Detecting Chromosome Instability in Cancer: Approaches to Resolve Cell-to-Cell Heterogeneity

Lepage, Chloe C.; Morden, Claire R.; Palmer, Michaela C. L.; Nachtigal, Mark W.; McManus, Kirk J.

doi:10.3390/cancers11020226

Cited by 40 publications

(48 citation statements)

References 136 publications

(215 reference statements)

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“…Putative CIN genes were identified as those inducing significant changes in surrogate markers of CIN, namely changes in nuclear areas (NAs) and micronucleus (MN) formation ( Figure 1A). Conceptually, changes in NAs correspond with large scale changes in DNA/chromosome complements, while micronuclei are hallmarks of CIN that typically arise due to chromosome mis-segregation events and defects in DSB repair (reviewed in [8]). In hTERT cells, scQuantIM identified 112 genes (68% of genes screened) that induced significant changes in cumulative NA frequency distributions (Kolmogorov-Smirnov (KS) test; p-value < 0.01) following silencing relative to siControl ( Figure 1B; Table S2), while 19 genes (12%) induced significant increases in MN formation ( Figure 1C; Table S3).…”

Section: Cross-species Analyses and Single-cell Quantitative Imaging mentioning

confidence: 99%

Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover

Thompson

Baergen

Lichtensztejn

et al. 2020

Cancers

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Chromosome instability (CIN), or progressive changes in chromosome numbers, is an enabling feature of many cancers; however, the mechanisms giving rise to CIN remain poorly understood. To expand our mechanistic understanding of the molecular determinants of CIN in humans, we employed a cross-species approach to identify 164 human candidates to screen. Using quantitative imaging microscopy (QuantIM), we show that silencing 148 genes resulted in significant changes in CIN-associated phenotypes in two distinct cellular contexts. Ten genes were prioritized for validation based on cancer patient datasets revealing frequent gene copy number losses and associations with worse patient outcomes. QuantIM determined silencing of each gene-induced CIN, identifying novel roles for each as chromosome stability genes. SKP1 was selected for in-depth analyses as it forms part of SCF (SKP1, CUL1, FBox) complex, an E3 ubiquitin ligase that targets proteins for proteolytic degradation. Remarkably, SKP1 silencing induced increases in replication stress, DNA double strand breaks and chromothriptic events that were ascribed to aberrant increases in Cyclin E1 levels arising from reduced SKP1 expression. Collectively, these data reveal a high degree of evolutionary conservation between human and budding yeast CIN genes and further identify aberrant mechanisms associated with increases in chromothriptic events.

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Section: Cross-species Analyses and Single-cell Quantitative Imaging mentioning

confidence: 99%

Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover

Thompson

Baergen

Lichtensztejn

et al. 2020

Cancers

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“…This is particularly relevant in the context of numerous genetic studies showing that aneuploid cells frequently exhibit phenotypic defects in many of the same pathways that cause CIN, including increases in micronucleus formation, chromosome missegregation events, cytokinetic defects, and anaphase bridges [19]. Thus, it is critical that researchers employ more accurate tools and approaches to clearly distinguish between aneuploidy and/or CIN (N-or S-CIN) within their studies (reviewed in [11]).…”

Section: Introductionmentioning

confidence: 99%

Chromosome Instability; Implications in Cancer Development, Progression, and Clinical Outcomes

Vishwakarma

McManus

2020

Cancers

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Chromosome instability (CIN) refers to an ongoing rate of chromosomal changes and is a driver of genetic, cell-to-cell heterogeneity. It is an aberrant phenotype that is intimately associated with cancer development and progression. The presence, extent, and level of CIN has tremendous implications for the clinical management and outcomes of those living with cancer. Despite its relevance in cancer, there is still extensive misuse of the term CIN, and this has adversely impacted our ability to identify and characterize the molecular determinants of CIN. Though several decades of genetic research have provided insight into CIN, the molecular determinants remain largely unknown, which severely limits its clinical potential. In this review, we provide a definition of CIN, describe the two main types, and discuss how it differs from aneuploidy. We subsequently detail its impact on cancer development and progression, and describe how it influences metastatic potential with reference to cancer prognosis and outcomes. Finally, we end with a discussion of how CIN induces genetic heterogeneity to influence the use and efficacy of several precision medicine strategies, including patient and risk stratification, as well as its impact on the acquisition of drug resistance and disease recurrence.

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“…The underlying molecular events driving micronucleus formation are often associated with chromosome instability (CIN; reviewed in [18,23]), an enabling feature and hallmark of many cancer types [24][25][26]. CIN is defined as an increase in the rate at which whole chromosomes, or large chromosome fragments are gained or lost [25], and is frequently associated with the formation of micronuclei.…”

Section: Introductionmentioning

confidence: 99%

An Automated, Single Cell Quantitative Imaging Microscopy Approach to Assess Micronucleus Formation, Genotoxicity and Chromosome Instability

Lepage

Thompson

Larson

et al. 2020

Cells

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Micronuclei are small, extranuclear bodies that are distinct from the primary cell nucleus. Micronucleus formation is an aberrant event that suggests a history of genotoxic stress or chromosome mis-segregation events. Accordingly, assays evaluating micronucleus formation serve as useful tools within the fields of toxicology and oncology. Here, we describe a novel micronucleus formation assay that utilizes a high-throughput imaging platform and automated image analysis software for accurate detection and rapid quantification of micronuclei at the single cell level. We show that our image analysis parameters are capable of identifying dose-dependent increases in micronucleus formation within three distinct cell lines following treatment with two established genotoxic agents, etoposide or bleomycin. We further show that this assay detects micronuclei induced through silencing of the established chromosome instability gene, SMC1A. Thus, the micronucleus formation assay described here is a versatile and efficient alternative to more laborious cytological approaches, and greatly increases throughput, which will be particularly beneficial for large-scale chemical or genetic screens.

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Detecting Chromosome Instability in Cancer: Approaches to Resolve Cell-to-Cell Heterogeneity

Cited by 40 publications

References 136 publications

Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover

Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover

Chromosome Instability; Implications in Cancer Development, Progression, and Clinical Outcomes

An Automated, Single Cell Quantitative Imaging Microscopy Approach to Assess Micronucleus Formation, Genotoxicity and Chromosome Instability

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