CEBP and ZEB2 alterations define three distinct subtypes of B-cell acute lymphoblastic leukemia.

B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous malignancy driven by diverse genetic alterations. Among these, CEBP family genes and ZEB2 are recurrently involved, yet the spectrum of genomic mechanisms and their clinical impact remain incompletely defined. Integrated genomic analyses of a cohort of 992 Philadelphia-negative adult B-ALL patients revealed multiple mechanisms of enhancer hijacking-mediated deregulation of CEBPA, CEBPB, CEBPD, and CEBPE, including IGH and several non-IGH fusions, as well as noncoding mutations in regulatory regions. Combined with gene expression analysis, we identified three distinct subtypes, defined by co-occurring CEBP and ZEB2 p.H1038R alterations (CEBP/ZEB2, n = 18 cases); isolated CEBP alterations (CEBPalt, n = 43), associated with frequent IKZF1 deletions and FLT3 deregulation; and isolated ZEB2 p.H1038R mutation (ZEB2alt, n = 15), associated with various additional genomic hits targeting ZEB2 and enhancing mutant ZEB2 expression. The three subtypes exhibited distinct clinical features, including age distribution (patients with CEBP/ZEB2 and ZEB2alt B-ALL were younger) and sex bias (female and male predominance in CEBPalt and ZEB2alt, respectively). Early treatment responses and outcomes also differed: patients with CEBP/ZEB2 B-ALL had a favorable early response, in contrast to patients with ZEB2alt B-ALL, who had high levels of minimal residual disease and a dismal prognosis. Collectively, our findings define CEBP and ZEB2 alterations as drivers of genetically and clinically distinct subtypes of adult B-ALL and provide a rationale for subtype-specific risk stratification. Preclinical experiments in CEBPalt B-ALL patient-derived xenografts demonstrated sensitivity to FLT3 inhibition, highlighting a potential therapeutic vulnerability.