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Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients

T C T M van der Pouw Kraan^1,*, C A Wijbrandts^2,*, L G M van Baarsen¹, A E Voskuyl³, F Rustenburg¹, J M Baggen¹, S M Ibrahim⁴, M Fero⁵, B A C Dijkmans³, P P Tak², C L Verweij¹

¹ VU Medical Center, Department of Molecular Cell Biology & Immunology, Amsterdam, The Netherlands
² Academic Medical Center, Division of Clinical Immunology and Rheumatology, University of Amsterdam, Amsterdam, The Netherlands
³ VU Medical Center, Department of Rheumatology, Amsterdam, The Netherlands
⁴ Section of Immunogenetics, University of Rostock, Rostock, Germany
⁵ Stanford Functional Genomics Facility, Stanford University, Stanford, California, USA

Correspondence to:
Dr C L Verweij
VU University Medical Centre, Department of Molecular and Cellular Biology & Immunology, J295, PO Box 7057, 1007 MB Amsterdam, The Netherlands;c.verweij{at}vumc.nl

Background: Rheumatoid arthritis (RA) is a heterogeneous disease with unknown cause.

Aim: To identify peripheral blood (PB) gene expression profiles that may distinguish RA subtypes.

Methods: Large-scale expression profiling by cDNA microarrays was performed on PB from 35 patients and 15 healthy individuals. Differential gene expression was analysed by significance analysis of microarrays (SAM), followed by gene ontology analysis of the significant genes. Gene set enrichment analysis was applied to identify pathways relevant to disease.

Results: A substantially raised expression of a spectrum of genes involved in immune defence was found in the PB of patients with RA compared with healthy individuals. SAM analysis revealed a highly significant elevated expression of interferon (IFN) type I regulated genes in patients with RA compared with healthy individuals, which was confirmed by gene ontology and pathway analysis, suggesting that this pathway was activated systemically in RA. A quantitative analysis revealed that increased expression of IFN-response genes was characteristic of approximately half of the patients (IFN^high patients). Application of pathway analysis revealed that the IFN^high group was largely different from the controls, with evidence for upregulated pathways involved in coagulation and complement cascades, and fatty acid metabolism, while the IFN^low group was similar to the controls.

Conclusion: The IFN type I signature defines a subgroup of patients with RA, with a distinct biomolecular phenotype, characterised by increased activity of the innate defence system, coagulation and complement cascades, and fatty acid metabolism.

Abbreviations: DC, dendritic cell; FLS, fibroblast-like synoviocytes; GSEA, gene set enrichment analysis; IFN, interferon; MTX, methotrexate; PB, peripheral blood; RA, rheumatoid arthritis; SAM, significance analysis of microarrays; SLE, systemic lupus erythematosus; SS, Sjögren’s syndrome

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