Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes

Myles J. Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John , David S. Watson, Sarah K. Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michele Bombardieri, Nora Ng, Maria DiCicco, Désirée van der HeijdeRobert Landewé, Annette van der Helm-van Mil, Alberto Cauli, Iain B McInnes, Christopher Buckley, Ernest Choy, Peter C Taylor, Michael J. Townsend, Costantino Pitzalis

Research output: Contribution to journalArticlepeer-review

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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-naïve patients, 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 the synovium linked to three distinct pathotypes, which imply the existence of divergent pathogenic pathways/activation states: fibroblastic pauci-immune pathotype; macrophage rich diffuse-myeloid pathotype; and a lympho-myeloid pathotype characterised by infiltration of B/T-lymphocytes and myeloid cells. Pro-myeloid inflammatory synovial gene signatures showed strong association with increased disease activity, and correlated with clinical response to initial DMARD (disease modifying antirheumatic drug) therapy, while plasma cell genes identified a poor prognosis subgroup with progressive structural damage.
Original languageEnglish
Pages (from-to)2455-2470.e5
JournalCell Reports
Issue number9
Publication statusPublished - 27 Aug 2019


  • PEAC
  • Pathobiology of Early Arthritis Cohort study
  • RNA sequencing
  • ectopic lymphoid structures
  • lymphoid neogenesis
  • personalized medicine
  • rheumatoid arthritis
  • synovial biopsy
  • transcriptomics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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