Comparative transcriptional profiling of key macrophage and fibroblast subpopulations in rheumatoid arthritis‐associated lung disease
Tracy Tabib, Ogechukwu Ezenwa, Joshua Sciurba, Eleanor B. Valenzi, John Sembrat, Brittany Cody, Jishnu Das, Robert Lafyatis, Dana P. AschermanObjective
Rheumatoid arthritis (RA) often involves extra‐articular complications, including interstitial lung disease (ILD) and/or pulmonary nodules. Transcriptomic profiling of lung tissue provides the opportunity to directly assess cell‐specific gene expression and corresponding pathway activation in different types of rheumatoid lung disease.
Methods
We used probe‐based, FLEX single‐cell RNA sequencing (scRNA‐seq) of fixed lung tissue specimens to compare gene expression profiles in macrophage and fibroblast populations contributing to tissue remodeling in RA‐ILD versus RA lung nodules. Additional comparison of differentially expressed genes (DEGs) in lung tissue explants from patients with idiopathic pulmonary fibrosis (IPF) elucidated the degree of overlap with RA‐ILD.
Results
FLEX scRNA‐seq of lung specimens from non‐diseased controls (n=4) and patients with RA‐ILD (n=9) or RA nodules (n=3) yielded clustering profiles mirroring UMAP distributions from conventional, poly(A) capture‐based scRNA‐seq of RA‐ILD, IPF, and control lung tissue. Comparative transcriptional profiling of macrophage and fibroblast subpopulations in RA‐ILD and RA lung nodules revealed only partial overlap, with differential upregulation of immunoregulatory, angioregulatory, and matrix assembly pathways in RA‐ILD fibroblasts that contrasted with selective upregulation of pathways promoting innate and adaptive immunity in macrophage populations comprising RA lung nodules. Comparison of DEGs between RA‐ILD and IPF lung‐derived macrophage and fibroblast populations demonstrated significant enhancement of profibrotic gene expression in both disease states.
Conclusions
FLEX scRNA‐seq of pulmonary macrophage and fibroblast subpopulations reveals key differences in transcriptional profile distinguishing RA‐ILD from RA lung nodules. Parallel comparison of cell type‐specific gene expression profiles between RA‐ILD and IPF demonstrates significant overlap in profibrotic transcriptional programs.