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Abstract
Loss of all or part of chromosome 7 [-7/del(7q)] is recurrent in myeloid neoplasms and associated with a poor response to chemotherapy. Chromosome 7-encoded genes that drive drug resistance and the consequences of combinatorial 7q tumor suppressor gene loss have remained unclear, the latter question being largely due to the challenges of modeling aneuploidy. Here, we use in silico data mining to uncover 7q genes involved in chemotherapy resistance. We establish murine models of del(7q) clonal hematopoiesis and drug resistance with multiplex CRISPR-Cas9-mediated inactivation of four genes, Cux1, Ezh2, Kmt2c, and Kmt2e. Post-genotoxic exposure, combined deficiency of Cux1 and Ezh2 preferentially promotes clonal myeloid expansion in vivo, with compounding defects in DNA damage recognition and repair. Experiments in human acute myeloid leukemia cell lines similarly illustrate central roles for CUX1 and EZH2 loss in cellular survival and DNA damage resolution following chemotherapy exposure. Transcriptome analysis reveals combined Cux1 and Ezh2 loss recapitulates -7 patient gene signatures and defective DNA damage response pathways, to a greater extent than single gene loss. This work reveals a genetic interaction between CUX1 and EZH2, and sheds light on how -7/del(7q) contributes to leukemogenesis and drug resistance characteristic of these adverse-risk neoplasms. These data support the concept of 7q as a contiguous gene syndrome region, in which combined loss of multiple gene drives pathogenesis. Further, our CRISPR-based approach may serve as a framework for interrogating other recurrent aneuploid events in cancer.