Transcriptome profiling by RNA-sequencing of the AML cell line MOLM-13.

All-trans retinoic acid (ATRA, RA) has powerful activity in APL; its efficacy in non-APL AML is still unclear, but may be boosted by epigenetic drugs such azanucleoside DNMT inhibitors (Blagitko-Dorfs et al. PLoS ONE 2013). In a randomized phase II study (DECIDER trial, NCT00867672) the addition of RA to decitabine (DAC) in newly diagnosed non-fit older AML patients resulted in a clinically meaningful extension of survival. We hypothesize that in vitro, the add-on of RA to DAC results in cooperative transcriptome changes (possibly associated with demethylation), which may explain at least in part this clinical result. The AML cell line MOLM-13 was treated with decitabine (DAC) ± ATRA in technical triplicates for 3 consecutive days (with daily change of media and DAC add-on). Cells were harvested and RNA was isolated after 72 hours, Fragment analysis by TapeStation confirmed RQN values ≥9.7. rRNA was removed and strand-specific libraries of each replicate were sequenced on an Illumina HiSeq 2500 with approximately 40 million reads per sample.