Genome-wide methylation profiling of KMT2A-rearranged infant Acute Lymphoblastic Leukemia (ALL) cells after treatment with azacitidine, decitabine and zebularine

Genome-wide methylation profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with three hypomethylating drugs (azacitidine, decitabine and zebularine) administered at low doses for 72 hours in vitro. We identified drug-specific and common differentially methylated regions and validated differentially expressed genes located within such regions, indicating commonalities in pathways targeted by azacitidine and decitabine in KMT2A-rearranged infant ALL. Of the three drugs, the most significant degree of hypomethylation was induced by decitabine followed by azacitidine, whereas zebularine did not exert a significant hypomethylating effect. Genome-wide methylation profiling of KMT2A-rearranged infant Acute Lymphoblastic Leukemia (ALL) cells after treatment with azacitidine, decitabine and zebularine Genomic DNA (750 ng) for each cell line and condition was treated with sodium bisulfite using the Zymo EZ DNA Methylation kit (Irvine). DNA was then hybridized to the Infinium MethylationEPIC BeadChip (Illumina). QC and data was filtered and quantile normalised in R. Following quality control checks, 773,929 probes were taken forward for downstream analyses. Differential methylation analysis of CpG sites was performed using limma, adjusting for pairing by cell line. Differential methylation analysis of regions was performed using DMRcate where CpGs were annotated and differentially methylated regions were identified.