Chromosome 8p-engineering and CRISPR-Cas9 viability screening reveal increased metastatic capacity of liver cancer cells targetable by patient-specific synthetic lethality [Cas9]

Large-scale chromosomal aberrations are prevalent in human cancer but their functional effects remain poorly understood. We describe the establishment of chromosome-engineered hepatocellular carcinoma cell lines using a dual guided CRISPR-Cas9 genome editing strategy. A mega base-sized region on chromosome 8p (chr8p) was heterozygously deleted mimicking a frequently observed copy number alteration (CNA) of solid tumors. Using this unique model system, we delineated the functional consequences of chr8p loss and its impact on metastatic behavior and patient survival. We found that metastasis associated genes on chr8p act in concert to induce an aggressive and invasive phenotype characteristic for chr8p deleted tumors. The conjunction of engineered chromosome-scale CNAs and genome-wide CRISPR-Cas9 viability screenings served as a powerful tool for the discovery of novel synthetic lethal targets and vulnerabilities accompanying patient-specific copy number changes. Using this target identification strategy, we showed that chr8p deletion sensitizes tumor cells to targeting of the reactive oxygen sanitizing enzyme Nudix hydrolase 17 (NUDT17). Small interfering RNA-mediated knockdown of NUDT17 alone, NUDT18 alone, combination of NUDT17 and NUDT18 or transfected with Control siRNAs. All four different treatments were performed in triplicates.