Transcriptome profiling by RNA-sequencing of the AML cell lines UCSD-AML1 and ELF-153.

DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q. Overall design: The AML cell lines UCSD-AML1 and ELF-153 were treated with decitabine (DAC) in technical triplicates for 4 consecutive days (with daily change of media and DAC add-on). Cells were harvested and RNA was isolated after 96 hours and after 144 hours, Fragment Analyzer QC confirmed RIN values =9.7. rRNA was removed and strand-specific libraries of each replicate were sequenced on an Illumina HiSeq 2500 with approximately 33 million reads per sample.