IKZF1 Deletion Is Strongly Associated with Risk of Relapse in Pediatric B Cell Precursor ALL with TCF3-PBX1

Recent progress in the treatment of pediatric B cell precursor (BCP)-ALL has improved the outcome of TCF3-PBX1 fusion positive BCP-ALL. However, approximately 10% of those cases still experience relapse and reliable genetic prognostic marker has not been identified in this sub-group. Recently, IKZF1 deletion was reported to be associated with poor outcomes in pediatric BCP-ALL. Therefore, we sought to determine whether IKZF1 deletion plays a role in determining poor outcomes in pediatric BCP-ALL patients with TCF3-PBX1 fusion.

Diagnostic bone marrow or peripheral blood samples of 53 pediatric TCF3-PBX1 fusion positive BCP-ALL patients treated according to Japan Association of Leukemia Study (JACLS) ALL02 protocol from April, 2002 to May, 2008 were examined in this study. The patients with Down syndrome were excluded in this genetic analysis. The diagnosis of BCP-ALL was based on morphological findings on bone marrow aspirates and immuno-phenotype analyses of leukemic cells by flow cytometry. Conventional cytogenetic analyses were done as part of the routine work-up. Molecular studies using quantitative RT-PCR for the detection of TCF3-PBX1 were performed as part of the routine work-up. The deletion of IKZF1, CDKN2A, CDKN2B, PAX5, ETV6, RB1, BTG1, EBF1 and the PAR1 region, which includes CRLF2, CSF2RA, and IL3RA was determined using multiplex ligation-dependent probe amplification (MLPA) in 53 patients whose diagnostic DNA samples were available. JAK2 mutations were also determined by direct sequencing of the exon 16, 20 and 21 in the patients with IKZF1 deletion.

The median age at diagnosis was 5 years (range 1 –14 years). The median leukocyte count at diagnosis was 21,800 × 10⁶ /L (range 2,700 – 183,300). The patients consisted of 28 male and 25 female patients. Twenty seven patients were categorized in NCI-SR and 26 patients in NCI-HR. Forty seven patients were classified as prednisolone good responder, six patients as prednisolone poor responder. The deletion of IKZF1 gene was present in 2 of 53 (3.8 %) patients, which was less frequent in BCP-ALL without TCF3-PBX1 fusion. JAK2 mutation was not determined in those two patients with IKZF1 deletion. The deletion of PAX5 was also less frequent (TCF3-PBX1 positive vs. negative: 17.9 % vs. 32.5 %). The deletion of CDKN2A and CDKN2B was identified in 12.8 % and 10.3 % of these patients, respectively, which was also less frequent than in BCP-ALL patients without TCF3-PBX1 (del. CDKN2A: 46.6 %, del. CDKN2B: 39.9 %). However, the deletion of RB1 was identified in 17.9 % of 53 patients, which was more than in those without TCF3-PBX1 fusion (3.0 %). The deletion of ETV6, EBF1 or BTG1 was not identified in 53 patients. Age at onset, initial WBC count and NCI risk were not associated with the relapse rate. Interestingly, patients with IKZF1 gene deletion had significantly higher relapse rate than those without IKZF1 deletion (2/2 vs. 5/51, p=0.015). However, the deletion of CDKN2A, CDKN2B, PAX5 and RB1 was not associated with the relapse rate.

This study determined that the presence of IKZF1 deletion was strongly correlated with risk of relapse in TCF3-PBX1 positive BCP-ALL, although the frequency was less than in those without TCF3-PBX1 negative. Thus, we expect that IKZF1 deletion might be an independent predictor of treatment outcome and represents a candidate of prognostic marker in pediatric BCP-ALL with TCF3-PBX1. Further molecular studies are required to determine genetic alterations in relapsed patients of TCF3-PBX1 positive BCP-ALL without IKZF1 deletion.

No relevant conflicts of interest to declare.