Targeting acute myeloid leukemia resistance with two novel combinations demonstrate superior efficacy in TP53, HLA-B, MUC4 and FLT3 mutations

Abstract

Acute myeloid leukemia (AML) is a genetically heterogeneous malignancy characterized by the clonal expansion of myeloid precursor cells. Despite the advent of venetoclax-based regimens, resistance mechanisms remain a major clinical challenge, particularly in patients with high-risk mutations such as TP53, MUC4, HLA-B and FLT3. Here, we evaluate two rational combination therapies, LY3009120 (pan-RAF) plus sapanisertib (mTOR) (LS), and ruxolitinib (JAK1/2) plus ulixertinib (ERK) (RU), across ten AML cell lines and a zebrafish embryo xenograft model. The study integrates real-time cell viability assays, xenograft imaging, and genetic analyses and relates responses to mutational profiles and benchmarks against first line treatment (venetoclax based combinations), the current standard for older and unfit AML. Both combinations outperformed or matched venetoclax-based comparators, with LS markedly reducing viability and RU showing robust efficacy in AML cell lines. In zebrafish, LS and RU suppressed leukemic burden with zero mortality and with modest effects on embryo length, indicating supportive but preliminary tolerability under the conditions tested. Mutation response analyses and clustering highlighted TP53, MUC4, HLA-B and FLT3 as correlates of LS and RU sensitivity, supporting mutation-informed prioritization. Collectively, our results nominate LS and RU as promising candidates, particularly in AML with TP53, FLT3, HLA-B or MUC4 alterations, and motivate prospective validation in stratified AML cohorts.