Prognostic significance of IKZF1 deletion subtypes in ph-negative BCP-ALL: Biallelic-null deletion predicts the worst survival in TP53-wild type patients

Abstract Background: Recent advances in molecular cytogenetic profiling of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) have identified IKZF1 deletions as an adverse prognostic marker, particularly in Philadelphia chromosome-negative (Ph–) cases. IKZF1 encodes the transcription factor IKAROS, and its deletions can be functionally classified into loss-of-function (LOF), dominant-negative (DN), and biallelic-null (homozygous) subtypes. However, the clinical relevance of these IKZF1 deletion subtypes remains uncertain, especially in the context of allogeneic hematopoietic cell transplantation (allo-HCT). Aims: To evaluate the prognostic impact of IKZF1 deletion subtypes in adult patients with BCP-ALL undergoing allo-HCT, with a focus on Ph-negative and TP53-wild type subgroups, and to determine whether biallelic-null IKZF1 deletion confers particularly poor post-transplant outcomes. Methods: We retrospectively analyzed 389 adult patients with BCP-ALL (201 Ph-positive, 188 Ph-negative) who received modified hyper-CVAD chemotherapy followed by allo-HCT between 2018 and 2024. IKZF1 deletions and alterations in 10 additional genes were identified via multiplex ligation-dependent probe amplification (MLPA). Targeted next-generation sequencing (NGS) of 73 genes was also performed. MRD monitoring was conducted using both NGS-based IGH/IGK rearrangement and multiparameter flow cytometry. IKZF1 deletions were categorized as LOF, DN (exons 4–7 deletion), or biallelic-null (homozygous deletion). Survival outcomes were assessed using Kaplan-Meier and competing risk models. Results: IKZF1 deletions were observed in 210 patients (158 Ph+ [78.6%] and 52 Ph– [27.7%]), comprising 125 LOF, 58 DN, and 27 biallelic-null deletions. In Ph+ BCP-ALL, IKZF1 status and subtype had no significant impact on survival outcomes. In contrast, in Ph– BCP-ALL, IKZF1 deletion was associated with inferior 3-year disease-free survival (DFS: 36.8% vs 54.1%, p=0.04) and higher cumulative incidence of relapse (CIR: 49.9% vs 35.2%, p=0.05). After excluding patients with TP53 mutations, the adverse impact of IKZF1 deletion on 3-year overall survival (OS) became more pronounced (55.4% vs 72.9%, p=0.037). In the TP53-wild type Ph– subgroup (n=187), biallelic-null IKZF1 deletions (n=6) were significantly associated with poorer 3-year OS (33.3%), 3-year post-HCT OS (33.3%), DFS (16.7%), and higher CIR (66.7%) compared to DN, LOF, and wild-type IKZF1 (all p < 0.05). No significant survival differences were observed between LOF and DN subtypes. Conclusions: IKZF1 deletion is a significant adverse prognostic marker in Ph-negative BCP-ALL, particularly in patients without TP53 mutations. Among IKZF1 deletion subtypes, biallelic-null (homozygous) deletions confer the worst survival outcomes despite allo-HCT, highlighting the need for intensified or alternative therapeutic strategies in this high-risk subgroup.