AML-373 Double mutant DNMT3A increases methylation damage in acute myeloid leukemia by inhibition of TDG function

• Published in: Clinical lymphoma, myeloma and leukemia myeloma and leukemia, 2024-09, Vol.24, p.S310-S310
• Main Authors: Boertjes, Emma, Massaar, Sanne, Zeilemaker, Annelieke, Konijnenburg, Jolinda, Kavelaars, Francois, Rijken, Melissa, Grob, Tim, Versluis, Jurjen, Sanders, Mathijs, Valk, Peter
• Format: Article
• Language: English
• Subjects: AML; DNMT3A; methylation damage; TDG
• ISSN: 2152-2650
• DOI: 10.1016/S2152-2650(24)01192-3

Mutations in DNMT3A, a de novo methyltransferase essential for the methylation of cytosines in a CpG dinucleotide context, are common early events in adult acute myeloid leukemia (AML). Methylation of cytosines can lead to DNA damage through spontaneous deanimation, which is normally repaired by the base excision repair enzymes MBD4 and TDG. Germline deficiency of MBD4 has been linked to increased risk of clonal hematopoiesis (CH) and AML with exceedingly high levels of methylation damage and mutations in DNMT3A. In MBD4-deficient AML, TDG does not compensate for MBD4 loss. Previous investigation suggests that DNMT3A and TDG interact, thereby positively influencing the repair activity of TDG. Nevertheless, it is unknown whether mutant DNMT3A could negatively impact the function of TDG. We investigated the impact of common DNMT3A mutations on TDG function to learn whether methylation damage repair is impaired. Targeted next-generation sequencing was performed to compare the driver landscape of single- (SM) versus double-mutated (DM) DNMT3A AML. Finally, we investigated whether overall methylation damage is increased in DM compared to SM. MBD4 and TDG repair activity was assessed in the presence of wildtype (WT) or mutant DNMT3A using glycosylase assays. Differences in survival and co-mutations were assessed in our AML cohort comprising 1,872 DNMT3A WT, 585 SM, and 88 DM patients. Whole-genome sequencing (WGS) was performed on diagnosis bone marrow aspirates from 6 DNMT3A WT, 7 SM, and 9 DM AML patients. WT DNMT3A potentiates the capacity of TDG to repair methylation damage. Mutant DNMT3A cotitrated with WT DNMT3A demonstrated weaker potentiation of TDG and resulted in inhibition at higher concentration. DNMT3A SM had a strong enrichment for DNMT3A R882 hotspot and NPM1 mutations, whereas there was a 10-fold increase in the IDH2 R172 hotspot mutation in DM. DNMT3A DM had a significantly worse overall survival (OS) compared to SM (HR=1.33, P=0.045). WGS uncovered a genome-wide increase in methylation damage when comparing DNMT3A DM to SM, which becomes even more prominent when DNMT3A mutations are positioned at the DNMT3A-TDG interaction interface. Double mutant DNMT3A is linked to increased methylation damage, diverging driver landscape and unfavorable overall survival.