KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function

Estrogen receptor alpha (ER alpha) is a ligand-activated nuclear receptor that directs proliferation and differentiation in selected cancer cell types including mammary-derived carcinomas. These master-regulatory functions of ER alpha require trans-acting elements such as the pioneer factor FOXA1 to establish a genomic landscape conducive to ER alpha control. Here, we identify the H3K4 methyltransferase KMT2C as necessary for hormone-driven ER alpha activity and breast cancer proliferation. KMT2C knockdown suppresses estrogen-dependent gene expression and causes H3K4me1 and H3K27ac loss selectively at ER alpha enhancers. Correspondingly, KMT2C loss impairs estrogen-driven breast cancer proliferation but has no effect on ER- breast cells. Whereas KMT2C loss disrupts estrogen-driven proliferation, it conversely promotes tumor outgrowth under hormone-depleted conditions. In accordance, KMT2C is one of the most frequently mutated genes in ER-positive breast cancer with KMT2C deletion correlating with significantly shorter progression-free survival on anti-estrogen therapy. From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ER alpha, displaying ongoing sensitivity to ER alpha antagonists. We conclude that KMT2C is a key regulator of ER alpha activity whose loss uncouples breast cancer proliferation from hormone abundance.