Background/Purpose: While the field of pediatric rheumatology has made enviable strides in improving the lives of children with juvenile idiopathic arthritis (JIA), there is still a great deal we do not understanding about the biology of treatment response and the achievement of remission. To gain a better understanding of how the adaptive immune system is altered during successful therapy for polyarticular JIA, we performed RNA sequencing (RNAseq) on purified CD4+ T cells during active disease and remission in a group of children with this disease.

Methods:  We isolated RNA from CD4+ T cells of children with 3 distinct phenotypes: children with active, treated polyarticular JIA (ADt, n=12), children on medication who fit criteria for clinical remission by the Wallace criteria (CRM, n=10), and 10 healthy children, a control group. All JIA patients were on dual therapy with methotrexate and etanercept, and non were taking glucocorticoids. RNA sequencing was performed using the Illumina HiSeq 2500. Differentially expressed genes (DEGs) were considered with a cut-off of fold change >2.0 and false discovery rate <0.05.

Results: A comparison of ADt vs CRM transcripts revealed 143 differentially expressed genes, included 140 genes upregulated and 3 down regulated in the ADt group. The comparison of CRM vs. HC transcripts revealed 145 differentially expressed genes (3 up-regulated and 142 down regulated). The latter findings corroborate previous results from mixed populations of peripheral blood cells demonstrating that the CRM state is not associated with normalization of leukocyte transcriptomes. The top canonical pathways from IPA based on these DE genes (ADt vs CRM) include oxidative phosphorylation, mitochondrial dysfunction, EIF2 signaling and antigen presentation pathways. DE genes identified in the CRM vs HC comparison also included antigen presentation pathways, allograft rejection signaling, and NFAT regulation. Principle component analysis (PCA) of the expression genes in CD4+ T cells showed that ADt clearly separated with CRM. It was interesting to note, that CRM and HC subjects clustered closer together than ADt and CRM samples.

Conclusion: Our studies show that treatment response in JIA is associated with transcriptional alterations in peripheral blood CD4+ T cells. These responses involve gene regulatory networks associated with T cell activation (e.g., oxidative phosphorylation, antigen presentation). However, children who fit criteria for CRM, while phenotypically normal, have ongoing, underlying immune abnormalities.

ACR Meeting Abstracts - https://acrabstracts.org/abstract/rnaseq-reveals-treatment-associated-gene-expression-dynamics-in-juvenile-idiopathic-arthritis-cd4-t-cells/