Multi-lineage transcriptional and cell communication signatures define evolving personalized mechanisms that initiate and perpetuate rheumatoid arthritis

Elevated anti-citrullinated protein antibodies (ACPA) levels in the peripheral blood are associated with an increased risk for developing rheumatoid arthritis (RA) and are hallmarks of established disease. Currently, no treatments are available that prevent progression to RA in at-risk individuals. In addition, diverse pathogenic mechanisms underlying a common clinical phenotype in RA complicate therapy because no single agent is universally effective in established disease. We propose that a unifying set of transcription factors (TFs) and their downstream pathways regulate pro-inflammatory cell communication networks, and that these networks allow multiple cell types to serve as pathogenic drivers in at-risk individuals and RA. To test this hypothesis, we identified ACPA-positive at-risk individuals, patients with early and established ACPA-positive RA and matched healthy controls. Single cell chromatin accessibility and transcriptomic profiles from peripheral blood mononuclear cells were integrated to define key TFs, TF-regulated targets and pathways. A distinctive TF signature was enriched in early RA, established RA and at-risk individuals that involved key pathogenic mechanisms in RA, especially SUMOylation, RUNX2, YAP1, NOTCH3, and β-Catenin Pathways. Interestingly, this signature was identified in multiple cell types and the pattern of cell type involvement varied among the at-risk and RA participants, supporting our hypothesis. Similar patterns of individualized gene expression patterns in varying cell types were confirmed in single cell studies of RA synovium. Cell communication analysis provided biological validation that diverse lineages can deliver the same core set of pro-inflammatory mediators to receiver cells in vivo that subsequently orchestrate rheumatoid inflammation. Longitudinal analysis showed that the signature cell type can evolve in individual at-risk participants but their core inflammatory mediator profile was stable. Cell-type-specific signature pathways could explain the personalized pathogenesis of RA and contribute to the diversity of clinical responses to targeted therapies. Overall, this study supports a new paradigm to understand how a common clinical phenotype could arise from diverse pathogenic mechanisms and demonstrates the relevance of peripheral blood cells to synovial disease.