Selective vulnerability of aneuploid human cancer cells to inhibition of the spindle assembly checkpoint

Abstract

Selective targeting of aneuploid cells is an attractive strategy for cancer treatment. Here, we mapped the aneuploidy landscapes of ~1,000 human cancer cell lines and classified them by their degree of aneuploidy. Next, we performed a comprehensive analysis of large-scale genetic and chemical perturbation screens, in order to compare the cellular vulnerabilities between neardiploid and highly-aneuploid cancer cells. We identified and validated an increased sensitivity of aneuploid cancer cells to genetic perturbation of core components of the spindle assembly checkpoint (SAC), which ensures the proper segregation of chromosomes during mitosis. Surprisingly, we also found highly-aneuploid cancer cells to be less sensitive to short-term exposures to multiple inhibitors of the SAC regulator TTK. To resolve this paradox and to uncover its mechanistic basis, we established isogenic systems of near-diploid cells and their aneuploid derivatives. Using both genetic and chemical inhibition of BUB1B, MAD2 and TTK, we found that the cellular response to SAC inhibition depended on the duration of the assay, as aneuploid cancer cells became increasingly more sensitive to SAC inhibition over time. The increased ability of aneuploid cells to slip from mitotic arrest and to keep dividing in the presence of SAC inhibition was coupled to aberrant spindle geometry and dynamics. This resulted in a higher prevalence of mitotic defects, such as multipolar spindles, micronuclei formation and failed cytokinesis. Therefore, although aneuploid cancer cells can overcome SAC inhibition more readily than diploid cells, the proliferation of the resultant aberrant cells is jeopardized. At the molecular level, analysis of spindle proteins identified a specific mitotic kinesin, KIF18A, whose levels were drastically reduced in aneuploid cancer cells. Aneuploid cancer cells were particularly vulnerable to KIF18A depletion, and KIF18A overexpression restored the sensitivity of aneuploid cancer cells to SAC inhibition. In summary, we identified an increased vulnerability of aneuploid cancer cells to SAC inhibition and explored its cellular and molecular underpinnings. Our results reveal a novel synthetic lethal interaction between aneuploidy and the SAC, which may have direct therapeutic relevance for the clinical application of SAC inhibitors.

Chromosomally unstable tumor cells specifically require KIF18A for proliferation

“…KIF18A KD increases the frequency of micronucleus formation as a result of chromosome alignment defects, and these micronucleated cells display reduced proliferation 20 . In support of this idea, recent work indicates that the frequency of KIF18A KD-dependent micronuclei is increased in cells with elevated chromosome number and correlates with reduced proliferation in aneuploid cells 47,48 .…”

Spindle Architectural Features Must Be Considered Along With Cell Size to Explain the Timing of Mitotic Checkpoint Silencing

“…Previous studies have shown that, in some experimental systems, tetraploidy can lengthen mitosis, but it is unclear if cell and spindle scaling contribute to this delay (Kuznetsova et al, 2015 ; Viganó et al, 2018 ; Paim and FitzHarris, 2019 ; Cohen-Sharir et al, 2020 ; Quinton et al, 2020 ). To investigate whether the differences in cell size and spindle geometry among the 4N clones affect their progression through mitosis, we measured the timing from cell rounding to anaphase onset (referred to as mitotic duration henceforth) using live-cell phase contrast microscopy ( Figure 3A and Supplementary Videos 11–15 ).…”

“…Our findings suggest that rather than multipolarity resulting from extra centrosomes, relatively subtle variations in spindle geometry, spindle pole size, microtubule abundance, and cell volume can affect mitotic progression and SAC silencing in tetraploid cells. Thus, even though spindle bipolarity may be preserved, other changes in cell size and spindle architecture—its geometry and composition—may promote mitotic dysfunction and contribute to the genomic instability caused by tetraploidy (Storchova and Kuffer, 2008 ; Dewhurst et al, 2014 ; Cohen-Sharir et al, 2020 ; Quinton et al, 2020 ).…”

“…For instance, cell cycle and mitotic progression were not perturbed in tetraploid yeast cells (Storchová et al, 2006 ), which may be due to the lack of spindle scaling in those strains. In contrast, tetraploid mammalian cells often progress through mitosis more slowly than their diploid counterparts (Kuznetsova et al, 2015 ; Paim and FitzHarris, 2019 ; Cohen-Sharir et al, 2020 ; Quinton et al, 2020 ), suggesting a possible delay in SAC silencing. Several recent studies, which explored the link between cell and spindle sizes and SAC function more closely (Gerhold et al, 2015 , 2018 ; Galli and Morgan, 2016 ; Kyogoku and Kitajima, 2017 ), also produced conflicting results.…”

Aneuploidy-driven genome instability triggers resistance to chemotherapy

“…Because of this, there are several ongoing efforts concentrated on understanding the contribution of cell intrinsic factors -such as genetic alterations and epigenetic changes -as well as cell extrinsic stimuli -such as cytokines and growth factors -as major players responsible for drug resistance (Vasan et al 2019). Recent papers identified an increased resistance of aneuploid cancer cell lines to multiple chemotherapies, and to drugs in general (Cohen-Sharir et al 2020). However, very little is known about how and why aneuploidy and the ensuing genomic instability impacts the therapeutic outcome.…”