Open Access Research article

Correlation analyses of clinical and molecular findings identify candidate biological pathways in systemic juvenile idiopathic arthritis

Xuefeng B Ling1, Claudia Macaubas2, Heather C Alexander3, Qiaojun Wen1, Edward Chen1, Sihua Peng1, Yue Sun2, Chetan Deshpande2, Kuang-Hung Pan4, Richard Lin4, Chih-Jian Lih4, Sheng-Yung P Chang3, Tzielan Lee5, Christy Sandborg5, Ann B Begovich3, Stanley N Cohen4 and Elizabeth D Mellins25*

Author affiliations

1 Department of Surgery, Stanford University, Stanford, CA 94305, USA

2 Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA

3 Celera Corporation, Alameda, CA 94502, USA

4 Department of Genetics, Stanford, CA 94305, USA

5 Division of Pediatric Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA

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Citation and License

BMC Medicine 2012, 10:125  doi:10.1186/1741-7015-10-125

Published: 23 October 2012



Clinicians have long appreciated the distinct phenotype of systemic juvenile idiopathic arthritis (SJIA) compared to polyarticular juvenile idiopathic arthritis (POLY). We hypothesized that gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with each disease would reveal distinct biological pathways when analyzed for significant associations with elevations in two markers of JIA activity, erythrocyte sedimentation rate (ESR) and number of affected joints (joint count, JC).


PBMC RNA from SJIA and POLY patients was profiled by kinetic PCR to analyze expression of 181 genes, selected for relevance to immune response pathways. Pearson correlation and Student's t-test analyses were performed to identify transcripts significantly associated with clinical parameters (ESR and JC) in SJIA or POLY samples. These transcripts were used to find related biological pathways.


Combining Pearson and t-test analyses, we found 91 ESR-related and 92 JC-related genes in SJIA. For POLY, 20 ESR-related and 0 JC-related genes were found. Using Ingenuity Systems Pathways Analysis, we identified SJIA ESR-related and JC-related pathways. The two sets of pathways are strongly correlated. In contrast, there is a weaker correlation between SJIA and POLY ESR-related pathways. Notably, distinct biological processes were found to correlate with JC in samples from the earlier systemic plus arthritic phase (SAF) of SJIA compared to samples from the later arthritis-predominant phase (AF). Within the SJIA SAF group, IL-10 expression was related to JC, whereas lack of IL-4 appeared to characterize the chronic arthritis (AF) subgroup.


The strong correlation between pathways implicated in elevations of both ESR and JC in SJIA argues that the systemic and arthritic components of the disease are related mechanistically. Inflammatory pathways in SJIA are distinct from those in POLY course JIA, consistent with differences in clinically appreciated target organs. The limited number of ESR-related SJIA genes that also are associated with elevations of ESR in POLY implies that the SJIA associations are specific for SJIA, at least to some degree. The distinct pathways associated with arthritis in early and late SJIA raise the possibility that different immunobiology underlies arthritis over the course of SJIA.

Arthritis; Inflammation; Juvenile idiopathic arthritis (JIA); Systemic JIA; Polyarticular JIA; Transcriptional analysis