Gene expression changes following DOT1L inhibitor treatment of DNMT3A-mutant AML cell lines. (A) Gene expression heat map (gene scaled and centered log2 counts per million) of top differentially expressed canyon-associated genes in OCI AML2 and OCI AML3 cell lines after 14 days of treatment with DOT1L inhibitor. (B) Relative expression determined by qRT-PCR of canyon-associated leukemogenic genes HOXA9, MEIS1, HOXB3, HOXB8, and the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in OCI AML 2 and OCI AML3 cells treated with 3 μM EPZ004777 or vehicle control for 14 days. qRT-PCR done in triplicate. Error bars represent standard deviation. (C) Ingenuity Pathway Analysis functional enrichment analysis of genes differentially expressed (false discovery rate [FDR] q value < 0.1) in AML cells after treatment with EPZ004777. P val, P value; prolif, proliferation. (D) GSEA of AML cells treated with EPZ004777. (E) Gene expression heat maps (gene scaled and centered log2 counts per million) of representative, core-enriched gene sets from GSEA. DN, downregulated; GO, gene ontogeny; inflamm, inflammatory; leuk, leukocyte; mDC, myeloid dendritic cell; meth, DNA methylation; Q-val, Q value; resp, response; signal size, enrichment signal strength of the leading edge subset of a gene set; trans, transition; UP, upregulated.