Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [ATAC-seq]

Pharmacologic targeting of epigenetic protein complexes has shown significant in vitro responses in AML. Early clinical trials in MLL-rearranged leukemia indicate rather transient responses and development of resistance. In an effort to define functional dependencies of MLL-fusions in acute myeloid leukemia, we identify the catalytic immunoproteasome subunit PSMB8 as an oncogene-specific vulnerability. Genetic and pharmacologic inactivation of PSMB8 results in impaired proliferation of murine and human leukemic cells while normal hematopoietic cells remain unaffected. Disruption of immunoproteasome function results in cellular enrichment of transcription factor BASP1, and consecutive repression of MLL-target genes. Pharmacologic targeting of PSMB8 improves efficacy of Menin-inhibitors, eradicates leukemia in primary human xenografts and shows preserved activity against Menin-inhibitor resistance mutations. This identifies and validates a cell-intrinsic mechanism whereby selectivity of proteostasis results in altered transcription factor abundance and repression of oncogene-specific transcriptional networks. Therapeutic targeting of PSMB8-dependent transcription in combination with Menin-inhibition could thus eradicate AML harboring MLL-rearrangements. Genome binding/occupancy profiling in MOLM-13 cells after 100nM PR-957 (ONX-0914) treatment or diluent control treatment for 48hours.