Mutations Synergize to Alter Epigenetic and Genomic Landscape of AML

Acute myeloid leukemia (AML) is an aggressive malignancy characterized by altered transcription, but the mechanisms by which mutations contribute to aberrant transcription in AML are not completely understood. The most common AML driver mutations include an internal tandem duplication in FLT3 (FLT3-ITD), causing constitutive activation of the encoded receptor tyrosine kinase, and a frameshift mutation in NPM1 (NPM1c), causing cytoplasmic localization of nucleophosmin, a protein typically found in the nucleolus. To investigate how each mutation contributes to epigenetic, genomic, and transcriptional changes, Yun and colleagues studied an allelic series of mouse models of AML induction in which mice harbored knock-in mutations of either Flt3-ITD, Npm1c, or both, with single mutants displaying premalignant phenotypes whereas double mutants developed aggressive disease. RNA-sequencing analysis of hematopoietic stem and progenitor cells (HSPC) from wild-type, single-mutant, or double-mutant mice revealed that, although single mutations modestly affected global gene expression, the combined mutations synergized to induce substantial differential expression. Given that transcriptional changes can be driven by alterations in chromatin accessibility as well as histone modifications, these two properties were assessed, showing that whereas each single mutation affected accessibility, only Flt3-ITD markedly affected chromatin modifications associated with regulatory activity in enhancer regions. Moreover, the combined mutations altered the 3-dimensional topology of promoter-associated DNA interactions in terms of genomic compartments that switched from active to inactive domains or vice versa. Integrated analysis of chromatin data in double-mutant versus wild-type HSPCs highlighted a cluster of cis-regulatory regions enriched for GATA and KLF motifs that had a decrease in marks associated with enhancer function, as well as a cluster enriched for PU.1, CEBP, RUNX, and AP-1 motifs that gained marks associated with enhancer function. Furthermore, this integrated analysis identified a novel superenhancer of the Hoxa locus, highly expressed in AML, in addition to functionally important network nodes for the maintenance of AML, including the transcription factor PU.1, that were validated through RNAi and CRISPR-mediated perturbation. Together, this work deconvolutes the synergistic epigenetic and genomic contributions of the most frequent driver mutations in AML.

Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, et al. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021 Sep 23 [Epub ahead of print].

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