Single-Cell Analysis Reveals Peripheral Helper T Cells in Rheumatoid Arthritis-Related Interstitial Lung Disease

Little is known about the pathogenesis of rheumatoid arthritis-related interstitial lung disease (RA-ILD). This study aimed to clarify the cellular and transcriptomic landscape of epithelial and immune cells in RA-ILD.

We performed single-cell RNA sequencing on fluorescence-activated cell sorted epithelial cells and immune cells from lung explants of four controls, three patients with non-RA connective tissue disease (CTD)-ILD, and five patients with RA-ILD. For T cell subclusters, we performed an integrative analysis with publicly available synovial T cell data. We performed immunofluorescence staining on lung sections from four controls, nine patients with RA-ILD, eight patients with non-RA CTD-ILD, and six patients with idiopathic pulmonary fibrosis.

We profiled 184,814 cells in total and identified 18 distinct cell clusters. We found fewer alveolar type II cells with reciprocally higher frequencies of other epithelial cell types (basal cells and ciliated cells) and fewer FCN1⁺ CD14⁺ monocytes in RA-ILD lungs. In T cell subset analysis, peripheral helper T (Tph) cells were exclusively observed in RA-ILD lungs. Compared with synovial Tph cells, lung Tph cells had elevated expression profiles of activation and lower cytotoxic and exhausted signatures. From gene ontology analysis, genes associated with the small GTPase-mediated signal transduction were enriched in lung Tph cells. On confirmatory immunofluorescence staining, Tph cells were specifically present in RA-ILD lungs.

We report a detailed transcriptomic analysis of the epithelial and immune cells in RA-ILD lungs and include a cross-tissue comparison that demonstrates organ-specific variations in the characteristics of Tph cells.