Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia

Abstract

Background: Despite best current therapy, up to 20% of pediatric patients with acute lymphoblastic leukemia (ALL) have a relapse. Recent genomewide analyses have identified a high frequency of DNA copy-number abnormalities in ALL, but the prognostic implications of these abnormalities have not been defined.

Methods: We studied a cohort of 221 children with high-risk B-cell-progenitor ALL with the use of single-nucleotide-polymorphism microarrays, transcriptional profiling, and resequencing of samples obtained at diagnosis. Children with known very-high-risk ALL subtypes (i.e., BCR-ABL1-positive ALL, hypodiploid ALL, and ALL in infants) were excluded from this cohort. A copy-number abnormality was identified as a predictor of poor outcome, and it was then tested in an independent validation cohort of 258 patients with B-cell-progenitor ALL.

Results: More than 50 recurring copy-number abnormalities were identified, most commonly involving genes that encode regulators of B-cell development (in 66.8% of patients in the original cohort); PAX5 was involved in 31.7% and IKZF1 in 28.6% of patients. Using copy-number abnormalities, we identified a predictor of poor outcome that was validated in the independent validation cohort. This predictor was strongly associated with alteration of IKZF1, a gene that encodes the lymphoid transcription factor IKAROS. The gene-expression signature of the group of patients with a poor outcome revealed increased expression of hematopoietic stem-cell genes and reduced expression of B-cell-lineage genes, and it was similar to the signature of BCR-ABL1-positive ALL, another high-risk subtype of ALL with a high frequency of IKZF1 deletion.

Conclusions: Genetic alteration of IKZF1 is associated with a very poor outcome in B-cell-progenitor ALL.

Figure 1. PAX5 and IKZF1 Sequence Mutations in High-Risk ALL in the Original Cohort

Panel A shows the functional domains of PAX5 and the location of missense mutations (arrowheads pointing down), frameshift mutations (diamonds), and splice-site mutations (arrowheads pointing to the right) detected in this study. In the domains, A denotes activating, H homeodomain, I inhibitory, O octapeptide domain, PD paired domain, and TD transactivating domain. Panel B shows structural modeling of the location of PAX5 paired-domain mutations. The DNA double helix is blue, the bipartite PAX5 paired domain is yellow, and ETS1, which interacts with and increases the affinity of DNA binding of PAX5, is green. Each mutation is predicted to disrupt the normal interaction of PAX5 with DNA, ETS1, or both. G24R is predicted to alter the flexibility of the DNA binding loop and interfere with the interaction of PAX5 with ETS1. D53V aligns R56, which in turn directly contacts DNA. R59G occurs at the junction with ETS1 and DNA and is likely to increase flexibility and destabilize both interactions. T75R clashes and causes electrostatic repulsion at R71, which is adjacent to the DNA binding site, and P80R has a direct effect on DNA binding, as previously described. Panel C shows the primary structure of IKAROS and the location of the six zinc fingers (green) and missense (arrowhead pointing down), frameshift (diamonds), and nonsense (arrowhead pointing up) mutations.

Figure 2. Associations between DNA Copy-Number Abnormality Predictors and Outcome in the Original and Validation Cohorts

Panel A shows the cumulative incidence of any event (relapse, death, or second malignant condition), and Panel B shows the cumulative incidence of any relapse among patients in the validation cohort after risk stratification with the use of the copy-number abnormality predictor based on data from the original cohort. Panel C shows the cumulative incidence of any event, and Panel D shows the cumulative incidence of relapse in the original cohort after risk stratification with the use of the copy-number abnormality predictor based on data from the validation cohort. High risk refers to patients who are predicted to be at high risk for events or relapse, and low risk refers to patients who are predicted to be at low risk for events or relapse.

Figure 3. Genetic Alterations of IKZF1, EBF1, and BTLA/CD200 and the Cumulative Incidence of Any Relapse in the Original Cohort

Panel A shows the cumulative incidence of relapse in the entire original cohort of patients with B-cell–progenitor ALL according to IKZF1, EBF1, and BTLA/CD200 alteration status. Panel B shows the cumulative incidence of relapse in the entire validation cohort, including patients with BCR-ABL1–positive B-cell–progenitor ALL. Panel C shows the cumulative incidence of relapse in the validation cohort after exclusion of patients with BCR-ABL1–positive B-cell–progenitor ALL. Only IKZF1 alterations were associated with poor outcome in both the original and validation cohorts. Five-year estimates of relapse are shown in the original cohort, and 10-year estimates are shown in the validation cohort. P values are calculated with the use of Gray’s test.