Evidence supporting a dominant negative mechanism for DNMT3A hotspot mutation-mediated leukemic cell transformation

Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in various hematological cancers. DNMT3AR882mut was recently shown to carry partially defective, dominant-negative or gain-of-function activities under different in vitro contexts. However, the causal roles for such a multifaceted effect of DNMT3AR882mut on leukemogenesis remain undefined. Here we report TF-1 leukemia cells as a robust system for modeling DNMT3AR882mut-dependent cell transformation phenotypes and for performing structure-function relationship studies of DNMT3AR882mut. We show that expression of DNMT3AR882mut and not its wildtype counterpart promotes TF-1 cell transformation and induces CpG hypomethylation predominantly at enhancers. Such effect by DNMT3AR882mut is dose-dependent, acts synergistically with that of IDH1 mutation, and resembles what was seen in human leukemia patients with DNMT3AR882mut. Both transformation- and hypomethylation-inducing capacities of DNMT3AR882mut rely on a motif involved in heterodimerization whereas its various chromatin-binding and enzymatic domains were dispensable. We also show bromodomain inhibition as a therapeutic means for treatment of murine leukemia carrying DNMT3AR882mut. Collectively, this study describes a useful model system for studying DNMT3AR882mut and supports a requirement for the dominant-negative effect of DNMT3AR882mut during leukemogenesis. TF-1 cells were stably expressed with either wild-type DNMT3A or its hematopoietic cancer-associated mutants. Genomic DNA was extracted and analyzed by the Illumina 450k Methylation array. Part of the data were submitted previously in GSE93727, including empty vector (GSM2461097, GSM2461098, GSM2461099, GSM2461100, and GSM2461101) and wild-type DNMT3A (GSM2461105, GSM2461106, and GSM2461107).