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There is a current imperative to unravel the hierarchy of molecular pathways that drive the transition of early to established disease in rheumatoid arthritis (RA). Herein, we report a comprehensive RNA sequencing analysis of the molecular pathways that drive early RA progression in the disease tissue (synovium), comparing matched peripheral blood RNA-seq in a large cohort of early treatment-naive patients, namely, the Pathobiology of Early Arthritis Cohort (PEAC). We developed a data exploration website ( to dissect gene signatures across synovial and blood compartments, integrated with deep phenotypic profiling. We identified transcriptional subgroups in synovium linked to three distinct pathotypes: fibroblastic pauci-immune pathotype, macrophage-rich diffuse-myeloid pathotype, and a lympho-myeloid pathotype characterized by infiltration of lymphocytes and myeloid cells. This is suggestive of divergent pathogenic pathways or activation disease states. Pro-myeloid inflammatory synovial gene signatures correlated with clinical response to initial drug therapy, whereas plasma cell genes identified a poor prognosis subgroup with progressive structural damage.

Original publication




Journal article


Cell rep

Publication Date





2455 - 2470.e5


PEAC, Pathobiology of Early Arthritis Cohort study, RNA sequencing, ectopic lymphoid structures, lymphoid neogenesis, personalized medicine, rheumatoid arthritis, synovial biopsy, transcriptomics, Adult, Aged, Antirheumatic Agents, Arthritis, Rheumatoid, Databases, Factual, Female, Humans, Interferons, Joints, Male, Middle Aged, Phenotype, Software, Transcriptome