OP0149 CD4+ T CELLS FROM CHILDREN WITH ACTIVE JUVENILE IDIOPATHIC ARTHRITIS SHOW ABERRANT CHROMATIN ORGANIZATION AND CTCF LOCALIZATION ASSOCIATED WITH TRANSCRIPTIONAL ABNORMALITIES
Authors: Evan Tarbell, Kaiyu Jiang, Teresa R. Hennon, Lucy Holmes, Patrick M. Gaffney, Tao Liu, Jim Jarvis
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Our group and others have shown that peripheral blood cells of children with juvenile idiopathic arthritis (JIA) display numerous transcriptional abnormalities. However, most of these studies have been performed on mixed cell types (peripheral blood mononuclear cells, whole blood). Little cell type specific data is available, making mechanistic inferences and links to disease pathogenesis difficult. <h3>Objectives</h3> To define transcriptional patterns in CD4+ T cells from children with polyarticular JIA and query mechanisms underlying transcriptional abnormalities. <h3>Methods</h3> We studied CD4+ T cells obtained from children with active polyarticular onset JIA and sought to identify epigenetic features associated with altered gene expression. We performed RNA-seq and ATAC-seq on a cohort of patients who had the active disease and were under treatment with methotrexate and etanercept (ADT), patients who fit criteria for clinical remission on medication (CRM), and healthy control children (HC). We used standard used the common dispersion protocol in EdgeR to identify differential gene expression. We used our recently developed and validated Hidden Markov ModeleR for ATAC-seq doftware to identify differentially accessible regions, comparing ADT, CRM, and HC samples. We integrated ATACseq and RNAseq data using the BETA software package. After preliminary analysis revealed a potential role for the transcriptional regulator, CCCTC binding factor (CTCF) in the observed transcriptional patterns, we performed ChIPseq and HiChIP studies on an independent group of JIA CD4+ T cell samples. <h3>Results</h3> We found widespread transcriptomic differences between ADT and either HC or CRM patients. We identified 4,062 genes that showed differential expression between ADT and HC samples. Gene expression patterns from CRM samples were nearly identical to healthy controls, suggesting that remission largely results in normalization of CD4+ T cell transcriptomes. We performed transcription factor motif analysis on the ATAC-seq identified accessible regions that were associated with differentially expressed genes. We identified the motif for the CCCTC-binding factor (CTCF) as being enriched within these accessible regions, compared to accessible regions associated with non-differentially expressed genes. We performed CTCF ChIP-seq and HiChIP on a second cohort of ADT and HC patients and were able to identify differential binding events, mediated by genetic alterations that interacted with differentially expressed genes. <h3>Conclusion</h3> Transcriptional abnormalities in CD4+ T cells of children with polyarticular JIA are associated with aberrant chromatin organization compared to healthy children. Some of this organization is due to aberrant localization of the transcriptional regulator CTCF, which is due, in some patients, to genetic variance. <h3>Disclosure of Interests</h3> None declared