Chromosome 7 Myeloid Tumor Suppressor Genes Cooperate in Chemotherapy Resistance

Loss of all or part of chromosome 7 [-7/del(7q)] is common in myeloid neoplasms and is associated with chemoresistance. -7/del(7q) occurs in de novo and therapy-related myeloid neoplasms (t-MN), high-risk secondary malignancies arising after prior exposure to chemotherapy or radiation. We previously reported that deficiency of CUX1, a 7q-encoded tumor suppressor gene, promotes hematopoietic stem and progenitor cell (HSPC) drug resistance, enabling HSPCs to persist during genotoxic insult, expand, and transform to t-MN. To comprehensively identify additional chromosome 7 genes putatively involved in drug resistance, we mined 13 chemotherapy resistance CRISPR-Cas9 genome-wide knockout screens performed in human cell lines. We included screens with daunorubicin, commonly used in the treatment of de novo acute myeloid leukemia, as well as screens with cisplatin and etoposide, chemotherapeutics that predispose to t-MN. Using loose thresholds for inclusion, we identified 113 genes that are potentially selected for by chemotherapy when edited. We prioritized candidates for validation based on those genes that were recurrent hits in more than one screen and genes with high expression levels in human HSPCs. Of the 9 top candidates tested in subsequent in vitro assays, we confirmed four genes to promote resistance when CRISPR-edited. This work yielded two 7q genes known to promote drug resistance when deficient, EZH2 and KMT2C/MLL3, validating our approach. We also identified novel drug resistance phenotypes for AHR and LUC7L2 deficiency. We demonstrate that combined deficiency in EZH2 and CUX1 leads to increased drug resistance in vitro and in vivo, to an extent greater than loss of either single gene alone. Transcriptome profiling additionally supports a genetic interaction between EZH2 and CUX1. In summary, chromosome 7 harbors multiple genes involved in chemotherapy resistance, supporting the concept of 7q as a contiguous gene syndrome. Furthermore, we reveal a previously unknown genetic interaction between the 7q genes CUX1 and EZH2. A refined understanding of the molecular pathways driving del(7q) pathogenesis and drug resistance will enable development of therapies designed to counter these treatment barriers.