IL-6 production through repression of UBASH3A gene via epigenetic dysregulation of super-enhancer in CD4(+) T cells in rheumatoid arthritis

BACKGROUND: Rheumatoid arthritis (RA) is associated with immune dysfunction. UBASH3A as a negative regulator of T cell receptors (TCRs) signaling is a susceptible factor in RA. The aim of this study was to determine the role of UBASH3A in RA pathogenesis, by assessing the role of super-enhancer (SE) in the control of UBASH3A expression in CD4(+) T cells and the contribution of the latter in proinflammatory cytokine production in patients with RA. METHODS: UBASH3A mRNA and protein levels were quantified by PCR and western blotting, respectively. The cells were treated with a locked nucleic acid to inhibit enhancer RNA (eRNA) expression. Chromatin immunoprecipitation was used to identify the factors recruited to UBASH3A loci displaying SE architecture. CD4(+) T cells were transfected with UBASH3A plasmids, and cytokine levels were measured by a cytometric bead array. RESULTS: UBASH3A was extracted as a RA susceptibility gene associated with SNPs in the SEs that are highly expressed in CD4(+) T cells by in silico screening. UBASH3A mRNA and protein expression levels were lower in CD4(+) T cells of RA patients than in the control. eRNA_1 and eRNA_3 knockdown reduced UBASH3A mRNA levels. RA patients exhibited accumulation of BTB and CNC homology 2 (BACH2), the silencing transcription factor, at the UBASH3A loci in CD4(+) T cells, but not the SE-defining factor, mediator complex subunit 1 (MED1)/bromodomain 4 (BRD4). However, opposite changes were observed in the control. Stimulation of TCRs expressed on CD4(+) T cells of RA patients resulted in interleukin (IL)-6 production, while UBASH3A over-expression significantly inhibited the production. CONCLUSIONS: In RA, transcription of UBASH3A is suppressed via epigenetic regulation of SE in CD4(+) T cells. Low UBASH3A levels result in excessive TCR signal activation with subsequent enhancement of IL-6 production. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s41232-022-00231-9.