Multi-omics analysis of AML cells treated with azacitidine reveals highly variable cell surface proteome remodeling

Acute myeloid leukemia (AML) is a heterogenous disease of abnormal hematopoietic differentiation with aberrant epigenetic alterations widely treated with azacitidine (AZA), a DNA methyltransferase inhibitor. To identify potential cell surface therapeutic targets for use in combination with AZA, we determined the effects of AZA treatment on four AML cell lines representing different stages of differentiation on three omics levels: the DNA methylome, the transcriptome, and the cell surface proteome. Untreated AML cell lines showed substantial overlap in their methylomes, transcriptomes, and cell surface proteomes. AZA treatment globally reduced DNA methylation in all cell lines, but changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, with TRPM4 being the only gene encoding a surface protein. Gene Set Enrichment Analysis (GSEA) of differentially-regulated RNA and surface proteins showed a decrease in metabolism pathways and an increase in immune defense response pathways, indicating a convergence of gene and protein regulation to common functional outcomes. Given the heterogeneous response of AZA in the four cell lines, we discuss potential therapeutic strategies in combination with AZA.