Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
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Jonathan A. Kropski | Timothy S. Blackwell | Nicholas E. Banovich | Latha Raju | James E. Loyd | J. Loyd | L. Ware | J. Kropski | T. Blackwell | A. Habermann | Chase J. Taylor | C. Jetter | N. Banovich | J. Sucre | L. Bui | A. Gutierrez | J. Roberson | S. Yahn | N. Winters | C. Calvi | L. Peter | M. Chung | Latha Raju | G. Ding | L. Wood | B. Richmond | A. Serezani | Simon B. Mallal | M. Bacchetta | R. Bremner | R. Walia | Wyatt J. McDonnell | Lorraine B. Ware | Arun C. Habermann | Austin J. Gutierrez | Linh T. Bui | Stephanie L. Yahn | Nichelle I. Winters | Carla L. Calvi | Lance Peter | Mei-I Chung | Christopher Jetter | Jamie Roberson | Guixiao Ding | Lori Wood | Jennifer MS Sucre | Bradley W. Richmond | Ana P. Serezani | Matthew J. Bacchetta | Ciara M. Shaver | Ross Bremner | Rajat Walia | C. Shaver | Simon Mallal | L. T. Bui
[1] A. Shilatifard,et al. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis , 2019, American journal of respiratory and critical care medicine.
[2] Paul J. Hoffman,et al. Comprehensive Integration of Single-Cell Data , 2018, Cell.
[3] Gregory W. Schwartz,et al. TooManyCells identifies and visualizes relationships of single-cell clades , 2019, Nature Methods.
[4] D. Rifkin,et al. The integrin αVβ6 binds and activates latent TGFβ3 , 2002 .
[5] Naftali Kaminski,et al. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. , 2006, American journal of respiratory and critical care medicine.
[6] J. Kropski,et al. Idiopathic pulmonary fibrosis: Epithelial-mesenchymal interactions and emerging therapeutic targets. , 2018, Matrix biology : journal of the International Society for Matrix Biology.
[7] S. Rosselot. Idiopathic pulmonary fibrosis. , 2014, Nursing standard (Royal College of Nursing (Great Britain) : 1987).
[8] Shengshou Hu,et al. Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction , 2019, Nature Genetics.
[9] Shandra L. Protzko,et al. An official American Thoracic Society/European Respiratory Society statement: Update of the international multidisciplinary classification of the idiopathic interstitial pneumonias. , 2013, American journal of respiratory and critical care medicine.
[10] J. W. Lee,et al. Extensive phenotyping of individuals at risk for familial interstitial pneumonia reveals clues to the pathogenesis of interstitial lung disease. , 2015, American journal of respiratory and critical care medicine.
[11] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[12] Ed Y. Tom,et al. Classification of usual interstitial pneumonia in patients with interstitial lung disease: assessment of a machine learning approach using high-dimensional transcriptional data. , 2015, The Lancet. Respiratory medicine.
[13] C. Nguyên,et al. Interactions Between β-Catenin and Transforming Growth Factor-β Signaling Pathways Mediate Epithelial-Mesenchymal Transition and Are Dependent on the Transcriptional Co-activator cAMP-response Element-binding Protein (CREB)-binding Protein (CBP)* , 2012, The Journal of Biological Chemistry.
[14] Sandrine Dudoit,et al. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets , 2018, bioRxiv.
[15] T. Deuse,et al. Distal Airway Stem Cells are Essential for Lung Regeneration. , 2015, Transplantation.
[16] Sandrine Dudoit,et al. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets , 2018 .
[17] A. Oberg,et al. Cellular senescence mediates fibrotic pulmonary disease , 2017, Nature Communications.
[18] J. Ajani,et al. iTALK: an R Package to Characterize and Illustrate Intercellular Communication , 2019, bioRxiv.
[19] Allon M. Klein,et al. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.
[20] Jonathan Haines,et al. Heterozygosity for a surfactant protein C gene mutation associated with usual interstitial pneumonitis and cellular nonspecific interstitial pneumonitis in one kindred. , 2002, American journal of respiratory and critical care medicine.
[21] B. Liu,et al. MicroRNA-338-3 p suppresses metastasis of lung cancer cells by targeting the EMT regulator Sox 4 , 2016 .
[22] Xiaoming Liu,et al. The Role of Sox Genes in Lung Morphogenesis and Cancer , 2012, International journal of molecular sciences.
[23] D. Sheppard,et al. Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix , 2006, Proceedings of the National Academy of Sciences.
[24] R. Satija,et al. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression , 2019, Genome Biology.
[25] Evan Z. Macosko,et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.
[26] Kevin Weiss,et al. Acellular normal and fibrotic human lung matrices as a culture system for in vitro investigation. , 2012, American journal of respiratory and critical care medicine.
[27] Ivana V. Yang,et al. A Common MUC 5 B Promoter Polymorphism and Pulmonary Fibrosis , 2011 .
[28] Jing Wang,et al. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs , 2019, Nucleic Acids Res..
[29] A. Nicholson,et al. Induction of epithelial-mesenchymal transition in alveolar epithelial cells by transforming growth factor-beta1: potential role in idiopathic pulmonary fibrosis. , 2005, The American journal of pathology.
[30] F. Sciurba,et al. MMP 1 and MMP 7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis , 2008 .
[31] N. Neff,et al. Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seq , 2014, Nature.
[32] Dawei Sun,et al. MicroRNA-138 Inhibits Cell Growth, Invasion, and EMT of Non-Small Cell Lung Cancer via SOX4/p53 Feedback Loop. , 2018, Oncology research.
[33] Fabian J Theis,et al. A cellular census of human lungs identifies novel cell states in health and in asthma , 2019, Nature Medicine.
[34] S. Herold,et al. Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia in vivo , 2019, The EMBO journal.
[35] Michael J. Cronce,et al. Multiple stromal populations contribute to pulmonary fibrosis without evidence for epithelial to mesenchymal transition , 2011, Proceedings of the National Academy of Sciences.
[36] Mark R. Looney,et al. Lineage-negative Progenitors Mobilize to Regenerate Lung Epithelium after Major Injury , 2014, Nature.
[37] M. Sander,et al. Sox9 plays multiple roles in the lung epithelium during branching morphogenesis , 2013, Proceedings of the National Academy of Sciences.
[38] Michael J. Cronce,et al. Type 2 alveolar cells are stem cells in adult lung. , 2013, The Journal of clinical investigation.
[39] Matthew J. Vincent,et al. p63+Krt5+ distal airway stem cells are essential for lung regeneration , 2014, Nature.
[40] Ivana V. Yang,et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. , 2011, The New England journal of medicine.
[41] M. Selman,et al. Idiopathic pulmonary fibrosis: new insights in its pathogenesis. , 2002, The international journal of biochemistry & cell biology.
[42] T. Jacks,et al. Identification of Bronchioalveolar Stem Cells in Normal Lung and Lung Cancer , 2005, Cell.
[43] Christoph Hafemeister,et al. Comprehensive integration of single cell data , 2018, bioRxiv.
[44] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[45] Stephen R Quake,et al. Microfluidic single-cell mRNA isolation and analysis. , 2006, Analytical chemistry.
[46] Naftali Kaminski,et al. A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis. , 2015, American journal of respiratory cell and molecular biology.
[47] Jianhong Ou,et al. Persistence of a novel regeneration-associated transitional cell state in pulmonary fibrosis , 2019 .
[48] B. Stripp,et al. Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis. , 2016, JCI insight.
[49] T. Blackwell,et al. Alveolar Epithelial Cells Undergo Epithelial-to-Mesenchymal Transition in Response to Endoplasmic Reticulum Stress* , 2011, The Journal of Biological Chemistry.
[50] T. Oury,et al. Animal models of fibrotic lung disease. , 2013, American journal of respiratory cell and molecular biology.
[51] D. Sheppard. Epithelial-mesenchymal interactions in fibrosis and repair. Transforming growth factor-β activation by epithelial cells and fibroblasts. , 2015, Annals of the American Thoracic Society.
[52] N. Kaminski,et al. The integrin alpha v beta 6 binds and activates latent TGF beta 1: a mechanism for regulating pulmonary inflammation and fibrosis. , 1999, Cell.
[53] Brent S. Pedersen,et al. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis , 2013, Nature Genetics.
[54] P. Wolters,et al. Alveolar epithelial cells express mesenchymal proteins in patients with idiopathic pulmonary fibrosis. , 2011, American journal of physiology. Lung cellular and molecular physiology.
[55] J. Loyd,et al. The genetic basis of idiopathic pulmonary fibrosis , 2015, European Respiratory Journal.
[56] Jin Woo Song,et al. Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. , 2009, American journal of respiratory and critical care medicine.
[57] Jianming Xu,et al. Local lung hypoxia determines epithelial fate decisions during alveolar regeneration , 2017, Nature Cell Biology.
[58] E. Neilson,et al. Contribution of epithelial-derived fibroblasts to bleomycin-induced lung fibrosis. , 2009, American journal of respiratory and critical care medicine.
[59] Erik Sundström,et al. RNA velocity of single cells , 2018, Nature.
[60] Burkhard Tümmler,et al. Faculty Opinions recommendation of A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. , 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.
[61] Naftali Kaminski,et al. Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis , 2019, bioRxiv.
[62] Fabian J Theis,et al. Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration , 2019, bioRxiv.
[63] Russell B. Fletcher,et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics , 2017, BMC Genomics.
[64] Ivana V. Yang,et al. Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis , 2013, Thorax.
[65] C. Piantadosi,et al. ABL kinase inhibition promotes lung regeneration through expansion of an SCGB1A1+ SPC+ cell population following bacterial pneumonia , 2019, Proceedings of the National Academy of Sciences.
[66] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[67] Grace X. Y. Zheng,et al. Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.
[68] N. Grishin,et al. Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. , 2009, American journal of human genetics.
[69] Manuel Serrano,et al. Cellular senescence: from physiology to pathology , 2014, Nature Reviews Molecular Cell Biology.
[70] W-B Hu,et al. MicroRNA-204 targets SOX4 to inhibit metastasis of lung adenocarcinoma. , 2019, European review for medical and pharmacological sciences.
[71] Irving L. Weissman,et al. A molecular cell atlas of the human lung from single cell RNA sequencing , 2019, Nature.
[72] Naftali Kaminski,et al. MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis , 2008, PLoS medicine.