Targeting eRNA-producing super-enhancers regulates TNFa expression and mitigates chronic inflammation in mice and patient-derived immune cells [CUT&RUN]

Chronic inflammatory diseases are driven by immune cell dysregulation and overproduction of pro-inflammatory molecules, such as tumor necrosis factor alpha (TNFa). Super-enhancers (SEs) and their enhancer RNAs (eRNAs) are critical gene expression regulators and offer therapeutic potential beyond protein-targeting approaches. We hypothesized that targeting eRNAs could reduce chronic inflammation by modulating TNFa expression. We generated TNF-9 knockout (KO) mice by deleting a Tnfa-regulating enhancer region. These mice exhibited significantly reduced Tnfa levels, improved disease outcomes, and diminished immune cell activation in models of rheumatoid arthritis (RA), psoriasis, and lipopolysaccharide (LPS)-induced sepsis. Integrative epigenomic and transcriptomic analysis identified additional LPS-responsive, eRNA-producing enhancers as therapeutic targets. Antisense oligonucleotide (ASO)-mediated knockdown of TNF-9 eRNA in mouse macrophages demonstrated decreased Tnfa expression and alleviated RA symptoms. Furthermore, ASO-mediated inhibition of the eRNA of the human homolog of TNF-9 similarly reduced TNFa levels. These findings support eRNA-targeted interventions as potential treatment for chronic inflammatory diseases. Overall design: CUT and RUN seq of BMDM from C57BL/6 mouse with or without LPS 1hr stimulation (with LPS stimulation : LPS, without LPS stimulation : UT). Chromatin profiling was conducted using three antibodies : H3K4me1 (me1), H3K27Ac (ac), and input control (IgG).