Cross-species single-cell and spatial transcriptomics map the conserved stromal remodeling landscape of inflammatory arthritis

Abstract

Rheumatoid arthritis (RA) is a condition characterized by chronic synovial inflammation and joint destruction. However, the precise networks linking cellular activation to stromal-mediated pathology remain poorly defined, hindering the development of targeted therapies. We integrated single-cell RNA sequencing (scRNA-seq) across multiple preclinical mouse models to construct a unified synovial inflammatory arthritis landscape, later validating our findings in a human RA dataset using Visium HD spatial transcriptomics. Unsupervised clustering of the mouse synovium resolved distinct structural, vascular, and immune niches. Interactome mapping identified Vascular Mural cells as central hubs receiving endothelial- and mural-derived Notch signaling. Downstream of this perivascular trigger, regulatory network analysis revealed a synchronized, stress-induced Atf3/Fos (AP-1) transcription factor regulon program coordinating myofibroblast differentiation. This pathway is conserved in human RA; a homologous matrix-remodeling gene expression module (SM01, including VIM , FN1 , MMP2 ) was highly active in human Activated FLS and Lining FLS. Visium HD spatial mapping physically positioned these circuitries, demonstrating that FN1 and THBS signaling networks co-localized in a highly active niche restricted to the synovial tissue’s edge. We define a conserved Notch/AP-1 to Fn1/THBS module regulatory axis operating within a distinct spatial niche. This model moves beyond traditional cellular profiling to identify therapeutic targets potentially useful towards simultaneously halting synovial inflammation and joint destruction.