Gene Copy Number Changes in Myeloid Leukemias.
Authors: Downing James R. 
Published: October 2019

Abstract
A wide range of genetic alterations contribute to the formation of leukemia. These alterations include, but are not limited to, point mutations, gene rearrangements, deletions, amplifications, and a diverse array of epigenetic changes that influence gene expression. Unfortunately, using present methodologies, the identification of all mutations within a leukemia cell is cost prohibitive. Therefore, a more measured approach is needed. In previous work on pediatric acute lymphoblastic leukemia (ALL), we demonstrated the power of genome-wide copy number analysis for the identification of recurrent mutations. Our analyses revealed deletion, amplification, point mutation, and structural rearrangement in genes encoding key regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL. PAX5 was the most frequent target of somatic mutation, being altered in 30% of cases. Deletions were also detected in E2A, EBF1, LEF1, Ikaros, and Aiolos. These findings suggest that direct disruption of pathways controlling B cell development and differentiation contributes to ALL pathogenesis. We have now extended our analysis to pediatric acute myeloid leukemia (AML). This analysis revealed a mean number of somatic copy number abnormalities (CNA) of 2.38 per cases, with gains equal to losses. Strikingly, the most frequent recurrent CNA were at the breakpoints of known chromosomal translocations, including t(8;21) and inv(16). Based on this observation, we examined genes with CNA in their 5’ or 3’ regions for their possible involvement in cryptic translocations. Using this approach, two cryptic translocations were identified: t(5;11) [NUP98-NSD1] in four cases, and t(6;11)[MLL-MLLT4] in two cases. A number of other genes were identified as the target of recurrent abnormalities, including amplification of CCDC26, ABCC4, and deletion of FAM20C, BCOR. The most frequent abnormality was the amplification of CCDC26 at 8q24.21 (N=15; focal in four cases, broad in 11 cases), which encodes a putative mediator of retinoic acid receptor signaling. The other recurrent lesions occurred in two or fewer cases. Thus many fewer recurrent lesions were identified in AML than in ALL. In addition to the CNA, we also sequenced genes previously shown to be mutated in AML including NRAS, KRAS, PTPN11, BRAF, SOS1, FLT3, CEPBA, NPM1, AML1, CKIT, ERG, TP53, PTEN, and GATA1. Mutations were identified in all genes except BRAF, or SOS1, with the frequency of mutations varying across the different AML genetic subtypes. FAB M7 cases had the highest frequency of CNA but had sequence mutations limited to GATA1. Mutations of FLT3, CEPBA, and NPM1 were most frequent in cases with no or miscellaneous cytogenetic abnormalities, whereas NRAS mutations were most frequent in t(8;21) and inv(16) cases. Importantly, approximately 20% of the cases with recurring translocations had no other sequence or numerical abnormalities. Collectively, these data demonstrate a marked difference in the spectrum of genetic lesions between AML and ALL, with AML having fewer CNA per cases, a lower frequency of recurrent lesions, and a higher frequency of cases lacking any CNA. These data suggest a fundamental difference in the type of collaborating mutations between AML and ALL.