A genome-wide RNAi screen for novel CIN genes using human artificial chromosome

Chromosome instability (CIN) remains among the most important problems in modern cancer research. In this study, we conducted a genome-wide RNAi screen to identify genes that contribute to CIN. To achieve this, we used a human artificial chromosome in a novel sensitized screen to measure CIN. We screened 18,658 genes for their roles in maintaining chromosomal stability and identified 834 candidates as potential CIN genes. A secondary RNAi screen identified 44 genes with the most pronounced CIN phenotypes. In guilt-by-association analysis using a published set of 8,498 proteins across a panel of 949 cancer cell lines, this cohort of 44 genes displayed a striking correlation with mitotic regulators. Furthermore, altered expression of these proteins was associated with a poor prognosis across multiple cancer types. Specifically, downregulation of AMY2B, ALAD, PDGFRA, PPIE, VEZ1, and TTC19 is associated with poor survival in two or more of the following: small cell lung cancer, lung adenocarcinoma, adrenocortical carcinoma, ovarian cancer, and breast cancer. The genes identified in this screen hold potential as prognostic markers for patient survival across several cancer types and could potentially serve as targets for the development of new therapeutic approaches aimed at mitigating CIN.