Single Cell RNA-seq and Mass Cytometry Reveals a Novel and a Targetable Population of Macrophages in Idiopathic Pulmonary Fibrosis

Abstract

In this study, we leveraged a combination of single cell RNAseq, cytometry by time of flight (CyTOF), and flow cytometry to study the biology of a unique macrophage population in pulmonary fibrosis. Using the profiling data from 312,928 cells derived from 32 idiopathic pulmonary fibrosis (IPF), 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we identified an expanded population of macrophages in IPF that have a unique transcriptional profile associated with pro-fibrotic signature. These macrophages attain a hybrid transitional state between alveolar and interstitial macrophages, are enriched with biological processes of pro-fibrotic immune cells, and express novel surface markers and genes that have not been previously reported. We then applied single cell CyTOF to simultaneously measure 37 markers to precisely phenotype the uniquely expanded macrophage subset in IPF lungs. The SPADE algorithm independently identified an expanded macrophage cluster, and validated CD84 and CD36 as novel surface markers that highly label this cluster. Using a separate validation cohort, we confirmed an increase in CD84++CD36++ macrophage population in IPF compared to control and COPD lungs by flow cytometry. Further, using the signature from the IPF-specific macrophages and the LINCS drug database, we predicted small molecules that could reverse the signature of IPF-specific macrophages, and validated two molecules, CRT and Cucur, using THP-1 derived human macrophages and precision-cut lung slices (PCLS) from IPF patients. Utilizing a multi-dimensional translational approach, our work identified a novel and targetable population of macrophages found in end-stage pulmonary fibrosis.One Sentence SummarySingle cell RNAseq, CyTOF, and flow cytometry reveal the presence of an aberrant macrophage population in pulmonary fibrosis

Macrophages in lung fibrosis

“…Furthermore, Ayaub et al . ( 45 ) analyzed the data reported by Adams et al . ( 44 ) in detail and found that in addition to a similar increase in SPP1 hi macrophages, these macrophages have intermediate features between AMs and IMs.…”

Regulatory Immune Cells in Idiopathic Pulmonary Fibrosis: Friends or Foes?

“…Highly proliferative osteopontin-expressing macrophages were identified through scRNA-seq and were found to mediate myofibroblast activation in the lungs of IPF patients (155). Similarly, another expanded population of pro-fibrotic CD36 + CD84 + macrophages in IPF were identified, which also showed increased expression of genes involved in ECM remodeling (156,PREPRINT).…”

Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

“…LAMs and LAM-like cells have been observed in disease contexts in adipose tissue from obese human individuals and from mice (Jaitin et al, 2019), injured and fibrotic liver (Perugorria et al, 2019;Ramachandran et al, 2019;Xiong et al, 2019), fibrotic lung (Ayaub et al, 2021;Reyfman et al, 2019), atherosclerotic aortic tissue (Cochain et al, 2018;Willemsen & de Winther, 2020), and Alzheimer's disease brain (Grubman et al, 2019;Keren-Shaul et al, 2017;Mathys et al, 2019). However, an understanding of their distribution and heterogeneity across human tissues is still lacking.…”