Menin-MLL complex cooperates with NF-Y to promote HCC survival [CUT&RUN]

Identification of new therapeutic targets in hepatocellular carcinoma (HCC) remains critical. Chromatin regulating complexes are frequently mutated or aberrantly expressed in HCC, suggesting dysregulation of chromatin environments is a key feature driving liver cancer. To investigate whether the altered chromatin state in HCC cells could be targeted, we designed and utilized an epigenome-focused CRISPR library that targets all genes involved in chromatin regulation. This focused approach allowed us to test multiple cell lines in both 2D and 3D growth conditions, which revealed striking differences in the essentiality of genes involved in ubiquitination and uncovered multiple chromatin regulators vital for HCC cell survival in 2D but whose loss promoted growth in 3D. We found the core subunits of the menin-MLL1 complex among the strongest essential genes for HCC survival in all screens and thoroughly characterized the mechanism through which menin-MLL1 complex promote HCC cell growth. Inhibition of the menin-MLL1 interaction led to global changes in occupancy of the complex and concomitant decreases in H3K4me3 and gene expression. We observed that increased chromatin accessibility at sites not bound by menin-MLL1 was associated with the recruitment of the pioneer transcription factor complex NF-Y. A CRISPR/Cas9 screen of chromatin regulators in the presence of the menin-MLL1 inhibitor SNDX-5613 revealed a synergistic effect on cell death when combining NF-YB loss and menin-MLL1 interaction inhibition. Together, these data show that menin-MLL1 is necessary for HCC cell survival and cooperates with NF-Y to regulate oncogenic gene transcription. CUT&RUN was performed for indicated antibodies following treatment of HLF cells with 5uM SNDX-5613 or DMSO for 24 hours