Abstract 1025: Genomic and metabolomic analysis of MAT2A inhibition reveals increased RNA splicing, lipid metabolism and cell cycle arrest in MTAP deleted tumor models

Abstract

Abstract Background: Approximately 15% of solid tumors harbor deletions in Methylthioadenosine phosphorylase (MTAP) (1). MTAP deletion confers enhanced sensitivity to Methionine Adenosyltransferase 2A (MAT2A) inhibition, which synthesizes the universal methyl donor and PRMT5 substrate S-Adenosyl Methionine (SAM) (2). MTAP loss results in the accumulation of its substrate methylthioadenosine (MTA) which partially inhibits PRMT5. PRMT5 symmetrically di-methylates arginine (SDMA) residues on proteins that are key to genomic integrity and proteostasis. Therefore, MTA accumulation and MAT2A inhibitor-driven abrogation of SAM significantly inhibit PRMT5 activity and key oncogenic signaling in MTAP deleted cancers. In this study, we sought to investigate the mechanistic and phenotypic implications of this synthetic lethal relationship. Methods: Using the HCT116 MTAP deleted isogenic pair and a panel of MTAP deleted cell lines, we evaluated the genomic and metabolomic effects of a proprietary MAT2A inhibitor using RNA sequencing (RNA-seq) and untargeted metabolomics respectively. Further, we investigated the effects of MAT2A inhibition across a large panel of MTAP WT and deleted cell lines in a multiplexed assay that assessed proliferation, apoptosis and cell cycle status. Results: MAT2A inhibition decreased SAM, and selectively decreased the proliferation and expression of SDMA in MTAP deleted cell lines. From RNA-seq data, MAT2A inhibition notably affected genes involved in p53 and plasma membrane signaling in the HCT116 MTAP deleted cell line compared to its parental counterpart. RNA-seq data also identified elevated frequency of alternative spliced transcripts that are involved in cell cycle, RNA processing and lipid metabolism pathways. In alignment with these observations, untargeted metabolomic analysis of MAT2A inhibition identified robust and selective changes in polyamine synthesis, oxidative stress and lipid metabolism in the HCT116 MTAP deleted cell line. With the changes in cell cycle related genes and previous reports indicating a role of lipid metabolism in cell cycle arrest , MAT2A inhibition increased expression of the G2/M cell cycle marker phospho-histone H3 and decreased proliferation in a larger percentage of MTAP deleted cell lines compared to MTAP WT cell lines. We further confirmed RNA-Seq data and observed increased p53 expression and a concordant decrease in the p53-regulated G2/M transition marker Cyclin B1 upon MAT2A inhibition in the HCT116 MTAP-deleted cell line. Conclusion: We have shown that MAT2A blockade results in distinct genomic and metabolomic effects that drives G2/M cell cycle arrest in MTAP deleted cell lines. Further analysis of these changes will help identify potential biomarkers that can further inform on the activity of MAT2A inhibition. We are currently targeting to enter clinical trials in 2021. Citation Format: Neil Bhola, Atieh Givmanesh, John Faulhaber, Melissa Fleury, Mark Lackner, Zineb Mounir, Divya Pankajakshan. Genomic and metabolomic analysis of MAT2A inhibition reveals increased RNA splicing, lipid metabolism and cell cycle arrest in MTAP deleted tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1025.