Targeting eRNA‐Producing Super‐Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient‐Derived Immune Cells

Abstract Chronic inflammatory diseases are driven by immune cell dysregulation and overproduction of pro‐inflammatory molecules, such as tumor necrosis factor alpha (TNFα). Super‐enhancers (SEs) and their enhancer RNAs (eRNAs) are critical gene expression regulators and offer therapeutic potential beyond protein‐targeting approaches. This work hypothesizes that targeting eRNAs could reduce chronic inflammation by modulating TNFα expression. This work generates TNF‐9 knockout (KO) mice by deleting a Tnfα‐regulating enhancer region. These mice exhibit significantly reduced Tnfα 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 identify additional LPS‐responsive, eRNA‐producing enhancers as therapeutic targets. Antisense oligonucleotide (ASO)‐mediated knockdown of TNF‐9 eRNA in mouse macrophages demonstrate decreased Tnfα expression and alleviated RA symptoms. Furthermore, ASO‐mediated inhibition of the eRNA of the human homolog of TNF‐9 similarly reduce TNFα levels. These findings support eRNA‐targeted interventions as potential treatment for chronic inflammatory diseases.