Accurate risk stratification is critical for ensuring that patients with high-risk ALL receive treatment of appropriate intensity and that low-risk patients are spared unnecessary toxic effects. Current risk stratification is based primarily on clinical variables, immunophenotype, detection of sentinel cytogenetic or molecular lesions, and early response to therapy.1
However, a substantial proportion of patients who have a relapse have no known poor-risk factors at the time of diagnosis.
We used high-resolution, genomewide copy-number analysis to identify genetic lesions associated with clinical outcome. Most striking was the strong association between deletions or mutations of IKZF1 and a poor outcome in two independent cohorts notable for different sample composition and treatment schedules. In multivariate analysis, the association between IKZF1 status and outcome was independent of age, leukocyte count at presentation, cytogenetic subtype, and levels of minimal residual disease; this indicates that detection of IKZF1 alterations at diagnosis might be useful in identifying patients with a high risk of treatment failure. Moreover, the gene-expression signatures of patients with poor-outcome (IKZF1-deleted) ALL in the original and validation cohorts were very similar to each other and to the signature of BCR-ABL1–positive ALL, a subtype of ALL in which IKZF1 deletion is very common. Since BCR-ABL1 ALL has a poor prognosis, these findings suggest that the mutation of IKZF1 is a key determinant of a poor outcome both in patients with BCR-ABL1–positive and patients with BCR-ABL1–negative disease. The similarity of the gene-expression signatures of BCR-ABL1–negative ALL with a mutation of IKZF1 and BCR-ABL1–positive ALL raises the possibility that patients with BCR-ABL1–negative ALL, deletion of IKZF1, and a poor outcome may have hitherto unidentified activating mutations in tyrosine kinases.
IKAROS is a transcription factor with well-established roles in lymphopoiesis and cancer.25
Normal IKAROS contains four N-terminal zinc fingers, which are required for DNA binding, and two C-terminal zinc fingers that mediate dimerization of IKAROS with itself and with other IKAROS family members. The development of all lymphoid lineages requires IKAROS,26
and in mice that are heterozygous for a dominant-negative Ikzf1
mutation, aggressive T-lineage hematopoietic disease develops.27 Ikzf1
is also a common target of integration in retroviral mutagenesis studies in mice.28
transcripts have been detected in normal hematopoietic cells and leukemic blasts.25
Isoforms lacking most or all of the N-terminal zinc fingers have attenuated DNA-binding capacity but retain their ability to undergo homodimerization and heterodimerization, and they thus act as dominant-negative inhibitors of IKAROS.29
Previous studies have shown expression of these aberrant IKAROS isoforms in ALL.25
Recently, we reported a very frequent deletion of IKZF1
–positive ALL and lymphoid blast crisis of chronic myeloid leukemia, suggesting that perturbation of IKAROS is a key event in the pathogenesis and progression of BCR-ABL1
Moreover, there was complete correlation between the extent of genomic deletion and the expression of aberrant IKAROS isoforms.5
For example, all patients expressing the dominant-negative Ik6 isoform, which lacks coding exons 3 through 6 and all N-terminal zinc fingers, had genomic deletions of exons 3 through 6.5
The present study shows that IKZF1 alterations occur in a substantial proportion of patients with BCR-ABL1–negative B-cell–progenitor ALL, predominantly in patients without other common recurrent cytogenetic abnormalities (38.8% of patients in the original cohort and 22.8% of the patients in the validation cohort with normal or miscellaneous karyotypic abnormalities had alterations of IKZF1). As in BCR-ABL1–positive ALL, IKZF1 deletions involved either the entire locus or sets of exons, and they are predicted to result in either haploinsufficiency or the expression of dominant-negative IKAROS isoforms. Moreover, we have identified sequence mutations of IKZF1 in ALL that are predicted to result in the loss of normal IKAROS function or expression of a novel dominant-negative isoform, G158S.
Using gene-set enrichment analysis, we found enrichment of hematopoietic stem-cell and progenitor genes and underexpression of B lymphoid genes in patients with ALL who had a poor outcome. This finding is consistent with the requirement for IKAROS in lymphoid development26
and the demonstration that expression of dominant-negative IKAROS isoforms impairs B lymphoid differentiation.30
Together, these data suggest that attenuation of normal IKAROS activity and the resulting block in lymphoid maturation render leukemic cells relatively resistant to eradication by chemotherapy. The clinical consequences of enrichment for genes that are characteristic of leukemia-initiating cells or stem cells, including their inherent drug-resistant mechanisms, remain to be determined.31
We did not find an association between clinical outcome and extensively studied loci such as CDKN2A/B32,33
status, despite the finding that PAX5
alterations were the most common lesions in the B-cell–differentiation pathway in both cohorts. PAX5
alterations may be important in establishing the leukemic clone, whereas alterations of IKZF1
may also contribute to resistance to chemotherapy. This finding is supported by recent data showing that IKZF1
alterations also emerge as new genetic alterations at the time of relapse in ALL.34
In summary, we identified an association between alterations of IKZF1
and the clinical outcome in B-cell–progenitor ALL in childhood. Integrated genomic analysis suggests that IKZF1
contributes directly to treatment resistance in ALL. These results provide a rationale for the integration of IKZF1
status in the evaluation of patients with ALL.