Abstract 2613: MYC controls DNA methylation on a global scale through DNMT3b upregulation in T-ALL and Burkitts Lymphoma

Abstract

Abstract Background: Oncogenic MYC is implicated in 60-70% of all human cancers, including T-cell acute lymphoblastic leukemia (T-ALL) and Burkitts lymphoma (BL). Genetic inactivation of MYC can cause tumor regression through cellular senescence in mouse models (exhibiting oncogene addiction), making it a promising therapeutic target. However, a pharmacological MYC inhibitor remains elusive, thus these findings cannot be translated into clinic. We are the first to demonstrate that MYC can control DNA methyl-transferase (DNMT) expression and thus, genome-wide DNA methylation; as an alternative strategy to disrupt the MYC network indirectly, we have chosen to target MYC-dependent DNMTs as a tumor-cell specific strategy. Experimental Procedures and Results: Utilizing expression profiling in patient-derived cell lines and clinical specimens, we found DNMT 1, 3a, and 3b to be overexpressed in MYC-driven T-ALL and BL compared to non-malignant tissue. Using transgenic inducible “tet-off” MYC-models in mouse T-ALL (EµSRα-tTA;tet-o-MYC) and human Burkitt’s lymphoma (P493-6), we have shown that DNMT1 and DNMT3b expression depend on high MYC expression levels in T-ALL and BL. Using patient-derived cell lines, we’ve shown that depletion of endogenous MYC caused a reduction of both DNMT1 and DNMT3b expression. Chromatin Immunoprecipitation (ChIP) profiling for MYC binding, further establishes the DNMT1 and DNMT3b promoters as bona fide targets of the MYC oncogene. Furthermore, shRNA-mediated knockdown of DNMT3b or pharmacological inhibition using NanaomycinA, indicates a tumor promoter function in the context of MYC-driven tumor maintenance in T-ALL. To further elucidate the consequence on DNA methylation and gene expression upon DNMT3b loss of function, Reduced Representation Bisulfite Sequencing and RNA-sequencing was performed to analyze alterations in DNA methylation and gene expression, respectively. We found that DNMT3b maintains CpG island DNA methylation near promoters, responsible for gene silencing during tumor maintenance. Accompanying changes in DNA methylation, we identified approximately one thousand differentially expressed genes upon DNMT3b knockdown, with upregulated genes responsible for controlling differentiation, transport, and development; while downregulated genes controlled processes including signal transduction, apoptosis, and regulation of cellular proliferation. Conclusion: Together, we provide novel evidence that MYC directly controls global DNA methylation through deregulation of DNMT1 and DNMT3b expression to maintain gene programs for T-ALL tumor maintenance. Furthermore, we provide evidence that targeted inhibition of individual DNMTs may reveal alternative tumor-specific therapies for T-ALL, BL, and other MYC-driven cancers. Citation Format: Candace J. Poole, Atul Lodh, Jan van Riggelen. MYC controls DNA methylation on a global scale through DNMT3b upregulation in T-ALL and Burkitts Lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2613.