RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance

Kennedy, V. E.; Peretz, C. A. C.; Walia, A.; Chyla, B.; Sun, Y.; Hill, J.; Tran, E.; Koh, A.; Ferng, T.; Pintar, S.; Jones, M.; Popescu, B.; Murad, N.; Roy, R.; Olshen, A.; Joshi, S.; Traer, E.; Dail, M.; Hamidi, H.; Altman, J.; Daver, N.; Levis, M.; McCloskey, J.; Perl, A.; Smith, C. C.

doi:10.1101/2025.02.02.636108

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bioRxiv · 10.1101/2025.02.02.636108

RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance

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Abstract

Despite efficacy of FLT3 and BCL2 inhibition in acute myeloid leukemia (AML), relapse limits survival. Mutation status and AML monocytic differentiation are implicated in resistance. On-treatment tumor evolution may select for genetically distinct clones or shifts in differentiation not resolvable by bulk sequencing. We performed multiomic single cell (SC) DNA/protein and RNA/protein profiling of patients treated on a clinical trial of the BCL2 inhibitor venetoclax and the FLT3 inhibitor gilteritinib (Ven/Git) to characterize immunophenotypic, transcriptional, and genetic clonal evolution on therapy. We found that while Ven/Gilt effectively eliminated FLT3 mutant clones, it selected for RAS mutations, RAS pathway activation and RAS-associated monocytic differentiation. In an in vitro model of monocytic differentiation associated with heightened RAS pathway activation, we demonstrated that MEK inhibition re-sensitized to Ven/Gilt. These data indicate RAS signaling is central to FLT3 and BCL2 inhibitor resistance, is tightly coupled to monocytic differentiation and can be overcome by RAS pathway inhibition. COIC.C.S. has provided educational talks for Astellas Pharma, served on advisory boards for Genentech/Abbvie and received research funding from Abbvie. B.C., Y.S. and J.H. are employees of Abbvie. M.S. and H.H. are or were previously employees of Genentech. FundingThis work was supported in part by Abbvie. C.C.S. is a Leukemia & Lymphoma Society Scholar in Clinical Research and a Damon Runyon-Richard Lumsden Foundation Clinical Investigator supported (in part) by the Damon Runyon Cancer Research Foundation (CI-99-18). Statement of SignificanceMutational and non-mutational RAS signaling activation drives clonal selection, monocytic differentiation and treatment resistance to FLT3 and BCL2 inhibition in AML. MEK inhibition can resensitize resistant AML cells, suggesting therapeutic potential for combined FLT3, BCL2 and RAS pathway inhibition in AML.

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Kennedy, V. E., Peretz, C. A. C., Walia, A., Chyla, B., Sun, Y., Hill, J., Tran, E., Koh, A., Ferng, T., Pintar, S., Jones, M., Popescu, B., Murad, N., Roy, R., Olshen, A., Joshi, S., Traer, E., Dail, M., Hamidi, H., Altman, J., Daver, N., Levis, M., McCloskey, J., Perl, A., Smith, C. C.. 2025-02-07. RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance. https://doi.org/10.1101/2025.02.02.636108

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