HOXD13 links positional identity to primary cilia-dependent signalling in synovial fibroblasts

Homeobox (HOX) transcription factors establish positional identity along the embryonic body axis, yet their functional roles in adult tissues remain poorly understood.

Synovial fibroblasts (SFs) and synovial tissue from rheumatoid arthritis (RA), osteoarthritis (OA), and noninflammatory donors were analysed using transcriptomic, epigenetic, and functional approaches. HOXD10, HOXD11, and HOXD13 were silenced in primary SFs, followed by RNA sequencing, gene set enrichment analysis, and assessment of proliferation, cell-cycle progression, and DNA damage responses. Primary cilia were assessed by immunofluorescence in SFs, and cilia-dependent Hedgehog signalling was evaluated using a GLI luciferase reporter assay.

HOXD10, HOXD11, and HOXD13 were selectively expressed in SFs from distal joints. We identify epigenetic mechanisms that maintain the anatomically restricted expression of these genes in adult SFs. Silencing of 5' HOXDs induces transcriptional changes in SFs that mirror joint-specific differences observed in RA. Notably, HOXD13 emerges as a key regulator of primary cilia function, influencing cell-cycle control and DNA damage responses, and genome stability. Consistent with these findings, we uncover joint-specific differences in primary cilia morphology, cell-cycle regulation, and DNA damage repair capacity in SFs.

Our results identify a previously unrecognised role for HOXD13 in linking embryonic positional identity to adult stromal cell function through primary cilia-dependent pathways. We propose that HOXD13-mediated regulation of primary cilia contributes to joint-specific SF phenotypes, providing a mechanistic framework linking positional identity to anatomically distinct fibroblast states. These findings suggest that developmental patterning genes can shape site-specific inflammatory responses.