Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL- rearranged B cell acute lymphoblastic leukemia

B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. As predicted by its prenatal origin, infant B-ALL (iB-ALL) shows an exceptionally silent DNA mutational landscape, suggesting that alternative epigenetic mechanisms may substantially contribute to its leukemogenesis. Here, we have integrated genome-wide DNA methylome and transcriptome data from 69 patients with de novo MLL-rearranged leukemia (MLLr) and non-MLLr iB-ALL leukemia uniformly treated according to the Interfant-99/06 protocol. iB-ALL methylome signatures display a plethora of common and specific alterations associated with chromatin states related to enhancer and transcriptional control in normal hematopoietic cells. DNA methylation, gene expression, and gene coexpression network analyses segregated MLLr away from non-MLLr iB-ALL and identified a coordinated and enriched expression of the AP-1 complex members FOS and JUN and RUNX factors in MLLr iB-ALL, consistent with the significant enrichment of hypomethylated CpGs in these genes. Integrative methylome-transcriptome analysis identified consistent cancer cell vulnerabilities, revealed a robust iB-ALL- specific gene expression-correlating dmCpG signature, and confirmed an epigenetic control of AP-1 and RUNX members in reshaping the molecular network of MLLr iB-ALL. Finally, pharmacological inhibition or functional ablation of AP-1 dramatically impaired MLLr-leukemic growth in vitro and in vivo using MLLr-iB-ALL patient-derived xenografts, providing rationale for new therapeutic avenues in MLLr-iB-ALL.

Automated summary

B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer, with infant B-ALL (iB-ALL) showing unique DNA mutational landscape and potential epigenetic mechanisms contributing to leukemogenesis. Integrated analysis of methylome and transcriptome data from MLLr and non-MLLr iB-ALL patients revealed chromatin state alterations and identified distinct gene expression patterns, particularly related to the AP-1 complex and RUNX factors in MLLr iB-ALL. Pharmacological inhibition of AP-1 showed promising potential in impairing MLLr-leukemic growth, suggesting a novel therapeutic approach for MLLr-iB-ALL.