Targeting convergent pathways prevents the differentiation of tissue-resident memory T cells from multilineage progenitors in the arthritic synovium

Introduction/Rationale: Rheumatoid arthritis is an autoimmune disease characterized by chronic, recurrent inflammation of the joints. We identified CD8 resident memory T cells (TRM) in human arthritic joints and demonstrated that TRM remain in the synovium during remission and mediate arthritis flares. However, the developmental origin and differentiation trajectory of TRM in the joints remain unclear.

Methods: Here, we use two parallel models of synovial TRM development: 1) an antigen-induced arthritis (AIA) murine model, and 2) a human synovial organoid model. Using 10x single-cell RNA sequencing, we discover the progenitor and differentiation pathways of synovial TRM. Antisense oligonucleotides (ASOs) targeting candidate signaling pathways were further applied either to human synovial organoids or through adoptive transfer experiments in the AIA model.

Results: Using 10x single-cell RNA sequencing, we discovered that synovial TRM derived from both circulating effector memory T cells (TEM) and central memory T cells (TCM) during murine arthritis. We further confirmed that both purified TEM and TCM were discretely differentiated into TRM in human synovial organoids. By integrating RNA sequencing data from both systems, we delineated convergent and divergent differentiation pathways and identified associated transcriptomic changes originating from these distinct progenitor pools. Among the genes expressed in the TRM convergent pathway was the transcription factor, RUNX3. Using ASOs to block RUNX3 expression, we prevented TRM formation along both TEM and TCM differentiation trajectories in human synovial organoids. Consistently, T cells treated with ASOs against Runx3 showed reduced TRM formation in murine arthritis.

Conclusion: Our results define the trajectory of TRM differentiation in the joint, highlighting these pathways as potential therapeutic targets for modulating chronic arthritis.