3D chromosomal landscape reveals miR‐146a dysfunctional enhancer in lupus and establishes a CRISPR‐mediated approach to inhibit the IFN pathway

The diminished expression of miR-146a in SLE contributes to the aberrant activation of the interferon pathway. Despite its significance, the underlying mechanism driving this reduced expression remains elusive. Considering the integral role of enhancers in steering gene expression, our study seeks to pinpoint the SLE-affected enhancers responsible for modulating miR-146a expression. Additionally, we aim to elucidate the mechanisms by which these enhancers influence miR-146a's contribution to the activation of interferon pathway.4C-seq and epigenomic profiles were applied to identify candidate enhancers of miR-146a. CRISPR activation was performed to screen functional enhancers. Differential analysis of chromatin accessibility was utilized to identify SLE-dysregulated enhancers and the mechanism underlying enhancer dysfunction was investigated by analyzing transcription factor binding. The therapeutic value of a lupus-related enhancer was further evaluated by targeting it in SLE patients' PBMCs through CRISPR activation approach.We identified shared and cell-specific enhancers of miR-146a in distinct immune cells. An enhancer, 32.5 kb downstream of miR-146a, possesses less accessibility in SLE, and its chromatin openness was negatively correlated with SLE disease activity. Moreover, C/EBPα, a down-regulated transcription factor in SLE patients, binds to the 32.5-kb enhancer and induces the epigenomic change of this locus. Furthermore, CRISPR-based activation of this enhancer in SLE PBMCs could inhibit the activity of interferon pathway.Our work defines a promising target for SLE intervention. We adopted integrative approaches to define cell-specific and functional enhancers of the SLE critical gene, and investigated the mechanism underlying its dysregulation mediated by a lupus-related enhancer.