The IKZF1 N159Y partial tandem duplication mutant drives chromatin remodeling, B-cell developmental defects and leukemia initiation

IKZF1 N159Y, present as a partial tandem duplication (hereafter N159Y), defines a distinct subtype of B-cell precursor acute lymphoblastic leukemia (B-ALL). The mechanistic basis of leukemogenesis of this mutation, in contrast to diverse IKZF1 alterations present across the spectrum of B-ALL, is unknown. Here we elucidate mechanisms of N159Y. We generated cell lines with heterozygous or hemizygous N159Y expression. Motif enrichment, luciferase assays, and AlphaFold3 modeling were used to evaluate altered DNA interactions. Inducible knock-in mouse models and in vitro colony-forming assays assessed developmental and self-renewal phenotypes. Cell fitness and cytotoxicity assays assessed epigenetic dependency. N159Y leukemia cells displayed a characteristic gene expression signature with activation of non-B lineage pathways and repression of B-cell identity genes. N159Y bound both canonical IKZF1 motifs and neomorphic bHLH motifs. Downregulated genes were associated with super-enhancer-linked B-cell developmental regulators. ChromHMM revealed gain of active and poised enhancers driven by N159Y. In IKZF1-null NALM6 cells, N159Y bound more sites than WT. In 293T cells, N159Y repressed the ETS motif-containing MCL1 promoter. N159Y leukemia cells showed dependency on EP300 and CREBBP , and sensitivity to A-485, JQ1, and vorinostat. In mouse models, N159Y caused a marked reduction of mature B cells with expansion of aberrant B-cell precursors, and was associated with leukemia development, while also conferring abnormal self-renewal capacity in vitro. We show that N159Y is a chromatin-remodeling transcription factor mutant with neomorphic chromatin-binding. It disrupts B cell development and induces B-ALL.