Genetic Dependencies Associated with Chromosomal Instability in Cancer Metastasis

Abstract

Recent studies have identified recurrent features of metastatic cancer cellssuch as their increased chromosomal instability (CIN) and frequent loss of the short arm of chromosome 17 (Chr17p). However, it remains unclear whether these features induce synthetic lethal vulnerabilities that can be used to specifically target metastatic disease. Using whole-genome CRISPR/Cas9 loss-of- function screens performed in matched primary and CIN-high brain-metastatic tumor models, we discovered that brain-metastatic cells exhibit increased sensitivity to the loss of diverse regulators of chromosome segregation. Knockout of one such regulator, NDE1, selectively inhibited the growth of brain-metastatic models in vitro and in vivo, an effect driven by the loss of STAG2 and consequent induction of CIN. Surprisingly, dependence on NDE1 was also highly correlated with loss of Chr17p across hundreds of cancer cell lines in DepMap, the result of losing the NDE1 paralog NDEL1, which resides at this locus. CIN and Chr17p loss are thus independently sufficient to drive NDE1 dependence in brain- metastatic cells, and the presence of both features increases NDE1 dependence additively. These findings demonstrate that metastasis evolution endows cancer cells with specific vulnerabilities, including one that is driven by two recurrently altered molecular features of metastatic disease.