Transcriptomic characterisation of Acute Myeloid Leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures
Background Acute myeloid leukemia (AML) is the most common type of acute leukemia, accounting for 20% of cases in children and adolescents. Genome-wide studies have identified genes that are commonly mutated in AML, including many epigenetic regulators involved in either DNA methylation (DNMT3A, TET2, IDH1/2) or histone post-translational modifications (ASXL1, EZH2, MLL1). Several cell lines derived from AML patients are widely used in cancer research. Whether important differences in these cell lines exist remains poorly characterised. Results Here, we used RNA sequencing (RNA-Seq) to contrast the transcriptome of four commonly used AML-derived cell lines: THP-1, NOMO-1, MOLM13 bearing the common initiating t(9;11) translocation, and MV4-11 bearing the t(4;11) translocation. Gene set and protein-protein interaction enrichment analyses, performed alongside expression profiling of master transcription regulator genes, revealed important differences in the transcriptome distinguishing these different AML models.  Conclusion The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research. Overall design: To compare these cell lines, we performed RNA-seq using deep sequencing (>120M paired end reads per sample).