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. RNA sequencing was performed using the Illumina HiSeq 2500 platform. In addition, we used the assay for transposase-accessible chromatin-sequencing (ATACseq) to survey open chromatin in a subset of these same patients (6 HC, and 5 ADT and CRM).

Results: Each of the 3 phenotypes was associated with its own its own chromatin accessibility signature as identified by ATACseq and its own transcriptional signature. We identified 16,039 accessible sites that were unique to HC, 38,451 that were unique to ADT, and 58,289 sites that were unique to CRM. Further analyses of the open regions unique to the HC cells showed that these regions were highly enriched (compared to genome background) for CCCTC-binding factor (CTCF) binding sites. These CTCF binding sites were absent in JIA CD4+ T cells. This finding suggests that aberrant 3D chromatin architecture (which is regulated by CTCF) may be a primary driver of the transcriptional aberrations observed in JIA. In contrast, open regions that were unique to the ADT state were highly enriched for NFIC and STAT4 binding sites. Both NFIC and STAT4 are known regulators of T cell activation, and the STAT4 locus has been identified as a region of genetic risk in JIA. Analysis of the combined RNAseq and ATACseq using BETA software demonstrated that the differences in chromatin accessibility had high regulatory potential for the differentially expressed genes, providing strong evidence that the chromatin changes and gene expression changes are causally linked. The CRM state was not associated with normalization of either the chromatin or transcriptional signatures of CD4+ T cells in children with JIA.

Conclusion:

Conclusion – Treatment response in JIA is associated with significant re-organization of chromatin and is accompanied by significant changes in transcription that can be attributed to the chromatin re-organization. Patterns of chromatin accessibility suggest important roles for chromatin regulators (e.g., CTCF) and transcription factors (NFIC, STAT4) in JIA. The achievement of CRM does not result in a normalization of either the transcriptome or the epigenome of CD4+ T cells.