Disparate Interferon Signaling and Shared Aberrant Basaloid Cells in Single-Cell Profiling of Idiopathic Pulmonary Fibrosis and Systemic Sclerosis-Associated Interstitial Lung Disease

Abstract

Idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated interstitial lung disease (SSc-ILD) differ in the predominant demographics and identified genetic risk alleles of effected patients, however both diseases frequently progress to respiratory failure and death. Contrasting advanced SSc-ILD to IPF provides insight to the role dysregulated immunity may play in pulmonary fibrosis. To analyze cell-type specific transcriptome commonalities and differences between IPF and SSc-ILD, we compared single-cell RNA-sequencing (scRNA-seq) of 21 explanted lung tissue specimens from patients with advanced IPF, SSc-ILD, and organ donor controls. Comparison of IPF and SSc-ILD tissue identified divergent patterns of interferon signaling, with interferon-gamma signaling upregulated in the SPP1hi and FABP4hi macrophages, cytotoxic T cells, and natural kill cells of IPF, while type I interferon signaling and production was upregulated in the corresponding SSc-ILD populations. Plasmacytoid dendritic cells were found in diseased lungs only, and exhibited upregulated cellular stress pathways in SSc-ILD compared to IPF. Alveolar type I cells were dramatically decreased in both IPF and SSc-ILD, with a distinct transcriptome signature separating these cells by disease. KRT5-/KRT17+ aberrant basaloid cells exhibiting markers of cellular senescence and epithelial-mesenchymal transition were identified in SSc-ILD for the first time. In summary, our study utilizes the enriched capabilities of scRNA-seq to identify key divergent cell types and pathways between IPF and SSc-ILD, providing new insights into the shared and distinct mechanisms between idiopathic and autoimmune interstitial lung diseases.

From pulmonary fibrosis to progressive pulmonary fibrosis: a lethal pathobiological jump

“…In a recent study performed in IPF and SSc-ILD lung tissues, p16 was predominantly localized to bronchiolized epithelium lining honeycomb cysts, specifically to KRT17 + basal epithelial cells that also coexpress KRT5 + (14). This finding is different from the reported by other authors (2,27,63), which found senescence markers in KRT5 -/KRT17 + epithelial cells, supporting the difficulty to identify with precision the senescent epithelial cells in fibrotic lungs.…”

“…More recently, the presence of KRT5 − /KRT17 + epithelial cells was confirmed in SSc-ILD, where they exhibit markers of EMT, elevated integrin αVβ6, a potent activator of latent TGF-β, and markers of cellular senescence including CDKN2A(p16), CDKN1A(p21) (63).…”

Cellular Senescence: Pathogenic Mechanisms in Lung Fibrosis

“…More recently, one single-cell RNA-seq cohort identified aberrant basaloid cells in IPF that co-expressed basal epithelial (TP63, KRT17, LAMB3, and LAMC2), mesenchymal (VIM, CDH2, FN1, COL1A1, TNC, and HMGA2), and senescence (CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15) signature genes [87]. Another study also described aberrant basaloid cells in IPF and systemic sclerosis-related ILDs whereby those cells expressed senescence markers, CDKN2A(gene for p16), CDKN1A(gene for p21), and GDF15 [88], and that cellular senescence was one of the profibrotic regulatory pathways identified in these cells. The new report of "transitional stem cells" or Krt 8 + alveolar differentiation intermediate cells displayed senescent phenotype.…”

Cellular Senescence: Pathogenic Mechanisms in Lung Fibrosis

“…More recently, one single-cell RNA-seq cohort identified aberrant basaloid cells in IPF that co-expressed basal epithelial (TP63, KRT17, LAMB3, and LAMC2), mesenchymal (VIM, CDH2, FN1, COL1A1, TNC, and HMGA2), and senescence (CDKN1A, CDKN2A, CCND1, CCND2, MDM2, and GDF15) signature genes [85]. Another study also described aberrant basaloid cells in IPF and systemic sclerosis-related ILDs, whereby those cells expressed senescence markers, CDKN2A (gene for p16), CDKN1A (gene for p21), and GDF15 [86], and that cellular senescence was one of the profibrotic regulatory pathways identified in these cells. The new report of "transitional stem cells" or Krt 8 + alveolar differentiation intermediate cells displayed a senescent phenotype.…”