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Open Access Highly Accessed Open Badges Research article

Genomic characterization of remission in juvenile idiopathic arthritis

Kaiyu Jiang13, Mark Barton Frank2, Yanmin Chen13, Jeanette Osban2 and James N Jarvis13*

Author Affiliations

1 Department of Pediatrics, Pediatric Rheumatology Research, University of Oklahoma Health Sciences Center, Basic Sciences Education Building 235A, Oklahoma City, OK 73104, USA

2 Microarray Research Facility, Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, 840 NE 13th Street, Oklahoma City, OK 73104, USA

3 Department of Pediatrics, Rheumatology Research, SUNY Buffalo Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14203

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Arthritis Research & Therapy 2013, 15:R100  doi:10.1186/ar4280

Published: 30 August 2013



The attainment of remission has become an important end point for clinical trials in juvenile idiopathic arthritis (JIA), although we do not yet have a full understanding of what remission is at the cell and molecular level.


Two independent cohorts of patients with JIA and healthy child controls were studied. RNA was prepared separately from peripheral blood mononuclear cells (PBMC) and granulocytes to identify differentially expressed genes using whole genome microarrays. Expression profiling results for selected genes were confirmed by quantitative, real-time polymerase chain reaction (RT-PCR).


We found that remission in JIA induced by either methotrexate (MTX) or MTX plus a TNF inhibitor (etanercept, Et) (MTX + Et) is characterized by numerous differences in gene expression in peripheral blood mononuclear cells and in granulocytes compared with healthy control children; that is, remission is not a restoration of immunologic normalcy. Network analysis of the differentially expressed genes demonstrated that the steroid hormone receptor superfamily member hepatocyte nuclear factor 4 alpha (HNF4α) is a hub in several of the gene networks that distinguished children with arthritis from controls. Confocal microscopy revealed that HNF4a is present in both T lymphocytes and granulocytes, suggesting a previously unsuspected role for this transcription factor in regulating leukocyte function and therapeutic response in JIA.


These findings provide a framework from which to understand therapeutic response in JIA and, furthermore, may be used to develop strategies to increase the frequency with which remission is achieved in adult forms of rheumatoid arthritis.

juvenile idiopathic arthritis; methotrexate; TNF inhibitor; gene expression; biomarker; microarray