Incidence and biological significance of IKZF1/Ikaros gene deletions in pediatric Philadelphia chromosome negative and Philadelphia chromosome positive B-cell precursor acute lymphoblastic leukemia.

In recent years, there have been a series of contradictory reports based on studies that employed single-nucleotide polymorphism (SNP) arrays regarding the incidence and prognostic significance of IKZF1 deletions in primary leukemic cells from pediatric patients with high-risk B-cell precursor ALL (BPL). Some of the initial reports have proposed that: i) genomic IKZF1 deletions (not alternative splicing) are the cause of expression of dominant-negative IK isoforms; and ii) IKZF1 is a haploinsufficient gene rendering its heterozygous deletions biologically and clinically significant. Mullighan et al. reported deletions of IKZF1 in 84% of Philadelphia chromosome positive (Ph) BPL patients, including 76% of pediatric and 91% of adult Ph BPL cases. The same Authors also reported a more than 25% frequency of IKZF1 deletions in Ph high-risk BPL patients. In both studies, IKZF1 deletions included homozygous/biallelic as well as heterozygous/monoallelic deletion of the entire gene locus as well as intragenic deletions. Likewise, Volejnikova et al. reported discordant results in 206 children with PhALL. Of 24 patients with overexpression of dominant-negative IK isoforms other than IK6, only one patient had a deletion within the IKZF1 locus and only half of the IK6 cases were found to have monoallelic IKZF1 deletions. The overall incidence of IKZF1 deletions was only 7%, and no patient had homozygous IKZF1 deletions and no patient had evidence of decreased IK protein expression even in the presence of monoallelic IKZF1 deletions. Although Mullighan et al. reported IKZF1 deletions as a significant predictor of poor outcome for high-risk BPL patients on the Children’s Oncology Group (COG) Study P9906, a subsequent study by Chen et al. could not confirm the independent prognostic significance of IKZF1 deletions for 499 high-risk BPL patients. We read with great interest the recent paper of Palmi et al. who reported an elegant study which raises further questions about the biological significance of IKZF1 deletions in pediatric BPL. They documented no homozygous IKZF1 deletions and heterozygous IKZF1 deletions were detected in only ~13% of their Ph BPL patient population. In approximately half of the cases with deletions (7.1%), the deletion involved the entire IKZF1 locus and in the other half a portion of the IKZF1 gene. Most importantly, IKZF1 deletions were not an independent prognostic factor of risk of relapse. In order to gain further insights into the incidence and biological significance of IKZF1 deletions, we examined the expression levels of IKZF1 transcripts in primary leukemic cells from 237 pediatric Ph BPL patients in sideby-side comparison with 122 pediatric Ph BPL cases and 74 normal bone marrow specimens in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database GSE 13159. BLAT analysis on IKZF1 target sequences deposited in Affymetrix NetAffxTM Analysis Center (http://www.affymetrix.com/analysis/index.affx) mapped the 10 probesets from the Affymetrix Human Genome U133 Plus 2.0 Arrays used in the analysis onto specific IKZF1