Lineage-Specific Metabolic Reprogramming Reveals LKB1 as Therapeutic Target in Acute Lymphoblastic Leukemia

Background & Hypothesis: The Philadelphia chromosome encoding the oncogenic BCR-ABL1 (Ph⁺) tyrosine kinase represents a common transforming oncogene in both chronic myeloid leukemia (CML) and a subset of pre-B acute lymphoblastic leukemia (ALL). While both diseases are driven by the same oncogene, biological and clinical characteristics differ between CML and Ph⁺ ALL. Given that oncogenic signaling from potent tyrosine kinases like BCR-ABL1 imposes significant metabolic requirements on energy supply, biogenesis and ability to survive metabolic stress, we investigated whether the divergent characteristics of BCR-ABL1 CML and Ph⁺ ALL have a metabolic basis.

Results: Interestingly, metabolic analyses demonstrated that patient-derived CML chronic phase (CML-CP) and Ph⁺ ALL cells have distinguishable glycolytic profiles. Consistent with a higher proliferative rate, Ph⁺ ALL cells rapidly exhausted the capacity of their glycolytic machinery when compared to CML-CP cells. Furthermore, when comparing their glycolytic reserve (i.e. spare glycolytic capacity needed to compensate for loss of mitochondrial ATP production), Ph⁺ ALL cells were shown to have a lower glycolytic reserve compared to CML-CP cells. These findings suggest that Ph⁺ ALL cells have less flexibility in adapting to metabolic stress. Searching for factors that mediate metabolic reprogramming to support rapid cellular proliferation and promote adaptation to metabolic stress in a lineage-specific manner, we identified the tumor suppressor LKB1 and its substrate AMPK which coordinate metabolism with cell growth.

To elucidate the potential lineage-specific functions of LKB1, genetic mouse models for 4-hydroxytamoxifen (4-OHT)-inducible deletion of Lkb1 in BCR-ABL1-driven myeloid leukemia (CML-like) and pre-B ALL (Ph⁺ ALL-like) were developed. Cre-mediated deletion of Lkb1 in myeloid leukemia mediated proliferation and stimulated aerobic glycolysis, as reflected by increases in both glucose consumption and lactate production. These findings are in agreement with previous findings in solid tumors and are consistent with the role of LKB1 as a tumor suppressor. In striking contrast, deletion of Lkb1 in pre-B ALL cells induced apoptosis and cell cycle arrest. In vivo, Lkb1 deletion in pre-B ALL cells delayed leukemia initiation and prolonged overall survival of transplant recipient mice. Furthermore, bioenergetics measurements of glycolytic and mitochondrial functions in response to various conditions of metabolic stress revealed that loss of Lkb1 function in pre-B ALL resulted in impaired metabolic adaptation. Likewise, metabolite profiling revealed that deletion of Lkb1 in pre-B ALL cells resulted in altered levels of metabolites from glycolysis, the TCA cycle, the pentose phosphate pathway, nucleotide metabolism, currency metabolites, amino acid metabolism and fatty acid metabolism. Importantly, C/EBPα-mediated lineage reprogramming of pre-B ALL cells into the myeloid lineage alleviated their dependency on Lkb1.

Similar to observations made with Cre-mediated deletion of Lkb1 in a model for BCR-ABL1 pre-B ALL, small molecule inhibition of AMPK using BML-275 (an ATP-competitive inhibitor) induced apoptosis in patient-derived pre-B ALL cells. Moreover, BML-275 had deleterious effects on metabolic adaptation in patient-derived pre-B ALL cells, but not in CML-CP cells. Finally, BML-275 synergized with pharmacological inhibition of PI3K/Akt signaling in inhibiting glycolytic function and eradicating patient-derived pre-B ALL cells. Combining BML-275 and a PI3K inhibitor (BKM120) exerted significantly more potent inhibitory effect on pre-B ALL progression than each agent alone, prolonging the overall survival of recipient mice.

Conclusions: Taken together, our findings demonstrate that LKB1/AMPK signaling plays lineage-specific roles in BCR-ABL1-driven CML and pre-B ALL. While LKB1/AMPK is an established tumor suppressor pathway in multiple cell types, our findings reveal a unique and previously unrecognized vulnerability of pre-B ALL cells.