Aneuploid Cancer Research Articles

Trichostatin A preferentially reverses the upregulation of gene-expression levels induced by gain of chromosome 7 in colorectal cancer cell lines.

Epithelial cancers are defined by a tumor-specific distribution of chromosomal aneuploidies that are maintained when cells metastasize and are conserved in cell lines derived from primary tumors. Correlations between genomic copy number and gene expression have been observed for different tumors including, colorectal (CRC), breast, and pancreatic cancer. These ploidy-driven transcriptional deregulations are characterized by low-level expression changes of most genes on the affected chromosomes. The emergence of these aberrations at an early stage of tumorigenesis and the strong selection for the maintenance of these aneuploidies suggest that aneuploidy-dependent transcriptional deregulations might contribute to cellular transformation and maintenance of the malignant phenotype. The histone deacetylase inhibitor (HDACi) Trichostatin A (TSA) has anticancer effects and is well known to lead to large-scale gene-expression changes. Here we assessed if TSA could disrupt the aneuploidy-driven gene expression in the aneuploid colon cancer cell line SW480 and the artificially generated aneuploid cell line DLD-1 + 7. We found that TSA increases transcriptional activity throughout the genome, yet inhibits aneuploidy-induced gene-expression changes on chromosome 7. Among the TSA affected genes on chromosome 7, we identified potential CRC oncogenes. These experiments represent the first attempt to explain how histone acetylation affects aneuploidy-driven gene-expression changes.

Inhibiting polo-like kinase 1 enhances radiosensitization via modulating DNA repair proteins in non-small-cell lung cancer.

To assure faithful chromosome segregation, cells make use of the spindle assembly checkpoint, which can be activated in aneuploid cancer cells. In this study, the efficacies of inhibiting polo-like kinase 1 (PLK1) on the radiosensitization of non-small-cell lung cancer (NSCLC) cells were studied. Clonogenic survival assay was performed to identify the effects of the PLK1 inhibitor on radiosensitivity within NSCLC cells. Mitotic catastrophe assessment was used to measure the cell death and histone H2AX protein (γH2AX) foci were utilized to assess the DNA double-strand breaks (DSB). The transcriptome was analyzed via unbiased profiling of microarray expression. The results showed that the postradiation mitotic catastrophe induction and the DSB repair were induced by PLK1 inhibitor BI-6727, leading to an increase in the radiosensitivity of NSCLC cells. BI-6727 in combination with radiation significantly induced the delayed tumor growth. PLK1-silenced NSCLC cells showed an altered mRNA and protein expression related to DNA damaging, replication, and repairing, including the DNA-dependent protein kinase (DNAPK) and topoisomerase II alpha (TOPO2A). Furthermore, inhibition of PLK1 blocked 2 important DNA repair pathways. To summarize, our study showed PLK1 kinase as an option in the therapy of NSCLC.

Aneuploid Cell Survival Relies upon Sphingolipid Homeostasis.

Aneuploidy, a hallmark of cancer cells, poses an appealing opportunity for cancer treatment and prevention strategies. Using a cell-based screen to identify small molecules that could selectively kill aneuploid cells, we identified the compound N-[2-hydroxy-1-(4-morpholinylmethyl)-2-phenylethyl]-decanamide monohydrochloride (DL-PDMP), an antagonist of UDP-glucose ceramide glucosyltransferase. DL-PDMP selectively inhibited proliferation of aneuploid primary mouse embryonic fibroblasts and aneuploid colorectal cancer cells. Its selective cytotoxic effects were based on further accentuating the elevated levels of ceramide, which characterize aneuploid cells, leading to increased apoptosis. We observed that DL-PDMP could also enhance the cytotoxic effects of paclitaxel, a standard-of-care chemotherapeutic agent that causes aneuploidy, in human colon cancer and mouse lymphoma cells. Our results offer pharmacologic evidence that the aneuploid state in cancer cells can be targeted selectively for therapeutic purposes, or for reducing the toxicity of taxane-based drug regimens. Cancer Res; 77(19); 5272-86. ©2017 AACR.

Abstract B21: CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions

Abstract CRISPR/Cas9 has emerged as a transformative new tool to systematically probe gene function. In this study, we compare the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies by performing parallel deep-coverage shRNA and CRISPR screens targeting 2722 genes across several cancer cell lines. CRISPR-based dropout screens identified more lethal genes compared to RNAi in all five cancer models, indicating that the identification of many cellular dependencies may require full gene inactivation, as induced by CRISPR but not RNAi. However, in two aneuploid cancer models we found that all genes within highly amplified regions, including non-expressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits in CRISPR-based screens. Using a CRISPR tiling array that encompassed all possible sgRNAs against the coding regions of 139 genes, sgRNAs targeting essential domains provide the most robust dropout phenotypes, suggesting that this approach might be used to define the protein domains that are required for cancer dependence. Collectively, these findings demonstrate the utility of CRISPR-based screens in the identification of cancer-dependent genes, but also reveal the need to carefully control for false-positive results especially in chromosomally unstable cancer lines. Note: This abstract was not presented at the conference. Citation Format: Diana Munoz, Frank P. Stegmeier, Michael Schlabach. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B21.

MYC regulated long non-coding RNAs could have roles in development of breast cancer

The deregulation of the cell cycle and checkpoint machinery in cancer presents a highly attractive therapeutic strategy. We review here the strategies used to exploit the dysregulated cell cycle, both through targeting kinases required for cell cycle progression, and checkpoint kinases to inappropriately force cells through the cell cycle. Appropriate control of the cell cycle is critical for proliferating normal cells, and we discuss the importance of defining tumour specific vulnerabilities that could be targeted with cell cycle kinase inhibitors. Recent studies have shown that ER-positive breast cancers rely on CDK4 to promote proliferation. TP53 mutant cancer cell lines are sensitive to WEE1 and CHK1 inhibitors in combination with chemotherapy, while PTEN-deficient aneuploid cancer cell lines are sensitive to TTK inhibitors.

Abstract 2050: Polyploid tumor cells: a chemoresistant cell type in triple-negative breast cancer

Abstract Background: Triple-negative breast cancers (TNBC) are associated with an extremely poor prognosis due to their aggressive behavior and rapid resistance to chemotherapy. Chemotherapy may select for resistant subclones and lead to tumor recurrence. Although, DNA aneuploidy has been a long known prognostic biomarker in breast cancer, the biological role of aneuploid or polyploid cancer cells in tumorigenesis and chemoresistance is largely undefined. Polyploid cells arise due to repeated rounds of DNA duplication in the absence of mitosis. Chemotherapeutic DNA-damaging agents or mitotic inhibitors can also induce formation of polyploid cells and subsequent senescence. However, recent reports indicate that polyploid cells represent a viable and proliferating subpopulation within a tumor that may escape chemotherapy and contribute to tumor recurrence. Methods: In this study, we examined the prevalence and functional significance of polyploidy occurring de novo or induced by chemotherapy in TNBC cell lines. DNA ploidy was analyzed in Hoechst 33342 stained cells using FACS. Cells with greater than 4N DNA content were defined as polyploid. Live-cell imaging was done to observe cell division patters in polyploid cells using IncuCyte Zoom. Cell proliferation was assessed in the absence and presence of chemotherapy drugs with distinct modes of action (docetaxel and paclitaxel: mitotic inhibitors, cisplatin: DNA cross-linking agent, and etoposide or VP16: topoisomerase inhibitor). RNAseq was performed to compare gene expression profiles between treatment-naive diploid and polyploid cells. Results: Hoechst 33342 staining determined the prevalence of polyploid cells in HCC1395(6.7%) and HCC1937 (5.8%) cells lines. Live-cell imaging in polyploid cells showed formation of mitotic structures suggesting multi-polar cell division. Cell proliferation assay revealed that polyploid cells grow slower than diploid cells and show reduced sensitivity to all four chemotherapy drugs. Docetaxel treatment resulted in induction of polyploidy and drug-induced senescence in parental TNBC cells. Drug-induced polyploid cells were resistant to subsequent docetaxel treatment. Time-lapse imaging showed budding of small daughter cells from polyploid senescent cells. Majority of senescent cells died, some cells survived and regenerated the diploid and polyploid subpopulations similar to those present in parental cells. RNAseq identified differentially expressed genes involved in G1-S and G2-M checkpoint pathways (BRCA1/2, RAD51), cell proliferation (Aurora kinase A/B) and apoptosis (BIM, BIRC3). Conclusions: Above findings indicate that there are molecular and functional differences between diploid and polyploid cells that are both naturally occurring or induced by chemotherapy. In our future studies, we will examine combinatorial approaches to overcome polyploidy-associated chemoresistance. Citation Format: Rekha Gyanchandani, Adrian Lee. Polyploid tumor cells: a chemoresistant cell type in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2050. doi:10.1158/1538-7445.AM2017-2050

Path Pendeccentric Connectivity Indices: Detour Matrix Based Molecular Descriptors for QSAR/QSPR Studies, Part 2

A pivotal role of tyrosine threonine kinase (TTK) has been established in tumor initiation, survival of genomically unstable and aneuploid cancer cells. In present study, path pendeccentric connectivity indices reported in part 1 of the manuscript were successfully applied for developing models for predicting TTK inhibitory activity of acetamide/carboxamide analogs. Diverse 2D and 3D molecular descriptors (MDs) were successfully utilized for developing models using artificial neural networks (ANN) and moving average analysis (MAA). The overall accuracy of prediction achieved for ANN and MAA based models was up to 96% for the training set and up to 92% during cross validation. The statistical utility of the said models was also evaluated through Matthews correlation coefficient, non error rate, sensitivity and intercorrelation analysis. Low IC50 values obtained for active ranges of the proposed MAA based models indicate the tremendous potential of said models for furnishing lead molecules for developing potent TTK inhibiting acetamide/carboxamide analogs.

Abstract 128: The next-generation CDK2/9 inhibitor CYC065 elicits marked antineoplastic effects in lung cancer by engaging antimetastatic pathways

Abstract We previously reported CDK2 antagonism with the first generation CDK2/9/7 inhibitor seliciclib (CYC202; Cyclacel) triggered anaphase catastrophe. This occurred when genomically unstable cancer cells with supernumerary centrosomes (a hallmark of cancer) fail to cluster excessive centrosomes at mitosis. This causes multipolar cell division and apoptotic death. Anaphase catastrophe is conferred after CDK2 antagonism of aneuploid cancer cells, sparing bipolar normal cells with two centrosomes. CYC065 (Cyclacel) is a next-generation CDK2/9 inhibitor that is undergoing clinical trial. Here, we explored CYC065 activity against lung cancer cells, some with known high metastatic potential. CYC065 substantially inhibited growth, triggered apoptosis, and induced anaphase catastrophe in murine (ED1, LKR13, and 393P) and human (Hop62, A549, and H1299) lung cancer cells. In marked contrast, these effects were largely unseen in bipolar immortalized pulmonary epithelial (murine C10 and human BEAS-2B) cells. We sought to explore whether CYC065 antineoplastic effects engaged antimetastatic pathways. In vitro migration and invasion assays were performed. CYC065 markedly inhibited migration and invasion of lung cancer cells (murine: 344SQ and KC2; human: A549 and H1299). Reverse Phase Protein Arrays (RPPAs) interrogated nearly 300 growth-regulatory proteins in murine (344SQ and KC2) and human (A549 and H1299) lung cancer cells over time (6, 12, 24, and 48 hours) after CYC065 or vehicle treatments. These lung cancer cells have high metastatic as well migration or invasive potentials. When highlighted proteins were clustered after CYC065 treatment, some species were clustered as significantly up-regulated or down-regulated in all cells over studied time points. Not surprisingly, up-regulated proteins included those involved in DNA damage or apoptosis. In addition to known CDK targets like phosphorylated retinoblastoma protein, novel proteins were markedly down-regulated, including mTOR pathway and integrin pathway proteins such as FAK phosphorylation and Src phosphorylation. Affected pathways were identified using Ingenuity Pathway Analysis (IPA). IPA revealed up-regulation of pathways that engaged ATM signaling, G2/M DNA damage checkpoint regulation, or apoptosis signaling. Down-regulated pathways affected mTOR signaling, cyclins, cell cycle regulation, or integrin pathways. Mouse studies will be presented that examine in vivo effects of CYC065 in reducing metastases. Taken together, the next-generation CDK2/9 inhibitor, CYC065, elicits marked antineoplastic effects by antagonizing migration and invasion of lung cancer cells. Comprehensive RPPA and IPA studies found that distinct pathways trigger these effects. Citation Format: Masanori Kawakami, Jason Roszik, Lin Zheng, Jonathan Kurie, Lisa Maria Mustachio, Xi Liu, Ethan Dmitrovsky. The next-generation CDK2/9 inhibitor CYC065 elicits marked antineoplastic effects in lung cancer by engaging antimetastatic pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 128. doi:10.1158/1538-7445.AM2017-128

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Abstract A35: Olaparib causes premature loss of cohesion in cancer cells

Abstract Although it has been decades since PARP inhibitors were initially discovered and various clinical trials have been performed, their mode of action in killing tumor cells subsequent to PARP inhibition is still not fully understood. We have recently identified poly(ADP-ribosyl)ation (PARylation) as a new post-translational modification of the cohesin complex, a key player in chromosome segregation during mitosis. We investigated the effect of PARP inhibition on mitosis in a panel of cells of cancer (cervical, breast, ovarian) and normal tissue origin. We treated cancerous and non-cancerous cell lines labelled with chromatin markers with a selected set of PARP inhibitors and imaged them with fluorescence live microscopy. Out of 5 tested inhibitors, a well-known and clinically relevant PARP inhibitor olaparib, induced strongest perturbations in mitotic progression. Olaparib induced a delay in entering anaphase, problems aligning chromosomes at the metaphase plate and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest. Cohesion fatigue, leading to cell death, was observed in cancer cell lines exhibiting S-phase stalling or G2/M arrest with increased protein levels of PARP1. Olaparib is known to entrap PARP1 at replication forks and thereby perturb replication fork movement. While its addition before the onset of mitosis did not result in mitotic defects, addition of olaparib only in S-phase was sufficient to cause mitotic phenotypes. Our results indicate that PARP inhibition by olaparib in S phase has downstream effects on mitotic progression. PARP1 RNAi in addition to olaparib treatment rescues the cohesion fatigue phenotype, suggesting that entrapment of PARP1 at the replication fork upon its inhibition is the main cause of cohesion fatigue. Cohesion fatigue was observed only in highly aneuploid cancer cells that are described to have an increased rate of chromosome mis-segregation. In conclusion, higher susceptibility of aneuploid cancer to cohesion fatigue and cell death upon olaparib treatment relative to normal cells would support its use as anti-mitotic chemotherapy. Citation Format: Eva Kukolj, Tanja Kaufmann, Amalie E. Dick, Robert Zeillinger, Daniel W. Gerlich, Dea Slade. Olaparib causes premature loss of cohesion in cancer cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr A35.

GTSE1 tunes microtubule stability for chromosome alignment and segregation by inhibiting the microtubule depolymerase MCAK.

The dynamic regulation of microtubules (MTs) during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore MTs have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The MT depolymerase MCAK (mitotic centromere-associated kinesin) can influence CIN through its impact on MT stability, but how its potent activity is controlled in cells remains unclear. In this study, we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumors, regulates MT stability during mitosis by inhibiting MCAK MT depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning as a result of MT instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, whereas artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus, GTSE1 inhibition of MCAK activity regulates the balance of MT stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability.

MPS1 kinase as a potential therapeutic target in medulloblastoma.

Medulloblastoma is the most common type of malignant brain tumor that affects children. Although recent advances in chemotherapy and radiation have improved outcomes, high-risk patients perform poorly with significant morbidity. Gene expression profiling has revealed that monopolar spindle 1 (MPS1) (TTK1) is highly expressed in medulloblastoma patient samples compared to that noted in normal cerebellum. MPS1 is a key regulator of the spindle assembly checkpoint (SAC), a mitotic mechanism specifically required for proper chromosomal alignment and segregation. The SAC can be activated in aneuploid cancer cells and MPS1 is overexpressed in many types of cancers. A previous study has demonstrated the effectiveness of inhibiting MPS1 with small-molecule inhibitors, but the role of MPS1 in medulloblastoma is unknown. In the present study, we demonstrated that MPS1 inhibition by shRNA or with a small-molecule drug, NMS-P715, resulted in decreased cell growth, inhibition of clonogenic potential and induction of apoptosis in cells belonging to both the Shh and group 3 medulloblastoma genomic signature. These findings highlight MPS1 as a rational therapeutic target for medulloblastoma.

DNA aneuploidy and breast cancer: a meta-analysis of 141,163 cases.

Background & AimsDNA ploidy, a DNA flow cytometry parameter, reflects tumor cell cycle. In breast cancer (BC), ploidy status characterizes genotypic stability and potential metastatic capacity. It is suggested that aneuploidy is an independent prognosticator for BC patients and could aid for individualized medicine. There are extensive studies concerning the prognostic significance of DNA aneuploidy, however, its clinical utility remains controversial. Herein we conducted a meta-analysis to determine the correlation between DNA ploidy status and BC characteristics and survival.MethodsThe electronic databases PubMed, EMBASE, and Web of Science were searched for relevant studies. The major investigated parameters were the BC aneuploidy rates in relation to tumor stage, size, lymph node metastasis, grading, estrogen receptor (ER) status, disease-free survival (DFS), and overall survival (OS). Hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs) for DFS and OS were extracted from each study before meta-analyzed. Risk ratios (RRs) were computed using the fixed-effect or random-effects model according to data heterogeneity, and the Mantel-Haenszel or the inverse-variance method was adopted where appropriate to obtain pooled estimates using RevMan 5.3. The Egger's test was conducted with Stata 11.ResultsPooled analyses of data from 29 studies involving a total of 141,163 cases showed that BC patients with more advanced tumors (stage I vs. stages II-IV, RR=0.84; 95% CI, 0.74 to 0.96; P=0.01), larger tumors (≤2 cm vs. >2 cm: RR=0.82; 95% CI, 0.77 to 0.87; P<0.00001), lymph node metastasis (pN0 vs. pN1-3: RR=0.85; 95% CI, 0.83 to 0.87, P<0.00001), poorer tumor proliferation (G2 vs. G1: RR=1.58; 95% CI, 1.40 to 1.79; P<0.00001; G3 vs. G1: RR=2.17; 95% CI, 1.77 to 2.67; P<0.00001; G3 vs. G2: RR=1.41; 95% CI, 1.25 to 1.60; P<0.00001), and ER− status (ER− vs. ER+: RR=1.32; 95% CI, 1.22 to 1.43; P<0.00001) were significantly more frequently aneuploid. BC patients with diploid tumors had better clinical outcomes than those with aneuploid cancers. The pooled HR estimates were0.73 (P<0.0001) for DFS and 0.72 (P=0.0001) for OS, respectively.ConclusionThis meta-analysis implies that DNA aneuploidy is a significant predictor for BC progression and survival, and should be focused on in the therapeutic planning.

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions.

CRISPR/Cas9 has emerged as a powerful new tool to systematically probe gene function. We compared the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies across multiple cancer cell lines. CRISPR dropout screens consistently identified more lethal genes than RNAi, implying that the identification of many cellular dependencies may require full gene inactivation. However, in two aneuploid cancer models, we found that all genes within highly amplified regions, including nonexpressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits. In addition, using a CRISPR tiling screen, we found that sgRNAs targeting essential domains generate the strongest lethality phenotypes and thus provide a strategy to rapidly define the protein domains required for cancer dependence. Collectively, these findings not only demonstrate the utility of CRISPR screens in the identification of cancer-essential genes, but also reveal the need to carefully control for false-positive results in chromosomally unstable cancer lines. We show in this study that CRISPR-based screens have a significantly lower false-negative rate compared with RNAi-based screens, but have specific liabilities particularly in the interrogation of regions of genome amplification. Therefore, this study provides critical insights for applying CRISPR-based screens toward the systematic identification of new cancer targets. Cancer Discov; 6(8); 900-13. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Aguirre et al., p. 914This article is highlighted in the In This Issue feature, p. 803.

Footprintless disruption of prosurvival genes in aneuploid cancer cells using CRISPR/Cas9 technology.

CRISPR/Cas9 has emerged as a powerful methodology for the targeted editing of genomic DNA sequences. Nevertheless, the intrinsic inefficiency of transfection methods required to use this technique with cultured cells requires the selection and isolation of successfully modified cells, which invariably subjects the cells to stress. Here we report a workflow that allows the isolation of genomically modified cells, even where loss of functional alleles constitutes a selective disadvantage owing to impaired ability to survive stress. Using targeted disruption of the Id1 and Id3 genes in murine B16-F10 and Ret melanoma cell lines as an example, we show that the method allows for the footprintless isolation of CRISPR/Cas9-modified aneuploid cancer cells. We also provide evidence that serial CRISPR/Cas9 modifications can occur, for example when initial homologous recombination events introduce cryptic PAM sequences, and demonstrate that multiple alleles can be successfully targeted in aneuploid cancer cells. By sequencing individual alleles we also found evidence for CRISPR/Cas9-induced transposable element insertion, albeit at a low frequency. This workflow should have broad application in the functional analysis of prosurvival gene function in cultured cells.

The Combination of DNA Ploidy Status and PTEN/6q15 Deletions Provides Strong and Independent Prognostic Information in Prostate Cancer.

Aberrant DNA content has been discussed as a potential prognostic feature in prostate cancer. We analyzed the clinical significance of DNA ploidy in combination with prognostic relevant deletions of PTEN and 6q15 in 3,845 prostate cancers. The DNA status was diploid in 67.8%, tetraploid in 25.6%, and aneuploid in 6.8% of tumors, and deletions of PTEN and 6q15 occurred in 17.8% and 20.3% of tumors. Abnormal DNA content and deletions were linked to high Gleason score, advanced tumor stage, and positive nodal stage (P < 0.0001 each). The risk of PSA recurrence increased from diploid to tetraploid and from tetraploid to aneuploid DNA status (P < 0.0001 each). However, 40% of patients with Gleason score ≥4+4 and 55% of patients with PSA recurrence had diploid cancers. This fraction decreased to 21% (Gleason ≥4+4) and 29% (PSA recurrence) if PTEN and/or 6q deletion data were added to ploidy data to identify cancers with an aberrant DNA status. The significance of combining both deletions and ploidy was further demonstrated in a combined recurrence analysis. Presence of deletions increased the risk of PSA recurrence in diploid (P < 0.0001), tetraploid (P < 0.0001), and aneuploid cancers (P = 0.0049), and the combination of ploidy data and deletions provided clinically relevant information beyond the CAPRA-S nomogram. Multivariate modeling including preoperatively and postoperatively available parameters identified the "combined DNA status" as a strong independent predictor of poor patient outcome. The combinatorial DNA content analysis involving general (ploidy) and specific events (deletions) has the potential for clinical utility in prostate cancer. Clin Cancer Res; 22(11); 2802-11. ©2016 AACR.

Molecular genetics of colorectal cancer

Colorectal cancer is the end result of an accumulation of destabilizing mutations and other genetic events, which occur in clones of colonocytes over many years. While each colorectal cancer is genetically unique, there are at least three distinct mechanisms by which the process occurs. The commonest is chromosomal instability, producing microsatellite stable, aneuploid cancers. The second is DNA promoter methylation that underlies CpG island methylation phenotype cancers, either microsatellite stable or unstable, and the third is loss of DNA mismatch repair, causing microsatellite unstable, diploid cancers. Cancers arising from these three mechanisms are biologically different and the differences have clinical implications.

A second transmissible cancer in Tasmanian devils

Clonally transmissible cancers are somatic cell lineages that are spread between individuals via the transfer of living cancer cells. There are only three known naturally occurring transmissible cancers, and these affect dogs, soft-shell clams, and Tasmanian devils, respectively. The Tasmanian devil transmissible facial cancer was first observed in 1996, and is threatening its host species with extinction. Until now, this disease has been consistently associated with a single aneuploid cancer cell lineage that we refer to as DFT1. Here we describe a second transmissible cancer, DFT2, in five devils located in southern Tasmania in 2014 and 2015. DFT2 causes facial tumors that are grossly indistinguishable but histologically distinct from those caused by DFT1. DFT2 bears no detectable cytogenetic similarity to DFT1 and carries a Y chromosome, which contrasts with the female origin of DFT1. DFT2 shows different alleles to both its hosts and DFT1 at microsatellite, structural variant, and major histocompatibility complex (MHC) loci, confirming that it is a second cancer that can be transmitted between devils as an allogeneic, MHC-discordant graft. These findings indicate that Tasmanian devils have spawned at least two distinct transmissible cancer lineages and suggest that transmissible cancers may arise more frequently in nature than previously considered. The discovery of DFT2 presents important challenges for the conservation of Tasmanian devils and raises the possibility that this species is particularly prone to the emergence of transmissible cancers. More generally, our findings highlight the potential for cancer cells to depart from their hosts and become dangerous transmissible pathogens.

Effects of aneuploidy on gene expression: implications for cancer.

Unbalanced chromosome content, so-called aneuploidy, is a hallmark of cancer cells. Changes in the copy numbers of chromosomes or large chromosomal regions significantly alter the expression of several hundreds of genes that are gained or lost. At the same time, aneuploidy per se affects the transcription of many genes throughout the entire genome, as several pathways are activated or inhibited in response to changes in chromosome copy number. In recent years, a large amount of quantitative genome, transcriptome and proteome data has enabled comparison of the changes in gene expression observed in aneuploid cancer cells, as well as in model aneuploid cells with defined karyotypes. Here, we summarize how aneuploidy shapes gene expression and how it may contribute to the phenotypes of cancer cells.

Replication stress activates DNA repair synthesis in mitosis.

Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis. Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs). CFSs are difficult-to-replicate loci that manifest as gaps or breaks on metaphase chromosomes (termed CFS 'expression'), particularly when cells have been exposed to replicative stress. The MUS81-EME1 structure-specific endonuclease promotes the appearance of chromosome gaps or breaks at CFSs following replicative stress. Here we show that entry of cells into mitotic prophase triggers the recruitment of MUS81 to CFSs. The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction. We propose that the attempted condensation of incompletely duplicated loci in early mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest that targeting this pathway could represent a new therapeutic approach.