RNA-seq in murine LSKs after Cux1 and/or Ezh2 loss, in the presence or absence of the DNA damaging agent N-ethyl-N-nitrosourea

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 datamining 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 response and repair. 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. Overall design: RNA-seq in control (shCtrl) and Cux1 knockdown (shCux1) murine hematopoietic progenitors transfected with CRISPR particles targeting Ezh2 (gEzh2), Kmt2c (gKmt2c), or an intron of Actin (gActin) as a control (4 replicates). A second RNA-seq experiment was performed in shCtrl and shCux1 murine hematopoietic progenitors treated with the Ezh2 inhibitor tazemetostat (Ezh2i) or vehicle, and the alkylating agent N-ethyl-N-nitrosurea (ENU).