The Diverse Consequences of Aneuploidy

Review Article | FOCUS https://doi.org/10.1038/s41556-018-0243-8Review Article | FOCUS https://doi.org/10.1038/s41556-018-0243-8 The diverse consequences of aneuploidy

Narendra Kumar Chunduri and Zuzana Storchová *

Aneuploidy, or imbalanced chromosome number, has profound effects on eukaryotic cells. In humans, aneuploidy is associated with various pathologies, including cancer, which suggests that it mediates a proliferative advantage under these conditions. Here, we discuss physiological changes triggered by aneuploidy, such as altered cell growth, transcriptional changes, proteotoxic stress, genomic instability and response to interferons, and how cancer cells adapt to the changing aneuploid genome.

ost eukaryotic organisms have their genome neatly orga- Mechanisms leading to aneuploidy have been thoroughly charac- nized in chromosomes, with characteristic number, size terized and there are several excellent reviews that summarize these Mand sequences that define the species. Yet, exceptions to discoveries30–32. Briefly, whole-chromosome aneuploidy is caused this so called euploidy (from ancient Greek eu—true, good) can by errors during chromosome segregation that result from incor- be found, such as aneuploidy that is characterized by copy num- rect attachments of the spindle microtubules to the kinetochore, a ber changes of whole chromosomes or chromosomal segments. proteinaceous complex that assembles at the centromeric region of Aneuploidy can be tolerated and occurs naturally in some uni- every chromosome33. The kinetochore enables the formation of a cellular eukaryotes, such as budding yeast, the pathogenic fungi stable attachment to the microtubules. Correct attachments create Candida albicans or parasites from genus Giardia, as well as in sev- tension between the spindle-generated forces and the forces general multicellular species1–6. In most contexts, whole-chromosome erated by sister chromatid cohesion that holds the sisters together aneuploidy has profound effects on cellular physiology. In humans, (Fig. 1a). Lack of attachments is recognized by the spindle assem- aneuploidy of autosomes is detrimental and only a few exceptions bly checkpoint (SAC) and corrected, while the activated checkpoint (trisomy of chromosomes 13, 18 and 21) are compatible with sur- delays anaphase onset until all chromosomes are properly attached34 vival, although accompanied with various pathologies. (Fig. 1b–d). Tension-less attachments are unstable and disassemble Aneuploidy is frequent in cancer, in which it is often associated to allow error correction35. Chromosome missegregation occurs due with a more complex phenotype called chromosomal instability to mutations or sporadic defects that impair mitotic spindle function, (CIN). CIN cells gain and lose chromosomes as they divide, thereby kinetochore structure, sister chromatid cohesion or SAC (Fig. 1e–g). creating progeny with variable aneuploid karyotypes. CIN and aneu- Mutations in genes regulating the chromosome segregation fidelity ploidy in cancer correlate with metastasis, resistance to drugs and in cancers are rather rare, but changes in their expression levels are disease progression7–14. Yet, exactly how aneuploidy affects eukary- frequently observed36,37. In addition, mutations in well-known onco- otic cells and how it contributes to tumorigenesis are only partially genes and tumour suppressor genes can trigger segregation errors. understood. Recent years have brought novel insights thanks to the Changes in transcriptional regulation of Rb-E2F and Ras affect the establishment of a wide palette of models of whole-chromosome fidelity of chromosome segregation by enhancing the expression aneuploidy. Moreover, next-generation sequencing and the broad of SAC genes or by causing sister chromatid cohesion defects38–41. use of -omics approaches have provided extensive data on chromo- Genes previously not linked to chromosome segregation may also some copy number changes and their consequences. In this Review, induce aneuploidy, as shown by two recent genetic screens42,43. we discuss recent insights into how aneuploidy affects cells and Furthermore, surrounding tissue may influence the occurrence organisms and relate these to findings from recent cancer analyses. of chromosome segregation defects, as a recent study demonstrated that epithelial tissue architecture promotes chromosome Occurrence and causes of aneuploidy segregation fidelity44. Whole-chromosomal aneuploidy arises from defects during chromo- Chromosome missegregation, particularly when coupled with some segregation in meiosis or mitosis. In particular, mammalian chromosome breakage, is often followed by irreversible cell cycle female meiosis is highly erroneous, resulting in aneuploid gametes arrest, impaired proliferation or cell death45–50. Thus, accumula- and subsequently in whole-organismal aneuploidy15,16. Early embryos tion of aneuploid cells in a tissue is affected not only by mutations often accumulate aneuploid cells due to mitotic errors, thus creat- that increase mitotic errors but also by those that facilitate survival ing a mosaic of euploid and aneuploid cells17,18. Later, the aneuploid immediately after abnormal mitosis47,51,52 and those that increase cells are removed from embryonic tissues by senescence or apoptosis, tolerance to stresses induced by aneuploidy53–55. Although these or become outgrown by euploid cells that proliferate better19,20. The types of mutation might be difficult to find experimentally, their frequency of aneuploid cells in mammalian tissue is difficult to esti- identification will help to understand how aneuploid cells arise and mate: whereas single-cell sequencing reveals less than 1% of aneuploid propagate in cancer. neurons and fibroblasts, the same tissues show frequent abnormal chromosome counts when evaluated by fluorescence in situ hybrid- Models of whole-chromosome aneuploidy ization21–24. For example, fluorescence in situ hybridization analysis of There are two main approaches to study aneuploidy and its cellular hepatocytes shows aneuploidy in as many as 50% of the cells, whereas consequences. First, acute aneuploidy can be induced by mutating single-cell sequencing indicates 4%21,25. Tissue-specific differences in genes involved in chromosome segregation or by impairing mito- aneuploidy were found also in other species, but the causes remain sis by adding inhibitors to cell cultures, specific tissues or even the unclear26. Importantly, aneuploidy is found in most malignant neopla- whole organism49,56–60 (Fig. 2a). This approach generates heteroge- sia, with occurrence depending on the cancer type and ranging up to neous aneuploid populations and allows the study of the immediate 90% in solid tumours and 35–60% in haematopoietic cancers27–29. cellular response to chromosome missegregation, that is, the acute

Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany. *e-mail: [email protected]

a Metaphase Prometaphase Amphitelic attachment Anaphase

SAC

b c d Absence of attachment Monotelic attachment Syntelic attachment

SAC SAC SAC

ef g Merotelic attachment Premature loss of sister Multipolar spindle chromatid cohesion

SAC

Kinetochore Microtubule Centrosome Cohesin SAC Engaged SAC SAC Satisfied SAC

Fig. 1 | Routes to whole-chromosome aneuploidy. a, The newly replicated sister chromatids that are held together by sister chromatid cohesion attach to microtubules via their respective kinetochores. During metaphase, each kinetochore has to attach to microtubules emanating from one spindle pole (centrosome); this amphitelic bipolar attachment results in a tension between sisters held together by sister chromatid cohesion and the pulling forces of the microtubules. Bipolar attachments of all chromatid pairs silence the checkpoint. In anaphase, the sister chromatid cohesion is dissolved and the chromosomes segregate to the opposite spindle poles. b, Lack of microtubule–kinetochore attachment. c, Monotelic attachment—that is, lack of attachment by one of the sister chromatids. Unattached kinetochores in b and c are recognized by the SAC and the progress to anaphase is halted until the error is corrected. d, Syntelic attachment—that is, when both sisters are attached to the same pole. This type of attachment is highly unstable and disassembles; the empty kinetochore is then recognized by the SAC. The events described in b–d lead to chromosome missegregation if uncorrected, for instance, due to a SAC defect. e, Merotelic attachment—that is, when one sister kinetochore attaches to microtubules emanating from both centrosomes. This attachment usually generates enough tension to remain stable and therefore escapes the SAC. Merotelically attached chromatids often lag during anaphase and may become missegregated. f, Lack of sister chromatid cohesion interferes with the establishment of bipolar attachment. g, Multipolar spindles owing to supernumerary centrosome lead to defective attachments and frequent merotely, particularly when the extra centrosomes cluster (depicted by connected arrows). Defects in the SAC interfere with error recognition and increase the frequency of missegregation. The arrows depict the direction in which chromosomes are pulled. consequences of aneuploidy. On the downside, the identities and Although the models of acute cellular response to aneuploidy copy numbers of the altered chromosomes remain unknown in and chronic consequences of aneuploidy differ in some aspects, this approach. Moreover, it may be difficult to distinguish whether together, they have broadened our knowledge and opened new the observed phenotypes are specific to chromosome copy number views on cancer. Importantly, both the acute and chronic response changes or caused by secondary effects of the treatments, such as to aneuploidy probably affect phenotypes of CIN cells, in which ongoing CIN. In a second approach, aneuploid cells are generated ongoing chromosome segregation errors further alter the already that differ from their isogenic counterparts only by the gain or loss aneuploid cells. Below, we focus in more detail on five phenotypes of one or two chromosomes. This allows the analysis of the chronic shared by most models of aneuploidy. For other aspects of aneu- consequences of defined aneuploidy in cells from patients with ploidy, such as the metabolic changes or the association with ageing, trisomy syndromes, or generated by a transfer of individual chro- we recommend recent reviews71,72. mosomes61–63, by targeted chromosome removal or silencing64–66, or through meiotic non-disjunction67 (Fig. 2b–e). Chromosome copy Effects on cell proliferation number changes introduced in budding yeast provide another use- In many aneuploid model systems, gain of a chromosome strongly ful model of aneuploidy68–70 (Fig. 2f–h). affects proliferation. The effects of aneuploidy can be positive

adInduced missegregation Transfect cells with plasmids with single or multiple gRNAs

Cas9

Single-cell cloning

Variable aneuploid progeny MonosomySurvive Nullisomy Die b

1 2345

6 789101112 e 13 14 15 16 17 18 19 20 21 22 YX Robertsonian WT translocations Trisomy syndrome patient Trisomic fibroblasts MEFs obtained Trisomy Chr. 1, from E13 embryos 13,16,19 c Micronucleation and isolation Mouse A9 donor cells

Selection +

Gene coding for antibiotic resistance 2N – 1 2N 2N + 1 Recipient Embryonic lethality Survival Embryonic lethality human cell line except for Chr. 19

fgh Haploid strain A Haploid strain B Diploid strain Triploid strain kar1Δ15 WT

Sporulation

GAL1–CEN3 + Kanamycin – Histidine + Galactose 2N – 12N + 1

Variable aneuploid progeny HIS3 cassette KanR cassette

Fig. 2 | Models of aneuploidy. a, Induced chromosome missegregation, either by drug treatment or by targeted mutagenesis, creates a heterogeneous population of aneuploid cells. This approach can be used both in vitro and in vivo. b, Cells from patients with trisomy syndromes provide material for cell cultures with the specific karyotype. c, Micronuclei-mediated chromosome transfer. Micronuclei carrying one or a few chromosomes are isolated and fused to the acceptor cell lines. Aneuploid cells are selected thanks to the resistance to antibiotics encoded on the transferred chromosome. d, Monosomic cells can be created by targeting chromosome-specific sequences via the CRISPR (clustered regularly interspaced short palindromic repeats)–Cas9 (CRISPR-associated protein 9) technique. e, Mating mice carrying Robertsonian translocations with wild-type (WT) mice produces embryos of variable karyotypes that can be used for the isolation of mouse embryonic fibroblasts (MEFs) with specific trisomies. f, Haploid disomic yeast cells can be created by mating wild-type cells with cells carrying the kar1 mutation. The mutation interferes with nuclear fusion during mating and only some chromosomes are randomly transferred. The specific disomy can be selected thanks to marker genes integrated on the chromosome of interest. g, Transcription across a centromere interferes with proper microtubule–kinetochore attachment in yeast cells, which leads to chromosome missegregation and progeny with missing or gained chromosomes. h, Sporulation of yeasts with odd ploidy results in spores with complex aneuploid karyotypes. 2N, diploid; Chr., chromosome; E13, embryonic day 13; gRNA, guide RNA. or negative, depending on the cell type, environment and which haploinsufficiency, when one gene copy of the allele is not sufficient chromosome is affected. Aneuploidy often confers a proliferative to support the wild-type phenotype. In neural and adult intestinal disadvantage with a delay in the G1 and S phases of the cell cycle, stem cells in Drosophila, aneuploidy decreases proliferation, which probably due to delayed accumulation of cyclins63,68,70,73–75. The leads to an accumulation of G1 cells, cell cycle exit and premature proliferation defects are caused by the expression of genes on the differentiation77. How, mechanistically, aneuploidy perturbs cell extra chromosome, as evidenced by at least two observations. First, cycle progression remains unclear, but many stress conditions, such aneuploid budding yeast harbouring yeast artificial chromosome as proteotoxic or genotoxic stress, identified in aneuploid cells (dis- with human and mouse DNA that cannot be transcribed in yeast cussed below) can interfere with G1–S progression78,79. do not suffer from cell cycle defects68. Second, even small changes By contrast, aneuploidy facilitates proliferation in murine embry- in the combined gene dosage of several genes impair proliferation, onic and human pluripotent stem cells80–82. Aneuploidy also confers although are not harmful when amplified individually76. Arm-level proliferative advantage to human trisomic cells as well as budding deletion of chromosome 3 in human cells29 and the loss of an entire yeasts and the pathogenic fungi C. albicans under stress condi- chromosome in diploid yeast cells70 also reduce proliferation. This tions6,69,83–85. In addition, there are chromosome-specific effects effect is probably a composite of aneuploidy-associated stresses and on proliferation. Budding yeast strains that are disomic for most

Genome Transcriptome Proteome Phenotype

Protein degradation Aneuploidy-induced stresses

Demand for HSP90 protein folding

Global effects on gene expression Misfolding and aggregate formation Chromosome-specific effects

Functional consequences of overexpression

Fig. 3 | Global and chromosome-specific changes in gene expression in response to aneuploidy. The presence of an extra chromosome leads to the production of surplus mRNA and proteins. This impairs protein homeostasis and stoichiometric balance of macromolecular complexes, leading to overwhelming of the protein-folding machinery, increased requirements for protein degradation pathways or the formation of protein aggregates. This general protein imbalance further impairs cellular physiology and propels global effects on gene expression. In addition, chromosome-specific effects due to increased expression of specific proteins (here illustrated by an increased transcription of a downstream target that is localized on a different chromosome) can be observed in aneuploid cells.

chromosomes delay the G1–S transition by 10–20 minutes, whereas with the copy number changes53,63,69,101–103. Importantly, the abun- gain of chromosome 1, 2, 5 or 9 causes no changes in proliferation68. dance of about 25% of all proteins on the affected chromosome Gain of chromosome 8 has a minor effect on the proliferation of becomes adjusted to diploid levels in both yeast and human cells human cells54 and gain of chromosome 12 seems to provide advan- and this predominantly affects the subunits of multi-molecular pro- tage to most cell types, as spontaneously arising cells with trisomy tein complexes63,101,102 (Fig. 3). This ‘dosage compensation’ is par- 12 often outgrow diploids in cell cultures80,81,86. Thus, proliferation ticularly apparent for proteins that are initially unstable but stabilize changes in aneuploid cells depend on the cell type, chromosome with age, most likely by binding to their partner104. The attenuated identity and environmental context, but the reasons for these differ- expression of genes encoded on the extra chromosome is mediated ences remain unclear. by the ubiquitin–proteasome system, as protein abundance can be rescued by proteasome inhibitors101,104. Gene expression changes in response to aneuploidy Besides these primary, chromosome-specific gene expres- Model systems with defined aneuploidy in budding and fis- sion changes, secondary trans-effects disturb the gene expression sion yeast68,69, engineered human and murine cell lines62,63,67, in network globally (Fig. 3). Aneuploidy-induced transcriptome Arabidopsis thaliana87 and in patient-derived cell lines and tis- deregulation observed in budding yeast resembles the so-called sues88–91 established that mRNA abundance largely scales with chro- environmental stress response that denotes common transcrip- mosome copy number (Fig. 3). These observations demonstrate tional changes following environmental stresses, such as starvation, the lack of general dosage compensation for whole-chromosome oxidative stress, heat shock and slow growth68,105,106. As the environ- aneuploidy, although there are some exceptions that affect mainly mental stress response also reflects redistributions of cells across sex chromosomes. In humans, additional copies of the X chromo- different cell cycle phases107, the observed changes may be partly some are dosage compensated via the long non-coding RNA XIST, attributed to the negative effect of aneuploidy on cell cycle progres- which in healthy women silences one of the X chromosomes92. sion. Analysis of mammalian aneuploid cells determined unique Accordingly, individuals with an extra X chromosome are mostly ‘aneuploidy stress responses’. This involves a conserved downreg- asymptomatic and only 10% of patients might be diagnosed93. In ulation of pathways involved in cell cycle regulation, nucleic acid Drosophila, dosage compensation was observed for both sex chro- metabolism and ribosomal biogenesis, and upregulation of regula- mosomes and autosomes94,95. Whereas the X chromosome and tors of autophagy, lysosomal pathways, membrane metabolism and chromosome 4, which was evolutionary derived from the X chro- glycolysis63,108,109. In addition, pathways related to the inflammatory mosome, are dosage compensated by chromosome-specific mecha- response, such as major histocompatibility complex and antigen nisms96,97, the underlying mechanisms for the autosomes remain processing and response to interferons (IFNs), are upregulated in unclear. Autosomal dosage compensation was also observed in human aneuploid cells49,103,109. aneuploid wild yeast isolates98, although the extent of this effect remains disputed99, and in C. albicans with monosomy 5 and tri- Proteotoxic stress somy 4/7b, in which 25–30% of the transcripts seem to be compen- Another prominent feature of aneuploid cells is proteotoxic stress sated to diploid levels100. However, with these exceptions, mRNA manifested by impaired protein folding, activation of degrada- levels mostly scale with the gene copy number. tion pathways and accumulation of cytoplasmic protein aggre- Analyses of protein abundance by mass spectrometry performed gates54,63,75,110,111. The protein aggregates accumulate in the cytoplasm in aneuploid budding yeasts and in human cells established that the due to reduced heat shock protein 90 (HSP90) folding capacity54,111. protein levels encoded on the affected chromosomes largely scale Accordingly, aneuploid budding yeast as well as human and murine

Nature Cell Biology | VOL 21 | JANUARY 2019 | 54–62 | www.nature.com/naturecellbiology 57 Review Article | FOCUS Reviewhttps://doi.org/10.1038/s41556-018-0243-8 Article | FOCUS NAture Cell BIology cells are sensitive to inhibitors of HSP90 (refs 54,68,110). Overexpression typical for aneuploids downregulates replicative factors. Indeed, of heat shock factor protein 1 (HSF1), a transcription factor that expression of the MCM2–7 helicase and other replication proteins regulates the expression of heat shock factors, rescues the protein- is downregulated following inhibition of HSP90 or depletion of the folding defects and the sensitivity to HSP90 inhibition in aneuploid transcription factor HSF1 (refs 54,118). Alternatively, replication factor human cells54. The protein-folding defect is probably due to the pro- levels can be affected by p53, which negatively regulates the expres- duction of surplus proteins from the supernumerary chromosomes sion of proliferative factors, including the MCM2–7 helicase119. The (Fig. 3). This overwhelms the chaperone machinery that is essential latter mechanism is supported by the finding that trisomic cells for protein folding and leads to the accumulation of misfolded or derived from DLD1 cells, a colorectal cancer cell line carrying a aggregated proteins. canonical TP53 cancer mutation, do not show downregulation of Misfolded and aggregated proteins must be removed, as fail- replicative proteins103. Thus, whereas increased DNA damage and ure to clear the aggregated proteins impairs cellular viability112. genomic instability are possible outcomes of chromosome gain, the Accordingly, aneuploid yeast and human cells rely on proteasomal causes of these phenotypes remain to be addressed in the future. degradation, as demonstrated by their increased sensitivity to the proteasomal inhibitor MG132 (refs 60,68). A genetic screen for Response to IFN aneuploidy-tolerating mutations determined a loss-of-function The response to type I IFNs is also consistently upregulated in mutation in UBP6 that increases the fitness of aneuploid yeast53. model mammalian aneuploids49,103,109. Increased expression of fac- UBP6 encodes a deubiquitinase, which is an enzyme that removes tors involved in IFN signalling and response, such as IFIT 3 (IFN- ubiquitin from the substrates of the proteasome, allowing them to induced protein with tetratricopeptide repeats 3), OASL1 (2′-5′ escape degradation113. Loss of a pleiotropic deubiquitinase Ubp3 -oligoadenylate synthase-like protein), STAT1 (signal transducer exacerbates the defects in aneuploid yeasts. This function is con- and activator of transcription 1) and others, has been observed in served, as the depletion of the human homologue USP10 impairs model trisomy and tetrasomy in RPE1, HCT116 or DLD1 cells103,109. the fitness of human cells following chromosome missegrega- The expression levels of pro-inflammatory cytokines increases tion55. These findings demonstrate the importance of the ubiqui- upon chromosome missegregation in human and murine cells49. tin–proteasome system in maintaining protein homeostasis and Moreover, activation of IFN signalling has been documented in cell the viability of aneuploids. lines with trisomy 21 (refs 120–122), murine models of Down’s syn- Another pathway of protein degradation is autophagy. drome123 and in patients with Down’s syndrome124. These observa- Accumulation of autophagosomes is increased in human and tions were previously attributed to the fact that four out of six IFN murine cells with chronic trisomy, and some aneuploid cells show receptors are located on chromosome 21 (ref. 125); however, recent increased sensitivity to the autophagy inhibitor chloroquine63,75,110. findings suggest that aneuploidy per se activates this pathway. Increased accumulation of foci positive for the autophagy marker DNA damage and genomic instability trigger an inflammatory LC3 was also observed immediately after chromosome misseg- response, which could explain the observed phenotype in aneuploid regation60,114. Although missegregating human cells accumulate cells. DNA is normally compartmentalized within the nucleus and autophagosomes, lysosomal activity appears to be compromised mitochondria, but the presence of DNA in the cytoplasm induces and autophagic flux, which reflects the protein turnover by autoph- type I IFNs and other cytokines through the cGAS–STING (cyclic agy, is diminished114. This indicates that acute protein overexpres- GMP–AMP synthase linked to stimulator of IFN genes) pathway of sion overwhelms cellular lysosomal degradation, thereby triggering innate immunity126. DNA damage and replication stress increase the lysosomal stress. This in turn activates TFEB, a transcription factor levels of cytosolic DNA present in so-called speckles or in micronu- required for the expression of lysosomal proteins114. Importantly, clei that are prone to rupture127–130. The levels of cytoplasmic DNA chronic aneuploidy does not lead to defects in autophagic flux and increase also in aneuploids103. Moreover, DNA damage elevates the to lysosomal stress63, suggesting that chronic aneuploid cells adapt expression levels of natural killer ligands and pro-inflammatory to protein imbalance by constitutive activation of autophagy and cytokines131–133. Such cytokines are observed in cells immediately lysosomal pathways. after chromosome missegregation where they might facilitate their clearance by the immune system49. Finally, whole-chromosomal Genomic instability aneuploidy in human primary fibroblasts induces DNA damage and Gain of a single chromosome often destabilizes the genome. In bud- oxidative stress and, subsequently, the senescence-associated secre- ding yeast, disomic cells show elevated chromosome missegrega- tory phenotype and senescence134. Recently, the senescence-associ- tion and increased spontaneous mutagenesis115. Similarly, human ated secretory phenotype was shown to arise due to IFN-β activation aneuploid cells frequently undergo abnormal mitoses and display in response to DNA damage via the cGAS–STING pathway135. Thus, increased levels of DNA damage75,116,117. The DNA damage that current evidence points towards DNA damage as a trigger of the arises is probably due to replication defects, given that both human inflammatory response and aneuploidy-induced genomic instabil- and yeast aneuploids are sensitive to replication inhibitors, and rep- ity may be a major contributor. lication stress markers, such as RPA32S33, are increased in human aneuploids49,115,117. Moreover, aneuploidy induces replication stress A paradox of aneuploidy and CIN in cancer at telomeres in human primary fibroblasts and murine haematopoi- Abnormal chromosome content and aberrant mitotic figures were etic stem cells43. Increased replication stress and DNA damage give noticed in cancer cells by David Hanselmann and Theodore Boveri rise to de novo chromosomal rearrangements in aneuploid cells117. more than a century ago136, and recent analyses of cancer genomes What mechanisms trigger the replication stress in aneuploids? confirmed the generality of this observation29,137. Despite its high The main culprit may be unbalanced protein expression, as yeast prevalence, the role of aneuploidy in tumorigenesis remains unclear aneuploids harbouring yeast artificial chromosome containing and is complicated by the paradoxical observation that aneuploidy human DNA do not show similar defects despite carrying a com- can act as both a tumour suppressor and a tumour-promoting parable amount of extra DNA68. Strikingly, both acute and chronic factor. In model systems, chromosome missegregation and aneu- aneuploidy reduces the expression of replication factors, including ploidy are anti-proliferative63,67,68, induce apoptosis51,60 or senes- the MCM2–7 helicase, the key replicative helicase required for repli- cence43,49,91,134, increase proteotoxic and genotoxic stress54,111,115,117 cation licencing and replisome progression60,117. What exactly causes and evoke innate immune responses49,103,122. Aneuploidy also the reduced expression of replication factors remains unclear. One inhibits the anchorage-independent growth on soft agar as well as possibility is that the proteotoxic stress and protein-folding defect tumour formation in nude mice138. In murine models of induced

58 Nature Cell Biology | VOL 21 | JANUARY 2019 | 54–62 | www.nature.com/naturecellbiology FOCUS | Review Article NAture Cell BIology FOCUShttps://doi.org/10.1038/s41556-018-0243-8 | Review Article aneuploidy, both tumour-suppressing and tumour-promoting Aneuploidy-induced Adaptations Therapeutic phenotypes are observed. Mice carrying heterozygous deletions of stresses strategies spindle assembly checkpoint genes, such as MAD1 (ref. 139), MAD2 Immune response Type I IFN response, Adaptive immunity, Immune activity 56 140 cGAS–STING, cytokines, (ref. ) and BUB1B (ref ), that lead to the accumulation of cells cytokines, T cell function with variable aneuploid karyotypes develop spontaneous and drug- recognition by NK cells induced tumours. Mutation of the gene encoding the kinesin-like Ipilimumab, motor protein CENPE (centromere-associated protein E) increases nivolumab, atezolizumab, the incidence of spleen lymphomas and lung adenomas, but inhibits sipileucel tumour formation in cancer-prone liver tissue58. By contrast, mice Genomic stability Replication stress, Replication stress, DNA damage, DNA damage, DNA damage, +/– +/– +/– with BUB1B or BUB3 /RAE1 mutations show tissue-specific mutagenesis mutagenesis, missegregation premature ageing and decreased tumour incidence despite similar LOH Cisplatin, 141,142 methotrexate, OG TSG rates of chromosome missegregation . In addition, individu- paclitaxel and others als with Down’s syndrome have an increased risk of developing 143 Proteostasis Proteotoxic Proteotoxic Proteotoxic leukaemia, but considerably low incidence of solid tumours . stress, stress, stress These findings suggest that the ability of aneuploidy to promote autophagy autophagy cancer depends on the tissue of origin and the degree of aneuploidy Chaperones, HSF1 and CIN. This could affect whether and how efficiently the cells HSF1, Epigallocatechin, adapt to the detrimental effects of aneuploidy (Fig. 4). chaperones 17AAG, ganetespib

Adaptations to aneuploidy-associated stresses in cancer Aneuploid cancers share some features with the model aneuploids, such as metabolic changes, genotoxic stress, proteotoxic stress and autophagy activation108,144–146. Whereas these stresses have a negative Healthy cells Aneuploid cells Senescence effect on model aneuploid cells, cancer cells find ways to adapt. For Cancer cells or death example, the expression levels of pro-proliferative genes that encode Proliferation replicative factors and ribosomal subunits are elevated in cancer, whereas they are downregulated in aneuploid model cell lines108,109. Overcoming the anti-proliferative effect of aneuploidy might be an important adaptation of transformed cells. Fig. 4 | Cellular responses and adaptations to whole-chromosome Cancers often experience proteotoxic stress, and constitutive aneuploidy. Following chromosome missegregation, cells experience activation of HSF1 is essential for many cancer types145. Inhibition numerous aneuploidy-induced stresses that are triggered by protein of HSP90-mediated protein folding is a therapy currently in clini- imbalance, DNA damage and activation of the inflammatory response. cal trials, with mixed results147,148 (Fig. 4). The drugs are mostly Surviving cells can adapt to these cell-intrinsic challenges, as well as to other applied to tumours that are driven by interactors of HSP90, such environmental stresses, by activation or inhibition of relevant pathways, which as HER2, EGFR (epidermal growth factor receptor), AKT, RAF is accelerated by elevated genomic instability. Thus, aneuploidy and CIN on and BRAF149,150, but the increased proteotoxic stress experienced the one hand trigger cellular stresses, but on the other hand also facilitate by cancer cells may occur partly due to their unbalanced aneuploid adaptation to the changing environment. Further increase of genomic karyotype148. Thus, additional benefit for treatment efficacy might and proteotoxic stress and activation of the adaptive immune response be gained when targeting aneuploid tumours. might serve as therapeutic strategies that are particularly efficient against Adaptation to aneuploidy-induced stresses is probably facili- aneuploidy tumours. 17AAG, 17-N-allylamino-17-demethoxygeldanamycin tated by genomic instability. Not only does the presence of an extra (also known as tanespimycin); LOH, loss of heterozygosity; NK, natural killer, chromosome elevate genomic instability115–117 but also, conversely, OG, oncogenes; TSG, tumour suppresor genes. defects in DNA replication and repair generate whole-chromosome aneuploidy, as incorrectly repaired double-stranded DNA breaks obstruct mitosis, chromosome segregation and cytokinesis151,152. lacking the motor protein Myo1, which is required for cytokine- Accordingly, cancer genome analyses demonstrate that whole-chro- sis160, in cells impaired by thiol peroxidase deficiency161, with dereg- mosome aneuploidy positively correlates with increased frequency ulated protein SUMOylation162, with telomerase insufficiency163 of point mutations as well as with the accumulation of de novo struc- and other defects caused by gene mutations164. In C. albicans, resis- tural rearrangements29,153,154. These ongoing cycles of chromosome tance to the broadly used antibiotic fluconazole often occurs via gains and losses drive amplifications of oncogenes or loss of tumour segmental aneuploidies6. In these cases, stress conditions stimulate suppressors155 and generate mutations that could potentially ben- the selection of aneuploid cells that gained protective mechanisms, efit tumour growth. However, if the genomic instability and DNA most likely by overexpression of the relevant genes due to increased damage reach a threshold, the cells undergo senescence and cell chromosome copy number, thereby restoring cellular homeostasis. death, which in turn inhibits tumorigenesis (Fig. 4). Indeed, high However, a gain of a specific chromosome may bring a novel set CIN levels correlate with improved prognosis for patients14. Thus, of adverse effects for the cells165. The idea that aneuploidy plays a an important adaptation of cancer cells may be to ‘stabilize’ and tol- similar role in cancer is supported by the findings that copy num- erate low or intermediate CIN levels and increasing their CIN load ber changes of some chromosomes are recurrent, occur in certain may serve as an efficient therapeutic strategy46,156,157 (Fig. 4). cancer types and may be associated with specific phenotypes and drug responses29,155,165. Aneuploidy as a driver of adaptation Aneuploidy may also drive tumour cell adaptation to the immune Cancers may need to adapt to the adverse effects of aneuploidy system. The cells of early cancer stages are eliminated by immune for survival. At the same time, aneuploidy per se drives adaptation CD8+, CD4+ and natural killer cells (reviewed in ref. 166). During to a stressful environment. In budding yeast, aneuploidy enables the course of tumour progression, cancer cells evolve from immu- adaptation to a broad range of stress conditions, such as elevated nogenic to immunosuppressive by ‘immunoediting’167,168, and eva- temperature84, endoplasmic reticulum stress158 or inhibition of sion of cancer cells from immune cells is an important hallmark of heat shock factors159. Aneuploidy also promotes survival in yeasts cancer144. Interestingly, aneuploidy in cancer correlates with immune

Nature Cell Biology | VOL 21 | JANUARY 2019 | 54–62 | www.nature.com/naturecellbiology 59 Review Article | FOCUS Reviewhttps://doi.org/10.1038/s41556-018-0243-8 Article | FOCUS NAture Cell BIology suppression and decreased immune cell infiltration, suggesting that 21. Knouse, K. A., Wu, J., Whittaker, C. A. & Amon, A. Single cell sequencing aneuploidy acts like an ‘invisible cloak’ to protect cancer cells from reveals low levels of aneuploidy across mammalian tissues. Proc. Natl Acad. 29,154 Sci. USA 111, 13409–13414 (2014). immune cells . How aneuploidy supports immune evasion in 22. Rehen, S. K. et al. Chromosomal variation in neurons of the developing cancers remains to be elucidated, but perhaps increased genomic and adult mammalian nervous system. Proc. Natl Acad. Sci. USA 98, instability elevates the chance of loss-of-heterozygosity events that 13361–13366 (2001). facilitate the loss of neoantigens or impair antigen presentation169. 23. Rehen, S. K. et al. Constitutional aneuploidy in the normal human brain. Taken together, the tumorigenic potential of aneuploidy may J. Neurosci. 25, 2176–2180 (2005). 24. Yurov, Y. B. et al. Aneuploidy and confned chromosomal mosaicism in the rely on the balance between its deleterious and advantageous developing human brain. PLoS ONE 2, e558 (2007). effects. Future studies should aim to address the molecular path- 25. Duncan, A. W. et al. Frequent aneuploidy among normal human ways involved in adaptation to aneuploidy as well as determine hepatocytes. Gastroenterology 142, 25–28 (2012). what the potential advantages aneuploidy provides to cancer cells. 26. Schoenfelder, K. P. et al. Indispensable pre-mitotic endocycles promote This will improve our understanding of how aneuploidy promotes aneuploidy in the Drosophila rectum. Development 141, 3551–3560 (2014). 27. Weaver, B. A. & Cleveland, D. W. Does aneuploidy cause cancer? Curr. tumour growth. Another particular challenge will be to identify Opin. Cell Biol. 18, 658–667 (2006). the mechanisms underlying the marked tissue specificity of the 28. Storchova, Z. & Kufer, C. Te consequences of tetraploidy and aneuploidy. cellular response to aneuploidy. Examination of the physiological J. Cell Sci. 121, 3859–3866 (2008). consequences of whole-chromosome aneuploidy, determination of 29. Taylor, A. M. et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 33, 676–689 (2018). the routes that allow to cope with them and identification of the 30. Gordon, D. J., Resio, B. & Pellman, D. Causes and consequences of advantages of aneuploidy may pinpoint novel therapeutic targets for aneuploidy in cancer. Nat. Rev. Genet. 13, 189–203 (2012). suppressing cancer growth. 31. Nagaoka, S. I., Hassold, T. J. & Hunt, P. A. Human aneuploidy: mechanisms and new insights into an age-old problem. Nat. Rev. Genet. 13, Received: 11 July 2018; Accepted: 31 October 2018; 493–504 (2012). Published online: 2 January 2019 32. Levine, M. S. & Holland, A. J. Te impact of mitotic errors on cell proliferation and tumorigenesis. Genes Dev. 32, 620–638 (2018). 33. Cheeseman, I. M. Te kinetochore. Cold Spring Harb. Perspect. Biol. 6, References a015826 (2014). 1. Peter, J. et al. Genome evolution across 1,011 Saccharomyces cerevisiae 34. Lara-Gonzalez, P., Westhorpe, F. G. & Taylor, S. S. Te spindle assembly isolates. Nature 556, 339–344 (2018). checkpoint. Curr. Biol. 22, R966–R980 (2012). 2. Duan, S. F. et al. Te origin and adaptive evolution of domesticated 35. Lampson, M. A. & Grishchuk, E. L. Mechanisms to avoid and correct populations of yeast from Far East Asia. Nat. Commun. 9, 2690 (2018). erroneous kinetochore–microtubule attachments. Biology (Basel) 6, 3. Pilo, D., Carvalho, S., Pereira, P., Gaspar, M. B. & Leitao, A. Is metal 1 (2017). contamination responsible for increasing aneuploidy levels in the Manila 36. Sansregret, L. & Swanton, C. Te role of aneuploidy in cancer evolution. clam Ruditapes philippinarum? Sci. Total Environ. 577, 340–348 (2017). Cold Spring Harb. Perspect. Med. 7, a028373 (2017). 4. Tumova, P., Uzlikova, M., Jurczyk, T. & Nohynkova, E. Constitutive 37. Simonetti, G., Bruno, S., Padella, A., Tenti, E. & Martinelli, G. Aneuploidy: aneuploidy and genomic instability in the single-celled eukaryote Giardia cancer strength or vulnerability? Int. J. Cancer https://doi.org/10.1002/ intestinalis. Microbiologyopen 5, 560–574 (2016). ijc.31718 (2018). 5. Leitao, A., Boudry, P. & Tiriot-Quievreux, C. Evidence of diferential 38. Hernando, E. et al. Rb inactivation promotes genomic instability by chromosome loss in aneuploid karyotypes of the Pacifc oyster. Crassostrea uncoupling cell cycle progression from mitotic control. Nature 430, gigas. Genome 44, 735–737 (2001). 797–802 (2004). 6. Selmecki, A., Forche, A. & Berman, J. Aneuploidy and isochromosome 39. Manning, A. L., Longworth, M. S. & Dyson, N. J. Loss of pRB causes formation in drug-resistant Candida albicans. Science 313, 367–370 (2006). centromere dysfunction and chromosomal instability. Genes Dev. 24, 7. Lee, A. J. et al. Chromosomal instability confers intrinsic multidrug 1364–1376 (2010). resistance. Cancer Res. 71, 1858–1870 (2011). 40. Cui, Y., Borysova, M. K., Johnson, J. O. & Guadagno, T. M. Oncogenic 8. Swanton, C. et al. Chromosomal instability determines taxane response. B-RafV600E induces spindle abnormalities, supernumerary centrosomes, and Proc. Natl Acad. Sci. USA 106, 8671–8676 (2009). aneuploidy in human melanocytic cells. Cancer Res. 70, 675–684 (2010). 9. Kuznetsova, A. Y. et al. Chromosomal instability, tolerance of mitotic errors 41. Orr, B. & Compton, D. A. A double-edged sword: how oncogenes and and multidrug resistance are promoted by tetraploidization in human cells. tumor suppressor genes can contribute to chromosomal instability. Front. Cell Cycle 14, 2810–2820 (2015). Oncol. 3, 164 (2013). 10. Turajlic, S. & Swanton, C. Metastasis as an evolutionary process. Science 42. Conery, A. R. & Harlow, E. High-throughput screens in diploid cells 352, 169–175 (2016). identify factors that contribute to the acquisition of chromosomal 11. Bakhoum, S. F. et al. Chromosomal instability drives metastasis through instability. Proc. Natl Acad. Sci. USA 107, 15455–15460 (2010). a cytosolic DNA response. Nature 553, 467–472 (2018). 43. Meena, J. K. et al. Telomerase abrogates aneuploidy-induced 12. Heng, H. H. et al. Stochastic cancer progression driven by non-clonal telomere replication stress, senescence and cell depletion. EMBO J. 34, chromosome aberrations. J. Cell Physiol. 208, 461–472 (2006). 1371–1384 (2015). 13. McClelland, S. E. Role of chromosomal instability in cancer progression. 44. Knouse, K. A., Lopez, K. E., Bachofner, M. & Amon, A. Chromosome Endocr. Relat. Cancer 24, T23–T31 (2017). segregation fdelity in epithelia requires tissue architecture. Cell 175, 14. Birkbak, N. J. et al. Paradoxical relationship between chromosomal 200–211 (2018). instability and survival outcome in cancer. Cancer Res. 71, 45. Castedo, M. et al. Cell death by mitotic catastrophe: a molecular defnition. 3447–3452 (2011). Oncogene 23, 2825–2837 (2004). 15. Hassold, T. & Hunt, P. To err (meiotically) is human: the genesis of human 46. Janssen, A., Kops, G. J. & Medema, R. H. Elevating the frequency of aneuploidy. Nat. Rev. Genet. 2, 280–291 (2001). chromosome mis-segregation as a strategy to kill tumor cells. Proc. Natl 16. Holubcova, Z., Blayney, M., Elder, K. & Schuh, M. Human oocytes. Acad. Sci. USA 106, 19108–19113 (2009). Error-prone chromosome-mediated spindle assembly favors 47. Tompson, S. L. & Compton, D. A. Proliferation of aneuploid human cells chromosome segregation defects in human oocytes. Science 348, is limited by a p53-dependent mechanism. J. Cell Biol. 188, 369–381 (2010). 1143–1147 (2015). 48. Hinchclife, E. H. et al. Chromosome missegregation during anaphase 17. Delhanty, J. D. et al. Detection of aneuploidy and chromosomal mosaicism triggers p53 cell cycle arrest through histone H3.3 Ser31 phosphorylation. in human embryos during preimplantation sex determination by fuorescent Nat. Cell Biol. 18, 668–675 (2016). in situ hybridisation, (FISH). Hum. Mol. Genet. 2, 1183–1185 (1993). 49. Santaguida, S. et al. Chromosome mis-segregation generates cell-cycle- 18. van Echten-Arends, J. et al. Chromosomal mosaicism in human arrested cells with complex karyotypes that are eliminated by the immune preimplantation embryos: a systematic review. Hum. Reprod. Update 17, system. Dev. Cell 41, 638–651 (2017). 620–627 (2011). 50. Soto, M. et al. p53 prohibits propagation of chromosome segregation errors 19. Bazrgar, M., Gourabi, H., Valojerdi, M. R., Yazdi, P. E. & Baharvand, H. that produce structural aneuploidies. Cell Rep. 19, 2423–2431 (2017). Self-correction of chromosomal abnormalities in human preimplantation 51. Lopez-Garcia, C. et al. BCL9L dysfunction impairs caspase-2 expression embryos and embryonic stem cells. Stem Cells Dev. 22, 2449–2456 (2013). permitting aneuploidy tolerance in colorectal cancer. Cancer Cell 31, 20. Bolton, H. et al. Mouse model of chromosome mosaicism reveals 79–93 (2017). lineage-specifc depletion of aneuploid cells and normal developmental 52. Sansregret, L. et al. APC/C dysfunction limits excessive cancer potential. Nat. Commun. 7, 11165 (2016). chromosomal instability. Cancer Discov. 7, 218–233 (2017).

53. Torres, E. M. et al. Identifcation of aneuploidy-tolerating mutations. Cell 84. Yona, A. H. et al. Chromosomal duplication is a transient evolutionary 143, 71–83 (2010). solution to stress. Proc. Natl Acad. Sci. USA 109, 21010–21015 (2012). 54. Donnelly, N., Passerini, V., Durrbaum, M., Stingele, S. & Storchova, Z. 85. Rutledge, S. D. et al. Selective advantage of trisomic human cells cultured in HSF1 defciency and impaired HSP90-dependent protein folding are non-standard conditions. Sci. Rep. 6, 22828 (2016). hallmarks of aneuploid human cells. EMBO J. 33, 2374–2387 (2014). 86. Baker, D. E. et al. Adaptation to culture of human embryonic stem cells and 55. Dodgson, S. E., Santaguida, S., Kim, S., Sheltzer, J. & Amon, A. Te oncogenesis in vivo. Nat. Biotechnol. 25, 207–215 (2007). pleiotropic deubiquitinase Ubp3 confers aneuploidy tolerance. Genes Dev. 87. Huettel, B., Kreil, D. P., Matzke, M. & Matzke, A. J. Efects of aneuploidy on 30, 2259–2271 (2016). genome structure, expression, and interphase organization in Arabidopsis 56. Michel, L. S. et al. MAD2 haplo-insufciency causes premature thaliana. PLoS Genet. 4, e1000226 (2008). anaphase and chromosome instability in mammalian cells. Nature 409, 88. Mao, R. et al. Primary and secondary transcriptional efects in the 355–359 (2001). developing human Down syndrome brain and heart. Genome Biol. 6, 57. Sotillo, R. et al. Mad2 overexpression promotes aneuploidy and R107 (2005). tumorigenesis in mice. Cancer Cell 11, 9–23 (2007). 89. Lockstone, H. E. et al. Gene expression profling in the adult Down 58. Weaver, B. A., Silk, A. D., Montagna, C., Verdier-Pinard, P. & Cleveland, D. W. syndrome brain. Genomics 90, 647–660 (2007). Aneuploidy acts both oncogenically and as a tumor suppressor. Cancer Cell 90. Halevy, T., Biancotti, J. C., Yanuka, O., Golan-Lev, T. & Benvenisty, N. 11, 25–36 (2007). Molecular characterization of Down syndrome embryonic stem cells 59. Foijer, F. et al. Chromosome instability induced by Mps1 and p53 mutation reveals a role for RUNX1 in neural diferentiation. Stem Cell Rep. 7, generates aggressive lymphomas exhibiting aneuploidy-induced stress. Proc. 777–786 (2016). Natl Acad. Sci. USA 111, 13427–13432 (2014). 91. Aziz, N. M. et al. Lifespan analysis of brain development, gene expression 60. Ohashi, A. et al. Aneuploidy generates proteotoxic stress and DNA damage and behavioral phenotypes in the Ts1Cje, Ts65Dn and Dp(16)1/Yey mouse concurrently with p53-mediated post-mitotic apoptosis in SAC-impaired models of Down syndrome. Dis. Model. Mech. 11, dmm031013 (2018). cells. Nat. Commun. 6, 7668 (2015). 92. Penny, G. D., Kay, G. F., Sheardown, S. A., Rastan, S. & Brockdorf, N. 61. Fournier, R. E. A general high-efciency procedure for production of Requirement for Xist in X chromosome inactivation. Nature 379, microcell hybrids. Proc. Natl Acad. Sci. USA 78, 6349–6353 (1981). 131–137 (1996). 62. Upender, M. B. et al. Chromosome transfer induced aneuploidy results in 93. Tartaglia, N. R., Howell, S., Sutherland, A., Wilson, R. & Wilson, L. A complex dysregulation of the cellular transcriptome in immortalized and review of trisomy X (47,XXX). Orphanet J. Rare Dis. 5, 8 (2010). cancer cells. Cancer Res. 64, 6941–6949 (2004). 94. Stenberg, P. et al. Bufering of segmental and chromosomal aneuploidies in 63. Stingele, S. et al. Global analysis of genome, transcriptome and proteome Drosophila melanogaster. PLoS Genet. 5, e1000465 (2009). reveals the response to aneuploidy in human cells. Mol. Syst. Biol. 8, 95. Zhang, Y. et al. Expression in aneuploid Drosophila S2 cells. PLoS Biol. 8, 608 (2012). e1000320 (2010). 64. Jiang, J. et al. Translating dosage compensation to trisomy 21. Nature 500, 96. Johansson, A. M., Stenberg, P., Bernhardsson, C. & Larsson, J. Painting of 296–300 (2013). fourth and chromosome-wide regulation of the 4th chromosome in 65. Adikusuma, F., Williams, N., Grutzner, F., Hughes, J. & Tomas, P. Targeted Drosophila melanogaster. EMBO J. 26, 2307–2316 (2007). deletion of an entire chromosome using CRISPR/Cas9. Mol. Ter. 25, 97. Gelbart, M. E. & Kuroda, M. I. Drosophila dosage compensation: a complex 1736–1738 (2017). voyage to the X chromosome. Development 136, 1399–1410 (2009). 66. Zuo, E. et al. CRISPR/Cas9-mediated targeted chromosome elimination. 98. Hose, J. et al. Dosage compensation can bufer copy-number variation in Genome Biol. 18, 224 (2017). wild yeast. eLife 4, e05462 (2015). 67. Williams, B. R. et al. Aneuploidy afects proliferation and spontaneous 99. Torres, E. M., Springer, M. & Amon, A. No current evidence for widespread immortalization in mammalian cells. Science 322, 703–709 (2008). dosage compensation in S. cerevisiae. eLife 5, e10996 (2016). 68. Torres, E. M. et al. Efects of aneuploidy on cellular physiology and cell 100. Tucker, C. et al. Transcriptional regulation on aneuploid chromosomes in division in haploid yeast. Science 317, 916–924 (2007). divers Candida albicans mutants. Sci. Rep. 8, 1630 (2018). 69. Pavelka, N. et al. Aneuploidy confers quantitative proteome changes and 101. Dephoure, N. et al. Quantitative proteomic analysis reveals posttranslational phenotypic variation in budding yeast. Nature 468, 321–325 (2010). responses to aneuploidy in yeast. eLife 3, e03023 (2014). 70. Beach, R. R. et al. Aneuploidy causes non-genetic individuality. Cell 169, 102. Liu, Y. et al. Systematic proteome and proteostasis profling in human 229–242 (2017). trisomy 21 fbroblast cells. Nat. Commun. 8, 1212 (2017). 71. Naylor, R. M. & van Deursen, J. M. Aneuploidy in cancer and aging. 103. Vigano, C. et al. Quantitative proteomic and phosphoproteomic comparison Annu. Rev. Genet. 50, 45–66 (2016). of human colon cancer DLD-1 cells difering in ploidy and chromosome 72. Zhu, J., Tsai, H.-J., Gordon, M. R. & Li, R. Cellular stress associated with stability. Mol. Biol. Cell 29, 1031–1047 (2018). aneuploidy. Dev. Cell 44, 420–431 (2018). 104. McShane, E. et al. Kinetic analysis of protein stability reveals age-dependent 73. Segal, D. J. & McCoy, E. E. Studies on Down’s syndrome in tissue culture. I. degradation. Cell 167, 803–815 (2016). Growth rates and protein contents of fbroblast cultures. J. Cell Physiol. 83, 105. Gasch, A. P. et al. Genomic expression programs in the response of yeast 85–90 (1974). cells to environmental changes. Mol. Biol. Cell 11, 4241–4257 (2000). 74. Torburn, R. R. et al. Aneuploid yeast strains exhibit defects in cell growth 106. Sheltzer, J. M., Torres, E. M., Dunham, M. J. & Amon, A. Transcriptional and passage through START. Mol. Biol. Cell 24, 1274–1289 (2013). consequences of aneuploidy. Proc. Natl Acad. Sci. USA 109, 75. Ariyoshi, K. et al. Induction of genomic instability and activation of 12644–12649 (2012). autophagy in artifcial human aneuploid cells. Mutat. Res. 790, 107. O’Duibhir, E. et al. Cell cycle population efects in perturbation studies. 19–30 (2016). Mol. Syst. Biol. 10, 732 (2014). 76. Bonney, M. E., Moriya, H. & Amon, A. Aneuploid proliferation defects in 108. Sheltzer, J. M. A transcriptional and metabolic signature of primary yeast are not driven by copy number changes of a few dosage-sensitive aneuploidy is present in chromosomally unstable cancer cells and informs genes. Genes Dev. 29, 898–903 (2015). clinical prognosis. Cancer Res. 73, 6401–6412 (2013). 77. Gogendeau, D. et al. Aneuploidy causes premature diferentiation of neural 109. Durrbaum, M. et al. Unique features of the transcriptional response to and intestinal stem cells. Nat. Commun. 6, 8894 (2015). model aneuploidy in human cells. BMC Genomics 15, 139 (2014). 78. Jonas, K., Liu, J., Chien, P. & Laub, M. T. Proteotoxic stress induces a 110. Tang, Y. C., Williams, B. R., Siegel, J. J. & Amon, A. Identifcation of cell-cycle arrest by stimulating Lon to degrade the replication initiator aneuploidy-selective antiproliferation compounds. Cell 144, 499–512 (2011). DnaA. Cell 154, 623–636 (2013). 111. Oromendia, A. B., Dodgson, S. E. & Amon, A. Aneuploidy causes 79. Barr, A. R. et al. DNA damage during S-phase mediates the proliferation- proteotoxic stress in yeast. Genes Dev. 26, 2696–2708 (2012). quiescence decision in the subsequent G1 via p21 expression. 112. Stefani, M. & Dobson, C. M. Protein aggregation and aggregate toxicity: Nat. Commun. 8, 14728 (2017). new insights into protein folding, misfolding diseases and biological 80. Liu, X. et al. Trisomy eight in ES cells is a common potential problem in evolution. J. Mol. Med. (Berl.) 81, 678–699 (2003). gene targeting and interferes with germ line transmission. Dev. Dyn. 209, 113. Hanna, J. et al. Deubiquitinating enzyme Ubp6 functions noncatalytically to 85–91 (1997). delay proteasomal degradation. Cell 127, 99–111 (2006). 81. Ben-David, U. et al. Aneuploidy induces profound changes in gene 114. Santaguida, S. & Amon, A. Aneuploidy triggers a TFEB-mediated lysosomal expression, proliferation and tumorigenicity of human pluripotent stem stress response. Autophagy 11, 2383–2384 (2015). cells. Nat. Commun. 5, 4825 (2014). 115. Sheltzer, J. M. et al. Aneuploidy drives genomic instability in yeast. Science 82. Zhang, M. et al. Aneuploid embryonic stem cells exhibit impaired 333, 1026–1030 (2011). diferentiation and increased neoplastic potential. EMBO J. 35, 116. Nicholson, J. M. et al. Chromosome mis-segregation and cytokinesis failure 2285–2300 (2016). in trisomic human cells. eLife 4, e05068 (2015). 83. Selmecki, A., Forche, A. & Berman, J. Genomic plasticity of the human 117. Passerini, V. et al. Te presence of extra chromosomes leads to genomic fungal pathogen Candida albicans. Eukaryot. Cell 9, 991–1008 (2010). instability. Nat. Commun. 7, 10754 (2016).

118. Sharma, K. et al. Quantitative proteomics reveals that Hsp90 inhibition 149. Mahalingam, D. et al. Targeting HSP90 for cancer therapy. Br. J. Cancer preferentially targets kinases and the DNA damage response. 100, 1523–1529 (2009). Mol. Cell. Proteomics 11, M111.014654 (2012). 150. Whitesell, L. & Lindquist, S. L. HSP90 and the chaperoning of cancer. 119. Spurgers, K. B. et al. Identifcation of cell cycle regulatory genes as principal Nat. Rev. Cancer 5, 761–772 (2005). targets of p53-mediated transcriptional repression. J. Biol. Chem. 281, 151. Burrell, R. A. et al. Replication stress links structural and numerical cancer 25134–25142 (2006). chromosomal instability. Nature 494, 492–496 (2013). 120. Tan, Y. H., Schneider, E. L., Tischfeld, J. & Epstein, C. J. & Ruddle, F. H. 152. Chan, Y. W., Fugger, K. & West, S. C. Unresolved recombination Human chromosome 21 dosage: efect on the expression of the interferon intermediates lead to ultra-fne anaphase bridges, chromosome breaks and induced antiviral state. Science 186, 61–63 (1974). aberrations. Nat. Cell Biol. 20, 92–103 (2018). 121. Iwamoto, T. et al. Infuences of interferon-γ on cell proliferation and 153. Duesberg, P., Rausch, C., Rasnick, D. & Hehlmann, R. Genetic instability of interleukin-6 production in Down syndrome derived fbroblasts. Arch. Oral cancer cells is proportional to their degree of aneuploidy. Proc. Natl Acad. Biol. 54, 963–969 (2009). Sci. USA 95, 13692–13697 (1998). 122. Sullivan, K. D. et al. Trisomy 21 consistently activates the interferon 154. Davoli, T., Uno, H., Wooten, E. C. & Elledge, S. J. Tumor aneuploidy response. eLife 5, e16220 (2016). correlates with markers of immune evasion and with reduced response 123. Ling, K. H. et al. Functional transcriptome analysis of the postnatal brain of to immunotherapy. Science 355, eaaf8399 (2017). the Ts1Cje mouse model for Down syndrome reveals global disruption of 155. Davoli, T. et al. Cumulative haploinsufciency and triplosensitivity interferon-related molecular networks. BMC Genomics 15, 624 (2014). drive aneuploidy patterns and shape the cancer genome. Cell 155, 124. Tanaka, M. H. et al. Expression of interferon-γ, interferon-α and related 948–962 (2013). genes in individuals with Down syndrome and periodontitis. Cytokine 60, 156. Kops, G. J., Foltz, D. R. & Cleveland, D. W. Lethality to human cancer cells 875–881 (2012). through massive chromosome loss by inhibition of the mitotic checkpoint. 125. Maroun, L. E. Interferon action and chromosome 21 trisomy (Down Proc. Natl Acad. Sci. USA 101, 8699–8704 (2004). syndrome): 15 years later. J. Teor. Biol. 181, 41–46 (1996). 157. Godek, K. M. et al. Chromosomal instability afects the tumorigenicity 126. Sun, L., Wu, J., Du, F., Chen, X. & Chen, Z. J. Cyclic GMP–AMP synthase of glioblastoma tumor-initiating cells. Cancer Discov. 6, is a cytosolic DNA sensor that activates the type I interferon pathway. 532–545 (2016). Science 339, 786–791 (2013). 158. Beaupere, C. et al. Genetic screen identifes adaptive aneuploidy as a key 127. Lan, Y. Y., Londono, D., Bouley, R., Rooney, M. S. & Hacohen, N. Dnase2a mediator of ER stress resistance in yeast. Proc. Natl Acad. Sci. USA 15, defciency uncovers lysosomal clearance of damaged nuclear DNA via 9586–9591 (2018). autophagy. Cell Rep. 9, 180–192 (2014). 159. Chen, G., Bradford, W. D., Seidel, C. W. & Li, R. Hsp90 stress potentiates 128. Mackenzie, K. J. et al. cGAS surveillance of micronuclei links genome rapid cellular adaptation through induction of aneuploidy. Nature 482, instability to innate immunity. Nature 548, 461–465 (2017). 246–250 (2012). 129. Harding, S. M. et al. Mitotic progression following DNA damage enables 160. Rancati, G. et al. Aneuploidy underlies rapid adaptive evolution pattern recognition within micronuclei. Nature 548, 466–470 (2017). of yeast cells deprived of a conserved cytokinesis motor. Cell 135, 130. Bartsch, K. et al. Absence of RNase H2 triggers generation of 879–893 (2008). immunogenic micronuclei removed by autophagy. Hum. Mol. Genet. 26, 161. Kaya, A. et al. Adaptive aneuploidy protects against thiol peroxidase 3960–3972 (2017). defciency by increasing respiration via key mitochondrial proteins. Proc. 131. Gasser, S., Orsulic, S., Brown, E. J. & Raulet, D. H. Te DNA damage Natl Acad. Sci. USA 112, 10685–10690 (2015). pathway regulates innate immune system ligands of the NKG2D receptor. 162. Ryu, H.-Y., Wilson, N. R., Mehta, S., Hwang, S. S. & Hochstrasser, M. Loss Nature 436, 1186–1190 (2005). of the SUMO protease Ulp2 triggers a specifc multichromosome 132. Rodier, F. et al. Persistent DNA damage signalling triggers senescence- aneuploidy. Genes Dev. 30, 1881–1894 (2016). associated infammatory cytokine secretion. Nat. Cell Biol. 11, 163. Millet, C., Ausiannikava, D., Le Bihan, T., Granneman, S. & Makovets, S. 973–979 (2009). Cell populations can use aneuploidy to survive telomerase insufciency. 133. Cohen, I. et al. IL-1α is a DNA damage sensor linking genotoxic stress Nat. Commun. 6, 8664 (2015). signaling to sterile infammation and innate immunity. Sci. Rep. 5, 164. Hughes, T. R. et al. Widespread aneuploidy revealed by DNA microarray 14756 (2015). expression profling. Nat. Genet. 25, 333–337 (2000). 134. Andriani, G. A. et al. Whole chromosome instability induces senescence 165. Chen, G. et al. Targeting the adaptability of heterogeneous aneuploids. Cell and promotes SASP. Sci. Rep. 6, 35218 (2016). 160, 771–784 (2015). 135. Yang, H., Wang, H., Ren, J., Chen, Q. & Chen, Z. J. cGAS is essential for 166. Vesely, M. D., Kershaw, M. H., Schreiber, R. D. & Smyth, M. J. Natural cellular senescence. Proc. Natl Acad. Sci. USA 114, E4612–E4620 (2017). innate and adaptive immunity to cancer. Annu. Rev. Immunol. 29, 136. Hardy, P. A. & Zacharias, H. Reappraisal of the Hansemann–Boveri 235–271 (2011). hypothesis on the origin of tumors. Cell Biol. Int. 29, 983–992 (2005). 167. Dunn, G. P., Bruce, A. T., Ikeda, H., Old, L. J. & Schreiber, R. D. Cancer 137. Knouse, K. A., Davoli, T., Elledge, S. J. & Amon, A. Aneuploidy in immunoediting: from immunosurveillance to tumor escape. Nat. Immunol. cancer: Seq-ing answers to old questions. Annu. Rev. Cancer Biol. 1, 3, 991–998 (2002). 335–354 (2017). 168. Schreiber, R. D., Old, L. J. & Smyth, M. J. Cancer immunoediting: 138. Sheltzer, J. M. et al. Single-chromosome gains commonly function as tumor integrating immunity’s roles in cancer suppression and promotion. Science suppressors. Cancer Cell 31, 240–255 (2017). 331, 1565–1570 (2011). 139. Iwanaga, Y. et al. Heterozygous deletion of mitotic arrest-defcient protein 1 169. McGranahan, N. et al. Allele-specifc HLA loss and immune escape in lung (MAD1) increases the incidence of tumors in mice. Cancer Res. 67, cancer evolution. Cell 171, 1259–1271 (2017). 160–166 (2007). 140. Dai, W. et al. Slippage of mitotic arrest and enhanced tumor development Acknowledgements in mice with BubR1 haploinsufciency. Cancer Res. 64, 440–445 (2004). The work on aneuploidy is supported by the German Research Foundation, grant 141. Baker, D. J. et al. BubR1 insufciency causes early onset of aging-associated agreement STO918/5-1 to Z.S. phenotypes and infertility in mice. Nat. Genet. 36, 744–749 (2004). 142. Baker, D. J. et al. Early aging-associated phenotypes in Bub3/Rae1 haploinsufcient mice. J. Cell Biol. 172, 529–540 (2006). Author contributions 143. Hasle, H., Clemmensen, I. H. & Mikkelsen, M. Risks of leukaemia and solid Both authors contributed equally. tumours in individuals with Down’s syndrome. Lancet 355, 165–169 (2000). 144. Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Competing interests Cell 144, 646–674 (2011). The authors declare no competing interests. 145. Dai, C. & Sampson, S. B. HSF1: guardian of proteostasis in cancer. Trends Cell Biol. 26, 17–28 (2016). 146. Perera, R. M. et al. Transcriptional control of autophagy–lysosome function Additional information drives pancreatic cancer metabolism. Nature 524, 361–365 (2015). Reprints and permissions information is available at www.nature.com/reprints. 147. Sidera, K. & Patsavoudi, E. HSP90 inhibitors: current development and Correspondence should be addressed to Z.S. potential in cancer therapy. Recent Pat. Anticancer Drug Discov. 9, 1–20 (2014). Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in 148. Bastola, P., Oien, D. B., Cooley, M. & Chien, J. Emerging cancer therapeutic published maps and institutional affiliations. targets in protein homeostasis. AAPS J. 20, 94 (2018). © Springer Nature Limited 2019

62 Nature Cell Biology | VOL 21 | JANUARY 2019 | 54–62 | www.nature.com/naturecellbiology