Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

Paul A Reyfman, James M 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, SeungHye 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 R 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 Perlman, Jacob I Sznajder, A Christine Argento, Colin T Gillespie, Jane Dematte, Manu Jain, Benjamin D Singer, Karen M Ridge, Anna P Lam, Ankit Bharat, Sangeeta M Bhorade, Cara J Gottardi, G R Scott Budinger, Alexander V Misharin

Research output: Contribution to journalArticle

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 controls.

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 in 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, novel 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 non-overlapping 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. The dataset is available at https://nupulmonary.org/resources/.

Original languageEnglish (US)
JournalAmerican Journal of Respiratory and Critical Care Medicine
DOIs
StateE-pub ahead of print - Dec 15 2018

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

Cite this

Reyfman, Paul A ; Walter, James M ; 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, SeungHye ; Gonzalez-Gonzalez, Francisco J ; Soberanes, Saul ; Watanabe, Satoshi ; Williams, Kinola J N ; Flozak, Annette S ; Nicholson, Trevor T ; Morgan, Vince K ; Winter, Deborah R ; 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 ; Sznajder, Jacob I ; Argento, A Christine ; Gillespie, Colin T ; Dematte, Jane ; Jain, Manu ; Singer, Benjamin D ; Ridge, Karen M ; Lam, Anna P ; Bharat, Ankit ; Bhorade, Sangeeta M ; Gottardi, Cara J ; Budinger, G R Scott ; Misharin, Alexander V. / Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. In: American Journal of Respiratory and Critical Care Medicine. 2018.
@article{237d01637b4449a19f578502b3526b96,
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 controls.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 in 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, novel 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 non-overlapping 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. The dataset is available at https://nupulmonary.org/resources/.",
author = "Reyfman, {Paul A} and Walter, {James M} and Nikita Joshi and Anekalla, {Kishore R} and McQuattie-Pimentel, {Alexandra C} and Stephen Chiu and Ramiro Fernandez and Mahzad Akbarpour and Ching-I Chen and Ziyou Ren and Rohan Verma and Hiam Abdala-Valencia and Kiwon Nam and Monica Chi and SeungHye Han 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 R} 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 Harris Perlman and Sznajder, {Jacob I} and Argento, {A Christine} and Gillespie, {Colin T} and Jane Dematte and Manu Jain and Singer, {Benjamin D} and Ridge, {Karen M} and Lam, {Anna P} and Ankit Bharat and Bhorade, {Sangeeta M} and Gottardi, {Cara J} and Budinger, {G R Scott} and Misharin, {Alexander V}",
year = "2018",
month = "12",
day = "15",
doi = "10.1164/rccm.201712-2410OC",
language = "English (US)",
journal = "American Journal of Respiratory and Critical Care Medicine",
issn = "1073-449X",
publisher = "American Thoracic Society",

}

Reyfman, PA, Walter, JM, Joshi, N, Anekalla, KR, McQuattie-Pimentel, AC, Chiu, S, Fernandez, R, Akbarpour, M, Chen, C-I, Ren, Z, Verma, R, Abdala-Valencia, H, Nam, K, Chi, M, Han, S, 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, H, Sznajder, JI, Argento, AC, Gillespie, CT, Dematte, J, Jain, M, Singer, BD, Ridge, KM, Lam, AP, Bharat, A, Bhorade, SM, Gottardi, CJ, Budinger, GRS & Misharin, AV 2018, 'Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis' American Journal of Respiratory and Critical Care Medicine. 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 A; Walter, James M; 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, SeungHye; Gonzalez-Gonzalez, Francisco J; Soberanes, Saul; Watanabe, Satoshi; Williams, Kinola J N; Flozak, Annette S; Nicholson, Trevor T; Morgan, Vince K; Winter, Deborah R; 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; Sznajder, Jacob I; Argento, A Christine; Gillespie, Colin T; Dematte, Jane; Jain, Manu; Singer, Benjamin D; Ridge, Karen M; Lam, Anna P; Bharat, Ankit; Bhorade, Sangeeta M; Gottardi, Cara J; Budinger, G R Scott; Misharin, Alexander V.

In: American Journal of Respiratory and Critical Care Medicine, 15.12.2018.

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 A

AU - Walter, James M

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, SeungHye

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 R

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

AU - Sznajder, Jacob I

AU - Argento, A Christine

AU - Gillespie, Colin T

AU - Dematte, Jane

AU - Jain, Manu

AU - Singer, Benjamin D

AU - Ridge, Karen M

AU - Lam, Anna P

AU - Bharat, Ankit

AU - Bhorade, Sangeeta M

AU - Gottardi, Cara J

AU - Budinger, G R Scott

AU - Misharin, Alexander V

PY - 2018/12/15

Y1 - 2018/12/15

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 controls.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 in 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, novel 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 non-overlapping 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. The dataset is available at https://nupulmonary.org/resources/.

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 controls.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 in 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, novel 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 non-overlapping 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. The dataset is available at https://nupulmonary.org/resources/.

U2 - 10.1164/rccm.201712-2410OC

DO - 10.1164/rccm.201712-2410OC

M3 - Article

JO - American Journal of Respiratory and Critical Care Medicine

JF - American Journal of Respiratory and Critical Care Medicine

SN - 1073-449X

ER -