Background/Purpose: To identify transcriptional changes in CD4+ T cells as children with polyarticular JIA transition from active disease to remission, and to identify underlying changes in chromatin architecture that account for these changes.

Methods: We isolated RNA from CD4+ T cells of children with 3 phenotypes: active, treated polyarticular JIA (ADT, n=12), children on medication who fit criteria for clinical remission (CRM, n=10), and 10 healthy children (HC). RNA sequencing was performed using the Illumina HiSeq 2500 platform. 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). We investigated whether regions of open chromatin that were unique to any of the 3 phenotypes (ADT, CRM, or HC) might show enrichment for specific transcriptional regulators, using standard computational approaches to determine whether unique peaks were associated with up-regulated genes, as determined by phenotype-to-phenotype comparisons of RNAseq data. We divided peaks into central and flanking regions then calculated the best match to each of 700+ motifs for each sub-region within each peak, and calculated enrichment by comparing the score of the best central match to the score of the best flanking matches.

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. Differential CTCF accessibility was identified within 2 of the known JIA risk haplotypes, those identified by the SNPs rs147992 (upstream of the IL2 gene) and rs2266959, an intronic region of the UBE2LR gene that also features H3K27ac+ enhancer marks in 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. 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: 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) in JIA and possible genetic determinants governing CTCF accessibility. The achievement of CRM does not result in a normalization of either the transcriptome or the epigenome of CD4+ T cells.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/treatment-response-in-polyarticular-jia-is-associated-with-transcriptional-changes-and-chromatin-reorganization-in-cd4-t-cells/