Transient Menin Inhibition Is Sufficient to Induce Irreversible Polycomb-Mediated Silencing and Potent Anti-Proliferative Effects in MLL-Rearranged AML

MLL-Fusion oncoproteins (MLL-FP) are potent oncogenes that drive an aggressive form of acute myeloid leukaemia (AML). MLL-FP activity can be disrupted by blocking its chromatin occupancy with MLL-Menin inhibitors, or by blocking its biochemical activity through inhibition of DOT1L. Despite these inhibitors having potent anti-leukaemia effects, our understanding of how Menin and DOT1L contribute to MLL-FP function remains incomplete. Here, using functional genomics, we uncover a key role for the non-canonical Polycomb repressive complex 1.1 (PRC1.1) in the silencing of MLL-FP target genes required for the efficacy of Menin and DOT1L inhibitors across a range of in vitro and in vivo MLL-FP models. Mechanistically, Menin inhibition elicits a PRC1.1-dependent selective deposition of the repressive H2AK119ub mark at key MLL-FP target genes, whereas DOT1L inhibition leads to a more global increase in H2AK119ub. Consistent with these differences, we demonstrate that the treatment-induced increase in PRC1.1 activity is specifically associated with loss of H3K79me2 rather than eviction of the MLL-FP or reduction in transcription. In addition, temporal analyses after Menin inhibition revealed that H3K79me2 loss precedes the deposition of H2AK119ub and H3K27me3, which correlates with the gradual downregulation of transcription. Upon this switch in chromatin state, Polycomb target genes undergo stable PRC2-mediated repression, leading to proliferation arrest and the irreversible commitment of leukaemia cells towards differentiation even after early drug withdrawal. Taken together, our findings demonstrate that Polycomb activity is required for the efficacy of these differentiation therapies and highlights why DOT1L is hijacked in MLL-leukaemia with important implications for future therapeutic strategies employing Menin inhibitors.