Genes with altered expression by 5-Aza treatment in myeloid leukemia cells through methylation in intron 1

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5-Azacitidine (5-Aza) is a hypomethylating agent with demonstrated therapeutic efficacy for myeloid leukemia. The aim of this study was to identify the genes that mediate the cell killing effect of 5-Aza against leukemia cells through their expression changes and DNA demethylation. RNA sequencing revealed 54 genes with increased transcription levels in both SKM-1 and KG-1a myeloid leukemia cell lines treated with 5-Aza. Long read sequencing revealed 79 genes in which intron 1 exhibited significant DNA demethylation after 5-Aza treatment. Forty-three genes showed both increased gene expression and DNA demethylation in intron 1 in cells treated with 5-Aza. Enrichment signaling pathway analysis demonstrated that genes were associated with “amino acid metabolism,” “neutrophil degranulation,” and “DNA damage response”. We evaluated the prognostic impacts of the 43 genes in acute myeloid leukemia patients using TCGA database. The results revealed that two genes ( HDC and MICALL2 ) with increased expression in leukemia cells after 5-Aza treatment were associated with better overall survival, while six genes ( BTG2 , CD52 , PECAM1 , PIK3IP1 , PTGS2 , and TREML2 ) correlated with worse overall survival. This study revealed that the epigenetic regulation by DNA demethylation in intron 1 has an important role of 5-Aza treatment in myeloid leukemia cells, and suggests novel targets for the development of combination therapy with 5-Aza. • The aim is to clarify the effect of DNA demethylation after 5-Azacitidine treatment. • Long read sequencing was conducted in AML/MDS cells treated with 5-Azacitidine. • Demethylation in intron 1 of genes correlates with the gene expression. • The cluster of genes identified in this study correlates with “DNA damage response”. • We identified 8 genes which correlate with prognosis in AML patients.

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