Copy Number Variations and IKZF1 Mutations In Pediatric CML

Chronic myeloid leukemia (CML) occurring in children and adolescents is associated with a number of clinical and molecular features that differ from the correspondent disease in patients in older age. Detailed molecular analyses of the genomic BCR-ABL1 breakpoints in a cohort of 60 pediatric individuals from the German CML-paed I and CML-paed II trial revealed a significantly different breakpoints distribution compared to adult CML. Especially the observed bimodal breakpoint distribution pattern in the BCR gene and a higher proportion of breakpoints within Alu repeat regions vary between pediatric CML and adult CML and resembles the pattern observed in adult BCR-ABL1-postitive acute lymphoblastic leukemia.

To identify additional genetic variations, in addition to the BCR-ABL1 fusion gene, high resolution whole-genome microarray analyses using Affymetrix Cytogenetics Whole-Genome 2.7M or CytoScan® HD arrays were performed in a selected sub-cohort of pediatric CML patients from the German CML-paed II trial; twenty individuals diagnosed in chronic phase (CP) and two individuals diagnosed in blast crisis (BC) were screened. In contrast to adult CML patients in whom about 25% of individuals in CP exhibit detectable CNVs, nearly 60% of pediatric patients have CNVs (1.9 CNVs per case) in this initial stage of CML. All identified CNVs were private and no recurrent genetic aberration was associated with early disease manifestation in children. Two patients in BC showed an increased number of CNVs (6.5 CNVs per case) which is in accordance with data from adult patients, indicating that additional secondary genetic events are associated with disease progression. One of the patients in lymphoid CML-BC harbored a deletion involving the IKZF1 gene, an aberration frequently observed in advanced disease stages in adult CML and ALL.

To further evaluate the incidence of IKZF1 mutations and their impact on the disease progression in pediatric CML patients, deep sequencing of IKZF1 was performed in 55 patients; 52 individuals in CP and 3 individuals in BC. Previously performed whole genome array analyses showed a deletion of exon 4 to 7 in the IKZF1 gene in one of the three analyzed patients in BC. Deep sequencing identified no additional mutation within IKZF1 in both remaining individuals. Interestingly, two patients in CP showed a single nucleotide insertion resulting in a premature stop codon, E35 and Y348 respectively. One patient developed imatinib resistantance 1.5 years after treatment onset. The second patient underwent stem cell transplantation 1 year after initial diagnosis. To date, with a follow-up of 7 and 6 years respectively, no patient progressed to advanced disease. These findings are in line with findings in adult CML, where IKZF1 aberrations are preferentially observed in advanced disease stages or imatinib resistant patients.