Subclonal IKZF1 Deletions Indicate a Multiclonal Evolution In BCR-ABL1-Positive B-Cell Precursor ALL

The transcription factor Ikaros, encoded by the IKZF1 gene, has multiple functions in different steps of hematopoiesis. Loss of function mutations in IKZF1 are frequently associated with BCR-ABL1-positive ALL. IKZF1 deletions comprise whole gene deletions as well as smaller intragenic deletions. All IKZF1 aberrations are associated with a poor prognosis in terms of overall survival and frequency of relapse.

IKZF1 deletions were evaluated in a cohort of 180 adult BCR-ABL1-positive B-cell precursor ALL cases. MLPA analysis was used to assess both whole gene and intragenic deletions, whereas breakpoint-specific consensus multiplex PCR [Caye et al., Haematologica, 2013] and real-time quantitative (RQ)-PCR were used to specifically detect the recurrent intragenic deletions Δ2-7, Δ2-8, Δ4-7 and Δ4-8. Intragenic IKZF1 deletions were detected in 129 patients (71.7%). More than one intragenic deletion was detected in a subset of 44 patients. Unexpectedly, in the majority of these patients (41/180 patients; 22.8%), significant differences in relative frequencies of single intragenic deletions were detected by RQ-PCR analysis. Together with the finding of more than two distinct intragenic deletions in 19/44 patients this clearly indicates the presence of subclonal or oligoclonal intragenic IKZF1 deletions. In the remaining 3/44 patients, number and frequencies of detected intragenic deletions rather suggested the presence of bi-allelic deletions within the whole leukemic bulk. Specificity of individual (sub-) clonal deletions was validated by Sanger sequencing. These data indicate that IKZF1 deletions arise independently in different subclones more frequently than it was estimated in earlier reports.

The quantitative breakpoint-specific PCR approach was additionally used to correlate the detection of intragenic IKZF1 mutations with established Ig/TCR-based monitoring of minimal residual disease (MRD) during/after treatment in a subset of 17 patients. Comparative IKZF1- and Ig/TCR-based MRD monitoring was performed on a total of 207 samples of initial diagnosis and follow-up. Whereas good correlation of Ig/TCR-MRD results and detection of IKZF1 deletions was seen in 9 out of 17 patients, different kinetics of Ig/TCR-MRD results and IKZF1-based leukemia monitoring in the remaining 8 patients were additionally indicative for the existence of IKZF1 deletions in leukemic subclones besides the major leukemic clone with their own kinetics of clearance and persistence.

Illegitimate RAG-mediated recombination has been proposed as responsible mechanism for recurrent intragenic deletions in IKZF1. Our data suggest that these lesions occur repeatedly during leukemogenesis and support a model of multiclonal evolution in BCR-ABL1-positive B-cell precursor ALL.