IKZF1 Deletions at Diagnose and Relapse of Childhood B-ALL

The transcription factor Ikaros is an essential regulator of lymphopoiesis and IKZF1 gene deletions have been associated with poor prognosis in acute lymphoblastic leukemia (ALL). Here we aim to assess the frequency and the prognostic impact of IKZF1 deletions in Turkish childhood B-ALL by using both deep sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA).

The patients cohort was comprised of 78 diagnose and 44 relapse samples of childhood B-ALL (17 paired diagnostic/relapse samples). The median age was 5 years (range, 0.4-17 years), and the median blast percentage at the time of diagnosis was 95% (range, 30-100). All patients were treated according to Berlin-Frankfurt-Munster (BFM) regimen. Patients were sequenced for the most frequent deletions of IKZF1 Δ 2-7, Δ4-7 and Δ4-8 by targeted deep sequencing (454 GS Junior platform, Roche) and also screened by MLPA (Multiplex ligation dependent probe amplification, SALSA kit, MRC Holland) for all exons of IKZF1 . IKZF1 deep sequencing plates were designed by IRONII study consortium. We used Coffalyser v9.4 software for the MLPA analyses, AVA and GENOMIZE programs for the deep sequencing results.

IKZF1 deletions were detected in 13% of the diagnose samples and 19% of the first relapsed materials. The detected Δ IKZF1 were listed in Table 1. Δ4-7 was the most common deletion both in diagnose and relapse that results in the expression of a dominant-negative IKAROS variant. The P#15,16,17 were wild type at the time of diagnosis however, gained Δ4-7 in the relapse. Furthermore, the P#3 displayed Δ4-7 both in diagnose and relapse time. We detected Δ2-7 in two first relapsed samples. The P#12 gained Δ4-8 deletion at second relapse in addition to Δ2-7 deletion. Deletions were both confirmed by deep sequencing and MLPA. In addition to NGS results, Δ1-6, Δ2-8, Δ2-3, exon1 and exon3 deletions were determined in five independent cases by MLPA. None of the patients who contained IKZF1 deletions showed somatic point mutations for the screened genomic regions. In the survival analysis, IKZF1 deletions were not found associated with lower overall survival rate (P=0,169).

According to these results, IKZF1 deletions occur more often in relapse than diagnosis, although based on limited patient numbers the event is showing a continuous and/or accumulated pattern. I KZF1 deletions is associated with increased risk of relapse and poor outcome in the literature. Here, we could not observe such effect. However, we detected more frequently IKZF1 deletions in the relapsed samples, which may contribute to development of therapy resistance in B-ALL.

Acknowledgments

This work was supported by TUBITAK (Project Number: 114S038) and and Scientific Research Coordination Unit of Istanbul University (Project no. 35624 and 20520). IKZF1 deep sequencing plates were designed by IRONII study consortium.

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