AML-328: Genomic Landscape of Copy-Neutral LOH and CNA in Intermediate-Risk AML: Recurrent Alterations in PHF6, SMC1A, and KMT2A Genes

The copy number alteration (CNA) and copy-neutral loss of heterozygosity (cnLOH) significantly contribute to the mutational profile of AML. In this study, we examined CNA and cnLOH in genes whose mutations are known to play a crucial role in the pathogenesis of AML. To identify CNA and cnLOH in NPM1, CBL, FLT3, JAK2, KIT, KRAS, MPL, NRAS, CALR, CSF3R, DNMT3A, IDH1, IDH2, TET2, ASXL1, BCOR, BCORL1, EZH2, KMT2A, SETBP1, NF1, PHF6, TP53, WT1, CEBPA, ETV6, GATA2, RUNX1, SF3B1, SRSF2, U2AF1, ZRSR2, RAD21, SMC1A, SMC3, and STAG2 genes in tumor genomes of intermediate-risk AML patients using chromosomal microarray analysis (CMA). We included 34 patients with AML who were treated in our center between 2017 and 2022. All patients belonged to an intermediate-risk group according to European LeukemiaNet (ELN-2022). Most of the patients (29/34) had a normal karyotype. Two patients had karyotype not belonging to a good or adverse group and in four cases karyotype could not be determined due to the absence of mitosis, although FISH ruled out adverse aberrations. FLT3 -ITD mutations were found in 13/34 (38%) of patients. CMA was performed on tumor DNA obtained during the primary diagnosis, either from fresh samples or from archival material. CMAwas carried out with ThermoFisher Scientific equipment using the CytoScan™ HT-CMA 96F array SNPoligonucleotide microarray in accordance with the manufacturer's protocol. Data were analyzed using Chromosome Analysis Suite and processed with Python 3.12.4 and SAS 9.4.We compared our CMA data with a triple-matched control dataset from 102 ostensibly healthy individuals (HI). The most frequent events were cnLOH of PHF6 (55.88% in patients vs 44.12% in HI) , SMC1A (53.94% in patients vs 53.92% in HI) , BCORL1 (50% in patients vs 36.27% in HI) and BCOR (35.29% in patients vs 32.35% in HI). In contrast, gain of KMT2A (14.71%) and cnLOH KMT2A (8.82%) were revealed only in patients. The high frequency of cnLOH (virtually, the homozygotizing of mutations) in the PHF6 , SMC1A , and BCOR genes may suggest their role as “second hits” in leukemia development. On the other hand, KMT2A alterations represent specific drivers of the disease.