β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (DNA methylation array)

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrate that this differentiated state is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the ACC epigenome. On chromatin, β-catenin binds master adrenal transcription factor SF1 and hijacks the adrenocortical super-enhancer landscape to maintain differentiation. Off chromatin, β-catenin binds histone methyltransferase EZH2, which is redistributed by the CIMP-high DNA methylation signature. SF1/β-catenin and EZH2/β-catenin complexes exist in normal adrenals and are selected for through all phases of ACC evolution. EZH2 inhibition in CIMP-high ACC favors EZH2/β-catenin assembly and purges SF1/β-catenin from chromatin, erasing differentiation and restraining cancer growth in vitro and in vivo. Our studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities. Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline) or EZH2 inhibitor EPZ-6438 (EZH2i) to evaluate the impact of EZH2 inhibition on the ACC epigenome. At endpoint, cells were harvested for DNA methylation array profiling by Illumina EPIC array. Alternatively, human adrenal glands were microdissected for zona fasciculata (ZF), zona reticularis (ZR), or fetal zone (FZ). After microdissection, DNA was extracted and submitted for methylation profiling by Illumina EPIC array. Donors for ZF and ZR samples are identified by number at the end of title (e.g. Donor 1 provided ZF1 and ZR1, Donor 3 provided ZF3 and ZR3 and so on). Fetal zone samples came from independent donors.