Abstract 5849: Integrated multi-omics of hydroxychloroquine evolved cancer cells reveal survival requires transcriptional upregulation of glycolysis, exocytosis, and chromosome fidelity, but not autophagy
Authors: Madison Clark, Silvia G. Vaena, Joe R. Delaney
Journal: Cancer Research (2024)

Abstract Repurposed drugs are undergoing a renaissance in the era of genomics, particularly in oncology. Over 2,300 FDA-approved and natural product small molecules now exist, but challenges remain in identifying which cancer patients may best benefit from such drugs. To best position repurposed drugs, mechanisms of action and resistance to the drug in a cancer cell setting must be determined. Hydroxychloroquine (HCQ) and chloroquine are repurposed drugs reported to disrupt autophagy, a molecular recycling pathway which is essential for tumor cell survival, chemotherapeutic resistance, and stem cell phenotypes. However, oncology trials with chloroquine have no biomarker or other genetic test to categorize patients who may best respond to HCQ therapy. It is unclear how tumors mechanistically evolve resistance to HCQ. We pursued a multi-omic strategy in OVCAR3 ovarian cancer and CCL218 colorectal cancer cells. Two genome-scale screens were performed. In the forward genetic screen, cell populations were passaged in 93-independent cultures for 15 drug pulse-chases with HCQ or vehicle control. Evolved cells were collected and processed for bulk RNA-seq, exome-seq, and single cell RNA-seq (scRNA-seq). In the reverse genetic screen, a pooled Brunello CRISPR-Cas9 library of 19,114 genes targeted by multiple sgRNAs was used in cells over three pulse-chases of HCQ or vehicle control treatments. HCQ evolved cells displayed remarkably few mutational differences, but substantial transcriptional differences. Bulk transcriptomes revealed multiple broad-spectrum pathways associated with resistance to HCQ, including upregulation of glycolysis, exocytosis, and chromosome condensation/segregation, as well as downregulation of translation and apoptosis. Analysis of scRNA-seq data indicated cell clusters were differentially reliant on cytoskeletal regulation, DNA repair, and metabolism. The genome-scale Cas9 screen identified remarkably few autophagy genes. However, an integrated analysis of Cas9 hits with RNA-seq upregulated genes confirmed glycolytic genes KDM3A, ENO2, and PDK3 were essential for HCQ resistance. Additional integrated hits were NEK2, involved in exocytosis, and chromosome condensation/segregation genes CDK1 and CENPA. Transcriptional plasticity was the primary mechanism by which cells evolved resistance to HCQ. Contrary to the widely presumed autophagy-related mode of cell death, the multi-omic analysis instead prioritized glycolytic metabolism, exocytosis, and chromosome condensation/segregation as most involved in cancer cell survival with HCQ. Integrated multi-omic analysis defined high-value biomarkers of HCQ sensitivity and resistance. Our analysis may serve as a model for how to better define the effects and positioning of repurposed drugs in oncology. Citation Format: Madison Clark, Silvia G. Vaena, Joe R. Delaney. Integrated multi-omics of hydroxychloroquine evolved cancer cells reveal survival requires transcriptional upregulation of glycolysis, exocytosis, and chromosome fidelity, but not autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5849.