1
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Yang H, Wu X, Xiao X, Chen J, Yu X, Zhao W, Wang F. Elucidating the causal associations and mechanisms between circulating immune cells and idiopathic pulmonary fibrosis: new insights from Mendelian randomization and transcriptomics. Front Immunol 2025; 15:1437984. [PMID: 39896814 PMCID: PMC11782250 DOI: 10.3389/fimmu.2024.1437984] [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: 05/24/2024] [Accepted: 12/31/2024] [Indexed: 02/04/2025] Open
Abstract
Background Growing evidence indicates an association between circulating immune cell phenotypes and idiopathic pulmonary fibrosis (IPF). Although studies have attempted to elucidate the causal relationship between the two, further clarification of the specific mechanisms and causal linkages is warranted. Objective We aimed to conduct a two-sample Mendelian randomization (MR) analysis with transcriptomics data analysis to elucidate the causal relationship between circulating immune cells and IPF and to explore potential biomarkers. Methods We first explored the bidirectional causal association between IPF and immune cell phenotypes using two-sample MR analysis. Genome-wide association studies data for immune cell phenotype and IPF were obtained from publicly available databases. A standardized instrumental variable screening process was used to select single nucleotide polymorphisms (SNPs) for inclusion in the MR. Five methods represented by IVW were used to assess causal effects. Subsequently, SNP-nearest genes combined with the transcriptomics data of IPF were subjected to multiple bioinformatics analyses such as TIMER, WGCNA, functional enrichment analysis, protein-protein interaction analysis, and ROC to identify IPF biomarkers. Finally, the single-cell RNA sequencing (scRNA-seq) data was used to validate our findings by single-cell analysis. Results The MR study identified 27 immune cell phenotypes causally associated with IPF, of which 20 were associated with a decreased risk of developing IPF and 7 were associated with an increased risk. CTSB (AUC=0.98), IL10 (AUC=0.83), and AGER (AUC=0.87) were identified as promising biomarkers of IPF. Single cell analysis showed differences in CD14+ CD16+ monocytes, CD16+ monocytes and Granulocyte-monocyte progenito between the IPF group and the healthy control group. The three hub genes were highly expressed in three immune cell subsets of IPF patients. It underscores the potential feasibility of three genes as biomarkers. Conclusions Our study demonstrates the causal associations of specific immune cell phenotypes with IPF through genetic methods and identifies CTSB, IL10, and AGER as biomarkers of IPF through bioinformatics analysis. These findings provide guidance for future clinical and basic research.
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Affiliation(s)
| | | | | | | | | | | | - Fei Wang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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2
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Kim SJ, Cecchini MJ, Woo E, Jayawardena N, Passos DT, Dick FA, Mura M. Spatially resolved gene expression profiles of fibrosing interstitial lung diseases. Sci Rep 2024; 14:26470. [PMID: 39488596 PMCID: PMC11531500 DOI: 10.1038/s41598-024-77469-5] [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: 07/25/2024] [Accepted: 10/22/2024] [Indexed: 11/04/2024] Open
Abstract
Fibrosing interstitial lung diseases (ILDs) encompass a diverse range of scarring disorders that lead to progressive lung failure. Previous gene expression profiling studies focused on idiopathic pulmonary fibrosis (IPF) and bulk tissue samples. We employed digital spatial profiling to gain new insights into the spatial resolution of gene expression across distinct lung microenvironments (LMEs) in IPF, chronic hypersensitivity pneumonitis (CHP) and non-specific interstitial pneumonia (NSIP). We identified differentially expressed genes between LMEs within each condition, and across histologically similar regions between conditions. Uninvolved regions in IPF and CHP were distinct from normal controls, and displayed potential therapeutic targets. Hallmark LMEs of each condition retained distinct gene signatures, but these could not be reproduced in matched lung tissue samples. Based on these profiles and unsupervised clustering, we grouped previously unclassified ILD cases into NSIP or CHP. Overall, our work uniquely dissects gene expression profiles between LMEs within and across different types of fibrosing ILDs.
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Affiliation(s)
- Seung J Kim
- Interstitial Lung Disease Research Laboratory, Lawson Health Research Institute, London, ON, Canada.
- London Health Sciences Research Institute, London, ON, Canada.
| | - Matthew J Cecchini
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Elissa Woo
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Nathashi Jayawardena
- Interstitial Lung Disease Research Laboratory, Lawson Health Research Institute, London, ON, Canada
- London Health Sciences Research Institute, London, ON, Canada
| | - Daniel T Passos
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Health Sciences Research Institute, London, ON, Canada
- Verspeeten Family Cancer Centre, London, ON, Canada
| | - Frederick A Dick
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Health Sciences Research Institute, London, ON, Canada
- Verspeeten Family Cancer Centre, London, ON, Canada
| | - Marco Mura
- Interstitial Lung Disease Research Laboratory, Lawson Health Research Institute, London, ON, Canada
- Division of Respirology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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3
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Nemeth J, Skronska-Wasek W, Keppler S, Schundner A, Groß A, Schoenberger T, Quast K, El Kasmi KC, Ruppert C, Günther A, Frick M. Adiponectin suppresses stiffness-dependent, profibrotic activation of lung fibroblasts. Am J Physiol Lung Cell Mol Physiol 2024; 327:L487-L502. [PMID: 39104319 PMCID: PMC11482465 DOI: 10.1152/ajplung.00037.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/05/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible respiratory disease with limited therapeutic options. A hallmark of IPF is excessive fibroblast activation and extracellular matrix (ECM) deposition. The resulting increase in tissue stiffness amplifies fibroblast activation and drives disease progression. Dampening stiffness-dependent activation of fibroblasts could slow disease progression. We performed an unbiased, next-generation sequencing (NGS) screen to identify signaling pathways involved in stiffness-dependent lung fibroblast activation. Adipocytokine signaling was downregulated in primary lung fibroblasts (PFs) cultured on stiff matrices. Re-activating adipocytokine signaling with adiponectin suppressed stiffness-dependent activation of human PFs. Adiponectin signaling depended on CDH13 expression and p38 mitogen-activated protein kinase gamma (p38MAPKγ) activation. CDH13 expression and p38MAPKγ activation were strongly reduced in lungs from IPF donors. Our data suggest that adiponectin-signaling via CDH13 and p38MAPKγ activation suppresses profibrotic activation of fibroblasts in the lung. Targeting of the adiponectin signaling cascade may provide therapeutic benefits in IPF.NEW & NOTEWORTHY A hallmark of idiopathic pulmonary fibrosis (IPF) is excessive fibroblast activation and extracellular matrix (ECM) deposition. The resulting increase in tissue stiffness amplifies fibroblast activation and drives disease progression. Dampening stiffness-dependent activation of fibroblasts could slow disease progression. We found that activation of the adipocytokine signaling pathway halts and reverses stiffness-induced, profibrotic fibroblast activation. Specific targeting of this signaling cascade may therefore provide therapeutic benefits in IPF.
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Affiliation(s)
- Julia Nemeth
- Institute of General Physiology, Ulm University, Ulm, Germany
| | | | - Sophie Keppler
- Institute of General Physiology, Ulm University, Ulm, Germany
| | | | - Alexander Groß
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Clemens Ruppert
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Andreas Günther
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
- Center for Interstitial and Rare Lung Diseases, Justus-Liebig University Giessen, Giessen, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, Ulm, Germany
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4
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Bonatti M, Pitozzi V, Caruso P, Pontis S, Pittelli MG, Frati C, Mangiaracina C, Lagrasta CAM, Quaini F, Cantarella S, Ottonello S, Villetti G, Civelli M, Montanini B, Trevisani M. Time-course transcriptome analysis of a double challenge bleomycin-induced lung fibrosis rat model uncovers ECM homoeostasis-related translationally relevant genes. BMJ Open Respir Res 2023; 10:e001476. [PMID: 37730279 PMCID: PMC10510891 DOI: 10.1136/bmjresp-2022-001476] [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: 09/28/2022] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is an irreversible disorder with a poor prognosis. The incomplete understanding of IPF pathogenesis and the lack of accurate animal models is limiting the development of effective treatments. Thus, the selection of clinically relevant animal models endowed with similarities with the human disease in terms of lung anatomy, cell biology, pathways involved and genetics is essential. The bleomycin (BLM) intratracheal murine model is the most commonly used preclinical assay to evaluate new potential therapies for IPF. Here, we present the findings derived from an integrated histomorphometric and transcriptomic analysis to investigate the development of lung fibrosis in a time-course study in a BLM rat model and to evaluate its translational value in relation to IPF. METHODS Rats were intratracheally injected with a double dose of BLM (days 0-4) and sacrificed at days 7, 14, 21, 28 and 56. Histomorphometric analysis of lung fibrosis was performed on left lung sections. Transcriptome profiling by RNAseq was performed on the right lung lobes and results were compared with nine independent human gene-expression IPF studies. RESULTS The histomorphometric and transcriptomic analyses provided a detailed overview in terms of temporal gene-expression regulation during the establishment and repair of the fibrotic lesions. Moreover, the transcriptomic analysis identified three clusters of differentially coregulated genes whose expression was modulated in a time-dependent manner in response to BLM. One of these clusters, centred on extracellular matrix (ECM)-related process, was significantly correlated with histological parameters and gene sets derived from human IPF studies. CONCLUSIONS The model of lung fibrosis presented in this study lends itself as a valuable tool for preclinical efficacy evaluation of new potential drug candidates. The main finding was the identification of a group of persistently dysregulated genes, mostly related to ECM homoeostasis, which are shared with human IPF.
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Affiliation(s)
- Martina Bonatti
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Department of Medicine Solna (MedS) and Center for Molecular Medicine (CMM), Karolinska Institutet, Solna, Sweden
| | - Vanessa Pitozzi
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Paola Caruso
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Silvia Pontis
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | | | - Caterina Frati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | - Federico Quaini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Cantarella
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- DKFZ - German Cancer Research Center, Heidelberg, Germany
| | - Simone Ottonello
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gino Villetti
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Maurizio Civelli
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Barbara Montanini
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, Parma, Italy
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5
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Kircali MF, Turanli B. Idiopathic Pulmonary Fibrosis Molecular Substrates Revealed by Competing Endogenous RNA Regulatory Networks. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:381-392. [PMID: 37540140 DOI: 10.1089/omi.2023.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic disease of the lung with poor prognosis. Fibrosis results from remodeling of the interstitial tissue. A wide range of gene expression changes are observed, but the role of micro RNAs (miRNAs) and circular RNAs (circRNA) is still unclear. Therefore, this study aimed to establish an messenger RNA (mRNA)-miRNA-circRNA competing endogenous RNA (ceRNA) regulatory network to uncover novel molecular signatures using systems biology tools. Six datasets were used to determine differentially expressed genes (DEGs) and miRNAs (DEmiRNA). Accordingly, protein-protein, mRNA-miRNA, and miRNA-circRNA interactions were constructed. Modules were determined and further analyzed in the Drug Gene Budger platform to identify potential therapeutic compounds. We uncovered common 724 DEGs and 278 DEmiRNAs. In the protein-protein interaction network, TMPRSS4, ESR2, TP73, CLEC4E, and TP63 were identified as hub protein coding genes. The mRNA-miRNA interaction network revealed two modules composed of ADRA1A, ADRA1B, hsa-miR-484 and CDH2, TMPRSS4, and hsa-miR-543. The DEmiRNAs in the modules further analyzed to propose potential circRNA regulators in the ceRNA network. These results help deepen the understanding of the mechanisms of IPF. In addition, the molecular leads reported herein might inform future innovations in diagnostics and therapeutics research and development for IPF.
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Affiliation(s)
- Muhammed Fatih Kircali
- School of Medicine, Marmara University, Istanbul, Türkiye
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
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6
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Wan J, Zhang Z, Tian S, Huang S, Jin H, Liu X, Zhang W. Single cell study of cellular diversity and mutual communication in chronic heart failure and drug repositioning. Genomics 2022; 114:110322. [PMID: 35219850 DOI: 10.1016/j.ygeno.2022.110322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/05/2022] [Accepted: 02/19/2022] [Indexed: 01/14/2023]
Abstract
Non-cardiomyocytes (non-CMs) play an important role in the process of cardiac remodeling of chronic heart failure. The mechanism of non-CMs transit and interact with each other remains largely unknown. Here, we try to characterize the cellular landscape of non-CMs in mice with chronic heart failure by using single-cell RNA sequencing (scRNA-seq) and provide potential therapeutic hunts. Cellular and molecular analysis revealed that the most affected cellular types are mainly fibroblasts and endothelial cells. Specially, Fib_0 cluster, the most abundant cluster in fibroblasts, was the only increased one, enriched for collagen synthesis genes such as Adamts4 and Crem, which might be responsible for the fibrosis in cardiac remodeling. End_0 cluster in endothelial cells was also the most abundant and only increased one, which has an effect of blood vessel morphogenesis. Cell communication further confirmed that fibroblasts and endothelial cells are the driving hubs in chronic heart failure. Furthermore, using fibroblasts and endothelial cells as the entry point of CMap technology, histone deacetylation (HDAC) inhibitors and HSP inhibitors were identified as potential anti-heart failure new drugs, which should be evaluated in the future. The combined application of scRNA-seq and CMap might be an effective way to achieve drug repositioning.
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Affiliation(s)
- Jingjing Wan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China; School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Zhen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Si Huang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Huizi Jin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Liu
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Weidong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China; School of Pharmacy, Second Military Medical University, Shanghai, China.
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7
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Qian W, Xia S, Yang X, Yu J, Guo B, Lin Z, Wei R, Mao M, Zhang Z, Zhao G, Bai J, Han Q, Wang Z, Luo Q. Complex Involvement of the Extracellular Matrix, Immune Effect, and Lipid Metabolism in the Development of Idiopathic Pulmonary Fibrosis. Front Mol Biosci 2022; 8:800747. [PMID: 35174208 PMCID: PMC8841329 DOI: 10.3389/fmolb.2021.800747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/06/2021] [Indexed: 01/02/2023] Open
Abstract
Background and objective: Idiopathic pulmonary fibrosis (IPF) is an aggressive fibrotic pulmonary disease with spatially and temporally heterogeneous alveolar lesions. There are no early diagnostic biomarkers, limiting our understanding of IPF pathogenesis. Methods: Lung tissue from surgical lung biopsy of patients with early-stage IPF (n = 7), transplant-stage IPF (n = 2), and healthy controls (n = 6) were subjected to mRNA sequencing and verified by real-time quantitative PCR (RT-qPCR), immunohistochemistry, Western blot, and single-cell RNA sequencing (scRNA-Seq). Results: Three hundred eighty differentially expressed transcripts (DETs) were identified in IPF that were principally involved in extracellular matrix (ECM) remodeling, lipid metabolism, and immune effect. Of these DETs, 21 (DMD, MMP7, POSTN, ECM2, MMP13, FASN, FADS1, SDR16C5, ACAT2, ACSL1, CYP1A1, UGT1A6, CXCL13, CXCL5, CXCL14, IL5RA, TNFRSF19, CSF3R, S100A9, S100A8, and S100A12) were selected and verified by RT-qPCR. Differences in DMD, FASN, and MMP7 were also confirmed at a protein level. Analysis of scRNA-Seq was used to trace their cellular origin to determine which lung cells regulated them. The principal cell sources of DMD were ciliated cells, alveolar type I/II epithelial cells (AT cells), club cells, and alveolar macrophages (AMs); MMP7 derives from AT cells, club cells, and AMs, while FASN originates from AT cells, ciliated cells, and AMs. Conclusion: Our data revealed a comprehensive transcriptional mRNA profile of IPF and demonstrated that ECM remodeling, lipid metabolism, and immune effect were collaboratively involved in the early development of IPF.
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Affiliation(s)
- Weiping Qian
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Shu Xia
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xiaoyun Yang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaying Yu
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bingpeng Guo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhengfang Lin
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Wei
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Mengmeng Mao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ziyi Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Gui Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Junye Bai
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Qian Han
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Zhongfang Wang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Qun Luo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
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8
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Li X, Cai H, Cai Y, Zhang Q, Ding Y, Zhuang Q. Investigation of a Hypoxia-Immune-Related Microenvironment Gene Signature and Prediction Model for Idiopathic Pulmonary Fibrosis. Front Immunol 2021; 12:629854. [PMID: 34194423 PMCID: PMC8236709 DOI: 10.3389/fimmu.2021.629854] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background There is growing evidence found that the role of hypoxia and immune status in idiopathic pulmonary fibrosis (IPF). However, there are few studies about the role of hypoxia and immune status in the lung milieu in the prognosis of IPF. This study aimed to develop a hypoxia-immune-related prediction model for the prognosis of IPF. Methods Hypoxia and immune status were estimated with microarray data of a discovery cohort from the GEO database using UMAP and ESTIMATE algorithms respectively. The Cox regression model with the LASSO method was used for identifying prognostic genes and developing hypoxia-immune-related genes. Cibersort was used to evaluate the difference of 22 kinds of immune cell infiltration. Three independent validation cohorts from GEO database were used for external validation. Peripheral blood mononuclear cell (PBMC) and bronchoalveolar lavage fluid (BALF) were collected to be tested by Quantitative reverse transcriptase-PCR (qRT-PCR) and flow cytometry from 22 clinical samples, including 13 healthy controls, six patients with non-fibrotic pneumonia and three patients with pulmonary fibrosis. Results Hypoxia and immune status were significantly associated with the prognosis of IPF patients. High hypoxia and high immune status were identified as risk factors for overall survival. CD8+ T cell, activated CD4+ memory T cell, NK cell, activated mast cell, M1 and M0 macrophages were identified as key immune cells in hypoxia-immune-related microenvironment. A prediction model for IPF prognosis was established based on the hypoxia-immune-related one protective and nine risk DEGs. In the independent validation cohorts, the prognostic prediction model performed the significant applicability in peripheral whole blood, peripheral blood mononuclear cell, and lung tissue of IPF patients. The preliminary clinical specimen validation suggested the reliability of most conclusions. Conclusions The hypoxia-immune-based prediction model for the prognosis of IPF provides a new idea for prognosis and treatment.
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Affiliation(s)
- Xinyu Li
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China
| | - Haozheng Cai
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Yufeng Cai
- School of Life Science, Central South University, Changsha, China
| | - Quyan Zhang
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China
| | - Yinghe Ding
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China
| | - Quan Zhuang
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
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9
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Iasella CJ, Hoji A, Popescu I, Wei J, Snyder ME, Zhang Y, Xu W, Iouchmanov V, Koshy R, Brown M, Fung M, Langelier C, Lendermon EA, Dugger D, Shah R, Lee J, Johnson B, Golden J, Leard LE, Kleinhenz ME, Kilaru S, Hays SR, Singer JP, Sanchez PG, Morrell MR, Pilewski JM, Greenland JR, Chen K, McDyer JF. Type-1 immunity and endogenous immune regulators predominate in the airway transcriptome during chronic lung allograft dysfunction. Am J Transplant 2021; 21:2145-2160. [PMID: 33078555 PMCID: PMC8607839 DOI: 10.1111/ajt.16360] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/25/2023]
Abstract
Chronic lung allograft dysfunction (CLAD) remains the major complication limiting long-term survival among lung transplant recipients (LTRs). Limited understanding of CLAD immunopathogenesis and a paucity of biomarkers remain substantial barriers for earlier detection and therapeutic interventions for CLAD. We hypothesized the airway transcriptome would reflect key immunologic changes in disease. We compared airway brush-derived transcriptomic signatures in CLAD (n = 24) versus non-CLAD (n = 21) LTRs. A targeted assessment of the proteome using concomitant bronchoalveolar lavage (BAL) fluid for 24 cytokines/chemokines and alloimmune T cell responses was performed to validate the airway transcriptome. We observed an airway transcriptomic signature of differential genes expressed (DGEs) in CLAD marked by Type-1 immunity and striking upregulation of two endogenous immune regulators: indoleamine 2, 3 dioxygenase 1 (IDO-1) and tumor necrosis factor receptor superfamily 6B (TNFRSF6B). Advanced CLAD staging was associated with a more intense airway transcriptome signature. In a validation cohort using the identified signature, we found an area under the curve (AUC) of 0.77 for CLAD LTRs. Targeted proteomic analyses revealed a predominant Type-1 profile with detection of IFN-γ, TNF-α, and IL-1β as dominant CLAD cytokines, correlating with the airway transcriptome. The airway transcriptome provides novel insights into CLAD immunopathogenesis and biomarkers that may impact diagnosis of CLAD.
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Affiliation(s)
- Carlo J. Iasella
- Department of Pharmacy and Therapeutics, University of
Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania
| | - Aki Hoji
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Iulia Popescu
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Jianxin Wei
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Mark E. Snyder
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Yingze Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Wei Xu
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Vera Iouchmanov
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Ritchie Koshy
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Mark Brown
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Monica Fung
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Charles Langelier
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Elizabeth A. Lendermon
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Daniel Dugger
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Rupal Shah
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Joyce Lee
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Bruce Johnson
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Jeffrey Golden
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Lorriana E. Leard
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Mary Ellen Kleinhenz
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Silpa Kilaru
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Steven R. Hays
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Jonathan P. Singer
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Pablo G. Sanchez
- Department of Cardiothoracic Surgery, University of
Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Matthew R. Morrell
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - Joseph M. Pilewski
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - John R. Greenland
- Division of Pulmonary, Critical Care, Allergy and Sleep
Medicine, University of California San Francisco, San Francisco, California
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
| | - John F. McDyer
- Division of Pulmonary, Allergy, and Critical Care Medicine,
Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh,
Pennsylvania
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10
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Baciu C, Sage A, Zamel R, Shin J, Bai XH, Hough O, Bhat M, Yeung JC, Cypel M, Keshavjee S, Liu M. Transcriptomic investigation reveals donor-specific gene signatures in human lung transplants. Eur Respir J 2021; 57:13993003.00327-2020. [PMID: 33122335 DOI: 10.1183/13993003.00327-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/05/2020] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Transplantation of lungs from donation after circulatory death (DCD) in addition to donation after brain death (DBD) became routine worldwide to address the global organ shortage. The development of ex vivo lung perfusion (EVLP) for donor lung assessment and repair contributed to the increased use of DCD lungs. We hypothesise that a better understanding of the differences between lungs from DBD and DCD donors, and between EVLP and directly transplanted (non-EVLP) lungs, will lead to the discovery of the injury-specific targets for donor lung repair and reconditioning. METHODS Tissue biopsies from human DBD (n=177) and DCD (n=65) donor lungs, assessed with or without EVLP, were collected at the end of cold ischaemic time. All samples were processed with microarray assays. Gene expression, network and pathway analyses were performed using R, Ingenuity Pathway Analysis and STRING. Results were validated with protein assays, multiple logistic regression and 10-fold cross-validation. RESULTS Our analyses showed that lungs from DBD donors have upregulation of inflammatory cytokines and pathways. In contrast, DCD lungs display a transcriptome signature of pathways associated with cell death, apoptosis and necrosis. Network centrality revealed specific drug targets to rehabilitate DBD lungs. Moreover, in DBD lungs, tumour necrosis factor receptor-1/2 signalling pathways and macrophage migration inhibitory factor-associated pathways were activated in the EVLP group. A panel of genes that differentiate the EVLP from the non-EVLP group in DBD lungs was identified. CONCLUSION The examination of gene expression profiling indicates that DBD and DCD lungs have distinguishable biological transcriptome signatures.
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Affiliation(s)
- Cristina Baciu
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Andrew Sage
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Ricardo Zamel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Jason Shin
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Xiao-Hui Bai
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Olivia Hough
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Mamatha Bhat
- Multiorgan Transplant Program, University Health Network, Toronto, ON, Canada.,Division of Gastroenterology, University of Toronto, Toronto, ON, Canada
| | - Jonathan C Yeung
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Multiorgan Transplant Program, University Health Network, Toronto, ON, Canada.,Toronto Lung Transplant Program, Dept of Surgery, University of Toronto, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Multiorgan Transplant Program, University Health Network, Toronto, ON, Canada.,Toronto Lung Transplant Program, Dept of Surgery, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shaf Keshavjee
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Multiorgan Transplant Program, University Health Network, Toronto, ON, Canada.,Toronto Lung Transplant Program, Dept of Surgery, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,These authors share senior authorship
| | - Mingyao Liu
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Multiorgan Transplant Program, University Health Network, Toronto, ON, Canada.,Toronto Lung Transplant Program, Dept of Surgery, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,These authors share senior authorship
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11
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McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019; 4:131597. [PMID: 31600171 PMCID: PMC6948862 DOI: 10.1172/jci.insight.131597] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary fibrosis (IPF) and 6 control lungs. Extent of fibrosis in each sample was assessed by microCT-measured alveolar surface density (ASD) and confirmed by histology. Regulatory gene expression networks were identified using linear mixed-effect models and dynamic regulatory events miner (DREM). Differential gene expression analysis identified a core set of genes increased or decreased before fibrosis was histologically evident that continued to change with advanced fibrosis. DREM generated a systems biology model (www.sb.cs.cmu.edu/IPFReg) that identified progressively divergent gene expression tracks with microRNAs and transcription factors that specifically regulate mild or advanced fibrosis. We confirmed model predictions by demonstrating that expression of POU2AF1, previously unassociated with lung fibrosis but proposed by the model as regulator, is increased in B lymphocytes in IPF lungs and that POU2AF1-knockout mice were protected from bleomycin-induced lung fibrosis. Our results reveal distinct regulation of gene expression changes in IPF tissue that remained structurally normal compared with moderate or advanced fibrosis and suggest distinct regulatory mechanisms for each stage.
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Affiliation(s)
- John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Siddhartha Jain
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Stijn E. Verleden
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Jose Herazo-Maya
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Milica Vukmirovic
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Argyrios Tzouvelekis
- Division of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Naoya Tanabe
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Fanny Chu
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johny Verschakelen
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven,Connecticut, USA
- Pathology and Laboratory Medicine Service, VA CT HealthCare System, West Haven, Connecticut, USA
| | - Dimitris V. Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junke Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jun Ding
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Karen Maes
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Laurens De Sadeleer
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robin Vos
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Arne Neyrinck
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ziv Bar-Joseph
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | | | - Wim A. Wuyts
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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Kassam I, Wu Y, Yang J, Visscher PM, McRae AF. Tissue-specific sex differences in human gene expression. Hum Mol Genet 2019; 28:2976-2986. [PMID: 31044242 PMCID: PMC6736104 DOI: 10.1093/hmg/ddz090] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/12/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Despite extensive sex differences in human complex traits and disease, the male and female genomes differ only in the sex chromosomes. This implies that most sex-differentiated traits are the result of differences in the expression of genes that are common to both sexes. While sex differences in gene expression have been observed in a range of different tissues, the biological mechanisms for tissue-specific sex differences (TSSDs) in gene expression are not well understood. A total of 30 640 autosomal and 1021 X-linked transcripts were tested for heterogeneity in sex difference effect sizes in n = 617 individuals across 40 tissue types in Genotype-Tissue Expression (GTEx). This identified 65 autosomal and 66 X-linked TSSD transcripts (corresponding to unique genes) at a stringent significance threshold. Results for X-linked TSSD transcripts showed mainly concordant direction of sex differences across tissues and replicate previous findings. Autosomal TSSD transcripts had mainly discordant direction of sex differences across tissues. The top cis-expression quantitative trait loci (eQTLs) across tissues for autosomal TSSD transcripts are located a similar distance away from the nearest androgen and estrogen binding motifs and the nearest enhancer, as compared to cis-eQTLs for transcripts with stable sex differences in gene expression across tissue types. Enhancer regions that overlap top cis-eQTLs for TSSD transcripts, however, were found to be more dispersed across tissues. These observations suggest that androgen and estrogen regulatory elements in a cis region may play a common role in sex differences in gene expression, but TSSD in gene expression may additionally be due to causal variants located in tissue-specific enhancer regions.
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Affiliation(s)
| | - Yang Wu
- Institute for Molecular Bioscience
| | - Jian Yang
- Institute for Molecular Bioscience
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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13
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Sivakumar P, Thompson JR, Ammar R, Porteous M, McCoubrey C, Cantu E, Ravi K, Zhang Y, Luo Y, Streltsov D, Beers MF, Jarai G, Christie JD. RNA sequencing of transplant-stage idiopathic pulmonary fibrosis lung reveals unique pathway regulation. ERJ Open Res 2019; 5:00117-2019. [PMID: 31423451 PMCID: PMC6689672 DOI: 10.1183/23120541.00117-2019] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/15/2019] [Indexed: 11/05/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), the scarring of lung parenchyma resulting in the loss of lung function, remains a fatal disease with a significant unmet medical need. Patients with severe IPF often develop acute exacerbations resulting in the rapid deterioration of lung function, requiring transplantation. Understanding the pathophysiological mechanisms contributing to IPF is key to develop novel therapeutic approaches for end-stage disease. We report here RNA-sequencing analyses of lung tissues from a cohort of patients with transplant-stage IPF (n=36), compared with acute lung injury (ALI) (n=11) and nondisease controls (n=19), that reveal a robust gene expression signature unique to end-stage IPF. In addition to extracellular matrix remodelling pathways, we identified pathways associated with T-cell infiltration/activation, tumour development, and cholesterol homeostasis, as well as novel alternatively spliced transcripts that are differentially regulated in the advanced IPF lung versus ALI or nondisease controls. Additionally, we show a subset of genes that are correlated with percent predicted forced vital capacity and could reflect disease severity. Our results establish a robust transcriptomic fingerprint of an advanced IPF lung that is distinct from previously reported microarray signatures of moderate, stable or progressive IPF and identifies hitherto unknown candidate targets and pathways for therapeutic intervention in late-stage IPF as well as biomarkers to characterise disease progression and enable patient stratification.
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Affiliation(s)
- Pitchumani Sivakumar
- Fibrosis Translational Research and Development, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - John Ryan Thompson
- Translational Bioinformatics, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Ron Ammar
- Translational Bioinformatics, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Mary Porteous
- Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Carly McCoubrey
- Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Edward Cantu
- Surgery Dept, University of Pennsylvania, Philadelphia PA, USA
| | - Kandasamy Ravi
- Integrated Genomics, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Yan Zhang
- Integrated Genomics, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Yi Luo
- Clinical Biomarkers, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Denis Streltsov
- Fibrosis Translational Research and Development, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Michael F Beers
- Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia PA, USA.,PENN Center for Pulmonary Biology, University of Pennsylvania, Philadelphia PA, USA
| | - Gabor Jarai
- Fibrosis Translational Research and Development, Bristol-Myers Squibb Research and Development, Princeton NJ, USA
| | - Jason D Christie
- Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia PA, USA.,PENN Center for Pulmonary Biology, University of Pennsylvania, Philadelphia PA, USA
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14
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Krauss E, Gehrken G, Drakopanagiotakis F, Tello S, Dartsch RC, Maurer O, Windhorst A, von der Beck D, Griese M, Seeger W, Guenther A. Clinical characteristics of patients with familial idiopathic pulmonary fibrosis (f-IPF). BMC Pulm Med 2019; 19:130. [PMID: 31319833 PMCID: PMC6637501 DOI: 10.1186/s12890-019-0895-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/11/2019] [Indexed: 11/29/2022] Open
Abstract
Background The aim of this study was to analyze the relative frequency, clinical characteristics, disease onset and progression in f-IPF vs. sporadic IPF (s-IPF). Methods Familial IPF index patients and their family members were recruited into the European IPF registry/biobank (eurIPFreg) at the Universities of Giessen and Marburg (UGMLC). Initially, we employed wide range criteria of f-IPF (e.g. relatives who presumably died of some kind of parenchymal lung disease). After narrowing down the search to occurrence of idiopathic interstitial pneumonia (IIP) in at least one first grade relative, 28 index patients were finally identified, prospectively interviewed and examined. Their family members were phenotyped with establishment of pedigree charts. Results Within the 28 IPF families, overall 79 patients with f-IPF were identified. In the same observation period, 286 f-IIP and s-IIP patients were recruited into the eurIPFreg at our UGMLC sites, corresponding to a familial versus s-IPF of 9.8%. The both groups showed no difference in demographics (61 vs. 79% males), smoking history, and exposure to any environmental triggers known to cause lung fibrosis. The f-IPF group differed by an earlier age at the onset of the disease (55.4 vs. 63.2 years; p < 0.001). On average, the f-IPF patients presented a significantly milder extent of functional impairment at the time point of inclusion vs. the s-IPF group (FVC 75% pred. vs. FVC 62% pred., p = 0.011). In contrast, the decline in FVC was found to be faster in the f-IPF vs. the s-IPF group (4.94% decline in 6 months in f-IPF vs. 2.48% in s-IPF, p = 0.12). The average age of death in f-IPF group was 67 years vs. 71.8 years in s-IPF group (p = 0.059). The f-IIP group displayed diverse inheritance patterns, mostly autosomal-dominant with variable penetrance. In the f-IPF, the younger generations showed a tendency for earlier manifestation of IPF vs. the older generation (58 vs. 66 years, p = 0.013). Conclusions The 28 f-IPF index patients presented an earlier onset and more aggressive natural course of the disease. The disease seems to affect consecutive generations at a younger age. Trial registration Nr. NCT02951416http://www.www.clinicaltrials.gov
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Affiliation(s)
- Ekaterina Krauss
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany
| | - Godja Gehrken
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany
| | - Fotios Drakopanagiotakis
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany
| | - Silke Tello
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany
| | - Ruth C Dartsch
- Agaplesion Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
| | - Olga Maurer
- Agaplesion Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
| | - Anita Windhorst
- Department of Medical Statistics, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Daniel von der Beck
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany
| | - Matthias Griese
- Children University Hospital, Campus Hauner, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Werner Seeger
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany.,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany.,Cardio-Pulmonary Institute, Giessen, Germany
| | - Andreas Guenther
- Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), European IPF Registry (eurIPFreg), Klinikstrasse 36, 35392, Giessen, Germany. .,European IPF Registry & Biobank (eurIPFreg), Giessen, Germany. .,Cardio-Pulmonary Institute, Giessen, Germany. .,Agaplesion Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany.
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15
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El Amrani K, Alanis-Lobato G, Mah N, Kurtz A, Andrade-Navarro MA. Detection of condition-specific marker genes from RNA-seq data with MGFR. PeerJ 2019; 7:e6970. [PMID: 31179178 PMCID: PMC6542349 DOI: 10.7717/peerj.6970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/07/2019] [Indexed: 12/19/2022] Open
Abstract
The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines.
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Affiliation(s)
- Khadija El Amrani
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Nancy Mah
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Kurtz
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
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16
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Ammar R, Sivakumar P, Jarai G, Thompson JR. A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection. PLoS One 2019; 14:e0215565. [PMID: 30998768 PMCID: PMC6472794 DOI: 10.1371/journal.pone.0215565] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease affecting ~5 million people globally. We have constructed an accurate model of IPF disease status using elastic net regularized regression on clinical gene expression data. Leveraging whole transcriptome microarray data from 230 IPF and 89 control samples from Yang et al. (2013), sourced from the Lung Tissue Research Consortium (LTRC) and National Jewish Health (NJH) cohorts, we identify an IPF gene expression signature. We performed optimal feature selection to reduce the number of transcripts required by our model to a parsimonious set of 15. This signature enables our model to accurately separate IPF patients from controls. Our model outperforms existing published models when tested with multiple independent clinical cohorts. Our study underscores the utility of elastic nets for gene signature/panel selection which can be used for the construction of a multianalyte biomarker of disease. We also filter the gene sets used for model input to construct a model reliant on secreted proteins. Using this approach, we identify the preclinical bleomycin rat model that is most congruent with human disease at day 21 post-bleomycin administration, contrasting with earlier timepoints suggested by other studies.
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Affiliation(s)
- Ron Ammar
- Translational Bioinformatics, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, United States of America
- * E-mail:
| | - Pitchumani Sivakumar
- Fibrosis, Translational Research & Development, Bristol-Myers Squibb, Princeton, NJ, United States of America
| | - Gabor Jarai
- Fibrosis, Translational Research & Development, Bristol-Myers Squibb, Princeton, NJ, United States of America
| | - John Ryan Thompson
- Translational Bioinformatics, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, United States of America
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17
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Burman A, Kropski JA, Calvi CL, Serezani AP, Pascoalino BD, Han W, Sherrill T, Gleaves L, Lawson WE, Young LR, Blackwell TS, Tanjore H. Localized hypoxia links ER stress to lung fibrosis through induction of C/EBP homologous protein. JCI Insight 2018; 3:99543. [PMID: 30135303 PMCID: PMC6141182 DOI: 10.1172/jci.insight.99543] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 07/05/2018] [Indexed: 02/06/2023] Open
Abstract
ER stress in type II alveolar epithelial cells (AECs) is common in idiopathic pulmonary fibrosis (IPF), but the contribution of ER stress to lung fibrosis is poorly understood. We found that mice deficient in C/EBP homologous protein (CHOP), an ER stress-regulated transcription factor, were protected from lung fibrosis and AEC apoptosis in 3 separate models where substantial ER stress was identified. In mice treated with repetitive intratracheal bleomycin, we identified localized hypoxia in type II AECs as a potential mechanism explaining ER stress. To test the role of hypoxia in lung fibrosis, we treated mice with bleomycin, followed by exposure to 14% O2, which exacerbated ER stress and lung fibrosis. Under these experimental conditions, CHOP-/- mice, but not mice with epithelial HIF (HIF1/HIF2) deletion, were protected from AEC apoptosis and fibrosis. In vitro studies revealed that CHOP regulates hypoxia-induced apoptosis in AECs via the inositol-requiring enzyme 1α (IRE1α) and the PKR-like ER kinase (PERK) pathways. In human IPF lungs, CHOP and hypoxia markers were both upregulated in type II AECs, supporting a conclusion that localized hypoxia results in ER stress-induced CHOP expression, thereby augmenting type II AEC apoptosis and potentiating lung fibrosis.
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Affiliation(s)
- Ankita Burman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan A. Kropski
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
| | - Carla L. Calvi
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Ana P. Serezani
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bruno D. Pascoalino
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Wei Han
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Taylor Sherrill
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Linda Gleaves
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - William E. Lawson
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
| | - Lisa R. Young
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Pediatrics, Division of Pulmonary Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy S. Blackwell
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
| | - Harikrishna Tanjore
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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18
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Imai-Matsushima A, Martin-Sancho L, Karlas A, Imai S, Zoranovic T, Hocke AC, Mollenkopf HJ, Berger H, Meyer TF. Long-Term Culture of Distal Airway Epithelial Cells Allows Differentiation Towards Alveolar Epithelial Cells Suited for Influenza Virus Studies. EBioMedicine 2018; 33:230-241. [PMID: 29937069 PMCID: PMC6085545 DOI: 10.1016/j.ebiom.2018.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/24/2022] Open
Abstract
As the target organ for numerous pathogens, the lung epithelium exerts critical functions in health and disease. However, research in this area has been hampered by the quiescence of the alveolar epithelium under standard culture conditions. Here, we used human distal airway epithelial cells (DAECs) to generate alveolar epithelial cells. Long-term, robust growth of human DAECs was achieved using co-culture with feeder cells and supplementation with epidermal growth factor (EGF), Rho-associated protein kinase inhibitor Y27632, and the Notch pathway inhibitor dibenzazepine (DBZ). Removal of feeders and priming with DBZ and a cocktail of lung maturation factors prevented the spontaneous differentiation into airway club cells and instead induced differentiation to alveolar epithelial cells. We successfully transferred this approach to chicken distal airway cells, thus generating a zoonotic infection model that enables studies on influenza A virus replication. These cells are also amenable for gene knockdown using RNAi technology, indicating the suitability of the model for mechanistic studies into lung function and disease.
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Affiliation(s)
- Aki Imai-Matsushima
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Laura Martin-Sancho
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Alexander Karlas
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Seiichiro Imai
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Tamara Zoranovic
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Andreas C Hocke
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine, Berlin, Germany
| | - Hans-Joachim Mollenkopf
- Max Planck Institute for Infection Biology, Core Facility Microarray/Genomics, Berlin, Germany
| | - Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
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19
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Greiffo FR, Eickelberg O, Fernandez IE. Systems medicine advances in interstitial lung disease. Eur Respir Rev 2017; 26:26/145/170021. [PMID: 28954764 DOI: 10.1183/16000617.0021-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 01/17/2023] Open
Abstract
Fibrotic lung diseases involve subject-environment interactions, together with dysregulated homeostatic processes, impaired DNA repair and distorted immune functions. Systems medicine-based approaches are used to analyse diseases in a holistic manner, by integrating systems biology platforms along with clinical parameters, for the purpose of understanding disease origin, progression, exacerbation and remission.Interstitial lung diseases (ILDs) refer to a heterogeneous group of complex fibrotic diseases. The increase of systems medicine-based approaches in the understanding of ILDs provides exceptional advantages by improving diagnostics, unravelling phenotypical differences, and stratifying patient populations by predictable outcomes and personalised treatments. This review discusses the state-of-the-art contributions of systems medicine-based approaches in ILDs over the past 5 years.
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Affiliation(s)
- Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany.,Division of Respiratory Sciences and Critical Care Medicine, Dept of Medicine, University of Colorado, Denver, CO, USA
| | - Isis E Fernandez
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
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20
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Yang C, Chen P, Zhang W, Du H. Bioinformatics-Driven New Immune Target Discovery in Disease. Scand J Immunol 2016; 84:130-6. [DOI: 10.1111/sji.12452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/11/2022]
Affiliation(s)
- C. Yang
- School of Chemistry and Biological Engineering; University of Science and Technology Beijing; Beijing China
| | - P. Chen
- School of Chemistry and Biological Engineering; University of Science and Technology Beijing; Beijing China
| | - W. Zhang
- School of Chemistry and Biological Engineering; University of Science and Technology Beijing; Beijing China
| | - H. Du
- School of Chemistry and Biological Engineering; University of Science and Technology Beijing; Beijing China
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21
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Nair GB, Matela A, Kurbanov D, Raghu G. Newer developments in idiopathic pulmonary fibrosis in the era of anti-fibrotic medications. Expert Rev Respir Med 2016; 10:699-711. [PMID: 27094006 DOI: 10.1080/17476348.2016.1177461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease with a fatal prognosis. Over the last decade, the concepts in pathobiology of pulmonary fibrosis have shifted from a model of chronic inflammation to dysregulated fibroproliferative repair in genetically predisposed patients. Although new breakthrough treatments are now available that slow the progression of the disease, several newer anti-inflammatory and anti-fibrotic drugs are under investigation. Patients with IPF often have coexistent conditions; prompt detection and interventions of which may improve the overall outcome of patients with IPF. Here, we summarize the present understanding of pathogenesis of IPF and treatment options for IPF in the current landscape of new anti-fibrotic treatment options.
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Affiliation(s)
- Girish B Nair
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA.,b Department of Medicine , SUNY Stony Brook School of Medicine , NY , USA
| | - Ajsza Matela
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA
| | - Daniel Kurbanov
- a Division of Pulmonary & Critical Care Medicine , Winthrop-University Hospital , Mineola , NY , USA
| | - Ganesh Raghu
- c Department of Medicine & Lab Medicine (Adjunct), Division of Pulmonary & Critical Care Medicine , University of Washington , Seattle , WA , USA
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