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Wei X, Jin C, Li D, Wang Y, Zheng S, Feng Q, Shi N, Kong W, Ma X, Wang J. Single-cell transcriptomics reveals CD8 + T cell structure and developmental trajectories in idiopathic pulmonary fibrosis. Mol Immunol 2024; 172:85-95. [PMID: 38936318 DOI: 10.1016/j.molimm.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Immune cells in the human lung are associated with idiopathic pulmonary fibrosis. However, the contribution of different immune cell subpopulations to the pathogenesis of pulmonary fibrosis remains unclear. We used single-cell RNA sequencing data to investigate the transcriptional profiles of immune cells in the lungs of 5 IPF patients and 3 subjects with non-fibrotic lungs. In an identifiable population of immune cells, we found increased percentage of CD8+ T cells in the T cell subpopulation in IPF. Monocle analyzed the dynamic immune status and cell transformation of CD8+ T cells, as well as the cytotoxicity and exhausted status of CD8+ T cell subpopulations at different stages. Among CD8+ T cells, we found differences in metabolic pathways in IPF and Ctrl, including lipid, amino acid and carbohydrate metabolic. By analyzing the metabolites of CD8+ T cells, we found that different populations of CD8+ T cells in IPF have unique metabolic characteristics, but they also have multiple identical up-regulated or down-regulated metabolites. In IPF, signaling pathways associated with fibrosis were enriched in CD8+ T cells, suggesting that CD8+ T cells may have an important contribution to fibrosis. Finally, we analyzed the interactions between CD8+ T cells and other cells. Together, these studies highlight key features of CD8+ T cells in the pathogenesis of IPF and help to develop effective therapeutic targets.
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Affiliation(s)
- Xuemei Wei
- Center of Respiratory and Critical Care Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830001, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi 830000, China
| | - Chengji Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou 570100, China
| | - Dewei Li
- Center of Respiratory and Critical Care Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830001, China
| | - Yujie Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou 570100, China
| | - Shaomao Zheng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou 570100, China
| | - Qiong Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou 570100, China
| | - Ning Shi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi 830000, China
| | - Weina Kong
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi 830000, China
| | - Xiumin Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi 830000, China.
| | - Jing Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou 570100, China; NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou 571199, China.
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2
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Nishioka Y, Araya J, Tanaka Y, Kumanogoh A. Pathological mechanisms and novel drug targets in fibrotic interstitial lung disease. Inflamm Regen 2024; 44:34. [PMID: 39026335 DOI: 10.1186/s41232-024-00345-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Interstitial lung diseases (ILDs) are a diverse group of conditions characterized by inflammation and fibrosis in the lung. In some patients with ILD, a progressive fibrotic phenotype develops, which is associated with an irreversible decline in lung function and a poor prognosis. MAIN BODY The pathological mechanisms that underlie this process culminate in fibroblast activation, proliferation, and differentiation into myofibroblasts, which deposit extracellular matrix proteins and result in fibrosis. Upstream of fibroblast activation, epithelial cell injury and immune activation are known initiators of fibrosis progression, with multiple diverse cell types involved. Recent years have seen an increase in our understanding of the complex and interrelated processes that drive fibrosis progression in ILD, in part due to the advent of single-cell RNA sequencing technology and integrative multiomics analyses. Novel pathological mechanisms have been identified, which represent new targets for drugs currently in clinical development. These include phosphodiesterase 4 inhibitors and other molecules that act on intracellular cyclic adenosine monophosphate signaling, as well as inhibitors of the autotaxin-lysophosphatidic acid axis and α v integrins. Here, we review current knowledge and recent developments regarding the pathological mechanisms that underlie progressive fibrotic ILD, including potential therapeutic targets. CONCLUSION Knowledge of the pathological mechanisms that drive progressive fibrosis in patients with ILD has expanded, with the role of alveolar endothelial cells, the immune system, and fibroblasts better elucidated. Drugs that target novel mechanisms hold promise for expanding the future therapeutic armamentarium for progressive fibrotic ILD.
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Affiliation(s)
| | - Jun Araya
- The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshiya Tanaka
- University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan.
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3
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Missarova A, Dann E, Rosen L, Satija R, Marioni J. Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biol 2024; 25:189. [PMID: 39026254 PMCID: PMC11256449 DOI: 10.1186/s13059-024-03334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Alsu Missarova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leah Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rahul Satija
- Center for Genomics and Systems Biology, NYU, New York, USA.
- New York Genome Center, New York, USA.
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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4
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Hose L, Schürmann M, Sudhoff H. Upregulation of key factors of viral entry of corona- and influenza viruses upon TLR3-signaling in cells from the respiratory tract and clinical treatment options by 1,8-Cineol. Phytother Res 2024. [PMID: 39020450 DOI: 10.1002/ptr.8280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
At the end of the 2019 coronavirus pandemic (COVID-19), highly contagious variants of coronaviruses had emerged. Together with influenza viruses, different variants of the coronavirus currently cause most colds and require appropriate drug treatment. We have investigated the expression of important factors for the replication of these viruses, namely transmembrane protease serine subtype 2 (TMPRSS2), neuropilin1 (NRP1), and angiotensin converting enzyme 2 (ACE2) or tumor necrosis factor-α (TNF-α) after toll like receptor-3 (TLR-3) stimulation using RT-qPCR and flow cytometry (FC) analysis. As model served primary fibroblasts derived from the lung and nasal cavity, as well as epidermal stem cells and fully matured respiratory epithelium. The stimulated cell cultures were treated with pharmaceuticals (Dexamethasone and Enzalutamide) and the outcome was compared with the phytomedicine 1,8-Cineol. The stimulation of TLR3 is sufficient to induce the expression of exactly those targets that were highly expressed in the corresponding culture type, specifically ACE2 and TMPRSS2 in respiratory epithelial stem cells and NRP1 in fibroblast cells. It seems this self-perpetuating cycle of infection-driven upregulation of key viral replication factors by the innate immune system represents an evolutionary advantage for viruses using these transcripts as viral replication factors. Likewise, to the standard pharmaceuticals with proven clinical efficiency, 1,8-Cineol was able to disrupt this self-perpetuating cycle. Considering the minor side effects and negligible pharmacological interactions with other drugs, it is conceivable that an adjuvant or combinatorial therapy with 1,8-Cineol for respiratory diseases caused by corona- or influenza viruses would be beneficial.
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Affiliation(s)
- Leonie Hose
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Bielefeld, Germany
| | - Matthias Schürmann
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Bielefeld, Germany
| | - Holger Sudhoff
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Bielefeld, Germany
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5
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McCall AS, Kropski JA. Biomarker-defined endotypes of pulmonary fibrosis. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00169-3. [PMID: 39025090 DOI: 10.1016/s2213-2600(24)00169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 07/20/2024]
Affiliation(s)
- A Scott McCall
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Veterans Affairs Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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6
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Hasegawa Y, Franks JM, Tanaka Y, Uehara Y, Read DF, Williams C, Srivatsan S, Pitstick LB, Nikolaidis NM, Shaver CM, Kropski J, Ware LB, Taylor CJ, Banovich NE, Wu H, Gardner JC, Osterburg AR, Yu JJ, Kopras EJ, Teitelbaum SL, Wikenheiser-Brokamp KA, Trapnell C, McCormack FX. Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. SCIENCE ADVANCES 2024; 10:eadl4913. [PMID: 38985878 PMCID: PMC11235167 DOI: 10.1126/sciadv.adl4913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/05/2024] [Indexed: 07/12/2024]
Abstract
The pathophysiology of silicosis is poorly understood, limiting development of therapies for those who have been exposed to the respirable particle. We explored mechanisms of silica-induced pulmonary fibrosis in human lung samples collected from patients with occupational exposure to silica and in a longitudinal mouse model of silicosis using multiple modalities including whole-lung single-cell RNA sequencing and histological, biochemical, and physiologic assessments. In addition to pulmonary inflammation and fibrosis, intratracheal silica challenge induced osteoclast-like differentiation of alveolar macrophages and recruited monocytes, driven by induction of the osteoclastogenic cytokine, receptor activator of nuclear factor κΒ ligand (RANKL) in pulmonary lymphocytes, and alveolar type II cells. Anti-RANKL monoclonal antibody treatment suppressed silica-induced osteoclast-like differentiation in the lung and attenuated pulmonary fibrosis. We conclude that silica induces differentiation of pulmonary osteoclast-like cells leading to progressive lung injury, likely due to sustained elaboration of bone-resorbing proteases and hydrochloric acid. Interrupting osteoclast-like differentiation may therefore constitute a promising avenue for moderating lung damage in silicosis.
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Affiliation(s)
- Yoshihiro Hasegawa
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Jennifer M. Franks
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yusuke Tanaka
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Yasuaki Uehara
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - David F. Read
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Claire Williams
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lori B. Pitstick
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Nikolaos M. Nikolaidis
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chase J. Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas E. Banovich
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Huixing Wu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Jason C. Gardner
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew R. Osterburg
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Jane J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Elizabeth J. Kopras
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Steven L. Teitelbaum
- Department of Pathology and Immunology, and Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathryn A. Wikenheiser-Brokamp
- Division of Pathology and Laboratory Medicine and Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Francis X. McCormack
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
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7
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Pir MS, Begar E, Yenisert F, Demirci HC, Korkmaz ME, Karaman A, Tsiropoulou S, Firat-Karalar EN, Blacque OE, Oner SS, Doluca O, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res 2024:gkae554. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete (1-3). While various independent approaches theoretically have the potential to reveal the entire list of ciliary genes, approximately 30% of the genes on the ciliary gene list still stand as ciliary candidates (4,5). These methods, however, have mainly relied on a single strategy to uncover ciliary candidate genes, making the categorization challenging due to variations in quality and distinct capabilities demonstrated by different methodologies. Here, we develop a method called CilioGenics that combines several methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF) network analysis, and text mining) to predict the ciliary capacity of each human gene. Our combined approach provides a CilioGenics score for every human gene that represents the probability that it will become a ciliary gene. Compared to methods that rely on a single method, CilioGenics performs better in its capacity to predict ciliary genes. Our top 500 gene list includes 258 new ciliary candidates, with 31 validated experimentally by us and others. Users may explore the whole list of human genes and CilioGenics scores on the CilioGenics database (https://ciliogenics.com/).
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Affiliation(s)
- Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Efe Begar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Hasan C Demirci
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Mustafa E Korkmaz
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Asli Karaman
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
- School of Medicine, Koç University, Istanbul 34450, Turkiye
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sukru S Oner
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkiye
| | - Osman Doluca
- Izmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, Izmir, Turkiye
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
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8
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Jin C, Chen Y, Wang Y, Li J, Liang J, Zheng S, Zhang L, Li Q, Wang Y, Ling F, Li Y, Zheng Y, Nie Q, Feng Q, Wang J, Yang H. Single-cell RNA sequencing reveals special basal cells and fibroblasts in idiopathic pulmonary fibrosis. Sci Rep 2024; 14:15778. [PMID: 38982264 PMCID: PMC11233624 DOI: 10.1038/s41598-024-66947-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most predominant type of idiopathic interstitial pneumonia and has an increasing incidence, poor prognosis, and unclear pathogenesis. In order to investigate the molecular mechanisms underlying IPF further, we performed single-cell RNA sequencing analysis on three healthy controls and five IPF lung tissue samples. The results revealed a significant shift in epithelial cells (ECs) phenotypes in IPF, which may be attributed to the differentiation of alveolar type 2 cells to basal cells. In addition, several previously unrecognized basal cell subtypes were preliminarily identified, including extracellular matrix basal cells, which were increased in the IPF group. We identified a special population of fibroblasts that highly expressed extracellular matrix-related genes, POSTN, CTHRC1, COL3A1, COL5A2, and COL12A1. We propose that the close interaction between ECs and fibroblasts through ligand-receptor pairs may have a critical function in IPF development. Collectively, these outcomes provide innovative perspectives on the complexity and diversity of basal cells and fibroblasts in IPF and contribute to the understanding of possible mechanisms in pathological lung fibrosis.
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Affiliation(s)
- Chengji Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yahong Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yujie Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jia Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Jin Liang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Shaomao Zheng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Lipeng Zhang
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiaoyu Li
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Yongchao Wang
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, 211800, China
| | - Fayu Ling
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yongjie Li
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Yu Zheng
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiuli Nie
- The Second Affiliated Clinical College, Hainan Medical University, Haikou, 570100, China
| | - Qiong Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China
| | - Jing Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital, Hainan Medical University, Haikou, 570100, China.
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, 571199, China.
| | - Huiling Yang
- School of Pharmacy, Guangdong Medical University, Dongguan, 523808, China.
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9
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Mapping the lung fibrosis transcriptome of mice and men. Nat Genet 2024:10.1038/s41588-024-01833-4. [PMID: 38969835 DOI: 10.1038/s41588-024-01833-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
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10
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Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson MS, DeRisi JL, Sperling AI, Shum AK. Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease. ACR Open Rheumatol 2024. [PMID: 38952015 DOI: 10.1002/acr2.11696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/10/2024] [Accepted: 04/26/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVE Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases. Establishing autoimmunity in ILD impacts prognosis and treatment. Patients with ILD are screened for autoimmunity by measuring antinuclear autoantibodies, rheumatoid factors, and other nonspecific tests. However, this approach may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. METHODS We use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct an autoantibody discovery screen of patients with ILD and controls. We screened for novel autoantigen candidates using PhIP-Seq. We next developed a radio-labeled binding assay and validated the leading candidate in 398 patients with ILD recruited from two academic medical centers and 138 blood bank individuals that formed our reference cohort. RESULTS PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among the 17 candidates, we validated CDHR5 and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, patients not previously diagnosed with autoimmunity. Using survival and transplant free-survival data available from one of the two centers, patients with CDHR5 autoantibodies showed worse survival compared with other patients with connective tissue disease ILD. CONCLUSION We used PhIP-Seq to define a novel CDHR5 autoantibody in a subset of select patients with ILD. Our data complement a recent study showing polymorphisms in the CDHR5-IRF7 gene locus strongly associated with titer of anticentromere antibodies in systemic sclerosis, creating a growing body of evidence suggesting a link between CDHR5 and autoimmunity.
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Affiliation(s)
| | | | - Sara E Vazquez
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Tania E Velez
- University of Chicago, Illinois, and University of Virginia, Charlottesville
| | | | | | | | | | | | | | | | - Imre Noth
- University of Virginia, Charlottesville
| | | | | | - Joseph L DeRisi
- University of California San Francisco and Chan Zuckerberg Biohub
| | - Anne I Sperling
- University of Chicago, Illinois, and University of Virginia, Charlottesville
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11
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Franzén L, Olsson Lindvall M, Hühn M, Ptasinski V, Setyo L, Keith BP, Collin A, Oag S, Volckaert T, Borde A, Lundeberg J, Lindgren J, Belfield G, Jackson S, Ollerstam A, Stamou M, Ståhl PL, Hornberg JJ. Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis. Nat Genet 2024:10.1038/s41588-024-01819-2. [PMID: 38951642 DOI: 10.1038/s41588-024-01819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/30/2024] [Indexed: 07/03/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. Here we generated spatially resolved transcriptome maps of human IPF (n = 4) and bleomycin-induced mouse pulmonary fibrosis (n = 6) to address these limitations. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by transforming growth factor beta signaling alongside predicted regulators, such as TP53 and APOE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.
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Affiliation(s)
- Lovisa Franzén
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Martina Olsson Lindvall
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael Hühn
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Victoria Ptasinski
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Laura Setyo
- Pathology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Benjamin P Keith
- Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Astrid Collin
- Animal Science and Technology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Steven Oag
- Animal Science and Technology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Volckaert
- Bioscience In Vivo, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Annika Borde
- Bioscience In Vivo, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Julia Lindgren
- Translational Genomics, Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Graham Belfield
- Translational Genomics, Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Sonya Jackson
- Late-Stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Ollerstam
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Marianna Stamou
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Patrik L Ståhl
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Jorrit J Hornberg
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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12
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Tsukui T, Wolters PJ, Sheppard D. Alveolar fibroblast lineage orchestrates lung inflammation and fibrosis. Nature 2024; 631:627-634. [PMID: 38987592 DOI: 10.1038/s41586-024-07660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Fibroblasts are present throughout the body and function to maintain tissue homeostasis. Recent studies have identified diverse fibroblast subsets in healthy and injured tissues1,2, but the origins and functional roles of injury-induced fibroblast lineages remain unclear. Here we show that lung-specialized alveolar fibroblasts take on multiple molecular states with distinct roles in facilitating responses to fibrotic lung injury. We generate a genetic tool that uniquely targets alveolar fibroblasts to demonstrate their role in providing niches for alveolar stem cells in homeostasis and show that loss of this niche leads to exaggerated responses to acute lung injury. Lineage tracing identifies alveolar fibroblasts as the dominant origin for multiple emergent fibroblast subsets sequentially driven by inflammatory and pro-fibrotic signals after injury. We identify similar, but not completely identical, fibroblast lineages in human pulmonary fibrosis. TGFβ negatively regulates an inflammatory fibroblast subset that emerges early after injury and stimulates the differentiation into fibrotic fibroblasts to elicit intra-alveolar fibrosis. Blocking the induction of fibrotic fibroblasts in the alveolar fibroblast lineage abrogates fibrosis but exacerbates lung inflammation. These results demonstrate the multifaceted roles of the alveolar fibroblast lineage in maintaining normal alveolar homeostasis and orchestrating sequential responses to lung injury.
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Affiliation(s)
- Tatsuya Tsukui
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paul J Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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13
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Melo-Narváez MC, Bramey N, See F, Heinzelmann K, Ballester B, Steinchen C, Jain E, Federl K, Hu Q, Dhakad D, Behr J, Eickelberg O, Yildirim AÖ, Königshoff M, Lehmann M. Stimuli-Specific Senescence of Primary Human Lung Fibroblasts Modulates Alveolar Stem Cell Function. Cells 2024; 13:1129. [PMID: 38994981 PMCID: PMC11240317 DOI: 10.3390/cells13131129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
Aging is the main risk factor for chronic lung diseases (CLDs) including idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Accordingly, hallmarks of aging like cellular senescence are increased in these patients in different lung cell types including fibroblasts. However, little is known about the different triggers that induce a senescence phenotype in different disease backgrounds and its role in CLD pathogenesis. Therefore, we characterized senescence in primary human lung fibroblasts (phLF) from control, IPF, or COPD patients at baseline and after exposure to disease-relevant insults (H2O2, bleomycin, TGF-β1) and studied their capacity to support progenitor cell potential in a lung organoid model. Bulk-RNA sequencing revealed that phLF from IPF and COPD activate different transcriptional programs but share a similar senescence phenotype at baseline. Moreover, H2O2 and bleomycin but not TGF-β1 induced senescence in phLF from different disease origins. Exposure to different triggers resulted in distinct senescence programs in phLF characterized by different SASP profiles. Finally, co-culture with bleomycin- and H2O2-treated phLF reduced the progenitor cell potential of alveolar epithelial progenitor cells. In conclusion, phLF from COPD and IPF share a conserved senescence response that varies depending on the insult and impairs alveolar epithelial progenitor capacity ex vivo.
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Affiliation(s)
- Maria Camila Melo-Narváez
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, German Center for Lung Research (DZL), 35043 Marburg, Germany
| | - Nora Bramey
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Fenja See
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Katharina Heinzelmann
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Beatriz Ballester
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
- Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Valencia, Spain
| | - Carina Steinchen
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Eshita Jain
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Kathrin Federl
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Qianjiang Hu
- Division of Pulmonary, Allergy & Critical Care, and Sleep Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Deepesh Dhakad
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Jürgen Behr
- Department of Medicine V, University Hospital Munich, Medical Faculty of the LMU Munich, 81377 Munich, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy & Critical Care, and Sleep Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Ali Önder Yildirim
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, University Hospital Munich, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Melanie Königshoff
- Division of Pulmonary, Allergy & Critical Care, and Sleep Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Mareike Lehmann
- Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Comprehensive Pneumology Center (CPC-M), German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, German Center for Lung Research (DZL), 35043 Marburg, Germany
- Lung Aging and Regeneration, Institute for Lung Health (ILH), 35392 Giessen, Germany
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14
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Zhang M, Zhang J, Hu H, Zhou Y, Lin Z, Jing H, Sun B. Multiomic analysis of monocyte-derived alveolar macrophages in idiopathic pulmonary fibrosis. J Transl Med 2024; 22:598. [PMID: 38937806 PMCID: PMC11209973 DOI: 10.1186/s12967-024-05398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Monocyte-derived alveolar macrophages (Mo_AMs) are increasingly recognised as potential pathogenic factors for idiopathic pulmonary fibrosis (IPF). While scRNAseq analysis has proven valuable in the transcriptome profiling of Mo_AMs, the integration analysis of multi-omics may provide additional dimensions of understanding of these cellular populations. METHODS We performed multi-omics analysis on 116 scRNAseq, 119 bulkseq and five scATACseq lung tissue samples from IPF. We built a large-scale IPF scRNAseq atlas and conducted the Monocle 2/3 as well as the Cellchat to explore the developmental path and intercellular communication on Mo_AMs. We also reported the difference in metabolisms, tissue repair and phagocytosis between Mo_AMs and tissue-resident alveolar macrophages (TRMs). To determine whether Mo_AMs affected pulmonary function, we projected clinical phenotypes (FVC%pred) from the bulkseq dataset onto the scRNAseq atlas. Finally, we used scATATCseq to uncover the upstream regulatory mechanisms and determine key drivers in Mo_AMs. RESULTS We identified three Mo_AMs clusters and the trajectory analysis further validated the origin of these clusters. Moreover, via the Cellchat analysis, the CXCL12/CXCR4 axis was found to be involved in the molecular basis of reciprocal interactions between Mo_AMs and fibroblasts through the activation of the ERK pathway in Mo_AMs. SPP1_RecMacs (RecMacs, recruited macrophages) were higher in the low-FVC group than in the high-FVC group. Specifically, compared with TRMs, the functions of lipid and energetic metabolism as well as tissue repair were higher in Mo_AMs than TRMs. But, TRMs may have higher level of phagocytosis than TRMs. SPIB (PU.1), JUNB, JUND, BACH2, FOSL2, and SMARCC1 showed stronger association with open chromatin of Mo_AMs than TRMs. Significant upregulated expression and deep chromatin accessibility of APOE were observed in both SPP1_RecMacs and TRMs. CONCLUSION Through trajectory analysis, it was confirmed that SPP1_RecMacs derived from Monocytes. Besides, Mo_AMs may influence FVC% pred and aggravate pulmonary fibrosis through the communication with fibroblasts. Furthermore, distinctive transcriptional regulators between Mo_AMs and TRMs implied that they may depend on different upstream regulatory mechanisms. Overall, this work provides a global overview of how Mo_AMs govern IPF and also helps determine better approaches and intervention therapies.
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Affiliation(s)
- Miaomiao Zhang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Jinghao Zhang
- Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, China
| | - Haisheng Hu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuan Zhou
- Department of Medicine II, Heart Center Bonn, University Hospital Bonn, Bonn, Germany
| | - ZhiWei Lin
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Jing
- Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Guangzhou, 510005, China.
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15
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Mannes PZ, Adams TS, Farsijani S, Barnes CE, Latoche JD, Day KE, Nedrow JR, Ahangari F, Kaminski N, Lee JS, Tavakoli S. Noninvasive assessment of the lung inflammation-fibrosis axis by targeted imaging of CMKLR1. SCIENCE ADVANCES 2024; 10:eadm9817. [PMID: 38896611 PMCID: PMC11186491 DOI: 10.1126/sciadv.adm9817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Precision management of fibrotic lung diseases is challenging due to their diverse clinical trajectories and lack of reliable biomarkers for risk stratification and therapeutic monitoring. Here, we validated the accuracy of CMKLR1 as an imaging biomarker of the lung inflammation-fibrosis axis. By analyzing single-cell RNA sequencing datasets, we demonstrated CMKLR1 expression as a transient signature of monocyte-derived macrophages (MDMφ) enriched in patients with idiopathic pulmonary fibrosis (IPF). Consistently, we identified MDMφ as the major driver of the uptake of CMKLR1-targeting peptides in a murine model of bleomycin-induced lung fibrosis. Furthermore, CMKLR1-targeted positron emission tomography in the murine model enabled quantification and spatial mapping of inflamed lung regions infiltrated by CMKLR1-expressing macrophages and emerged as a robust predictor of subsequent lung fibrosis. Last, high CMKLR1 expression by bronchoalveolar lavage cells identified an inflammatory endotype of IPF with poor survival. Our investigation supports the potential of CMKLR1 as an imaging biomarker for endotyping and risk stratification of fibrotic lung diseases.
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Affiliation(s)
- Philip Z. Mannes
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Samaneh Farsijani
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Aging and Population Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Clayton E. Barnes
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph D. Latoche
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kathryn E. Day
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jessie R. Nedrow
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Sina Tavakoli
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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16
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Han G, Yan D, Sun Z, Fang J, Chang X, Wilson L, Liu Y. Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses. Hum Genomics 2024; 18:69. [PMID: 38902839 DOI: 10.1186/s40246-024-00638-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. RESULTS Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study. CONCLUSION In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.
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Affiliation(s)
- Gang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA
| | - Dongyan Yan
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Zhe Sun
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Jiyuan Fang
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Xinyue Chang
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Lucas Wilson
- Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA
| | - Yushi Liu
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
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17
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Shin KWD, Atalay MV, Cetin-Atalay R, O'Leary EM, Glass ME, Szafran JCH, Woods PS, Meliton AY, Shamaa OR, Tian Y, Mutlu GM, Hamanaka RB. ATF4 and mTOR regulate metabolic reprogramming in TGF-β-treated lung fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598694. [PMID: 38915485 PMCID: PMC11195155 DOI: 10.1101/2024.06.12.598694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Idiopathic pulmonary fibrosis is a fatal disease characterized by the TGF-β-dependent activation of lung fibroblasts, leading to excessive deposition of collagen proteins and progressive replacement of healthy lung with scar tissue. We and others have shown that fibroblast activation is supported by metabolic reprogramming, including the upregulation of the de novo synthesis of glycine, the most abundant amino acid found in collagen protein. How fibroblast metabolic reprogramming is regulated downstream of TGF-β is incompletely understood. We and others have shown that TGF-β-mediated activation of the Mechanistic Target of Rapamycin Complex 1 (mTORC1) and downstream upregulation of Activating Transcription Factor 4 (ATF4) promote increased expression of the enzymes required for de novo glycine synthesis; however, whether mTOR and ATF4 regulate other metabolic pathways in lung fibroblasts has not been explored. Here, we used RNA sequencing to determine how both ATF4 and mTOR regulate gene expression in human lung fibroblasts following TGF-β. We found that ATF4 primarily regulates enzymes and transporters involved in amino acid homeostasis as well as aminoacyl-tRNA synthetases. mTOR inhibition resulted not only in the loss of ATF4 target gene expression, but also in the reduced expression of glycolytic enzymes and mitochondrial electron transport chain subunits. Analysis of TGF-β-induced changes in cellular metabolite levels confirmed that ATF4 regulates amino acid homeostasis in lung fibroblasts while mTOR also regulates glycolytic and TCA cycle metabolites. We further analyzed publicly available single cell RNAseq data sets and found increased expression of ATF4 and mTOR metabolic targets in pathologic fibroblast populations from the lungs of IPF patients. Our results provide insight into the mechanisms of metabolic reprogramming in lung fibroblasts and highlight novel ATF4 and mTOR-dependent pathways that may be targeted to inhibit fibrotic processes.
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Affiliation(s)
- Kun Woo D Shin
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | | | - Rengul Cetin-Atalay
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Erin M O'Leary
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Mariel E Glass
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Jennifer C Houpy Szafran
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Parker S Woods
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Angelo Y Meliton
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Obada R Shamaa
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Yufeng Tian
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Gökhan M Mutlu
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
| | - Robert B Hamanaka
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637
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18
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Vásquez-Pacheco E, Marega M, Lingampally A, Fassy J, Truchi M, Goth K, Trygub L, Taghizadeh S, Bartkuhn M, Alexopoulos I, Dong Y, Lebrigand K, Gunther A, Chen C, Zhang J, Chao CM, Al Alam D, El Agha E, Mari B, Bellusci S, Rivetti S. Highlighting fibroblast plasticity in lung fibrosis: the WI-38 cell line as a model for investigating the myofibroblast and lipofibroblast switch. Theranostics 2024; 14:3603-3622. [PMID: 38948058 PMCID: PMC11209726 DOI: 10.7150/thno.93519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/14/2024] [Indexed: 07/02/2024] Open
Abstract
Background: Myofibroblasts (MYFs) are generally considered the principal culprits in excessive extracellular matrix deposition and scar formation in the pathogenesis of lung fibrosis. Lipofibroblasts (LIFs), on the other hand, are defined by their lipid-storing capacity and are predominantly found in the alveolar regions of the lung. They have been proposed to play a protective role in lung fibrosis. We previously reported that a LIF to MYF reversible differentiation switch occurred during fibrosis formation and resolution. In this study, we tested whether WI-38 cells, a human embryonic lung fibroblast cell line, could be used to study fibroblast differentiation towards the LIF or MYF phenotype and whether this could be relevant for idiopathic pulmonary fibrosis (IPF). Methods: Using WI-38 cells, Fibroblast (FIB) to MYF differentiation was triggered using TGF-β1 treatment and FIB to LIF differentiation using Metformin treatment. We also analyzed the MYF to LIF and LIF to MYF differentiation by pre-treating the WI-38 cells with TGF-β1 or Metformin respectively. We used IF, qPCR and bulk RNA-Seq to analyze the phenotypic and transcriptomic changes in the cells. We correlated our in vitro transcriptome data from WI-38 cells (obtained via bulk RNA sequencing) with the transcriptomic signature of LIFs and MYFs derived from the IPF cell atlas as well as with our own single-cell transcriptomic data from IPF patients-derived lung fibroblasts (LF-IPF) cultured in vitro. We also carried out alveolosphere assays to evaluate the ability of the proposed LIF and MYF cells to support the growth of alveolar epithelial type 2 cells. Results: WI-38 cells and LF-IPF display similar phenotypical and gene expression responses to TGF-β1 and Metformin treatment. Bulk RNA-Seq analysis of WI-38 cells and LF-IPF treated with TGF-β1, or Metformin indicate similar transcriptomic changes. We also show the partial conservation of the LIF and MYF signature extracted from the Habermann et al. scRNA-seq dataset in WI-38 cells treated with Metformin or TGF-β1, respectively. Alveolosphere assays indicate that LIFs enhance organoid growth, while MYFs inhibit organoid growth. Finally, we provide evidence supporting the MYF to LIF and LIF to MYF reversible switch using WI-38 cells. Conclusions: WI-38 cells represent a versatile and reliable model to study the intricate dynamics of fibroblast differentiation towards the MYF or LIF phenotype associated with lung fibrosis formation and resolution, providing valuable insights to drive future research.
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Affiliation(s)
- Esmeralda Vásquez-Pacheco
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Manuela Marega
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Helios Universitätsklinikum Wuppertal-Universität Witten/Herdecke, Department of Pediatrics, Centre for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | - Arun Lingampally
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Julien Fassy
- Université Côte d'Azur, CNRS UMR7275, IPMC, FHU-OncoAge, IHU RespiERA, Sophia Antipolis, Valbonne, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS UMR7275, IPMC, FHU-OncoAge, IHU RespiERA, Sophia Antipolis, Valbonne, France
| | - Kerstin Goth
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Lisa Trygub
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Sara Taghizadeh
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Marek Bartkuhn
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Ioannis Alexopoulos
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Ying Dong
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS UMR7275, IPMC, FHU-OncoAge, IHU RespiERA, Sophia Antipolis, Valbonne, France
| | - Andreas Gunther
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, Zhejiang, China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine. The First Affiliated Hospital of Wenzhou Medical University, 325000 Wenzhou, Zhejiang, China
| | - JinSan Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, Zhejiang, China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine. The First Affiliated Hospital of Wenzhou Medical University, 325000 Wenzhou, Zhejiang, China
| | - Cho-Ming Chao
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Department of Pediatrics, Centre for Clinical and Translational Research (CCTR), Helios University Hospital Wuppertal, Witten/Herdecke University, 42283 Wuppertal, Germany
| | | | - Elie El Agha
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), 35392 Giessen, Germany
| | - Bernard Mari
- Université Côte d'Azur, CNRS UMR7275, IPMC, FHU-OncoAge, IHU RespiERA, Sophia Antipolis, Valbonne, France
| | - Saverio Bellusci
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, Zhejiang, China
- Laboratory of Extracellular Lung Matrix Remodelling, Department of Internal Medicine, Cardio-Pulmonary Institute and Institute for Lung Health, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefano Rivetti
- Cardio-Pulmonary Institute and Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
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19
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Li L, Wang T, Chen Z, Liang J, Ding H. Multi-cohort analysis reveals immune subtypes and predictive biomarkers in tuberculosis. Sci Rep 2024; 14:13345. [PMID: 38858405 PMCID: PMC11164950 DOI: 10.1038/s41598-024-63365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
Tuberculosis (TB) remains a significant global health threat, necessitating effective strategies for diagnosis, prognosis, and treatment. This study employs a multi-cohort analysis approach to unravel the immune microenvironment of TB and delineate distinct subtypes within pulmonary TB (PTB) patients. Leveraging functional gene expression signatures (Fges), we identified three PTB subtypes (C1, C2, and C3) characterized by differential immune-inflammatory activity. These subtypes exhibited unique molecular features, functional disparities, and cell infiltration patterns, suggesting varying disease trajectories and treatment responses. A neural network model was developed to predict PTB progression based on a set of biomarker genes, achieving promising accuracy. Notably, despite both genders being affected by PTB, females exhibited a relatively higher risk of deterioration. Additionally, single-cell analysis provided insights into enhanced major histocompatibility complex (MHC) signaling in the rapid clearance of early pathogens in the C3 subgroup. This comprehensive approach offers valuable insights into PTB pathogenesis, facilitating personalized treatment strategies and precision medicine interventions.
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Affiliation(s)
- Ling Li
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Tao Wang
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Zhi Chen
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Jianqin Liang
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China
| | - Hong Ding
- The Eighth Medical Center of the PLA General Hospital, Beijing, 100091, People's Republic of China.
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20
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Adewale AT, Sharma S, Mouawad J, Nguyen XX, Bradshaw AD, Feghali-Bostwick C. IGF-II Regulates Lysyl Oxidase Propeptide and Mediates its Effects in part via Basic Helix-Loop-Helix E40. Matrix Biol 2024; 132:S0945-053X(24)00078-7. [PMID: 38852924 DOI: 10.1016/j.matbio.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Pulmonary fibrosis (PF) is a clinically severe and commonly fatal complication of Systemic Sclerosis (SSc). Our group has previously reported profibrotic roles for Insulin-like Growth Factor II (IGF-II) and Lysyl Oxidase (LOX) in SSc-PF. We sought to identify downstream regulatory mediators of IGF-II. In the present work, we show that SSc lung tissues have higher baseline levels of the total (N-glycosylated/unglycosylated) LOX-Propeptide (LOX-PP) than normal lung tissues. LOX-PP-mediated changes were consistent with the extracellular matrix (ECM) deregulation implicated in SSc-PF progression. Furthermore, Tolloid-like 1 (TLL1) and Bone Morphogenetic Protein 1 (BMP1), enzymes that can cleave ProLOX to release LOX-PP, were increased in SSc lung fibrosis and the bleomycin (BLM)-induced murine lung fibrosis model, respectively. In addition, IGF-II regulated the levels of ProLOX, active LOX, LOX-PP, BMP1, and isoforms of TLL1. The Class E Basic Helix-Loop-Helix protein 40 (BHLHE40) transcription factor localized to the nucleus in response to IGF-II. BHLHE40 silencing downregulated TLL1 isoforms and LOX-PP, and restored significant features of ECM deregulation triggered by IGF-II. Our findings indicate that IGF-II, BHLHE40, and LOX-PP may serve as targets of therapeutic intervention to halt SSc-PF progression.
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Affiliation(s)
- Adegboyega Timothy Adewale
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Shailza Sharma
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
| | - Joe Mouawad
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Xinh-Xinh Nguyen
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Amy D Bradshaw
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carol Feghali-Bostwick
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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21
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Guo Y, Yu L, Guo L, Xu L, Li Q. A Regularized Bayesian Dirichlet-multinomial Regression Model for Integrating Single-cell-level Omics and Patient-level Clinical Study Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597391. [PMID: 38895417 PMCID: PMC11185671 DOI: 10.1101/2024.06.04.597391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The abundance of various cell types can vary significantly among patients with varying phenotypes and even those with the same phenotype. Recent scientific advancements provide mounting evidence that other clinical variables, such as age, gender, and lifestyle habits, can also influence the abundance of certain cell types. However, current methods for integrating single-cell-level omics data with clinical variables are inadequate. In this study, we propose a regularized Bayesian Dirichlet-multinomial regression framework to investigate the relationship between single-cell RNA sequencing data and patient-level clinical data. Additionally, the model employs a novel hierarchical tree structure to identify such relationships at different cell-type levels. Our model successfully uncovers significant associations between specific cell types and clinical variables across three distinct diseases: pulmonary fibrosis, COVID-19, and non-small cell lung cancer. This integrative analysis provides biological insights and could potentially inform clinical interventions for various diseases.
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Affiliation(s)
- Yanghong Guo
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, Texas, U.S.A
| | - Lei Yu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Lei Guo
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, Texas, U.S.A
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22
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Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
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23
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Wu Y, Shi W, Li H, Liu C, Shimizu K, Li R, Zhang C. Specneuzhenide improves bleomycin-induced pulmonary fibrosis in mice via AMPK-dependent reduction of PD-L1. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155318. [PMID: 38493719 DOI: 10.1016/j.phymed.2023.155318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/29/2023] [Accepted: 12/25/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Pulmonary fibrosis (PF) is an escalating global health issue, characterized by rising rates of morbidity and mortality annually. Consequently, further investigation of potential damage mechanisms and potential preventive strategies for PF are warranted. Specnuezhenide (SPN), a prominent secoiridoid compound derived from Ligustrum lucidum Ait, exhibits anti-inflammatory and anti-oxidative capacities, indicating the potential therapeutic actions on PF. However, the underlying mechanisms of SPN on PF remain unclear. PURPOSE This work was aimed at investigating the protective actions of SPN on PF and the potential mechanism. METHODS In vivo, mice were administrated with bleomycin (BLM) to establish PF model. PF mice were treated with SPN (45/90 mg/kg) by gavage. In vitro, we employed TGF-β1 (10 ng/mL)-induced MLE-12 and PLFs cells, which then were treated with SPN (5, 10, 20 µM). DARTS assay, biofilm interference experiment and molecular docking were performed to investigate the molecular target of SPN. RESULTS In vivo, we found SPN treatment improved survival rate, alleviated pathological changes through reducing BLM-induced extracellular matrix (ECM) deposition, as well as BLM-induced epithelial-mesenchymal transition (EMT). In vitro, SPN inhibited EMT and lung fibroblast transdifferentiation. Mechanistically, SPN activated the AMPK protein to decrease the abnormally high level of PD-L1. Furthermore, the compound C, known as an AMPK inhibitor, exhibited a significant hindrance to the inhibition of SPN on TGF-β1-caused fibroblast transdifferentiation and proliferation. This outcome could be attributed to the fact that compound C could eliminate the inhibitory effects of SPN on PD-L1 expression. Interestingly, DARTS assay, biofilm interference experiment and molecular docking results all indicated that SPN could bind to AMPK, which suggested that SPN might be a potential agonist targeting AMPK protein. CONCLUSION Altogether, the results in our work illustrated that SPN promoted AMPK-dependent reduction of PD-L1 protein, contributing to the inhibition of fibrosis progression. Thus, SPN may represent a potential AMPK agonist for PF treatment.
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Affiliation(s)
- Yanliang Wu
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wen Shi
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Haini Li
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Chang Liu
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Kuniyoshi Shimizu
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Forest and Forest Products Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Renshi Li
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Chaofeng Zhang
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Chinese Medicine Resources, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China.
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24
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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: a robust and accurate method to identify feature gene sets and annotate cells. Nucleic Acids Res 2024; 52:e46. [PMID: 38647069 PMCID: PMC11109959 DOI: 10.1093/nar/gkae307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/25/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024] Open
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.
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Affiliation(s)
- Qi Gao
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Jichun Xie
- Department of Biostatistics and Bioinformatics, Duke University, USA
- Department of Mathematics, Duke University, USA
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25
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Yang C, Tan Y, Li Z, Hu L, Chen Y, Zhu S, Hu J, Huai T, Li M, Zhang G, Rao D, Fei G, Shao M, Ding Z. Pulmonary redox imbalance drives early fibroproliferative response in moderate/severe coronavirus disease-19 acute respiratory distress syndrome and impacts long-term lung abnormalities. Ann Intensive Care 2024; 14:72. [PMID: 38735020 PMCID: PMC11089033 DOI: 10.1186/s13613-024-01293-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/10/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND COVID-19-associated pulmonary fibrosis remains frequent. This study aimed to investigate pulmonary redox balance in COVID-19 ARDS patients and possible relationship with pulmonary fibrosis and long-term lung abnormalities. METHODS Baseline data, chest CT fibrosis scores, N-terminal peptide of alveolar collagen III (NT-PCP-III), transforming growth factor (TGF)-β1, superoxide dismutase (SOD), reduced glutathione (GSH), oxidized glutathione (GSSG) and malondialdehyde (MDA) in bronchoalveolar lavage fluid (BALF) were first collected and compared between SARS-CoV-2 RNA positive patients with moderate to severe ARDS (n = 65, COVID-19 ARDS) and SARS-CoV-2 RNA negative non-ARDS patients requiring mechanical ventilation (n = 63, non-ARDS). Then, correlations between fibroproliferative (NT-PCP-III and TGF-β1) and redox markers were analyzed within COVID-19 ARDS group, and comparisons between survivor and non-survivor subgroups were performed. Finally, follow-up of COVID-19 ARDS survivors was performed to analyze the relationship between pulmonary abnormalities, fibroproliferative and redox markers 3 months after discharge. RESULTS Compared with non-ARDS group, COVID-19 ARDS group had significantly elevated chest CT fibrosis scores (p < 0.001) and NT-PCP-III (p < 0.001), TGF-β1 (p < 0.001), GSSG (p < 0.001), and MDA (p < 0.001) concentrations on admission, while decreased SOD (p < 0.001) and GSH (p < 0.001) levels were observed in BALF. Both NT-PCP-III and TGF-β1 in BALF from COVID-19 ARDS group were directly correlated with GSSG (p < 0.001) and MDA (p < 0.001) and were inversely correlated with SOD (p < 0.001) and GSH (p < 0.001). Within COVID-19 ARDS group, non-survivors (n = 28) showed significant pulmonary fibroproliferation (p < 0.001) with more severe redox imbalance (p < 0.001) than survivors (n = 37). Furthermore, according to data from COVID-19 ARDS survivor follow-up (n = 37), radiographic residual pulmonary fibrosis and lung function impairment improved 3 months after discharge compared with discharge (p < 0.001) and were associated with early pulmonary fibroproliferation and redox imbalance (p < 0.01). CONCLUSIONS Pulmonary redox imbalance occurring early in COVID-19 ARDS patients drives fibroproliferative response and increases the risk of death. Long-term lung abnormalities post-COVID-19 are associated with early pulmonary fibroproliferation and redox imbalance.
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Affiliation(s)
- Chun Yang
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Yuanyuan Tan
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Zihao Li
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Lei Hu
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Yuanyuan Chen
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Shouliang Zhu
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Jiawei Hu
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Tingting Huai
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Mingqing Li
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Guobin Zhang
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China
| | - Dewang Rao
- Anhui Medical University, #81 Meishan Road, Hefei, 230032, Anhui, China
| | - Guanghe Fei
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China.
| | - Min Shao
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China.
| | - Zhenxing Ding
- The First Affiliated Hospital of Anhui Medical University, #218 Jixi Road, Hefei, 230022, Anhui, China.
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26
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Burgess CL, Huang J, Bawa PS, Alysandratos KD, Minakin K, Ayers LJ, Morley MP, Babu A, Villacorta-Martin C, Yampolskaya M, Hinds A, Thapa BR, Wang F, Matschulat A, Mehta P, Morrisey EE, Varelas X, Kotton DN. Generation of human alveolar epithelial type I cells from pluripotent stem cells. Cell Stem Cell 2024; 31:657-675.e8. [PMID: 38642558 PMCID: PMC11147407 DOI: 10.1016/j.stem.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/31/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Alveolar epithelial type I cells (AT1s) line the gas exchange barrier of the distal lung and have been historically challenging to isolate or maintain in cell culture. Here, we engineer a human in vitro AT1 model system via directed differentiation of induced pluripotent stem cells (iPSCs). We use primary adult AT1 global transcriptomes to suggest benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, enriched in these cells. Next, we generate iPSC-derived alveolar epithelial type II cells (AT2s) and find that nuclear YAP signaling is sufficient to promote a broad transcriptomic shift from AT2 to AT1 gene programs. The resulting cells express a molecular, morphologic, and functional phenotype reminiscent of human AT1 cells, including the capacity to form a flat epithelial barrier producing characteristic extracellular matrix molecules and secreted ligands. Our results provide an in vitro model of human alveolar epithelial differentiation and a potential source of human AT1s.
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Affiliation(s)
- Claire L Burgess
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pushpinder S Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Kasey Minakin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lauren J Ayers
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apoorva Babu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Bibek R Thapa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Adeline Matschulat
- The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xaralabos Varelas
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
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27
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Saviano A, Roehlen N, Baumert TF. Tight Junction Proteins as Therapeutic Targets to Treat Liver Fibrosis and Hepatocellular Carcinoma. Semin Liver Dis 2024; 44:180-190. [PMID: 38648796 DOI: 10.1055/s-0044-1785646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In the last decade tight junction proteins exposed at the surface of liver or cancer cells have been uncovered as mediators of liver disease biology: Claudin-1 and Occludin are host factors for hepatitis C virus entry and Claudin-1 has been identified as a driver for liver fibrosis and hepatocellular carcinoma (HCC). Moreover, Claudins have emerged as therapeutic targets for liver disease and HCC. CLDN1 expression is upregulated in liver fibrosis and HCC. Monoclonal antibodies (mAbs) targeting Claudin-1 have completed preclinical proof-of-concept studies for treatment of liver fibrosis and HCC and are currently in clinical development for advanced liver fibrosis. Claudin-6 overexpression is associated with an HCC aggressive phenotype and treatment resistance. Claudin-6 mAbs or chimeric antigen receptor-T cells therapies are currently being clinically investigated for Claudin-6 overexpressing tumors. In conclusion, targeting Claudin proteins offers a novel clinical opportunity for the treatment of patients with advanced liver fibrosis and HCC.
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Affiliation(s)
- Antonio Saviano
- Inserm, U1110, Institute of Translational Medicine and Liver Disease, Strasbourg, France
- University of Strasbourg, Strasbourg, France
- Service d'hépato-gastroentérologie, Pôle Hépato-digestif, Institut-Hospitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Natascha Roehlen
- Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Diseases, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas F Baumert
- Inserm, U1110, Institute of Translational Medicine and Liver Disease, Strasbourg, France
- University of Strasbourg, Strasbourg, France
- Service d'hépato-gastroentérologie, Pôle Hépato-digestif, Institut-Hospitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut Universitaire de France, Paris, France
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28
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Selman M, Pardo A. Idiopathic Pulmonary Fibrosis: From Common Microscopy to Single-Cell Biology and Precision Medicine. Am J Respir Crit Care Med 2024; 209:1074-1081. [PMID: 38289233 DOI: 10.1164/rccm.202309-1573pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/29/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico; and
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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29
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Bhattacharyya A, Khan R, Lee JY, Tassew G, Oskouian B, Allende ML, Proia RL, Yin X, Ortega JG, Bhattacharya M, Saba JD. Gene therapy with AAV9-SGPL1 in an animal model of lung fibrosis. J Pathol 2024; 263:22-31. [PMID: 38332723 PMCID: PMC10987276 DOI: 10.1002/path.6256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease of the lung that leads rapidly to respiratory failure. Novel approaches to treatment are urgently needed. The bioactive lipid sphingosine-1-phosphate (S1P) is increased in IPF lungs and promotes proinflammatory and profibrotic TGF-β signaling. Hence, decreasing lung S1P represents a potential therapeutic strategy for IPF. S1P is degraded by the intracellular enzyme S1P lyase (SPL). Here we find that a knock-in mouse with a missense SPL mutation mimicking human disease resulted in reduced SPL activity, increased S1P, increased TGF-β signaling, increased lung fibrosis, and higher mortality after injury compared to wild type (WT). We then tested adeno-associated virus 9 (AAV9)-mediated overexpression of human SGPL1 (AAV-SPL) in mice as a therapeutic modality. Intravenous treatment with AAV-SPL augmented lung SPL activity, attenuated S1P levels within the lungs, and decreased injury-induced fibrosis compared to controls treated with saline or only AAV. We confirmed that AAV-SPL treatment led to higher expression of SPL in the epithelial and fibroblast compartments during bleomycin-induced lung injury. Additionally, AAV-SPL decreased expression of the profibrotic cytokines TNFα and IL1β as well as markers of fibroblast activation, such as fibronectin (Fn1), Tgfb1, Acta2, and collagen genes in the lung. Taken together, our results provide proof of concept for the use of AAV-SPL as a therapeutic strategy for the treatment of IPF. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Aritra Bhattacharyya
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ranjha Khan
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Joanna Y. Lee
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Gizachew Tassew
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Babak Oskouian
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Maria L. Allende
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard L. Proia
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xiaoyang Yin
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Javier G. Ortega
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mallar Bhattacharya
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Julie D. Saba
- Department of Pediatrics, University of California, San Francisco, CA, USA
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30
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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31
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Herbst CJ, Lopez-Rodriguez E, Gluhovic V, Schulz S, Brandt R, Timm S, Abledu J, Falivene J, Pennitz P, Kirsten H, Nouailles G, Witzenrath M, Ochs M, Kuebler WM. Characterization of Commercially Available Human Primary Alveolar Epithelial Cells. Am J Respir Cell Mol Biol 2024; 70:339-350. [PMID: 38207121 DOI: 10.1165/rcmb.2023-0320ma] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
In vitro lung research requires appropriate cell culture models that adequately mimic in vivo structure and function. Previously, researchers extensively used commercially available and easily expandable A549 and NCI-H441 cells, which replicate some but not all features of alveolar epithelial cells. Specifically, these cells are often restricted by terminally altered expression while lacking important alveolar epithelial characteristics. Of late, human primary alveolar epithelial cells (hPAEpCs) have become commercially available but are so far poorly specified. Here, we applied a comprehensive set of technologies to characterize their morphology, surface marker expression, transcriptomic profile, and functional properties. At optimized seeding numbers of 7,500 cells per square centimeter and growth at a gas-liquid interface, hPAEpCs formed regular monolayers with tight junctions and amiloride-sensitive transepithelial ion transport. Electron microscopy revealed lamellar body and microvilli formation characteristic for alveolar type II cells. Protein and single-cell transcriptomic analyses revealed expression of alveolar type I and type II cell markers; yet, transcriptomic data failed to detect NKX2-1, an important transcriptional regulator of alveolar cell differentiation. With increasing passage number, hPAEpCs transdifferentiated toward alveolar-basal intermediates characterized as SFTPC-, KRT8high, and KRT5- cells. In spite of marked changes in the transcriptome as a function of passaging, Uniform Manifold Approximation and Projection plots did not reveal major shifts in cell clusters, and epithelial permeability was unaffected. The present work delineates optimized culture conditions, cellular characteristics, and functional properties of commercially available hPAEpCs. hPAEpCs may provide a useful model system for studies on drug delivery, barrier function, and transepithelial ion transport in vitro.
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Affiliation(s)
- Christopher J Herbst
- Institute of Physiology
- German Center for Cardiovascular Research, Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Berlin, Germany
- German Center for Lung Research, Deutsches Zentrum für Lungenforschung (DZL), Berlin, Germany
| | | | | | | | | | - Sara Timm
- Core Facility Electron Microscopy, and
| | | | | | - Peter Pennitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany; and
| | - Geraldine Nouailles
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ochs
- Institute of Functional Anatomy
- Core Facility Electron Microscopy, and
- German Center for Lung Research, Deutsches Zentrum für Lungenforschung (DZL), Berlin, Germany
| | - Wolfgang M Kuebler
- Institute of Physiology
- German Center for Cardiovascular Research, Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Berlin, Germany
- German Center for Lung Research, Deutsches Zentrum für Lungenforschung (DZL), Berlin, Germany
- Keenan Research Centre, St. Michael's Hospital, and
- Departments of Surgery and
- Physiology, University of Toronto, Toronto, Ontario, Canada
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32
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Cai Q, Peng M. Identification of CNKSR1 as a biomarker for "cold" tumor microenvironment in lung adenocarcinoma: An integrative analysis based on a novel workflow. Heliyon 2024; 10:e29126. [PMID: 38628722 PMCID: PMC11019179 DOI: 10.1016/j.heliyon.2024.e29126] [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: 02/02/2024] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Background Therapies targeting PD1/PD-L1 pathway have revolutionized the treatment of lung cancer. However, anti-PD1/PD-L1 therapies have proven beneficial for only a select group of lung adenocarcinoma (LUAD) patients and generally do not work for immuno-cold tumors characterized by a lack of immune cell infiltration. Identifying novel biomarkers is vital to broad therapeutic options for LUAD patients with no response to anti-PD1/PD-L1 immunotherapies. Methods Our study has developed a novel strategy to identify a promising biomarker that addresses the limitations of anti-PD1/PD-L1 immunotherapy in treating immunological cold tumors. We exacted LUAD RNA-seq data from the Cancer Genome Atlas database (TCGA). Using several machine learning methods, we identified the candidate biomarker. Based on the expression level of PD-L1 and the identified biomarker, samples were categorized into four groups. We further used ESTIMATE, ssGSEA, and CIBERSORT algorithms to calculate the immune infiltration level of each group. The results were validated in three independent bulk datasets and one scRNA-seq dataset. Immunohistochemistry (IHC) assessments were performed in clinical samples to further evaluate the coexpression of CNKSR1 and PD-L1, and to compare CD8 + T cell infiltration among groups. Results After comprehensive analyses, CNKSR1 was identified as a novel promising biomarker for immuno-cold LUAD. CNKSR1 mRNA expression levels exhibited a negative correlation with both PD-L1 mRNA expression and the extent of immune cell infiltration in LUAD. Besides, in contrast to the significant association between the expression of PD-L1 and the majority of other well-established or widely studied immune checkpoint molecules, a mutually exclusive expression pattern is observed between CNKSR1 and these molecules. The aforementioned results were consistent in validation datasets. The prognostic model built based on the CNKSR1 coexpression module also showed robust predictive performance. Additionally, IHC assessments have confirmed that the coexpression of CNKSR1 and PD-L1 is rare in LUAD samples. Notably, LUADs in the high-CNKSR1 group, characterized by high CNKSR1 but low PD- L1 expression, demonstrated reduced infiltration of CD8+ T cells. Conclusions In summary, CNKSR1 emerges as a promising biomarker for immune-cold LUADs, and the study into CNKSR1 modulating T-cell infiltration may lead to the identification of compensatory molecules to enhance the effectiveness of current immunotherapy for LUAD.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Mou Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
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33
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Chen Y, Wang T, Liang F, Han J, Lou Z, Yu Y, Li J, Zhan T, Gu Y, Dong L, Jiang B, Zhang W, Wu M, Lu Y. Nicotinamide phosphoribosyltransferase prompts bleomycin-induced pulmonary fibrosis by driving macrophage M2 polarization in mice. Theranostics 2024; 14:2794-2815. [PMID: 38773984 PMCID: PMC11103509 DOI: 10.7150/thno.94482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/24/2024] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is an irreversible, fatal interstitial lung disease lacking specific therapeutics. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the nicotinamide adenine dinucleotide (NAD) salvage biosynthesis pathway and a cytokine, has been previously reported as a biomarker for lung diseases; however, the role of NAMPT in pulmonary fibrosis has not been elucidated. Methods: We identified the NAMPT level changes in pulmonary fibrosis by analyzing public RNA-Seq databases, verified in collected clinical samples and mice pulmonary fibrosis model by Western blotting, qRT-PCR, ELISA and Immunohistochemical staining. We investigated the role and mechanism of NAMPT in lung fibrosis by using pharmacological inhibition on NAMPT and Nampt transgenic mice. In vivo macrophage depletion by clodronate liposomes and reinfusion of IL-4-induced M2 bone marrow-derived macrophages (BMDMs) from wild-type mice, combined with in vitro cell experiments, were performed to further validate the mechanism underlying NAMPT involving lung fibrosis. Results: We found that NAMPT increased in the lungs of patients with IPF and mice with bleomycin (BLM)-induced pulmonary fibrosis. NAMPT inhibitor FK866 alleviated BLM-induced pulmonary fibrosis in mice and significantly reduced NAMPT levels in bronchoalveolar lavage fluid (BALF). The lung single-cell RNA sequencing showed that NAMPT expression in monocytes/macrophages of IPF patients was much higher than in other lung cells. Knocking out NAMPT in mouse monocytes/macrophages (Namptfl/fl;Cx3cr1CreER) significantly alleviated BLM-induced pulmonary fibrosis in mice, decreased NAMPT levels in BALF, reduced the infiltration of M2 macrophages in the lungs and improved mice survival. Depleting monocytes/macrophages in Namptfl/fl;Cx3cr1CreER mice by clodronate liposomes and subsequent pulmonary reinfusion of IL-4-induced M2 BMDMs from wild-type mice, reversed the protective effect of monocyte/macrophage NAMPT-deletion on lung fibrosis. In vitro experiments confirmed that the mechanism of NAMPT engaged in pulmonary fibrosis is related to the released NAMPT by macrophages promoting M2 polarization in a non-enzyme-dependent manner by activating the STAT6 signal pathway. Conclusions: NAMPT prompts bleomycin-induced pulmonary fibrosis by driving macrophage M2 polarization in mice. Targeting the NAMPT of monocytes/macrophages is a promising strategy for treating pulmonary fibrosis.
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Affiliation(s)
- Yaling Chen
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Tong Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jia Han
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yifan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jinsheng Li
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Tianwei Zhan
- Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Yuqing Gu
- Department of Pharmacology, School of Pharmacy, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Lingjun Dong
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang Province, China
| | - Bo Jiang
- Department of Pharmacology, School of Pharmacy, Zhejiang University, Hangzhou, Zhejiang Province, China
- Department of Clinical Pharmacology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weiping Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yunbi Lu
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
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34
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Read J, Reid AT, Thomson C, Plit M, Mejia R, Knight DA, Lize M, El Kasmi K, Grainge CL, Stahl H, Schuliga M. Alveolar epithelial cells of lung fibrosis patients are susceptible to severe virus-induced injury. Clin Sci (Lond) 2024; 138:537-554. [PMID: 38577922 DOI: 10.1042/cs20240220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/06/2024]
Abstract
Patients with pulmonary fibrosis (PF) often experience exacerbations of their disease, characterised by a rapid, severe deterioration in lung function that is associated with high mortality. Whilst the pathobiology of such exacerbations is poorly understood, virus infection is a trigger. The present study investigated virus-induced injury responses of alveolar and bronchial epithelial cells (AECs and BECs, respectively) from patients with PF and age-matched controls (Ctrls). Air-liquid interface (ALI) cultures of AECs, comprising type I and II pneumocytes or BECs were inoculated with influenza A virus (H1N1) at 0.1 multiplicity of infection (MOI). Levels of interleukin-6 (IL-6), IL-36γ and IL-1β were elevated in cultures of AECs from PF patients (PF-AECs, n = 8-11), being markedly higher than Ctrl-AECs (n = 5-6), 48 h post inoculation (pi) (P<0.05); despite no difference in H1N1 RNA copy numbers 24 h pi. Furthermore, the virus-induced inflammatory responses of PF-AECs were greater than BECs (from either PF patients or controls), even though viral loads in the BECs were overall 2- to 3-fold higher than AECs. Baseline levels of the senescence and DNA damage markers, nuclear p21, p16 and H2AXγ were also significantly higher in PF-AECs than Ctrl-AECs and further elevated post-infection. Senescence induction using etoposide augmented virus-induced injuries in AECs (but not viral load), whereas selected senotherapeutics (rapamycin and mitoTEMPO) were protective. The present study provides evidence that senescence increases the susceptibility of AECs from PF patients to severe virus-induced injury and suggests targeting senescence may provide an alternative option to prevent or treat the exacerbations that worsen the underlying disease.
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Affiliation(s)
- Jane Read
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Andrew T Reid
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - Claire Thomson
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- Saint Vincent's Hospital, Sydney, NSW, Australia
| | | | - Ross Mejia
- John Hunter Hospital, Newcastle, NSW, Australia
| | - Darryl A Knight
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Providence Health Care Research Institute, Vancouver, British Columbia, Canada
| | - Muriel Lize
- Boehringer Ingelheim Pharma GmbH & Co. KG, Germany
| | | | - Christopher L Grainge
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- John Hunter Hospital, Newcastle, NSW, Australia
| | - Heiko Stahl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Germany
| | - Michael Schuliga
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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35
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McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: A robust and accurate method to identify feature gene sets and annotate cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.24.541352. [PMID: 37577619 PMCID: PMC10418061 DOI: 10.1101/2023.05.24.541352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multiomic cellular profiles. It is conveniently available as an open-source R package.
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37
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Basil MC, Alysandratos KD, Kotton DN, Morrisey EE. Lung repair and regeneration: Advanced models and insights into human disease. Cell Stem Cell 2024; 31:439-454. [PMID: 38492572 PMCID: PMC11070171 DOI: 10.1016/j.stem.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The respiratory system acts as both the primary site of gas exchange and an important sensor and barrier to the external environment. The increase in incidences of respiratory disease over the past decades has highlighted the importance of developing improved therapeutic approaches. This review will summarize recent research on the cellular complexity of the mammalian respiratory system with a focus on gas exchange and immunological defense functions of the lung. Different models of repair and regeneration will be discussed to help interpret human and animal data and spur the investigation of models and assays for future drug development.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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38
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Shi X, Chen Y, Shi M, Gao F, Huang L, Wang W, Wei D, Shi C, Yu Y, Xia X, Song N, Chen X, Distler JHW, Lu C, Chen J, Wang J. The novel molecular mechanism of pulmonary fibrosis: insight into lipid metabolism from reanalysis of single-cell RNA-seq databases. Lipids Health Dis 2024; 23:98. [PMID: 38570797 PMCID: PMC10988923 DOI: 10.1186/s12944-024-02062-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Pulmonary fibrosis (PF) is a severe pulmonary disease with limited available therapeutic choices. Recent evidence increasingly points to abnormal lipid metabolism as a critical factor in PF pathogenesis. Our latest research identifies the dysregulation of low-density lipoprotein (LDL) is a new risk factor for PF, contributing to alveolar epithelial and endothelial cell damage, and fibroblast activation. In this study, we first integrative summarize the published literature about lipid metabolite changes found in PF, including phospholipids, glycolipids, steroids, fatty acids, triglycerides, and lipoproteins. We then reanalyze two single-cell RNA-sequencing (scRNA-seq) datasets of PF, and the corresponding lipid metabolomic genes responsible for these lipids' biosynthesis, catabolism, transport, and modification processes are uncovered. Intriguingly, we found that macrophage is the most active cell type in lipid metabolism, with almost all lipid metabolic genes being altered in macrophages of PF. In type 2 alveolar epithelial cells, lipid metabolic differentially expressed genes (DEGs) are primarily associated with the cytidine diphosphate diacylglycerol pathway, cholesterol metabolism, and triglyceride synthesis. Endothelial cells are partly responsible for sphingomyelin, phosphatidylcholine, and phosphatidylethanolamines reprogramming as their metabolic genes are dysregulated in PF. Fibroblasts may contribute to abnormal cholesterol, phosphatidylcholine, and phosphatidylethanolamine metabolism in PF. Therefore, the reprogrammed lipid profiles in PF may be attributed to the aberrant expression of lipid metabolic genes in different cell types. Taken together, these insights underscore the potential of targeting lipid metabolism in developing innovative therapeutic strategies, potentially leading to extended overall survival in individuals affected by PF.
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Affiliation(s)
- Xiangguang Shi
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yahui Chen
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Fei Gao
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Lihao Huang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Dong Wei
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Chenyi Shi
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuexin Yu
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Xueyi Xia
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Nana Song
- Department of Nephrology, Zhongshan Hospital, Fudan University, Fudan Zhangjiang Institute, Shanghai, People's Republic of China
| | - Xiaofeng Chen
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jörg H W Distler
- Department of Internal Medicine 3 and Institute for Clinical Immunology, University of Erlangen, Nuremberg, Germany
| | - Chenqi Lu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jingyu Chen
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China.
- Center for Lung Transplantation, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jiucun Wang
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China.
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
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Patel M, Post Y, Hill N, Sura A, Ye J, Fisher T, Suen N, Zhang M, Cheng L, Pribluda A, Chen H, Yeh WC, Li Y, Baribault H, Fletcher RB. A WNT mimetic with broad spectrum FZD-specificity decreases fibrosis and improves function in a pulmonary damage model. Respir Res 2024; 25:153. [PMID: 38566174 PMCID: PMC10985870 DOI: 10.1186/s12931-024-02786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Wnt/β-catenin signaling is critical for lung development and AT2 stem cell maintenance in adults, but excessive pathway activation has been associated with pulmonary fibrosis, both in animal models and human diseases such as idiopathic pulmonary fibrosis (IPF). IPF is a detrimental interstitial lung disease, and although two approved drugs limit functional decline, transplantation is the only treatment that extends survival, highlighting the need for regenerative therapies. METHODS Using our antibody-based platform of Wnt/β-catenin modulators, we investigated the ability of a pathway antagonist and pathway activators to reduce pulmonary fibrosis in the acute bleomycin model, and we tested the ability of a WNT mimetic to affect alveolar organoid cultures. RESULTS A WNT mimetic agonist with broad FZD-binding specificity (FZD1,2,5,7,8) potently expanded alveolar organoids. Upon therapeutic dosing, a broad FZD-binding specific Wnt mimetic decreased pulmonary inflammation and fibrosis and increased lung function in the bleomycin model, and it impacted multiple lung cell types in vivo. CONCLUSIONS Our results highlight the unexpected capacity of a WNT mimetic to effect tissue repair after lung damage and support the continued development of Wnt/β-catenin pathway modulation for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Mehaben Patel
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Yorick Post
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Natalie Hill
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Asmiti Sura
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Jay Ye
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Trevor Fisher
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Nicholas Suen
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Mengrui Zhang
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Leona Cheng
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Ariel Pribluda
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Hui Chen
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Wen-Chen Yeh
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Yang Li
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Hélène Baribault
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA
| | - Russell B Fletcher
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA, 94080, USA.
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Li PL, Chen DF, Li XT, Hao RC, Zhao ZD, Li ZL, Yin BF, Tang J, Luo YW, Wu CT, Nie JJ, Zhu H. Microgel-based carriers enhance skeletal stem cell reprogramming towards immunomodulatory phenotype in osteoarthritic therapy. Bioact Mater 2024; 34:204-220. [PMID: 38235309 PMCID: PMC10792171 DOI: 10.1016/j.bioactmat.2023.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/13/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Skeletal stem cells (SSC) have gained attentions as candidates for the treatment of osteoarthritis due to their osteochondrogenic capacity. However, the immunomodulatory properties of SSC, especially under delivery operations, have been largely ignored. In the study, we found that Pdpn+ and Grem1+ SSC subpopulations owned immunoregulatory potential, and the single-cell RNA sequencing (scRNA-seq) data suggested that the mechanical activation of microgel carriers on SSC induced the generation of Pdpn+Grem1+Ptgs2+ SSC subpopulation, which was potent at suppressing macrophage inflammation. The microgel carriers promoted the YAP nuclear translocation, and the activated YAP protein was necessary for the increased expression of Ptgs2 and PGE2 in microgels-delivered SSC, which further suppressed the expression of TNF-ɑ, IL-1β and promoted the expression of IL-10 in macrophages. SSC delivered with microgels yielded better preventive effects on articular lesions and macrophage activation in osteoarthritic rats than SSC without microgels. Chemically blocking the YAP and Ptgs2 in microgels-delivered SSC partially abolished the enhanced protection on articular tissues and suppression on osteoarthritic macrophages. Moreover, microgel carriers significantly prolonged SSC retention time in vivo without increasing SSC implanting into osteoarthritic joints. Together, our study demonstrated that microgel carriers enhanced SSC reprogramming towards immunomodulatory phenotype to regulate macrophage phenotype transformation for effectively osteoarthritic therapy by promoting YAP protein translocation into nucleus. The study not only complement and perfect the immunological mechanisms of SSC-based therapy at the single-cell level, but also provide new insight for microgel carriers in stem cell-based therapy.
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Affiliation(s)
- Pei-Lin Li
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Da-Fu Chen
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Road Xinjiekou 31, Beijing, 100035, PR China
| | - Xiao-Tong Li
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Rui-Cong Hao
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Zhi-Dong Zhao
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
- People's Liberation Army General Hospital, Road Fuxing 28, Beijing, 100853, PR China
| | - Zhi-Ling Li
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Bo-Feng Yin
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Jie Tang
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Yu-Wen Luo
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Road Xinjiekou 31, Beijing, 100035, PR China
| | - Chu-Tse Wu
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
| | - Jing-Jun Nie
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Road Xinjiekou 31, Beijing, 100035, PR China
| | - Heng Zhu
- Department of Stem Cells and Regenerative Medicine, Beijing Institute of Radiation Medicine, Road Taiping 27, Beijing, 100850, PR China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China
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Castro CFG, Nardiello C, Hadzic S, Kojonazarov B, Kraut S, Gierhardt M, Schäffer J, Bednorz M, Quanz K, Heger J, Korfei M, Wilhelm J, Hecker M, Bartkuhn M, Arnhold S, Guenther A, Seeger W, Schulz R, Weissmann N, Sommer N, Pak O. The Role of the Redox Enzyme p66Shc in Biological Aging of the Lung. Aging Dis 2024; 15:911-926. [PMID: 37548932 PMCID: PMC10917546 DOI: 10.14336/ad.2023.0715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/15/2023] [Indexed: 08/08/2023] Open
Abstract
The mitochondrial adaptor protein p66Shc has been suggested to control life span in mice via the release of hydrogen peroxide. However, the role of p66Shc in lung aging remains unsolved. Thus, we investigated the effects of p66Shc-/- on the aging of the lung and pulmonary circulation. In vivo lung and cardiac characteristics were investigated in p66Shc-/- and wild type (WT) mice at 3, 12, and 24 months of age by lung function measurements, micro-computed tomography (µCT), and echocardiography. Alveolar number and muscularization of small pulmonary arteries were measured by stereology and vascular morphometry, respectively. Protein and mRNA levels of senescent markers were measured by western blot and PCR, respectively. Lung function declined similarly in WT and p66Shc-/- mice during aging. However, µCT analyses and stereology showed slightly enhanced signs of aging-related parameters in p66Shc-/- mice, such as a decline of alveolar density. Accordingly, p66Shc-/- mice showed higher protein expression of the senescence marker p21 in lung homogenate compared to WT mice of the corresponding age. Pulmonary vascular remodeling was increased during aging, but aged p66Shc-/- mice showed similar muscularization of pulmonary vessels and hemodynamics like WT mice. In the heart, p66Shc-/- prevented the deterioration of right ventricular (RV) function but promoted the decline of left ventricular (LV) function during aging. p66Shc-/- affects the aging process of the lung and the heart differently. While p66Shc-/- slightly accelerates lung aging and deteriorates LV function in aged mice, it seems to exert protective effects on RV function during aging.
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Affiliation(s)
- Claudia F. Garcia Castro
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Claudio Nardiello
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Stefan Hadzic
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Baktybek Kojonazarov
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Simone Kraut
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Mareike Gierhardt
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Julia Schäffer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Mariola Bednorz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Karin Quanz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Jacqueline Heger
- Institute of Physiology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Martina Korfei
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Jochen Wilhelm
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Matthias Hecker
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Marek Bartkuhn
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Stefan Arnhold
- Institute of Veterinary Anatomy, Histology and Embryology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Andreas Guenther
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- European IPF Registry & Biobank (eurIPFreg), Giessen, Germany.
- Agaplesion Evangelisches Krankenhaus Mittelhessen, Giessen, Germany
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
| | - Rainer Schulz
- Institute of Physiology, Justus-Liebig University of Giessen, Giessen, Germany.
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
| | - Oleg Pak
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus- Liebig University of Giessen, Giessen, Germany.
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Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung. Nat Genet 2024; 56:595-604. [PMID: 38548990 PMCID: PMC11018522 DOI: 10.1038/s41588-024-01702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis. Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA sequencing of lung tissue from 66 individuals with pulmonary fibrosis and 48 unaffected donors. Using a pseudobulk approach, we mapped expression quantitative trait loci (eQTLs) across 38 cell types, observing both shared and cell-type-specific regulatory effects. Furthermore, we identified disease interaction eQTLs and demonstrated that this class of associations is more likely to be cell-type-specific and linked to cellular dysregulation in pulmonary fibrosis. Finally, we connected lung disease risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression and implicates context-specific eQTLs as key regulators of lung homeostasis and disease.
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Affiliation(s)
- Heini M Natri
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christina B Del Azodi
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sagrika Chugh
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Kendle
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - David K Flaherty
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brittany K Matlock
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carla L Calvi
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy S Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Lorraine B Ware
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Bacchetta
- Department of Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rajat Walia
- Department of Thoracic Disease and Transplantation, Norton Thoracic Institute, Phoenix, AZ, USA
| | - Ciara M Shaver
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Davis J McCarthy
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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43
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Zheng M, Zhu W, Gao F, Zhuo Y, Zheng M, Wu G, Feng C. Novel inhalation therapy in pulmonary fibrosis: principles, applications and prospects. J Nanobiotechnology 2024; 22:136. [PMID: 38553716 PMCID: PMC10981316 DOI: 10.1186/s12951-024-02407-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Pulmonary fibrosis (PF) threatens millions of people worldwide with its irreversible progression. Although the underlying pathogenesis of PF is not fully understood, there is evidence to suggest that the disease can be blocked at various stages. Inhalation therapy has been applied for lung diseases such as asthma and chronic obstructive pulmonary disease, and its application for treating PF is currently under consideration. New techniques in inhalation therapy, such as the application of microparticles and nanoparticles, traditional Chinese medicine monomers, gene therapy, inhibitors, or agonists of signaling pathways, extracellular vesicle interventions, and other specific drugs, are effective in treating PF. However, the safety and effectiveness of these therapeutic techniques are influenced by the properties of inhaled particles, biological and pathological barriers, and the type of inhalation device used. This review provides a comprehensive overview of the pharmacological, pharmaceutical, technical, preclinical, and clinical experimental aspects of novel inhalation therapy for treating PF and focus on therapeutic methods that significantly improve existing technologies or expand the range of drugs that can be administered via inhalation. Although inhalation therapy for PF has some limitations, the advantages are significant, and further research and innovation about new inhalation techniques and drugs are encouraged.
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Affiliation(s)
- Meiling Zheng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100010, China
- Peking University People's Hospital, Beijing, 100032, China
| | - Wei Zhu
- Department of Ophthalmology, Changshu No. 2 People's Hospital, Changshu, 215500, China
| | - Fei Gao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, China
| | - Yu Zhuo
- Department of Medical Oncology Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100010, China
| | - Mo Zheng
- Department of Medical Oncology Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100010, China
| | - Guanghao Wu
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Cuiling Feng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100010, China.
- Peking University People's Hospital, Beijing, 100032, China.
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44
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Abel TR, Kosarek NN, Parvizi R, Jarnagin H, Torres GM, Bhandari R, Huang M, Toledo DM, Smith A, Popovich D, Mariani MP, Yang H, Wood T, Garlick J, Pioli PA, Whitfield ML. Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586316. [PMID: 38585776 PMCID: PMC10996484 DOI: 10.1101/2024.03.22.586316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Systemic sclerosis (SSc) is an autoimmune disease characterized by skin fibrosis, internal organ involvement and vascular dropout. We previously developed and phenotypically characterized an in vitro 3D skin-like tissue model of SSc, and now analyze the transcriptomic (scRNA-seq) and epigenetic (scATAC-seq) characteristics of this model at single-cell resolution. SSc 3D skin-like tissues were fabricated using autologous fibroblasts, macrophages, and plasma from SSc patients or healthy control (HC) donors. SSc tissues displayed increased dermal thickness and contractility, as well as increased α-SMA staining. Single-cell transcriptomic and epigenomic analyses identified keratinocytes, macrophages, and five populations of fibroblasts (labeled FB1 - 5). Notably, FB1 APOE-expressing fibroblasts were 12-fold enriched in SSc tissues and were characterized by high EGR1 motif accessibility. Pseudotime analysis suggests that FB1 fibroblasts differentiate from a TGF-β1-responsive fibroblast population and ligand-receptor analysis indicates that the FB1 fibroblasts are active in macrophage crosstalk via soluble ligands including FGF2 and APP. These findings provide characterization of the 3D skin-like model at single cell resolution and establish that it recapitulates subsets of fibroblasts and macrophage phenotypes observed in skin biopsies.
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45
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Zhang H, Mulqueen RM, Iannuzo N, Farrera DO, Polverino F, Galligan JJ, Ledford JG, Adey AC, Cusanovich DA. txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. Genome Biol 2024; 25:78. [PMID: 38519979 PMCID: PMC10958877 DOI: 10.1186/s13059-023-03150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/20/2023] [Indexed: 03/25/2024] Open
Abstract
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.
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Affiliation(s)
- Hao Zhang
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Ryan M Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Natalie Iannuzo
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Dominique O Farrera
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Francesca Polverino
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Arizona, Tucson, AZ, USA
- Banner - University Medicine North, Pulmonary - Clinic F, Tucson, AZ, USA
| | - James J Galligan
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Julie G Ledford
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA.
- Oregon Health & Science University, Knight Cardiovascular Institute, Portland, OR, USA.
| | - Darren A Cusanovich
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.
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46
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Carter H, Costa RM, Adams TS, Gilchrist T, Emch CE, Bame M, Oldham JM, Linderholm AL, Noth I, Kaminski N, Moore BB, Gurczynski SJ. Dendritic Cell - Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.584457. [PMID: 38559175 PMCID: PMC10980010 DOI: 10.1101/2024.03.15.584457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring and loss of lung function. With limited treatment options, patients succumb to the disease within 2-5 years. The molecular pathogenesis of IPF regarding the immunologic changes that occur is poorly understood. We characterize a role for non-canonical aryl-hydrocarbon receptor signaling (ncAHR) in dendritic cells (DCs) that leads to production of IL-6 and IL-17, promoting fibrosis. TLR9 signaling in myofibroblasts is shown to regulate production of TDO2 which converts tryptophan into the endogenous AHR ligand kynurenine. Mice with augmented ncAHR signaling were created by crossing floxed AHR exon-2 deletion mice (AHR Δex2 ) with mice harboring a CD11c-Cre. Bleomycin was used to study fibrotic pathogenesis. Isolated CD11c+ cells and primary fibroblasts were treated ex-vivo with relevant TLR agonists and AHR modulating compounds to study how AHR signaling influenced inflammatory cytokine production. Human datasets were also interrogated. Inhibition of all AHR signaling rescued fibrosis, however, AHR Δex2 mice treated with bleomycin developed more fibrosis and DCs from these mice were hyperinflammatory and profibrotic upon adoptive transfer. Treatment of fibrotic fibroblasts with TLR9 agonist increased expression of TDO2. Study of human samples corroborate the relevance of these findings in IPF patients. We also, for the first time, identify that AHR exon-2 floxed mice retain capacity for ncAHR signaling.
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Xu F, Tong Y, Yang W, Cai Y, Yu M, Liu L, Meng Q. Identifying a survival-associated cell type based on multi-level transcriptome analysis in idiopathic pulmonary fibrosis. Respir Res 2024; 25:126. [PMID: 38491375 PMCID: PMC10941445 DOI: 10.1186/s12931-024-02738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive disease with a five-year survival rate of less than 40%. There is significant variability in survival time among IPF patients, but the underlying mechanisms for this are not clear yet. METHODS AND RESULTS We collected single-cell RNA sequence data of 13,223 epithelial cells taken from 32 IPF patients and bulk RNA sequence data from 456 IPF patients in GEO. Based on unsupervised clustering analysis at the single-cell level and deconvolution algorithm at bulk RNA sequence data, we discovered a special alveolar type 2 cell subtype characterized by high expression of CCL20 (referred to as ATII-CCL20), and found that IPF patients with a higher proportion of ATII-CCL20 had worse prognoses. Furthermore, we uncovered the upregulation of immune cell infiltration and metabolic functions in IPF patients with a higher proportion of ATII-CCL20. Finally, the comprehensive decision tree and nomogram were constructed to optimize the risk stratification of IPF patients and provide a reference for accurate prognosis evaluation. CONCLUSIONS Our study by integrating single-cell and bulk RNA sequence data from IPF patients identified a special subtype of ATII cells, ATII-CCL20, which was found to be a risk cell subtype associated with poor prognosis in IPF patients. More importantly, the ATII-CCL20 cell subtype was linked with metabolic functions and immune infiltration.
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Affiliation(s)
- Fei Xu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yun Tong
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Wenjun Yang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yiyang Cai
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Meini Yu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Qingkang Meng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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48
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Lin KZ, Qiu Y, Roeder K. eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings. BMC Bioinformatics 2024; 25:113. [PMID: 38486150 PMCID: PMC10941434 DOI: 10.1186/s12859-024-05724-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. RESULTS We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. CONCLUSIONS eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
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Affiliation(s)
- Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Yixuan Qiu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, People's Republic of China
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
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49
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Zhou BW, Liu HM, Xu F, Jia XH. The role of macrophage polarization and cellular crosstalk in the pulmonary fibrotic microenvironment: a review. Cell Commun Signal 2024; 22:172. [PMID: 38461312 PMCID: PMC10924385 DOI: 10.1186/s12964-024-01557-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024] Open
Abstract
Pulmonary fibrosis (PF) is a progressive interstitial inflammatory disease with a high mortality rate. Patients with PF commonly experience a chronic dry cough and progressive dyspnoea for years without effective mitigation. The pathogenesis of PF is believed to be associated with dysfunctional macrophage polarization, fibroblast proliferation, and the loss of epithelial cells. Thus, it is of great importance and necessity to explore the interactions among macrophages, fibroblasts, and alveolar epithelial cells in lung fibrosis, as well as in the pro-fibrotic microenvironment. In this review, we discuss the latest studies that have investigated macrophage polarization and activation of non-immune cells in the context of PF pathogenesis and progression. Next, we discuss how profibrotic cellular crosstalk is promoted in the PF microenvironment by multiple cytokines, chemokines, and signalling pathways. And finally, we discuss the potential mechanisms of fibrogenesis development and efficient therapeutic strategies for the disease. Herein, we provide a comprehensive summary of the vital role of macrophage polarization in PF and its profibrotic crosstalk with fibroblasts and alveolar epithelial cells and suggest potential treatment strategies to target their cellular communication in the microenvironment.
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Affiliation(s)
- Bo-Wen Zhou
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Hua-Man Liu
- Department of General Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Fei Xu
- Department of Pneumology and Critical Care Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Xin-Hua Jia
- Department of Pneumology and Critical Care Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China.
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50
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Lee JY, Reyes NS, Ravishankar S, Zhou M, Krasilnikov M, Ringler C, Pohan G, Wilson C, Ang KKH, Wolters PJ, Tsukui T, Sheppard D, Arkin MR, Peng T. An in vivo screening platform identifies senolytic compounds that target p16INK4a+ fibroblasts in lung fibrosis. J Clin Invest 2024; 134:e173371. [PMID: 38451724 PMCID: PMC11060735 DOI: 10.1172/jci173371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
The appearance of senescent cells in age-related diseases has spurred the search for compounds that can target senescent cells in tissues, termed senolytics. However, a major caveat with current senolytic screens is the use of cell lines as targets where senescence is induced in vitro, which does not necessarily reflect the identity and function of pathogenic senescent cells in vivo. Here, we developed a new pipeline leveraging a fluorescent murine reporter that allows for isolation and quantification of p16Ink4a+ cells in diseased tissues. By high-throughput screening in vitro, precision-cut lung slice (PCLS) screening ex vivo, and phenotypic screening in vivo, we identified a HSP90 inhibitor, XL888, as a potent senolytic in tissue fibrosis. XL888 treatment eliminated pathogenic p16Ink4a+ fibroblasts in a murine model of lung fibrosis and reduced fibrotic burden. Finally, XL888 preferentially targeted p16INK4a-hi human lung fibroblasts isolated from patients with idiopathic pulmonary fibrosis (IPF), and reduced p16INK4a+ fibroblasts from IPF PCLS ex vivo. This study provides proof of concept for a platform where p16INK4a+ cells are directly isolated from diseased tissues to identify compounds with in vivo and ex vivo efficacy in mice and humans, respectively, and provides a senolytic screening platform for other age-related diseases.
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Affiliation(s)
- Jin Young Lee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Nabora S. Reyes
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Supriya Ravishankar
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Minqi Zhou
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Maria Krasilnikov
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Christian Ringler
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | | | | | | | - Paul J. Wolters
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Tatsuya Tsukui
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | - Dean Sheppard
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
| | | | - Tien Peng
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep
- Bakar Aging Research Institute, UCSF, San Francisco, California, USA
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