Chromosome 5q deletion drives evolution of aneuploidy in myeloid neoplasms with complex karyotype

Clonal acquisition of multiple chromosomal abnormalities in hematopoietic stem and progenitor cells (HSPCs) is a hallmark of high-risk acute myeloid leukemia with complex karyotype (AML-CK). AML-CK is associated with TP53 mutations and chromosome 5q deletions [del(5q)]; however, the drivers and clonal trajectories of aneuploid evolution in HSPCs remain unknown. We developed a patient-derived induced pluripotent stem cell (iPSC) model in which preleukemic HSPCs clonally evolve to distinct, highly aneuploid states after transient mitotic inhibition. By tracking chromosome evolution at single-cell resolution, we show that TP53-mutant HSPCs with del(5q), but not TP53 mutation alone, evolve complex chromosomal changes. Clonal evolution was marked by the stepwise acquisition of numerical and structural chromosome changes seen in patients with AML-CK, with individual abnormalities conferring a fitness advantage. iPSC-derived aneuploid HSPCs and primary samples from patients with AML-CK exhibited a conserved gene expression signature marked by upregulation of PTEN, cohesins, and the antiapoptotic factor BCL2, indicative of a shared aneuploid cell state in HSPCs. The clinical BCL2 inhibitor venetoclax eradicated BCL2-dependent aneuploid clones, with resistant clones undergoing a lineage switch to upregulate alternative BCL2 factors. In summary, we demonstrate that mutant TP53 and del(5q) drive chromosome evolution marked by stepwise acquisition of individual abnormalities. Moreover, aneuploid HSPCs exhibit a shared gene expression state that confers unique, targetable therapeutic vulnerabilities in AML-CK.