Genetic heterogeneity and metabolic plasticity cooperate in the establishment of resistance to molecular therapy in FLT3-ITD-positive AML cells

The rapid emergence of drug resistance still represents a major obstacle for effective cancer cure in the clinical setting. Genetic alterations are generally considered the main cause of patient relapse, but the crucial contribution given by non-genetic factors is now becoming clear. In our work, we used FLT3-ITD-positive Acute Myeloid Leukemia (AML) as a model system to investigate the genetic and non-genetic mechanisms involved in drug resistance to molecular therapies. Our data revealed that upon tyrosine kinase inhibitor (TKI) treatment, the passage into a quiescent drug-tolerant persister (DTP) state was necessary for the emergence of a genetically distinct fully resistant population. Moreover, we provided evidence that the transition through the DTP state was characterized by a step of metabolic rewiring from glycolysis to fatty acid oxidation (FAO), which became a fundamental metabolic requirement for persister cells survival. In addition, we observed that rare genetic alterations present at the level of the parental population favored the selection of pre-existing mutated clones (PMCs) during TKI treatment. Nevertheless, pre-existing genetic alterations alone were not sufficient for the establishment of full resistance. Accordingly, also PMCs needed a step of drug adaptation, in part dependent on FAO, before their emergence. Our analysis also revealed that nutrient requirements during the metabolic rewiring phase were modulated by the Randle cycle metabolic circuit. Overall, our study identifies new potential bioenergetic vulnerabilities to target DTPs in FLT3-ITD-positive AML and highlights how both genetic and phenotypic factors concomitantly contribute to the development of full drug resistance.