IDH3 regulates citrate homeostasis to control metabolic fitness and venetoclax resistance of AML stem cells

Targeting metabolic dependencies of leukemic stem cells (LSC) may open avenues to improve outcomes of patients suffering from acute myeloid leukemia (AML). LSCs rely heavily on an active tricarboxylic acid (TCA) cycle and mitochondrial oxidative phosphorylation whereas healthy hematopoietic stem and progenitor cells (HSPCs) possess more metabolic flexibility. Here, we identify the TCA cycle enzyme isocitrate dehydrogenase 3 (IDH3) as a critical and selective regulator of LSC maintenance. IDH3 is more abundant in LSCs compared to healthy HSPCs, and TCA cycle activity correlates with inferior clinical outcomes of AML patients. Knockdown of IDH3A, the catalytic subunit of the complex, impairs colony-forming potential and bone marrow organoid as well as in vivo engraftment of AML, while sparing healthy hematopoiesis. Mechanistically, IDH3A downregulation reduces TCA cycle flux and leads to accumulation of intracellular citrate, impairing both glycolysis and oxidative phosphorylation. The resulting bioenergetic crisis activates AMPK and suppresses mTORC1, leading to reduced translational activity and an imbalance of anti-apoptotic proteins. Consequently, IDH3A-KD cells show enhanced susceptibility to BCL2 inhibition by venetoclax in vitro and in vivo. In a clinical cohort, LSCs from patients resistant to venetoclax/azacitidine (Ven/Aza) exhibit transcriptomic programs indicative of active TCA cycle and glycolysis. We demonstrate that downregulation of IDH3A activity and subsequent citrate accumulation directly affect these pathways and shift AML stem cells towards a metabolic state of increased vulnerability. In summary, we establish IDH3 as a metabolic rheostat in LSCs and suggest targeting the IDH3A-citrate axis to overcome Ven/Aza resistance of AML patients.