Comparative transcriptional profiling of key macrophage and fibroblast subpopulations in rheumatoid arthritis-associated lung disease.

Abstract

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. 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. 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. 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.