Purpose Although IKZF1 deletion ( IKZF1) confers a higher risk of relapse in childhood B-cell acute lymphoblastic leukemia (B-ALL), it is uncertain whether treatment intensification will reverse this risk and improve outcomes. The Malaysia-Singapore ALL 2010 study (MS2010) prospectively upgraded the risk assignment of patients with IKZF1 to the next highest level and added imatinib to the treatment of all patients with BCR- ABL1 fusion. Patients and Methods In total, 823 patients with B-ALL treated in the Malyasia-Singapore ALL 2003 study (MS2003; n = 507) and MS2010 (n = 316) were screened for IKZF1 using the multiplex ligation-dependent probe amplification assay. The impact of IKZF1 on the 5-year cumulative incidence of relapse (CIR) was compared between the two studies. Results Patient characteristics were similar in both cohorts, including IKZF1 frequencies (59 of 410 [14.4%] v 50 of 275 [18.2%]; P = .2). In MS2003, where IKZF1 was not used in risk assignment, IKZF1 conferred a significantly higher 5-year CIR (30.4% v 8.1%; P = 8.7 × 10), particularly in the intermediate-risk group who lacked high-risk features (25.0% v 7.5%; P = .01). For patients with BCR-ABL1-negative disease, IKZF1 conferred a higher 5-year CIR (20.5% v 8.0%; P = .01). In MS2010, the 5-year CIR of patients with IKZF1 significantly decreased to 13.5% ( P = .05) and no longer showed a significant difference in patients with BCR-ABL1-negative disease (11.4% v 4.4%; P = .09). The 5-year overall survival for patients with IKZF1 improved from 69.6% in MS2003 to 91.6% in MS2010 ( P = .007). Conclusion Intensifying therapy for childhood B-ALL with IKZF1 significantly reduced the risk of relapse and improved overall survival. Incorporating IKZF1 screening significantly improved treatment outcomes in contemporary ALL therapy.

In childhood B-ALL, among the recently described subtypes were DUX4 and PAX5 altered (PAX5alt). Using whole transcriptome RNA sequencing (RNA-Seq) in 377 B-ALL children from MaSpore ALL 2003/2010 (MS2003/MS2010) studies, we found that, after hyperdiploid and ETV6-RUNX1, the third and fourth most common subtypes were DUX4 (n= 51; 14%) and PAX5alt (n= 36; 10%). DUX4 also formed the largest genetic subtype among patients with poor Day 33 MRD (n=12/44). But despite the poor MRD, outcome of DUX4 B-ALL was excellent (5-year cumulative risk of relapse (CIR) 8.9% [95% CI, 2.8% to 19.5%], 5-year OS 97.8% [95% CI, 85.3% to 99.7%]). In MS2003, 21% DUX4 B-ALL had poor peripheral blood (PB) response to prednisolone at day 8, higher than other subtypes (8%; P=0.03). In MS2010, with vincristine at day 1, no day 8 poor PB response was observed in DUX4 subtype (P=0.03). PAX5alt group had an intermediate risk of relapse (5-year CIR 18.1%) but when IKZF1 was not deleted, outcome was excellent with no relapse among 23 patients. Compared to MS2003, outcome of PAX5alt B-ALL with IKZF1 co-deletion was improved by treatment intensification in MS2010 (5-year CIR 80.0% vs 0%; P=0.05). In conclusion, despite its poor initial response, DUX4 B-ALL had a favorable overall outcome, and the prognosis of PAX5alt was strongly dependent on IKZF1 co-deletion.

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