MLL (KMT2A)-rearranged Acute Lymphoblastic Leukemias Are Addicted to S-Adenosyl Methionine (SAM): Implications for Therapy

Abstract

MLL (KMT2A)-rearranged acute lymphoblastic leukemia (MLLr ALL) is an aggressive subset associated with poor survival and relapse representing 5% of childhood ALL cases and 75% of infant leukemias. Though current intensive chemotherapy regimens have improved survival in childhood ALL overall, they fail to cure many of these high-risk patient subgroups and inflict significant long-term side effects, demonstrating the urgent need for novel therapies. While exploring the effect of different amino acid depletion strategies, we observed rapid induction of apoptosis upon methionine restriction (MR) in MLLr cells. The histone methyltransferase function of the MLL fusion protein complex requires increased amounts of the methionine metabolite s-adenosylmethionine (SAM) to maintain its hypermethylated state, creating a selective sensitivity of MLLr ALL for perturbations in methionine availability. To explore how MR impinges on MLLr cells' metabolic state we performed global metabolomics on SEM cells and observed rapid effects on metabolism, with 416 metabolites out of the 650 measured differing significantly upon 12 hours of MR. We performed in parallel mRNA sequencing on SEM cells to understand the effect of MR on gene expression and identified 1351 differentially expressed genes. Integrated transcriptomics and metabolomics analysis revealed several key pathways interlinked with SAM, including the folate cycle, polyamine synthesis, arginine/redox metabolism, nucleotide synthesis, and the creatine/urea cycle, with several SAM-dependent enzymes and key byproducts in these pathways being significantly reduced upon MR. Moreover, addition of SAM completely rescued MLLr cell lines from methionine depletion induced apoptosis, an effect not observed in non-MLLr cells, confirming the critical role of SAM in this leukemia subset. To better understand the effect of methionine and SAM restriction on epigenetic modifications, we looked at histone methylation in a panel of MLLr and non-MLLr B-ALL cell lines and observed a global suppression of methylation upon MR specifically in the pediatric MLLr cells. Additionally, gene expression analysis revealed downregulation of key MLL fusion target genes associated with proliferation and maintenance of the oncogenic phenotype in response to MR, including ZMYND8, ERG, BCL2, PROM1, HMX3, HOXA10, HMGA2, and PBX3. Several of these gene targets are known to be transcriptionally upregulated in MLLr leukemia via aberrant H3K79 methylation. Consistent with this notion, knockdown of the H3K79 demethylase, KDM2B, displayed a more MR-resistant phenotype than its wildtype counterparts. Taken together, MR has a direct effect on global histone methylation in MLLr ALL cells, which in turn disturbs the MLL gene signature critical for their survival. Lastly, immunocompromised mice were engrafted with MLLr SEM cells and treated with a 95% MR diet while leukemia progression was monitored by flow cytometry. The MR diet was well tolerated with minimal weight loss, methionine levels in plasma were roughly 50% reduced compared to controls, and that alone was enough to significantly delay leukemic growth (p = 0.015). While several compounds targeting MAT2A, the enzyme that produces SAM from methionine, are currently in Phase 1 clinical trials, the availability of an FDA approved methionine-free formula for infants allows for rapid translation to the clinic. As a follow-up, we also performed a drug screen using 214 compounds to identify drugs that interact with MR, showing that vinca-alkaloids, including vincristine, strongly synergize. Validation experiments demonstrate that MR triggers a stress induced G2 arrest, priming cells for mitotic spindle destruction with vincristine. In vivo experiments are currently underway using patient-derived xenografts exploring synergistic potential of vincristine with targeting methionine metabolism. In summary, we found that MLLr leukemic cells are selectively vulnerable to perturbations of the methionine cycle due to their increased need for SAM to maintain hypermethylation and aberrant gene activation. Limiting methionine and/or SAM availability provides an attractive adjuvant therapy potentiating the effects of current or novel (targeted) therapies for MLLr leukemia.