Structures and therapeutic mechanisms in ZNF384-r B-cell acute lymphoblastic leukemia

ZNF384 gene rearrangement (ZNF384-r) is one of the major genetic lesion in 4% B-cell acute lymphoblastic leukemia (B-ALL) patients. However, the exact pathogenic mechanism leading to the leukemia outbreak remains elusive. Here, we determined the crystal structure of the ZNF384 zinc finger (ZF) domains 3-4 (2.0 Å). This helped to obtain the model ZNF384-DNA complex by AlphaFold 3, SAXS and X-ray crystallography. Site directed mutagenesis identified key residues Q68 in ZF3 and Q98 in ZF4 that were essential for transcriptional activity. Clinical characteristics of 10 new cases of ZNF384-r B-ALL were reported and integrated multi-omics profiling identified ID2 as a ZNF384-r-dependent target gene that was frequently associated with poor prognosis. Abnormal ID2 expression delineated a clinically adverse subgroup characterized by more severe differentiation arrest and immunosuppressive signature. Supportively, targeting ID2 in ZNF384-r cells induced mitochondrial apoptosis and effectively suppressed leukemia progression in patient derived xenograft (PDX) mice. Altogether, this study not only revealed the DNA engagement mechanism in oncogenic ZNF384-r fusion, but also highlighted ID2 as a promising therapeutic target in B-ALL.