Microscopy-based high-content analyses identify novel chromosome instability genes including SKP1

Abstract

Cancer is a devastating disease responsible for ~80,000 deaths in Canada each year. Chromosome instability (CIN) is an abnormal phenotype frequently observed in cancer, characterized by an increase in the rate at which chromosomes or chromosomal fragments are gained or lost. CIN underlies the development of aggressive, drug resistant cancers, disease recurrence, and poor prognoses. Despite this, the majority of CIN genes have yet to be elucidated, highlighting the need for studies aimed at identifying the defective genes that underlie CIN. This thesis describes the development and utilization of imaged-based assays designed to detect CIN phenotypes (i.e. nuclear size changes and micronucleus formation) following gene silencing. Mitotic chromosome spread analyses validated that changes in CIN phenotypes corresponded with numerical and structural chromosome defects by silencing the established CIN gene, SMC1A (Chapter 3). The assays were multiplexed in a high-content, siRNA-based screen of 164 candidate genes in hTERT and HT1080, which identified 148 putative CIN genes. Validation of 10 genes (e.g. SKP1) was performed in hTERT and HCT116, which confirmed gene silencing induced chromosome changes (Chapter 4). SKP1 is a component of the SKP1-CUL1-F-box protein (SCF) E3 ubiquitin ligase complex, which regulates degradation of numerous proteins within pathways that maintain chromosome stability. Accordingly, the aberrant biology underlying CIN in SKP1 silenced cells was investigated further using immunofluorescence, microscopy, and biochemical techniques (Chapter 5). A high-content screen of all 68 F-box genes was performed to determine which F-box proteins/SCF complexes regulate chromosome stability. EMI1, SKP2, and FBXL7 induced CIN phenotypes similar to SKP1, suggesting that the corresponding SCF complexes are required for chromosome stability. Increases in the levels of SCF substrates Survivin and CCNE1, were detected in SKP1 silenced cells. Replication stress, DNA damage, centromeric protein mislocalization, and centrosome defects were also observed, all of which are mechanisms known to underlie CIN. Significantly, a novel screen for CIN phenotypes was developed and employed in this study, which expedited human CIN gene identification and provided critical insights into the fundamental biological mechanisms that regulate chromosome stability. Importantly, characterizing the aberrant genes/mechanisms that underlie CIN and oncogenesis could ultimately reveal novel cancer therapeutic targets.