Transcriptomic profiling of KMT2A-rearranged infant acute lymphoblastic leukemia (ALL) cells after treatment witith azacitidine and decitabine.

Transcriptomic profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with two hypomethylating drugs (azacitidine and decitabine) administered at low doses for 72 hours in vitro. We identified changes in gene expression following treatment with hypomethylating agents, with decitabine exerting a greater effect than azacitidine. Total RNA (500 ng) for each cell line and condition was used as input for library preparation using the Illumina Stranded mRNA Prep kit (Illumina). A total of 54 poly A stranded libraries (6 controls, 6 azacitidine-treated and 6 decitabine-treated cell lines in triplicate) were sequenced to a depth of >20 million paired-end reads (150 bp) per sample using a NovaSeq 6000 (Illumina). Raw data was demultiplexed, underwent quality control, aligned and mapped to the trancriptome (hg38). Differential expression analysis was performed to identify differentially expressed genes comparing treatment with untreated control for each cell line.