Targeting BRD9 in KMT2A-rearranged Acute Myeloid Leukemia to citcumvent MEN1 inhibitor resistance
Acute myeloid leukemia (AML) with KMT2A rearrangement (KMT2Ar) has a poor clinical prognosis. Oncogene program of this AML subtype is driven by the interaction between KMT2A and its cofactor MEN1. MEN1 inhibitors (MEN1i) target this interaction and show therapeutic promise in relapsed/refractory KMT2Ar AML. However, ~40% of the treated patients develop resistance to MEN1i caused by acquired MEN1 mutations, highlighting an unmet need for alternative therapies. AML cells with KMT2Ar rely on a core set of transcription factors including IRF8, MEF2D, and MYC, known as the transcription factor (TF) addiction pathway. In this study, we investigated the roles of BRD9, a subunit of human BRG1/BRM-associated factor chromatin remodeling complex, in regulating the TF addiction pathway, and therapeutic potential of BRD9 degraders on MEN1i-resistant KMT2Ar AML cells.
A BRD9 degrader (dBRD9A) was used to deplete BRD9 in AML cell lines and primary AML samples. We measured the effects of dBRD9A treatment on cell viability and differentiation as the primary readout of drug potency. ATAC-seq and RNA-seq were employed to identify the changes of chromatin accessibility and transcriptome following BRD9 depletion. Functional relevance of the identified gene targets were further confirmed by performing genetic rescue experiments.
The Depmap CRISPR screen data revealed that BRD9 is essential in KMT2Ar or KMT2A mutations (KMT2A+) leukemic cell lines. Chemical depletion of BRD9 confirmed that BRD9 loss induces growth defect and myeloid differentiation. Subsequently, transcriptomic analysis of MOLM13 cells (KMT2Ar) revealed rapid downregulation of IRF8 and MYC after 3 h BRD9 depletion. The transcriptomic changes coincided with reduced chromatin accessibility of IRF8 and MYC super enhancers that contain the consensus binding sequence of MYB. Interestingly, the effects of BRD9 depletion were attenuated in the cells genetically reconstituted with IRF8 and MYC. Next, we studied the effects of BRD9 depletion in a panel of primary KMT2Ar AML samples with either high or low expression of IRF8. The IRF8-high samples displayed higher sensitive to dBRD9A treatment than the IRF8-low samples. Moreover, the expression of the TF addiction genes were preferentially downregulated in the IRF8-high AML samples after BRD9 degradation. Furthermore, we uncovered that BRD9 and MEN1 independently regulate the genes associated with the TF addiction and the KMT2A/MEN1 pathway, respectively. Due to this regulatory independency, BRD9 depletion could reduce the viability of both wild-type and MEN-1 mutated MV4-11 (KMT2Ar) cell lines.
BRD9 cooperates with MYB to activate the TF addiction genes and sustains the growth of KMT2Ar AML cells. Translationally, the TF addiction pathway is independent from the KMT2A/MEN1 regulatory pathway. Anti-BRD9 agents remain effective in AML cells with MEN1 mutations, suggesting their potential to be used to treat KMT2Ar patients who are resistant to MEN1i.