Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis

Paul Andrew Reyfman, James McCauley Walter, Nikita Joshi, Kishore R. Anekalla, Alexandra C. McQuattie-Pimentel, Stephen Chiu, Ramiro Fernandez, Mahzad Akbarpour, Ching I. Chen, Ziyou Ren, Rohan Verma, Hiam Abdala-Valencia, Kiwon Nam, Monica Chi, Seung Hye Han, Francisco J. Gonzalez-Gonzalez, Saul Soberanes, Satoshi Watanabe, Kinola J.N. Williams, Annette S. FlozakTrevor T. Nicholson, Vince K. Morgan, Deborah Rachelle Winter, Monique Hinchcliff, Cara L. Hrusch, Robert D. Guzy, Catherine A. Bonham, Anne I. Sperling, Remzi Bag, Robert B. Hamanaka, Gökhan M. Mutlu, Anjana V Yeldandi, Stacy A. Marshall, Ali Shilatifard, Luis A N Amaral, Harris R Perlman, Jacob I Sznajder, A. Christine Argento, Colin Thomas Gillespie, Jane Dematte, Manu Jain, Benjamin Singer, Karen M Ridge, Anna P Lam, Ankit Bharat, Sangeeta Maruti Bhorade, Cara Gottardi, GR Scott Budinger, Alexander Misharin*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

504 Scopus citations


Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, nove population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to nonoverlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. We developed a web-based tool to explore these data. Conclusions: We generated a single-cell atlas of pulmonary fibrosis. Using this atlas, we demonstrated heterogeneity within alveolar macrophages and epithelial cells from subjects with pulmonary fibrosis. These results support the feasibility of discovery-based approaches using next-generation sequencing technologies to identify signaling pathways for targeting in the development of personalized therapies for patients with pulmonary fibrosis.

Original languageEnglish (US)
Pages (from-to)1517-1536
Number of pages20
JournalAmerican Journal of Respiratory and Critical Care Medicine
Issue number12
Early online dateDec 15 2018
StatePublished - Jun 15 2019


  • Alveolar macrophages
  • Alveolar type II cells
  • Pulmonary fibrosis
  • RNA sequencing

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine
  • Critical Care and Intensive Care Medicine


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