Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis

Abstract

We provide a single cell atlas of Idiopathic Pulmonary Fibrosis (IPF), a fatal interstitial lung disease, focusing on resident lung cell populations. By profiling 312,928 cells from 32 IPF, 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we demonstrate that IPF is characterized by changes in discrete subpopulations of cells in the three major parenchymal compartments: the epithelium, endothelium and stroma. Among epithelial cells, we identify a novel population of IPF enriched aberrant basaloid cells that co-express basal epithelial markers, mesenchymal markers, senescence markers, developmental transcription factors and are located at the edge of myofibroblast foci in the IPF lung. Among vascular endothelial cells in the in IPF lung parenchyma we identify an expanded cell population transcriptomically identical to vascular endothelial cells normally restricted to the bronchial circulation. We confirm the presence of both populations by immunohistochemistry and independent datasets. Among stromal cells we identify fibroblasts and myofibroblasts in both control and IPF lungs and leverage manifold-based algorithms diffusion maps and diffusion pseudotime to infer the origins of the activated IPF myofibroblast. Our work provides a comprehensive catalogue of the aberrant cellular transcriptional programs in IPF, demonstrates a new framework for analyzing complex disease with scRNAseq, and provides the largest lung disease single-cell atlas to date.

Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis

“…Finally, we took advantage of a recently available scRNASeq dataset submitted on bioRχiv to interrogate enrichment for IPF fibroblast and myofibroblast marker genes. [8] The fibroblast marker genes, HAS1 and HAS2, were detected in less than 7 patients and were therefore excluded from our FF signature. The myofibroblast markers genes, COL8A1 and ACTA2, were detected in 13/13 and in 12/13 patients, respectively.…”

“…It is worth mentioning that we found no significant overlap between these collagen-related genes and the list of genes differentially expressed in myofibroblasts in IPF compared to control lung reported in a recent bioRχiv scRNAseq study. [8] This suggest that scRNAseq and our LCM approach could be considered complementary strategies to interrogate different aspects of IPF pathomechanisms.…”

“…Comparator cells are challenging to define given the potential diverse origins and phenotypes of myo/fibroblasts in IPF and importantly the paucity of interstitial fibroblasts which can be captured from healthy control lung. Moreover, recent scRNASeq data available on bioRχiv,[8] suggest that “pathological ACTA2-expressing IPF myofibroblasts represent an extreme pole of a continuum connected to a quiescent ACTA2-negative stromal population rather than resident or activated fibroblasts in control lung”. We herein report on the generation of a composite gene expression profile from more than 60 individual FF derived from 13 patients.…”

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

“…3a). These included 6 published datasets [63][64][65][66][67][68] and 16 datasets that are not yet published [69][70][71][72][73] . In the case of unpublished data, we only obtained singlecell expression counts for the three genes, as well as the total UMI counts per cell, cell identity annotations, and the relevant anonymous clinical variables (age and sex, as well as smoking status when ascertained).…”

Cell-intrinsic differences between human airway epithelial cells from children and adults

“…A novel CFTR-producing population, the ionocyte (Montoro et al, 2018;Plasschaert et al, 2018), has been described, and we have new insight into cellular differentiation through the resolution of differentiation intermediates; for example, basal luminal progenitor cells (Mori et al, 2015;Rock et al, 2011;Watson et al, 2015), which are defined by an intermediate keratin profile (TP63-/KRT5+/KRT8+/KRT4+/KRT13+) (Braga et al, 2019;García et al, 2019). Efforts in mapping pathologic states have identified mucous ciliated cells (ciliated cells which co-express a number of genes typically associated with goblet cells and are more frequent in asthmatic patients (Braga et al, 2019)), as well as novel pathological epithelial cell subtypes in idiopathic pulmonary fibrosis (Adams et al, 2019;Habermann et al, 2019;Reyfman et al, 2019). In addition, region-specific differences exist in airway epithelial cell phenotype within the bronchial tree such that basal, ciliated and secretory populations in the nasal epithelium differ phenotypically (and maybe functionally) from their counterparts in the large or small airways (Braga et al, 2019;Deprez et al, 2019;Kumar et al, 2011;Travaglini et al, 2019).…”