Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

Abstract

Genomic, transcriptomic and proteomic profiles of human aneuploid cells reveal that mRNA levels increase with gene copy number, but protein levels are partially compensated. Aneuploid cells also exhibit common alterations in several pathways, including an activation of autophagy.

Autophagy regulates the survival of cells with chromosomal instability

“…The frequency of elevated autophagy was significantly higher in the high-CIN cells generated by Rad21 depletion, which also have a high frequency of elevated ROS generation, DNA damage and aneuploidy [ 22 ]. This is consistent with data from human cells showing that increased levels of aneuploidy correlate with elevated Atg8/LC3 and p62 [ 13 , 14 ]. In that work, the effect of ongoing karyotypic variation (CIN) on autophagy was not tested, possibly because it is difficult to maintain proliferation in vertebrate CIN cells without additional changes such as p53 loss [ 1 ], which would itself impact autophagy.…”

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

“…Firstly, compensated proteins were enriched for subunits of macromolecular protein complexes (15.6% versus 1.8% in the background set). This observation matches several observations in aneuploid yeast and human (including cancer) cell lines 46,47,[53][54][55][56] that also detected protein complex subunits to be highly prevalent amongst compensated proteins. It can be explained by the fact that individual subunits of macromolecular complexes are typically unstable unless assembled into a stable complex 46 .…”

Reduction of chromosomal instability and inflammation is a common aspect of adaptation to aneuploidy

“…Activation of PERK is aimed at reducing translational loading of the ER by reducing the global levels of translation (61,71). Consistent with this, we observed a reduction of processes related to translation, peptide biosynthesis, and RNA processing in the early aneuploid clones, responses that have been reported in other aneuploid models as well (72–74). How these alterations related to proteotoxic stress translate into CIN awaits further investigation.…”

“…It has been shown by us and others that proliferation rates strongly correlate to the number of imbalanced genes (4,6,10,13,40). If adaptation to aneuploidy is indeed not solely driven by karyotype simplification but other processes contribute to the adaptation process, we predicted that the impact of imbalanced genes on proliferation rates will be less pronounced in adapted clones as compared to their early counterparts.…”

“…The most obvious path to adaptation would be karyotype correction, where aneuploid clones revert to a (more) euploid karyotype. Since RNA levels largely scale with DNA copy number (4–6,10–14), we first utilized the transcriptome data to extract karyotype information (Fig. 2A: red regions reflect gains, blue regions reflect losses).…”

“…Aneuploidy manifests deleterious effects at both the organismal and cellular levels, resulting in developmental defects and reduced cellular proliferation (2)(3)(4)(5)(6)(7)(8). The detrimental effects of aneuploidy have been attributed to imbalances in coding genetic material (4,9).…”

“…Aneuploidy has also been linked to enhanced genetic instability (4,25) and replication stress (4,23,(26)(27)(28)(29), which can be caused by imbalances in crucial protein complexes (26). Besides, numerous studies have reported metabolic alterations in response to aneuploidy (4,6,(30)(31)(32)(33). These metabolic alterations might be caused by the enhanced energy requirements to deal with the challenges induced by the aneuploid state.…”

“…The disruption of proteostasis upon aneuploidy results in an increased burden on protein synthesis, folding and degradation machineries, often leading to proteotoxic stress (18). Indeed, in both aneuploid yeast and human cell models, indications of proteotoxic stress and a higher dependency on processes related to the maintenance of proteostasis have been extensively documented (6,7,13,(19)(20)(21)(22)(23)(24).…”

“…It is widely acknowledged that aneuploidy results in the altered expression of the genes located on the involved chromosome(s). While RNA expression largely scales with DNA copy number (4)(5)(6)(10)(11)(12)(13)(14), large-scale dosage compensation is observed at the protein level in an attempt to maintain complex stoichiometry and appropriate levels of dosage sensitive factors (6,10,13,(15)(16)(17). The disruption of proteostasis upon aneuploidy results in an increased burden on protein synthesis, folding and degradation machineries, often leading to proteotoxic stress (18).…”

Aneuploidy-induced proteostasis disruption impairs mitochondrial functions and mediates aggregation of mitochondrial precursor proteins through SQSTM1/p62

“…1b, c). The p62 abundance further increased upon treatment with an inhibitor of autophagosome-lysosome fusion Bafilomycin A1 (BafA1), confirming the existence of normal autophagic flux in the polysomic cells as previously reported (8,18). The size and number of p62 bodies per cell surface area also increase in polysomic cells (Fig.…”

“…The mild, but chronic overexpression of hundreds of unneeded proteins in cells with extra chromosomes alters proteome landscape of the cell and triggers aneuploidy-associated stress response. As a consequence, human cells with additional chromosomes suffer from proteotoxic stress, as documented by increased sensitivity to chaperone inhibitors, accumulation of ubiquitinand p62-positive cytosolic bodies, and increased lysosomal stress (8,9,(14)(15)(16)(17). By analyzing the phenotypes of five cell lines with different extra chromosomes, we show that the number and size of p62-positive cytosolic bodies tightly correlate with the number of extra protein-coding genes in polysomic cells (Fig.…”

“…Abundance of p62 in aneuploid cells scales with the amount of extra DNA. We and others have previously shown that aneuploid cells accumulate autophagy and lysosomal markers on both transcriptome and proteome levels (8,(14)(15)(16)18). Among the most abundant proteins within this category was the selective autophagy receptor p62, which forms highly abundant cytosolic p62-bodies in polysomic cells.…”

“…1a). The karyotypes were confirmed by chromosome painting and sequencing (8,33). The cell lines were labeled according to their karyotype as HCT116 3/3 (trisomy of chromosome 3), 5/3 (trisomy of chromosome 5), 5/4 (tetrasomy of chromosome 5), 13/3 (trisomy of chromosome 13) and 21/3 (trisomy of chromosome 21).…”

“…2, 3). We hypothesize that the impaired protein folding and imbalanced protein homeostasis due to aneuploidy induces protein aggregation (8,15,17,49,50,65) into cytosolic p62-positive bodies, which sequester unimported mitochondrial proteins. The reduced import of essential mitochondrial proteins into mitochondria impairs mitochondrial health (Fig.…”

“…Polysomic cell lines were derived from the near-diploid human colon carcinoma cell line HCT116 (ATCC No. CCL-247) expressing H2B-GFP by microcell-mediated chromosome transfer as previously described (8,33). Parental HCT116 (WT), HCT116 21/3 (trisomy of chromosome 21), 13/3 (trisomy of chromosome 13), 5/3 (trisomy of chromosome 5), 3/3 (trisomy of chromosome 3), and 5/4 (tetrasomy of chromosome 5) were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10 % Fetal Bovine Serum and 5 % Penicillin/Streptomycin and incubated at 37 °C with 5 % CO 2 atmosphere.…”

“…Human cells with extra chromosomes (polysomy) also frequently exhibit slower proliferation rates when compared to their diploid counterparts. Moreover, they manifest an array of phenotypic changes, including features of proteotoxic stress, as evidenced by an increased sensitivity to inhibitors targeting protein folding and turnover, elevated replication stress and accumulation of DNA damage and structural rearrangements, activation of the innate immune response and reduced translation (5,(8)(9)(10)(11)(12)(13). Similar effects were also observed in acute response to aneuploidy, immediately after induced chromosome missegregation (14)(15)(16).…”

“…targets them for degradation. Cytosolic p62-bodies accumulate in aneuploid cells arising immediately after induced chromosome missegregation as well as in cells with constitutive chromosome gain (8,(14)(15)(16)18). The causes of p62 accumulation remain only partially understood.…”

“…In acute response to chromosome missegregation, p62, which is an autophagy substrate, accumulates due to saturated autophagy (14,15). In cells with constitutive chromosome gain, the increased expression of p62 is observed on both transcriptome and proteome levels (8,16,18), likely in response to the excess or misfolded proteins, or in response to increased oxidative stress. Taken together, accumulation of cytosolic p62 bodies is integral to the cellular response to aneuploidy, although their function remains unclear.…”

Evolutionary Expression of HER2 Conferred by Chromosome Aneuploidy on Circulating Gastric Cancer Cells Contributes to Developing Targeted and Chemotherapeutic Resistance

“…In situ coexamination of Chr8 aneuploidy and cHER2 phenotyping on CTCs performed with HER2-iFISH revealed that aneuploid Chr8 (multiploidy of Chr8 in particular) contributed to acquisition of the posttherapeutic cHER2 þ phenotype on CTCs, which is in accordance with the published observations, showing correlation between protein expression and chromosomal copy-number variations in budding yeast (35). The impact of chromosome number variation on the noncoding protein contributes to compensatory posttranslational mechanisms which reduce protein expression when their encoding genes are in excess (36,37). Similarly, it is reasonable to speculate that aneuploid Chr8 with extra copies of chromosome in CTCs may have an impact on noncoding HER2 protein in a similar way.…”

Unique features of the transcriptional response to model aneuploidy in human cells

“…This yielded 18 genes whose expression is more than 1.4 fold increased and 5 genes whose expression is more than 1.4 fold decreased in all analyzed aneuploids (Figure 4 , Table 2 ). The changes in mRNA levels are consistent with proteomics measurements in 7 out of 8 proteins for which the data are available [ 15 ] (Table 2 ). Importantly, expression of only one of these 23 genes (FRY) is similarly upregulated by the stress stimuli, suggesting that the recurrent expression changes are indeed in response to aneuploidy.…”

“…Moreover, pathways that are activated or inhibited by aneuploidy may serve as novel targets for cancer treatment. This has been recently demonstrated by the fact that aneuploid cells are more sensitive to drugs inhibiting HSP90, autophagy inhibitors and inhibitors of the AMPK kinase, which strongly correlates with the identified increased requirements for autophagy, protein folding and energy metabolism in aneuploid mammalian cells ([ 15 , 30 ] and this work). Further research should elucidate the efficacy of this approach.…”

“…The similarity of cellular response to inhibition of autophagy and to aneuploidy might suggest that aneuploidy inhibits autophagy. This however is not true as we previously documented by an observation that autophagic flux (the dynamic flow through autophagy) is in aneuploids as efficient as in diploids [15]. Inhibition of basal autophagy by bafilomycin A1 treatment causes proteotoxic stress [35].…”

“… The column “Protein levels” shows how often corresponding changes of the protein levels were identified by Stingele et al [ 15 ] (number of cell lines with altered protein expression/number of cell lines where the protein was quantified; NA – proteomics data not available). The rows 1-18 show upregulated genes; the rows 1- 5 (below) show downregulated genes.…”

“…Importantly, the duration of the cell cycle of the complex aneuploid cell lines is indistinguishable from diploids (Additional file 1 : Figure S2). Previously, it has been proposed that the transcriptional changes identified in aneuploid cells are caused by the slow growth, which is typical for model trisomic cell lines [ 3 , 14 , 15 ]. Thus, our finding indicates that the response to aneuploidy in mammalian cells is not always associated with a slower progression through the cell cycle, and thereby the slower proliferation cannot be the only cause of the identified transcriptional changes.…”

“…Recently, we established de novo human aneuploid cell lines that were derived from diploid and chromosomally stable cells by a micronuclei-mediated chromosome transfer [ 15 ]. We performed transcriptional analysis of the original diploid cell lines and their trisomic and tetrasomic derivatives (HCT116: trisomy of chromosome 3 – 3/3; tetrasomy of chromosome 5 - 5/4; RPE1: trisomy of chromosome 5 and 12 - 5/3 12/3, trisomy of chromosome 21 - 21/3, see Methods for further details) and calculated the aneuploid-to-diploid fold change for all detected mRNAs.…”

“…Since chromosome missegregation was shown to trigger oxidative stress [ 24 , 33 ], we analysed the transcriptional response to oxidative stress inducers nitric oxide and hydrogen dioxide. Aneuploidy was also recently linked to DNA damage and replication stress [ 34 ], therefore we analyzed the response to the replication inhibitor hydroxyurea and transcription inhibition by actinomycin D. Further, aneuploidy was shown to trigger proteotoxic stress and to activate autophagy [ 3 , 15 , 30 , 31 ]. Therefore, we compared the response to aneuploidy to the transcriptional changes elicited by cells grown under hypoxic conditions, which is known to result in energy and ER stress with subsequent proteotoxic stress.…”

“…In general, the effect of bafilomycin A1 further emphasizes the role of autophagy in mammalian aneuploids. Aneuploidy leads to activation of autophagy in human and mouse cells [ 15 , 30 ] and aneuploid cells are more sensitive to the autophagy inhibiting drug chloroquine [ 30 ]. The consistent upregulation of lysosomes and lytic vacuoles appears to be specific for mammalian cells as it was not observed in aneuploid yeasts and plants [ 19 ].…”

“…Similarly, we tested the transcriptional changes in cells where autophagy was inhibited, a condition known to trigger proteotoxic stress. The comparison with transcription profiles of cells grown on high or low glucose was of particular interest, because aneuploid cells show changes in the metabolic pathways and higher energy demands [ 3 , 14 , 15 ]. Remarkably, we found that none of the stress conditions triggers response similar to ARP.…”

“…The ARP is characterized by strong downregulation of DNA and RNA metabolism, which correlates with the slow growth observed in nearly all aneuploid cells analyzed to date. Indeed, many factors required for DNA replication are less abundant, such as the heterohexameric replicative helicase MCM (Additional file 2 : Table S1), and this may partially explain the previously observed slow progression through the S-phase [ 15 ]. However, the complex aneuploid cell lines progress through interphase at a rate closely matching the rate of the corresponding diploid cell lines and yet the levels of factors involved in replication are similarly decreased (Additional file 1 : Figure S2).…”

“…Genome-wide expression profiling of HCT116- and RPE1- derived aneuploid cells lines was conducted in three replicates by IMGM laboratories GmbH (Martinsried, Germany) as previously described [ 15 ]. cDNA was hybridized on Agilent Whole Human Genome Oligo microarrays (4x44K format) for HCT116 diploid and HCT116 5/4, or Agilent SurePrint G3 Human GE microarrays (8x60K) for the other cell lines according to a One-Color based hybridization protocol.…”

“…Following model aneuploid cell lines were used for data analysis: parental cell line HCT116 (human colon carcinoma cell line): HCT116 3/3 (trisomy 3), HCT116 5/4 (tetrasomy 5) [ 43 ]; parental cell line HCT116 H2B-GFP: HCT116 5/4 (tetrasomy 5) [ 15 ], HPT1, HPT2 (hypertetraploids with complex karyotypes, A.Y.K. unpublished data); parental cell line RPE1 (human retinal pigment epithelial cell line, hTERT immortalized): RPE15/3 12/3 (trisomy 5, 12); parental cell line RPE1 H2B-GFP: RPE1 21/3 (trisomy 21) [ 15 ]; parental cell line DLD1 (human colon adenocarcinoma cell line): DLD1 3/3 (trisomy 3), DLD1 7/3 (trisomy 7), DLD1 13/3 (trisomy 13) [ 13 ], parental cell line HE35 (human embryonic cell line): HE35 8/3, clones 1–3 [ 17 ].…”

“…unpublished data); parental cell line RPE1 (human retinal pigment epithelial cell line, hTERT immortalized): RPE15/3 12/3 (trisomy 5, 12); parental cell line RPE1 H2B-GFP: RPE1 21/3 (trisomy 21) [15]; parental cell line DLD1 (human colon adenocarcinoma cell line): DLD1 3/3 (trisomy 3), DLD1 7/3 (trisomy 7), DLD1 13/3 (trisomy 13) [13], parental cell line HE35 (human embryonic cell line): HE35 8/3, clones 1–3 [17]. …”

“…The HCT116- and RPE1- derived tri- and tetrasomic cell lines have been described previously [ 15 ]. The post- tetraploid cell lines HPT1 and HPT2 were generated by expansion of individual tetraploids formed by induced inhibition of cytokinesis through dihydrocytochalasin treatment.…”

“…The post- tetraploid cell lines HPT1 and HPT2 were generated by expansion of individual tetraploids formed by induced inhibition of cytokinesis through dihydrocytochalasin treatment. The DNA content was determined by flow cytometry, standard karyotyping, chromosome painting and array comparative genomic hybridization as in [ 15 ]. Cells were maintained in 10 cm dishes in Dulbecco’s Modified Eagle Medium (DMEM) at 37°C and 5% CO2.…”

“…A similar response was identified in a study comparing transcriptome data from disomic and complex aneuploid strains of budding yeast, partial aneuploids of fission yeast, aneuploid Arabidopsis thaliana plant cells, mouse cell lines with Robertsonian translocations that lead to trisomies, and human cells from patients with trisomy syndromes [ 19 ]. Additionally, comparative transcriptomics and proteomics of model human trisomic and tetrasomic cells identified a common pattern in the transcriptional response to aneuploidy [ 15 ]. These studies pointed out similarities in the response to aneuploidy in most eukaryotes.…”

“…Second, specific pathways might be activated in a cellular response to aneuploidy. Recent attempts to uncover the consequences of aneuploidy suggest that aneuploidy indeed instigates a specific response in eukaryotic cells [ 3 , 15 , 19 ]. Haploid yeast strains carrying an additional chromosome (hereafter referred to as disomes) exhibit a common transcriptional signature that has been previously identified in budding yeast as a so called environmental stress response that is triggered upon various exogenous stresses, such as oxidative stress, heat shock or slow growth [ 3 , 20 ].…”

“…In most aneuploid cells the chromosome dosage changes lead to correlating changes in mRNA (e.g. [ 3 , 12 - 15 ]) as well as on protein levels [ 6 , 15 , 16 ]. These analyses further revealed that besides the increased abundance of transcripts and proteins originating from the aneuploid chromosome, the expression of multiple other genes is altered as well [ 3 , 13 , 15 , 17 ].…”

Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns

“…In line with observations in other cell types 1 , 3 , 5 , most whole chromosome CNAs were detrimental to cellular fitness in HMECs and RPTECs, with some exceptions. However, convergent karyotypic evolution improved proliferation rates, coincident with reduced stress signatures.…”

Cellular Stress Associated with Aneuploidy

“…The replication defects observed were in part related to an imbalance in the production of the six subunits of the MCM2-7 helicase. This finding was consistent with a previous dataset from the same group using similar aneuploid cell lines that found a general downregulation of proteins involved in DNA replication (Stingele et al, 2012). …”

“…Mouse embryonic fibroblasts (MEFs) trisomic for chromosome 1, 13, 16, or 19 were also found to have proliferation defects (Williams et al, 2008). Similar growth impairment was observed in human colorectal carcinoma HCT116 cells carrying extra copies of chromosome 3 or 5 (Stingele et al, 2012). However, specific aneuploidy can confer growth advantages under specific conditions.…”

“…Other than UPS, activation of lysosomal-mediated autophagy was also detected upon aneuploidy induction in human HCT116 and retinal pigment epithelial RPE-1 cell lines (Stingele et al, 2012). Increased p62/sequestosome expression, generally triggered by oxidative stress to sequester misfolded protein into aggregates, was found in aneuploid cells.…”

“…Cell cycle delays associated with replication stress may be a cause of the perturbation in cell cycle/proliferative dynamics observed for aneuploid cells in the past (Segal and McCoy, 1974; Stingele et al, 2012; Williams et al, 2008). …”

“…However, it was less pronounced when compared with RNA expression. For instance, SILAC analysis of HCT116 cells tetrasomic for chromosome 5 in comparison with a diploid cell line found the median ratio of protein levels to be 1.6-fold for genes encoded on chromosome 5 (Stingele et al, 2012). A similar observation was made in a stable near-haploid leukemia cell line disomic for chromosome 8 (Burckstummer et al, 2013).…”

“…In addition to increased DNA damage, aneuploid cells experiencing replication stress (including those harboring DNA damage) are also subject to several other fates, such as cell cycle delays, DNA condensation defect, inappropriate mitotic entry, senescence, and even immunological recognition and destruction (Andriani et al, 2016; Blank et al, 2015; Burrell et al, 2013; Lamm et al, 2016; Meena et al, 2015; Santaguida et al, 2017; Soto et al, 2017). Cell cycle delays associated with replication stress may be a cause of the perturbation in cell cycle/proliferative dynamics observed for aneuploid cells in the past (Segal and McCoy, 1974; Stingele et al, 2012; Williams et al, 2008).…”

“…In MEFs trisomic for one of four specific chromosomes, each trisomy displayed alterations in glutamine use and the production of ammonium and lactate, and a subset of karyotypes exhibited increased glucose uptake (Williams et al, 2008). Trisomic and tetrasomic HCT116 cell lines generated through microcell-mediated chromosome transfer (MMCT) showed specific downregulation in proteins involved in DNA, RNA, and carbohydrate metabolism, whereas other pathways such as mitochondrial metabolism were upregulated (Stingele et al, 2012). The observed alteration of DNA metabolic pathways is consistent with DNA replication defects that have also been noted for aneuploid cells (see following section).…”

Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy

“…We then removed the drug and monitored cell proliferation over time either in the absence (Figures 1B and 1C) or in the presence of a chemotherapeutic agent and other anti-cancer agents (Figures 1D-1F). In agreement with previous reports (Dobles et al, 2000;Kops et al, 2004;Michel et al, 2004;Santaguida et al, 2017Sheltzer et al, 2017;Stingele et al, 2012;Tang et al, 2011;Williams et al, 2008), induction of CIN led to decreased proliferation, observed over a range of concentrations of reversine, corresponding to different degrees of mitotic errors (Figures 1B,1C,. To test the effects of CIN on cell proliferation in the presence of a chemotherapeutic agent, cancer cell lines were exposed to a battery of chemotherapeutic drugs after reversine removal (Figure 1D).…”

“…See also Figure S7. 2015;Sheltzer et al, 2017;Stingele et al, 2012;Tang et al, 2011;Torres et al, 2007;Williams et al, 2008). On the other hand, recent studies have also suggested that aneuploidy might facilitate cell proliferation under specific conditions.…”

“…Several studies showed that cells harboring aneuploidies are slower in cell-cycle progression with a major G1 delay (Kops et al, 2004;Santaguida et al, 2017Sheltzer et al, 2017;Stingele et al, 2012;Tang et al, 2011;Torres et al, 2007;Williams et al, 2008). Interestingly, it has been recently proposed that this detrimental effect of aneuploidy on cell proliferation could increase resistance to particular chemotherapeutics (Replogle et al, 2020).…”

“…Examples of this include aneuploidy-specific drug resistance in Candida albicans (Selmecki et al, 2006(Selmecki et al, , 2009 and Saccharomyces cerevisae (Chen et al, 2012(Chen et al, , 2015, and trisomy-driven proliferation under stress conditions in colorectal cancer cell lines (Rutledge et al, 2016). These aneuploidy-specific phenotypes might be the consequence of transcriptomic and proteomic changes imposed by specific chromosome gains and losses (Gemoll et al, 2013;Habermann et al, 2007;Pavelka et al, 2010;Santaguida et al, 2017Stingele et al, 2012;Torres et al, 2007).…”

“…Chromosome mis-segregation leads to abnormal karyotypes, a condition known as aneuploidy . The presence of aneuploid karyotypes affects several processes and has many cellular consequences (Chunduri and Storchova ´, 2019; Zhu et al, 2018;Weaver and Cleveland, 2008;Levine and Holland, 2018), including genome instability (Ohashi et al, 2015, Passerini et al, 2016, Santaguida et al, 2017, Sheltzer et al, 2011, metabolic alterations (Williams et al, 2008), and proteotoxic stress (Ohashi et al, 2015;Stingele et al, 2012). In humans, aneuploidy is the primary cause of spontaneous abortions and leads to severe developmental defects, such as those present in patients with Down syndrome (trisomy 21) (Roper and Reeves, 2006).…”

Monosomies, trisomies and segmental aneuploidies differentially affect chromosomal stability

“…In line with previous studies, we found that the cellular fitness of the vast majority of our aneuploid clones was decreased (Sheltzer et al, , 2012Stingele et al, 2012;Torres et al, 2007;Williams et al, 2008). We found a significant correlation between the number of imbalanced genes and reduced proliferation rates, and both the gains and losses of genes contributed to this correlation.…”

“…To investigate this, we first evaluated autophagic flux, by examining the conversion between LC3B-I to LC3B-II on autophagosomes (Kabeya et al, 2000;Mizushima et al, 2004). This conversion indicates an activated autophagy pathway which aids in the degradation of misfolded/unfolded proteins upon proteotoxic stress and has previously been shown to be upregulated in trisomic cell lines and in cells where aneuploidy was induced with inhibitors Stingele et al, 2012). We tested 3 of our trisomic clones that displayed a variety of CIN levels but we could not detect a significant increase in LC3B-II in these clones (Fig.…”

“…Cells deal with the excess of unincorporated proteins by performing dosage compensation (Brennan et al, 2019;Dephoure et al, 2014;Torres et al, 2007Torres et al, , 2010Kojima and Cimini, 2019). This has been shown to occur both in trisomies (Stingele et al, 2012) as well as in monosomies (Chunduri et al, 2021). Although both monosomies and trisomies perform dosage compensation, the critical difference between monosomies and trisomies might be their distinct mechanism for dosage compensation and the associated stress pathways that are induced.…”

“…To further investigate the relation between CIN and gained coding genes, we aimed to elucidate a potential causal relationship. It has been extensively shown that gaining extra coding DNA leads to an excess of proteins being expressed from the involved chromosome (Dephoure et al, 2014;Liu et al, 2017;Pavelka et al, 2010;Stingele et al, 2012;Torres et al, 2010). Both chromosome gains and losses lead to specific protein imbalances.…”

“…For instance, CIN has been suggested to be the result of specific gains or losses of chromosomes that contain key regulators of proper segregation in mitosis (Nicholson et al, 2015;Zhu et al, 2012). Furthermore, it has been shown that the presence of extra chromosomes disrupts proteostasis and saturation of the protein folding machinery can result in misfolded proteins, aggregate formation and activation of protein degradation pathways (Dürrbaum et al, 2014;Stingele et al, 2012Stingele et al, , 2013Tang et al, 2011). Subsequently, this can result in the deregulation of specific proteins that highly depend on the chaperone machinery.…”