenterology and Hepatology, Northwestern University, Evanston, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Northwestern University, Evanston, IL, USA
| | | | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, USA.
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.
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2
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Watanabe S, Markov NS, Lu Z, Piseaux Aillon R, Soberanes S, Runyan CE, Ren Z, Grant RA, Maciel M, Abdala-Valencia H, Politanska Y, Nam K, Sichizya L, Kihshen HG, Joshi N, McQuattie-Pimentel AC, Gruner KA, Jain M, Sznajder JI, Morimoto RI, Reyfman PA, Gottardi CJ, Budinger GRS, Misharin AV. Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis. Proc Natl Acad Sci U S A 2021; 118:e2101100118. [PMID: 33972447 PMCID: PMC8157939 DOI: 10.1073/pnas.2101100118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pulmonary fibrosis is a relentlessly progressive and often fatal disease with a paucity of available therapies. Genetic evidence implicates disordered epithelial repair, which is normally achieved by the differentiation of small cuboidal alveolar type 2 (AT2) cells into large, flattened alveolar type 1 (AT1) cells as an initiating event in pulmonary fibrosis pathogenesis. Using models of pulmonary fibrosis in young adult and old mice and a model of adult alveologenesis after pneumonectomy, we show that administration of ISRIB, a small molecule that restores protein translation by EIF2B during activation of the integrated stress response (ISR), accelerated the differentiation of AT2 into AT1 cells. Accelerated epithelial repair reduced the recruitment of profibrotic monocyte-derived alveolar macrophages and ameliorated lung fibrosis. These findings suggest a dysfunctional role for the ISR in regeneration of the alveolar epithelium after injury with implications for therapy.
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Affiliation(s)
- Satoshi Watanabe
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Department of Respiratory Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8641, Japan
| | - Nikolay S Markov
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Ziyan Lu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Raul Piseaux Aillon
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Saul Soberanes
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Constance E Runyan
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Ziyou Ren
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Rogan A Grant
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Mariana Maciel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Hiam Abdala-Valencia
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yuliya Politanska
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Kiwon Nam
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Lango Sichizya
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Hermon G Kihshen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Nikita Joshi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Alexandra C McQuattie-Pimentel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Katherine A Gruner
- Mouse Histology and Phenotyping Laboratory, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611
| | - Manu Jain
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Jacob I Sznajder
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Paul A Reyfman
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Cara J Gottardi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - G R Scott Budinger
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611;
| | - Alexander V Misharin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611;
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3
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McQuattie-Pimentel AC, Ren Z, Joshi N, Watanabe S, Stoeger T, Chi M, Lu Z, Sichizya L, Aillon RP, Chen CI, Soberanes S, Chen Z, Reyfman PA, Walter JM, Anekalla KR, Davis JM, Helmin KA, Runyan CE, Abdala-Valencia H, Nam K, Meliton AY, Winter DR, Morimoto RI, Mutlu GM, Bharat A, Perlman H, Gottardi CJ, Ridge KM, Chandel NS, Sznajder JI, Balch WE, Singer BD, Misharin AV, Budinger GS. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging. J Clin Invest 2021; 131:140299. [PMID: 33586677 PMCID: PMC7919859 DOI: 10.1172/jci140299] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Alveolar macrophages orchestrate the response to viral infections. Age-related changes in these cells may underlie the differential severity of pneumonia in older patients. We performed an integrated analysis of single-cell RNA-Seq data that revealed homogenous age-related changes in the alveolar macrophage transcriptome in humans and mice. Using genetic lineage tracing with sequential injury, heterochronic adoptive transfer, and parabiosis, we found that the lung microenvironment drove an age-related resistance of alveolar macrophages to proliferation that persisted during influenza A viral infection. Ligand-receptor pair analysis localized these changes to the extracellular matrix, where hyaluronan was increased in aged animals and altered the proliferative response of bone marrow-derived macrophages to granulocyte macrophage colony-stimulating factor (GM-CSF). Our findings suggest that strategies targeting the aging lung microenvironment will be necessary to restore alveolar macrophage function in aging.
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Affiliation(s)
| | - Ziyou Ren
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Nikita Joshi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Satoshi Watanabe
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Monica Chi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ziyan Lu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Lango Sichizya
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raul Piseaux Aillon
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ching-I Chen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Saul Soberanes
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Zhangying Chen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Paul A. Reyfman
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - James M. Walter
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kishore R. Anekalla
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jennifer M. Davis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kathryn A. Helmin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Constance E. Runyan
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiam Abdala-Valencia
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kiwon Nam
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Angelo Y. Meliton
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Chicago Hospitals, Chicago, Illinois, USA
| | - Deborah R. Winter
- Department of Medicine, Division of Rheumatology, Northwestern University, Chicago, Illinois, USA
| | - Richard I. Morimoto
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, USA
| | - Gökhan M. Mutlu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Chicago Hospitals, Chicago, Illinois, USA
| | - Ankit Bharat
- Department of Surgery, Division of Thoracic Surgery, Northwestern University, Chicago, Illinois, USA
| | - Harris Perlman
- Department of Medicine, Division of Rheumatology, Northwestern University, Chicago, Illinois, USA
| | - Cara J. Gottardi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karen M. Ridge
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Navdeep S. Chandel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jacob I. Sznajder
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - William E. Balch
- The Scripps Research Institute Department of Chemical Physiology, La Jolla, California, USA
| | - Benjamin D. Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, USA
| | - Alexander V. Misharin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - G.R. Scott Budinger
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
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4
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Joshi N, Watanabe S, Verma R, Jablonski RP, Chen CI, Cheresh P, Markov NS, Reyfman PA, McQuattie-Pimentel AC, Sichizya L, Lu Z, Piseaux-Aillon R, Kirchenbuechler D, Flozak AS, Gottardi CJ, Cuda CM, Perlman H, Jain M, Kamp DW, Budinger GRS, Misharin AV. A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages. Eur Respir J 2020; 55:1900646. [PMID: 31601718 PMCID: PMC6962769 DOI: 10.1183/13993003.00646-2019] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023]
Abstract
Ontologically distinct populations of macrophages differentially contribute to organ fibrosis through unknown mechanisms.We applied lineage tracing, single-cell RNA sequencing and single-molecule fluorescence in situ hybridisation to a spatially restricted model of asbestos-induced pulmonary fibrosis.We demonstrate that tissue-resident alveolar macrophages, tissue-resident peribronchial and perivascular interstitial macrophages, and monocyte-derived alveolar macrophages are present in the fibrotic niche. Deletion of monocyte-derived alveolar macrophages but not tissue-resident alveolar macrophages ameliorated asbestos-induced lung fibrosis. Monocyte-derived alveolar macrophages were specifically localised to fibrotic regions in the proximity of fibroblasts where they expressed molecules known to drive fibroblast proliferation, including platelet-derived growth factor subunit A. Using single-cell RNA sequencing and spatial transcriptomics in both humans and mice, we identified macrophage colony-stimulating factor receptor (M-CSFR) signalling as one of the novel druggable targets controlling self-maintenance and persistence of these pathogenic monocyte-derived alveolar macrophages. Pharmacological blockade of M-CSFR signalling led to the disappearance of monocyte-derived alveolar macrophages and ameliorated fibrosis.Our findings suggest that inhibition of M-CSFR signalling during fibrosis disrupts an essential fibrotic niche that includes monocyte-derived alveolar macrophages and fibroblasts during asbestos-induced fibrosis.
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Affiliation(s)
- Nikita Joshi
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- These authors contributed equally to this work
| | - Satoshi Watanabe
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Respiratory Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- These authors contributed equally to this work
| | - Rohan Verma
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- These authors contributed equally to this work
| | - Renea P Jablonski
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Medicine, Section of Pulmonary and Critical Care, The University of Chicago, Chicago, IL, USA
| | - Ching-I Chen
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul Cheresh
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexandra C McQuattie-Pimentel
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ziyan Lu
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Raul Piseaux-Aillon
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David Kirchenbuechler
- Center for Advanced Microscopy, Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Annette S Flozak
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cara J Gottardi
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Carla M Cuda
- Division of Rheumatology, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Jesse Brown VA Medical Center, Chicago, IL, USA
| | - David W Kamp
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Jesse Brown VA Medical Center, Chicago, IL, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Jesse Brown VA Medical Center, Chicago, IL, USA
- These authors contributed equally to this work
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- These authors contributed equally to this work
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5
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Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, Verma R, Abdala-Valencia H, Nam K, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Watanabe S, Williams KJN, Flozak AS, Nicholson TT, Morgan VK, Winter DR, Hinchcliff M, Hrusch CL, Guzy RD, Bonham CA, Sperling AI, Bag R, Hamanaka RB, Mutlu GM, Yeldandi AV, Marshall SA, Shilatifard A, Amaral LAN, Perlman H, Sznajder JI, Argento AC, Gillespie CT, Dematte J, Jain M, Singer BD, Ridge KM, Lam AP, Bharat A, Bhorade SM, Gottardi CJ, Budinger GRS, Misharin AV. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 199:1517-1536. [PMID: 30554520 PMCID: PMC6580683 DOI: 10.1164/rccm.201712-2410oc] [Citation(s) in RCA: 696] [Impact Index Per Article: 139.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/14/2019] [Indexed: 11/30/2022] Open
Abstract
Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to nonoverlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. We developed a web-based tool to explore these data. Conclusions: We generated a single-cell atlas of pulmonary fibrosis. Using this atlas, we demonstrated heterogeneity within alveolar macrophages and epithelial cells from subjects with pulmonary fibrosis. These results support the feasibility of discovery-based approaches using next-generation sequencing technologies to identify signaling pathways for targeting in the development of personalized therapies for patients with pulmonary fibrosis.
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Affiliation(s)
- Paul A. Reyfman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - James M. Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Nikita Joshi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | - Stephen Chiu
- Division of Thoracic Surgery, Department of Surgery
| | | | | | - Ching-I Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Rohan Verma
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Kiwon Nam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Monica Chi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - SeungHye Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Saul Soberanes
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Satoshi Watanabe
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Annette S. Flozak
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | | | | | - Cara L. Hrusch
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Robert D. Guzy
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Catherine A. Bonham
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Anne I. Sperling
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Remzi Bag
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Robert B. Hamanaka
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | - Gökhan M. Mutlu
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois; and
| | | | - Stacy A. Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Luis A. N. Amaral
- Department of Chemical and Biological Engineering, Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois
| | | | - Jacob I. Sznajder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - A. Christine Argento
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Division of Thoracic Surgery, Department of Surgery
| | - Colin T. Gillespie
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Division of Thoracic Surgery, Department of Surgery
| | - Jane Dematte
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Karen M. Ridge
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Anna P. Lam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Ankit Bharat
- Division of Thoracic Surgery, Department of Surgery
| | | | - Cara J. Gottardi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
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6
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Walter JM, Ren Z, Yacoub T, Reyfman PA, Shah RD, Abdala-Valencia H, Nam K, Morgan VK, Anekalla KR, Joshi N, McQuattie-Pimentel AC, Chen CI, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Aillon RP, Watanabe S, Williams KJN, Lu Z, Paonessa J, Hountras P, Breganio M, Borkowski N, Donnelly HK, Allen JP, Amaral LA, Bharat A, Misharin AV, Bagheri N, Hauser AR, Budinger GRS, Wunderink RG. Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia. Am J Respir Crit Care Med 2019; 199:1225-1237. [PMID: 30398927 PMCID: PMC6519857 DOI: 10.1164/rccm.201804-0650oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Rationale: The identification of informative elements of the host response to infection may improve the diagnosis and management of bacterial pneumonia. Objectives: To determine whether the absence of alveolar neutrophilia can exclude bacterial pneumonia in critically ill patients with suspected infection and to test whether signatures of bacterial pneumonia can be identified in the alveolar macrophage transcriptome. Methods: We determined the test characteristics of alveolar neutrophilia for the diagnosis of bacterial pneumonia in three cohorts of mechanically ventilated patients. In one cohort, we also isolated macrophages from alveolar lavage fluid and used the transcriptome to identify signatures of bacterial pneumonia. Finally, we developed a humanized mouse model of Pseudomonas aeruginosa pneumonia to determine if pathogen-specific signatures can be identified in human alveolar macrophages. Measurements and Main Results: An alveolar neutrophil percentage less than 50% had a negative predictive value of greater than 90% for bacterial pneumonia in both the retrospective (n = 851) and validation cohorts (n = 76 and n = 79). A transcriptional signature of bacterial pneumonia was present in both resident and recruited macrophages. Gene signatures from both cell types identified patients with bacterial pneumonia with test characteristics similar to alveolar neutrophilia. Conclusions: The absence of alveolar neutrophilia has a high negative predictive value for bacterial pneumonia in critically ill patients with suspected infection. Macrophages can be isolated from alveolar lavage fluid obtained during routine care and used for RNA-Seq analysis. This novel approach may facilitate a longitudinal and multidimensional assessment of the host response to bacterial pneumonia.
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Affiliation(s)
- James M. Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Tyrone Yacoub
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Paul A. Reyfman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Raj D. Shah
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | | | - Kiwon Nam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Vince K. Morgan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Kishore R. Anekalla
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Nikita Joshi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | | | - Ching-I Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Monica Chi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - SeungHye Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | | | - Saul Soberanes
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Raul P. Aillon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Satoshi Watanabe
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | | | - Ziyan Lu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Joseph Paonessa
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Peter Hountras
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Madonna Breganio
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Nicole Borkowski
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Helen K. Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Jonathan P. Allen
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois; and
| | - Luis A. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Ankit Bharat
- Division of Thoracic Surgery, Department of Surgery, Feinberg School of Medicine, and
| | | | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Alan R. Hauser
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois; and
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7
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Soberanes S, Misharin AV, Jairaman A, Morales-Nebreda L, McQuattie-Pimentel AC, Cho T, Hamanaka RB, Meliton AY, Reyfman PA, Walter JM, Chen CI, Chi M, Chiu S, Gonzalez-Gonzalez FJ, Antalek M, Abdala-Valencia H, Chiarella SE, Sun KA, Woods PS, Ghio AJ, Jain M, Perlman H, Ridge KM, Morimoto RI, Sznajder JI, Balch WE, Bhorade SM, Bharat A, Prakriya M, Chandel NS, Mutlu GM, Budinger GS. Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis. Cell Metab 2019; 29:503. [PMID: 30726761 PMCID: PMC6377562 DOI: 10.1016/j.cmet.2018.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Soberanes S, Misharin AV, Jairaman A, Morales-Nebreda L, McQuattie-Pimentel AC, Cho T, Hamanaka RB, Meliton AY, Reyfman PA, Walter JM, Chen CI, Chi M, Chiu S, Gonzalez-Gonzalez FJ, Antalek M, Abdala-Valencia H, Chiarella SE, Sun KA, Woods PS, Ghio AJ, Jain M, Perlman H, Ridge KM, Morimoto RI, Sznajder JI, Balch WE, Bhorade SM, Bharat A, Prakriya M, Chandel NS, Mutlu GM, Budinger GRS. Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis. Cell Metab 2019; 29:335-347.e5. [PMID: 30318339 PMCID: PMC6365216 DOI: 10.1016/j.cmet.2018.09.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/11/2018] [Accepted: 09/17/2018] [Indexed: 12/28/2022]
Abstract
Urban particulate matter air pollution induces the release of pro-inflammatory cytokines including interleukin-6 (IL-6) from alveolar macrophages, resulting in an increase in thrombosis. Here, we report that metformin provides protection in this murine model. Treatment of mice with metformin or exposure of murine or human alveolar macrophages to metformin prevented the particulate matter-induced generation of complex III mitochondrial reactive oxygen species, which were necessary for the opening of calcium release-activated channels (CRAC) and release of IL-6. Targeted genetic deletion of electron transport or CRAC channels in alveolar macrophages in mice prevented particulate matter-induced acceleration of arterial thrombosis. These findings suggest metformin as a potential therapy to prevent some of the premature deaths attributable to air pollution exposure worldwide.
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Affiliation(s)
- Saul Soberanes
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Alexander V Misharin
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Amit Jairaman
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Luisa Morales-Nebreda
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Alexandra C McQuattie-Pimentel
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Takugo Cho
- Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA
| | - Robert B Hamanaka
- Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA
| | - Angelo Y Meliton
- Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA
| | - Paul A Reyfman
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - James M Walter
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Ching-I Chen
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Monica Chi
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Stephen Chiu
- Department of Surgery, Northwestern University, Chicago, IL 60611, USA
| | - Francisco J Gonzalez-Gonzalez
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Matthew Antalek
- Rice Institute for Biomedical Research, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Hiam Abdala-Valencia
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Sergio E Chiarella
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Kaitlyn A Sun
- Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA
| | - Parker S Woods
- Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA
| | - Andrew J Ghio
- United States Environmental Protections Agency, Chapel Hill, NC 27599, USA
| | - Manu Jain
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Harris Perlman
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Karen M Ridge
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Richard I Morimoto
- Rice Institute for Biomedical Research, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Jacob I Sznajder
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - William E Balch
- Scripps Research, Department of Molecular Medicine, La Jolla, CA 92037, USA
| | - Sangeeta M Bhorade
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Ankit Bharat
- Department of Surgery, Northwestern University, Chicago, IL 60611, USA
| | - Murali Prakriya
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Navdeep S Chandel
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA
| | - Gökhan M Mutlu
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA; Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC6026, Chicago, IL 60637, USA.
| | - G R Scott Budinger
- Department of Medicine and Pulmonary and Critical Care Medicine, Northwestern University, 240 E Huron Street, M300, Chicago, IL 60611, USA.
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9
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Ferguson KT, McQuattie-Pimentel AC, Malsin ES, Sporn PHS. Dynamics of Influenza-induced Lung-Resident Memory T Cells, Anatomically and Functionally Distinct Lung Mesenchymal Populations, and Dampening of Acute Lung Injury by Neutrophil Transfer of Micro-RNA-223 to Lung Epithelial Cells. Am J Respir Cell Mol Biol 2018; 59:397-399. [PMID: 29641210 PMCID: PMC6189642 DOI: 10.1165/rcmb.2018-0047ro] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/09/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Keith T. Ferguson
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Alexandra C. McQuattie-Pimentel
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Elizabeth S. Malsin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Peter H. S. Sporn
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
- Medical and Research Services, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
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10
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McQuattie-Pimentel AC, Budinger GRS, Ballinger MN. Monocyte-derived Alveolar Macrophages: The Dark Side of Lung Repair? Am J Respir Cell Mol Biol 2018; 58:5-6. [PMID: 29286855 DOI: 10.1165/rcmb.2017-0328ed] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | - G R Scott Budinger
- 1 Division of Pulmonary and Critical Care Northwestern University Chicago, Illinois and
| | - Megan N Ballinger
- 2 Division of Pulmonary, Critical Care and Sleep Medicine The Ohio State University Columbus, Ohio
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11
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Bharat A, McQuattie-Pimentel AC, Budinger GRS. Non-classical monocytes in tissue injury and cancer. Oncotarget 2017; 8:106171-106172. [PMID: 29290937 PMCID: PMC5739722 DOI: 10.18632/oncotarget.22584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/18/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ankit Bharat
- Ankit Bharat: Division of Thoracic Surgery, Department of Surgery and Division of Pulmonary & Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexandra C McQuattie-Pimentel
- Ankit Bharat: Division of Thoracic Surgery, Department of Surgery and Division of Pulmonary & Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - G R Scott Budinger
- Ankit Bharat: Division of Thoracic Surgery, Department of Surgery and Division of Pulmonary & Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, IL, USA
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12
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Misharin AV, Morales-Nebreda L, Reyfman PA, Cuda CM, Walter JM, McQuattie-Pimentel AC, Chen CI, Anekalla KR, Joshi N, Williams KJN, Abdala-Valencia H, Yacoub TJ, Chi M, Chiu S, Gonzalez-Gonzalez FJ, Gates K, Lam AP, Nicholson TT, Homan PJ, Soberanes S, Dominguez S, Morgan VK, Saber R, Shaffer A, Hinchcliff M, Marshall SA, Bharat A, Berdnikovs S, Bhorade SM, Bartom ET, Morimoto RI, Balch WE, Sznajder JI, Chandel NS, Mutlu GM, Jain M, Gottardi CJ, Singer BD, Ridge KM, Bagheri N, Shilatifard A, Budinger GRS, Perlman H. Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span. J Exp Med 2017; 214:2387-2404. [PMID: 28694385 PMCID: PMC5551573 DOI: 10.1084/jem.20162152] [Citation(s) in RCA: 642] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/02/2017] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
Misharin et al. elucidate the fate and function of monocyte-derived alveolar macrophages during the course of pulmonary fibrosis. These cells persisted throughout the life span, were enriched for the expression of profibrotic genes, and their genetic ablation ameliorated development of pulmonary fibrosis. Little is known about the relative importance of monocyte and tissue-resident macrophages in the development of lung fibrosis. We show that specific genetic deletion of monocyte-derived alveolar macrophages after their recruitment to the lung ameliorated lung fibrosis, whereas tissue-resident alveolar macrophages did not contribute to fibrosis. Using transcriptomic profiling of flow-sorted cells, we found that monocyte to alveolar macrophage differentiation unfolds continuously over the course of fibrosis and its resolution. During the fibrotic phase, monocyte-derived alveolar macrophages differ significantly from tissue-resident alveolar macrophages in their expression of profibrotic genes. A population of monocyte-derived alveolar macrophages persisted in the lung for one year after the resolution of fibrosis, where they became increasingly similar to tissue-resident alveolar macrophages. Human homologues of profibrotic genes expressed by mouse monocyte-derived alveolar macrophages during fibrosis were up-regulated in human alveolar macrophages from fibrotic compared with normal lungs. Our findings suggest that selectively targeting alveolar macrophage differentiation within the lung may ameliorate fibrosis without the adverse consequences associated with global monocyte or tissue-resident alveolar macrophage depletion.
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Affiliation(s)
- Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Carla M Cuda
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Alexandra C McQuattie-Pimentel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ching-I Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Nikita Joshi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kinola J N Williams
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Hiam Abdala-Valencia
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Tyrone J Yacoub
- Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL
| | - Monica Chi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Stephen Chiu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL.,Division of Thoracic Surgery, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Francisco J Gonzalez-Gonzalez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Khalilah Gates
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Anna P Lam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Trevor T Nicholson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Philip J Homan
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Saul Soberanes
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Salina Dominguez
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Vince K Morgan
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Rana Saber
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Alexander Shaffer
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Monique Hinchcliff
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ankit Bharat
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL.,Division of Thoracic Surgery, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Sergejs Berdnikovs
- Division of Allergy and Immunology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Sangeeta M Bhorade
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Elizabeth T Bartom
- Division of Thoracic Surgery, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institutes, La Jolla, CA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Gökhan M Mutlu
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Cara J Gottardi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Neda Bagheri
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ali Shilatifard
- Division of Thoracic Surgery, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Harris Perlman
- Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL
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13
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Chiarella SE, Gonzalez-Gonzalez FJ, McQuattie-Pimentel AC, Singer BD, Budinger GS, Schleimer RP, Gottardi CJ. Defining the Cell Type through Which the Asthma-Associated Intercellular Junction Protein Alpha-T-Catenin Drives Asthma Phenotypes in Mice. J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Bharat A, Bhorade SM, Morales-Nebreda L, McQuattie-Pimentel AC, Soberanes S, Ridge K, DeCamp MM, Mestan KK, Perlman H, Budinger GRS, Misharin AV. Flow Cytometry Reveals Similarities Between Lung Macrophages in Humans and Mice. Am J Respir Cell Mol Biol 2016; 54:147-9. [PMID: 26274047 DOI: 10.1165/rcmb.2015-0147le] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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