Endocrine therapies target the activation of the oestrogen receptor alpha (ERa) via distinct
mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using
drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific
epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with
invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal
genomics analysis of reprogrammed regulatory regions identifies individual drug-induced
epigenetic states involving large topologically associating domains (TADs) and the activation
of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB)
through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the
constitutive activation of oestrogen receptors alpha (ERa) in AI-resistant cells, partly via the
biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERa binding is reduced
and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a
subset of ERa-positive patients.