Abstract 90: A cell cycle-related genomic and transcriptomic signature distinguish aneuploid and euploid acute myeloid leukemia

Chromosome gain or loss, which is the hallmark of aneuploidy, occurs in about 10% of adult Acute Myeloid Leukemia (AML) cases (Farag et al. IJO 2002, Breems et al. JCO 2008), despite inducing a dramatic reduction of cellular fitness in non-malignant cells (Torres et al. Science 2007). The study aimed to identify AML-specific molecular mechanisms having a causative and/or tolerogenic role towards aneuploidy. We performed 100 bp paired-end whole exome sequencing (WES, Illumina Hiseq2000) of 38 aneuploid (A) and 34 euploid (E) AML cases, identified according to cytogenetic analysis and SNP array (CytoScan HD, Affymetrix). Variants were called with GATK, MuTect and VarScan. We also compared the transcriptomic profile of leukemic bone marrow cells from 21 A-AML and 28 E-AML cases (HTA 2.0, Affymetrix). A-AML showed a significantly higher mutation load compared with E-AML (median number of variants: 25 and 15, respectively, p<.001) and a specific pattern of genomic lesions. Indeed, mutations in myeloid transcription factors and chromatin modifiers preferentially occurred in E-AML (p = .04 and p<.01, respectively), while A-AML was enriched for alterations in cell cycle-related genes (p<.01), with 70% of cases carrying at least one of those mutations (vs. 35% of E-AML, p<.01). The mutated genes played different functions across cell cycle phases, including DNA replication, centrosome dynamics, chromatid cohesion, chromosome segregation and spindle-assembly checkpoint. Moreover, 29% of A-AML displayed mutations of TP53 or a TP53-related gene (DDIAS, USP10), compared with 5.9% of E-AML cases (p = .01), with enrichment for a transcriptional signature of p53 downregulation in the aneuploid cohort (p<.05). Among the differentially expressed genes, we identified a cell cycle-related signature characterized by increased CDC20 and UBE2C and reduced RAD50, ATR and CCNA1 in A-AML (p<.001), confirmed at protein level, which was able to separate A-AML and E-AML. A-AML also showed upregulation of a KRAS transcriptional signature, irrespective of KRAS mutational status (p<.05). Our data show a link between aneuploidy and genomic instability in AML and highlight novel molecular mechanisms for the acquisition and/or maintenance of the aneuploid phenotype. Deregulation of the cell cycle machinery and DNA damage/repair checkpoints, either through mutations, copy number and transcriptomic alterations, cooperate with leukemogenic pathways, as KRAS signaling, to develop A-AML and overcome the unfitness barrier. This evidence suggests that a number of A-AML patients may benefit from pharmacological reactivation of TP53 and inhibition of KRAS pathway.