TP53 inactivation confers resistance to the menin inhibitor revumenib in Acute Myeloid Leukemia

Abstract

Abstract Acute myeloid leukemia (AML) is a heterogeneous and aggressive hematologic malignancy associated with poor outcomes and limited treatment options. A subset of AML cases are characterized by KMT2A rearrangements (KMT2Ar), which often co-occur with secondary mutations, most commonly in RAS. Recent studies have highlighted that TP53 mutations also occur in this context and are often associated with resistance to conventional and targeted therapies. Menin inhibitors, such as revumenib, have demonstrated promising activity in treating AML with KMT2Ar or NPM1 mutations by disrupting the menin-KMT2A interaction critical for leukemogenesis. While acquired resistance involving somatic mutations in the MEN1 gene has been observed during treatment, the mechanisms responsible for de novo resistance remains unknown. Given the accelerating clinical development of menin inhibitors, both as monotherapies and in combination with chemotherapy or other targeted agents, understanding genetic factors that affect treatment response is increasingly important. Identifying such biomarkers can inform patient stratification and guide the development of rational drug combinations, especially in treatment-refractory AML. To investigate the role of TP53 in menin inhibitor sensitivity, we analyzed primary patient datasets and confirmed that TP53 mutations and KMT2Ar frequently co-occur in pediatric AML, which correlated with inferior clinical outcomes. To model this genetically, we generated isogenic TP53 wild-type and TP53 knockout MV4-11 cells, a KMT2Ar AML cell line responsive to menin inhibition. This allowed us to directly evaluate the impact of TP53 loss on response to revumenib. We found that TP53-mutant cells were intrinsically resistant to revumenib, in contrast to their wild-type counterparts. The TP53-mutant cells failed to activate canonical p53 transcriptional targets upon treatment, indicating impaired apoptotic signaling. Furthermore, gene expression analysis and BH3 profiling revealed dysregulation of the apoptosis regulators BCL-2 and MCL-1, suggesting a shift toward an apoptosis-resistant state. Building on the results, we then examined combination treatments. In TP53-WT cells, revumenib synergized with the BCL-2 inhibitor venetoclax, consistent with previously reported activity. However, this synergy was lost in TP53-mutant cells, demonstrating that functional TP53 is required for the apoptotic response to this combination. Notably, TP53-mutant cells displayed enhanced sensitivity to the combination of revumenib and an MCL-1 inhibitor, suggesting that MCL-1 becomes a dominant survival factor in the absence of TP53. Together, these results highlight a therapeutic vulnerability in TP53-mutant AML that could be exploited using menin and MCL-1 co-targeting. Importantly, this strategy may offer improved tolerability compared to dual BCL-2/MCL-1 inhibition, which has overlapping toxicity profiles. Our findings suggest that TP53 mutational status may serve as a predictive biomarker for response to menin inhibitors and help guide the selection of rational drug combinations. Specifically, co-targeting MCL-1 in TP53-mutant AML may overcome intrinsic resistance to menin inhibition and improve therapeutic outcomes in this high-risk subset. In summary, this study provides the first direct evidence that TP53 mutations confer de novo resistance to menin inhibition in KMT2A-rearranged AML. By uncovering how TP53 loss rewires apoptotic signaling and alters drug sensitivity, we offer a mechanistic rationale for pairing menin inhibitors with MCL-1 inhibitors in genetically defined patient subsets. These findings underscore the importance of integrating biomarker-driven strategies into future clinical trials of menin inhibitor-based therapies and lay the groundwork for developing tailored treatments for patients with high-risk, TP53-mutant AML.