Transcriptomic alterations including p53 pathway dysregulation prime DNMT3A mutant cells for transformation

DNMT3A mutations are prevalent in haematologic malignancies. Our mouse model introduced the murine homologue (R878H) of the human ‘hotspot’ R882H mutation into the mouse Dnmt3a locus, resulting in globally reduced DNA methylation in all tissues. Mice with heterozygous R878H mutations developed g-radiation induced thymic lymphoma more rapidly than control mice, suggesting a vulnerability to stress stimuli in Dnmt3aR878H/+ cells. In competitive transplantations, Dnmt3aR878H/+ Lin-Sca-1+Kit+ (LSK) cells had a competitive advantage over WT cells, indicating a self-renewal phenotype at the expense of differentiation. RNA-sequencing of Dnmt3aR878H/+ LSKs exposed to low dose g-radiation showed downregulation of the p53 pathway. Accordingly, reduced PUMA expression was observed by flow cytometry in the bone marrow of g-irradiated Dnmt3aR878H/+ mice due to altered p53 signalling. These findings provide new insights as to how DNMT3A mutations cause subtle changes in the transcriptome of LSK cells which contribute to their increased self-renewal and propensity for malignant transformation. To investigate the transcriptomic changes taking place in response to g-irradiation in Dnmt3aR878H/+ mutant LSK cells, we utilised RNA-seq. The RNAseq samples included in this submission were taken from bone marrow LSK cells of 4-week-old female mice in the following conditions: 4 replicate Dnmt3aR878H/+ untreated samples, 4 replicate WT untreated samples, 3 replicate Dnmt3aR878H/+ irradiated samples, and 2 replicate WT irradiated samples.