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. Flozak & 29 others Trevor 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 journalArticle

11 Citations (Scopus)

Abstract

Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, 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
Volume199
Issue number12
DOIs
StatePublished - Jun 15 2019

Fingerprint

Single-Cell Analysis
Pulmonary Fibrosis
Lung
RNA Sequence Analysis
Alveolar Macrophages
Alveolar Epithelial Cells
Atlases
Population
Idiopathic Pulmonary Fibrosis
In Situ Hybridization
Fibrosis
Stem Cells

Keywords

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

ASJC Scopus subject areas

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

Cite this

Reyfman, Paul Andrew ; Walter, James McCauley ; Joshi, Nikita ; Anekalla, Kishore R. ; McQuattie-Pimentel, Alexandra C. ; Chiu, Stephen ; Fernandez, Ramiro ; Akbarpour, Mahzad ; Chen, Ching I. ; Ren, Ziyou ; Verma, Rohan ; Abdala-Valencia, Hiam ; Nam, Kiwon ; Chi, Monica ; Han, Seung Hye ; Gonzalez-Gonzalez, Francisco J. ; Soberanes, Saul ; Watanabe, Satoshi ; Williams, Kinola J.N. ; Flozak, Annette S. ; Nicholson, Trevor T. ; Morgan, Vince K. ; Winter, Deborah Rachelle ; Hinchcliff, Monique ; Hrusch, Cara L. ; Guzy, Robert D. ; Bonham, Catherine A. ; Sperling, Anne I. ; Bag, Remzi ; Hamanaka, Robert B. ; Mutlu, Gökhan M. ; Yeldandi, Anjana V ; Marshall, Stacy A. ; Shilatifard, Ali ; Amaral, Luis A N ; Perlman, Harris R ; Sznajder, Jacob I ; Christine Argento, A. ; Gillespie, Colin Thomas ; Dematte, Jane ; Jain, Manu ; Singer, Benjamin ; Ridge, Karen M ; Lam, Anna P ; Bharat, Ankit ; Bhorade, Sangeeta Maruti ; Gottardi, Cara ; Budinger, GR Scott ; Misharin, Alexander. / Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis. In: American journal of respiratory and critical care medicine. 2019 ; Vol. 199, No. 12. pp. 1517-1536.
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title = "Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis",
abstract = "Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, 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.",
keywords = "Alveolar macrophages, Alveolar type II cells, Pulmonary fibrosis, RNA sequencing",
author = "Reyfman, {Paul Andrew} and Walter, {James McCauley} and Nikita Joshi and Anekalla, {Kishore R.} and McQuattie-Pimentel, {Alexandra C.} and Stephen Chiu and Ramiro Fernandez and Mahzad Akbarpour and Chen, {Ching I.} and Ziyou Ren and Rohan Verma and Hiam Abdala-Valencia and Kiwon Nam and Monica Chi and Han, {Seung Hye} and Gonzalez-Gonzalez, {Francisco J.} and Saul Soberanes and Satoshi Watanabe and Williams, {Kinola J.N.} and Flozak, {Annette S.} and Nicholson, {Trevor T.} and Morgan, {Vince K.} and Winter, {Deborah Rachelle} and Monique Hinchcliff and Hrusch, {Cara L.} and Guzy, {Robert D.} and Bonham, {Catherine A.} and Sperling, {Anne I.} and Remzi Bag and Hamanaka, {Robert B.} and Mutlu, {G{\"o}khan M.} and Yeldandi, {Anjana V} and Marshall, {Stacy A.} and Ali Shilatifard and Amaral, {Luis A N} and Perlman, {Harris R} and Sznajder, {Jacob I} and {Christine Argento}, A. and Gillespie, {Colin Thomas} and Jane Dematte and Manu Jain and Benjamin Singer and Ridge, {Karen M} and Lam, {Anna P} and Ankit Bharat and Bhorade, {Sangeeta Maruti} and Cara Gottardi and Budinger, {GR Scott} and Alexander Misharin",
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Reyfman, PA, Walter, JM, Joshi, N, Anekalla, KR, McQuattie-Pimentel, AC, Chiu, S, Fernandez, R, Akbarpour, M, Chen, CI, Ren, Z, Verma, R, Abdala-Valencia, H, Nam, K, Chi, M, Han, SH, Gonzalez-Gonzalez, FJ, Soberanes, S, Watanabe, S, Williams, KJN, Flozak, AS, Nicholson, TT, Morgan, VK, Winter, DR, Hinchcliff, M, Hrusch, CL, Guzy, RD, Bonham, CA, Sperling, AI, Bag, R, Hamanaka, RB, Mutlu, GM, Yeldandi, AV, Marshall, SA, Shilatifard, A, Amaral, LAN, Perlman, HR, Sznajder, JI, Christine Argento, A, Gillespie, CT, Dematte, J, Jain, M, Singer, B, Ridge, KM, Lam, AP, Bharat, A, Bhorade, SM, Gottardi, C, Budinger, GRS & Misharin, A 2019, 'Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis', American journal of respiratory and critical care medicine, vol. 199, no. 12, pp. 1517-1536. https://doi.org/10.1164/rccm.201712-2410OC

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

In: American journal of respiratory and critical care medicine, Vol. 199, No. 12, 15.06.2019, p. 1517-1536.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis

AU - Reyfman, Paul Andrew

AU - Walter, James McCauley

AU - Joshi, Nikita

AU - Anekalla, Kishore R.

AU - McQuattie-Pimentel, Alexandra C.

AU - Chiu, Stephen

AU - Fernandez, Ramiro

AU - Akbarpour, Mahzad

AU - Chen, Ching I.

AU - Ren, Ziyou

AU - Verma, Rohan

AU - Abdala-Valencia, Hiam

AU - Nam, Kiwon

AU - Chi, Monica

AU - Han, Seung Hye

AU - Gonzalez-Gonzalez, Francisco J.

AU - Soberanes, Saul

AU - Watanabe, Satoshi

AU - Williams, Kinola J.N.

AU - Flozak, Annette S.

AU - Nicholson, Trevor T.

AU - Morgan, Vince K.

AU - Winter, Deborah Rachelle

AU - Hinchcliff, Monique

AU - Hrusch, Cara L.

AU - Guzy, Robert D.

AU - Bonham, Catherine A.

AU - Sperling, Anne I.

AU - Bag, Remzi

AU - Hamanaka, Robert B.

AU - Mutlu, Gökhan M.

AU - Yeldandi, Anjana V

AU - Marshall, Stacy A.

AU - Shilatifard, Ali

AU - Amaral, Luis A N

AU - Perlman, Harris R

AU - Sznajder, Jacob I

AU - Christine Argento, A.

AU - Gillespie, Colin Thomas

AU - Dematte, Jane

AU - Jain, Manu

AU - Singer, Benjamin

AU - Ridge, Karen M

AU - Lam, Anna P

AU - Bharat, Ankit

AU - Bhorade, Sangeeta Maruti

AU - Gottardi, Cara

AU - Budinger, GR Scott

AU - Misharin, Alexander

PY - 2019/6/15

Y1 - 2019/6/15

N2 - 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.

AB - 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.

KW - Alveolar macrophages

KW - Alveolar type II cells

KW - Pulmonary fibrosis

KW - RNA sequencing

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EP - 1536

JO - American Journal of Respiratory and Critical Care Medicine

JF - American Journal of Respiratory and Critical Care Medicine

SN - 1073-449X

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