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Xie Z, Wang Y, Chen T, Fan W, Wei L, Liu B, Situ X, Zhan Q, Fu T, Tian T, Li S, He Q, Zhou J, Wang H, Du J, Tseng HR, Lei Y, Tang KJ, Ke Z. Circulating tumor cells with increasing aneuploidy predict inferior prognosis and therapeutic resistance in small cell lung cancer. Drug Resist Updat 2024; 76:101117. [PMID: 38996549 DOI: 10.1016/j.drup.2024.101117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/23/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024]
Abstract
AIMS Treatment resistance commonly emerges in small cell lung cancer (SCLC), necessitating the development of novel and effective biomarkers to dynamically assess therapeutic efficacy. This study aims to evaluate the clinical utility of aneuploid circulating tumor cells (CTCs) for risk stratification and treatment response monitoring. METHODS A total of 126 SCLC patients (two cohorts) from two independent cancer centers were recruited as the study subjects. Blood samples were collected from these patients and aneuploid CTCs were detected. Aneuploid CTC count (ACC) and aneuploid CTC score (ACS), were used to predict progression-free survival (PFS) and overall survival (OS). The performance of the ACC and the ACS was evaluated by calculating the area under the receiver operating characteristic (ROC) curve (AUC). RESULTS Compared to ACC, ACS exhibited superior predictive power for PFS and OS in these 126 patients. Moreover, both univariate and multivariate analyses revealed that ACS was an independent prognostic factor. Dynamic ACS changes reflected treatment response, which is more precise than ACC changes. ACS can be used to assess chemotherapy resistance and is more sensitive than radiological examination (with a median lead time of 2.8 months; P < 0.001). When patients had high ACS levels (> 1.115) at baseline, the combination of immunotherapy and chemotherapy resulted in longer PFS (median PFS, 7.7 months; P = 0.007) and OS (median OS, 16.3 months; P = 0.033) than chemotherapy alone (median PFS, 4.9 months; median OS, 13.6 months). CONCLUSIONS ACS could be used as a biomarker for risk stratification, treatment response monitoring, and individualized therapeutic intervention in SCLC patients.
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Affiliation(s)
- Zhongpeng Xie
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yanxia Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Tingfei Chen
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Wei Fan
- Cyttel Biomedical Technology Co., Ltd, Taizhou 225300, China
| | - Lihong Wei
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Bixia Liu
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaohua Situ
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qinru Zhan
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Tongze Fu
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Tian Tian
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Shuhua Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qiong He
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jianwen Zhou
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Huipin Wang
- Molecular Diagnostic Center, Zhongshan City People's Hospital, Zhongshan 528403, China
| | - Juan Du
- Molecular Diagnostic Center, Zhongshan City People's Hospital, Zhongshan 528403, China
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA.
| | - Yiyan Lei
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China.
| | - Ke-Jing Tang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, SunYat-Sen University, Guangzhou 510080, China; Department of Pharmacy, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Cyttel Biomedical Technology Co., Ltd, Taizhou 225300, China.
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Dutcher HA, Hose J, Howe H, Rojas J, Gasch AP. The response to single-gene duplication implicates translation as a key vulnerability in aneuploid yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589582. [PMID: 38659764 PMCID: PMC11042342 DOI: 10.1101/2024.04.15.589582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Aneuploidy produces myriad consequences in health and disease, yet models of the deleterious effects of chromosome amplification are still widely debated. To distinguish the molecular determinants of aneuploidy stress, we measured the effects of duplicating individual genes in cells with varying chromosome duplications, in wild-type cells and cells sensitized to aneuploidy by deletion of RNA-binding protein Ssd1. We identified gene duplications that are nearly neutral in wild-type euploid cells but significantly deleterious in euploids lacking SSD1 or SSD1+ aneuploid cells with different chromosome duplications. Several of the most deleterious genes are linked to translation; in contrast, duplication of other translational regulators, including eI5Fa Hyp2, benefit ssd1Δ aneuploids over controls. Using modeling of aneuploid growth defects, we propose that the deleterious effects of aneuploidy emerge from an interaction between the cumulative burden of many amplified genes on a chromosome and a subset of duplicated genes that become toxic in that context. Our results suggest that the mechanism behind their toxicity is linked to a key vulnerability in translation in aneuploid cells. These findings provide a perspective on the dual impact of individual genes and overall genomic burden, offering new avenues for understanding aneuploidy and its cellular consequences.
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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Vande Zande P, Zhou X, Selmecki A. The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress. Annu Rev Microbiol 2023; 77:341-361. [PMID: 37307856 PMCID: PMC10599402 DOI: 10.1146/annurev-micro-041320-112443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fungal species have dynamic genomes and often exhibit genomic plasticity in response to stress. This genome plasticity often comes with phenotypic consequences that affect fitness and resistance to stress. Fungal pathogens exhibit genome plasticity in both clinical and agricultural settings and often during adaptation to antifungal drugs, posing significant challenges to human health. Therefore, it is important to understand the rates, mechanisms, and impact of large genomic changes. This review addresses the prevalence of polyploidy, aneuploidy, and copy number variation across diverse fungal species, with special attention to prominent fungal pathogens and model species. We also explore the relationship between environmental stress and rates of genomic changes and highlight the mechanisms underlying genotypic and phenotypic changes. A comprehensive understanding of these dynamic fungal genomes is needed to identify novel solutions for the increase in antifungal drug resistance.
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Affiliation(s)
- Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
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Heng J, Heng HH. Genome Chaos, Information Creation, and Cancer Emergence: Searching for New Frameworks on the 50th Anniversary of the "War on Cancer". Genes (Basel) 2021; 13:genes13010101. [PMID: 35052441 PMCID: PMC8774498 DOI: 10.3390/genes13010101] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 12/26/2022] Open
Abstract
The year 2021 marks the 50th anniversary of the National Cancer Act, signed by President Nixon, which declared a national “war on cancer.” Powered by enormous financial support, this past half-century has witnessed remarkable progress in understanding the individual molecular mechanisms of cancer, primarily through the characterization of cancer genes and the phenotypes associated with their pathways. Despite millions of publications and the overwhelming volume data generated from the Cancer Genome Project, clinical benefits are still lacking. In fact, the massive, diverse data also unexpectedly challenge the current somatic gene mutation theory of cancer, as well as the initial rationales behind sequencing so many cancer samples. Therefore, what should we do next? Should we continue to sequence more samples and push for further molecular characterizations, or should we take a moment to pause and think about the biological meaning of the data we have, integrating new ideas in cancer biology? On this special anniversary, we implore that it is time for the latter. We review the Genome Architecture Theory, an alternative conceptual framework that departs from gene-based theories. Specifically, we discuss the relationship between genes, genomes, and information-based platforms for future cancer research. This discussion will reinforce some newly proposed concepts that are essential for advancing cancer research, including two-phased cancer evolution (which reconciles evolutionary contributions from karyotypes and genes), stress-induced genome chaos (which creates new system information essential for macroevolution), the evolutionary mechanism of cancer (which unifies diverse molecular mechanisms to create new karyotype coding during evolution), and cellular adaptation and cancer emergence (which explains why cancer exists in the first place). We hope that these ideas will usher in new genomic and evolutionary conceptual frameworks and strategies for the next 50 years of cancer research.
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Affiliation(s)
- Julie Heng
- Harvard College, 16 Divinity Ave, Cambridge, MA 02138, USA;
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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Mishra A, Forche A, Anderson MZ. Parasexuality of Candida Species. Front Cell Infect Microbiol 2021; 11:796929. [PMID: 34966696 PMCID: PMC8711763 DOI: 10.3389/fcimb.2021.796929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022] Open
Abstract
While most fungi have the ability to reproduce sexually, multiple independent lineages have lost meiosis and developed parasexual cycles in its place. Emergence of parasexual cycles is particularly prominent in medically relevant fungi from the CUG paraphyletic group of Candida species. Since the discovery of parasex in C. albicans roughly two decades ago, it has served as the model for Candida species. Importantly, parasex in C. albicans retains hallmarks of meiosis including genetic recombination and chromosome segregation, making it a potential driver of genetic diversity. Furthermore, key meiotic genes play similar roles in C. albicans parasex and highlights parallels between these processes. Yet, the evolutionary role of parasex in Candida adaptation and the extent of resulting genotypic and phenotypic diversity remain as key knowledge gaps in this facultative reproductive program. Here, we present our current understanding of parasex, the mechanisms governing its regulation, and its relevance to Candida biology.
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Affiliation(s)
- Abhishek Mishra
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, ME, United States
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
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7
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Huang M, Ma Y, Lv C, Li S, Lu F, Zhang S, Wang DD, Lin PP, Yang Y. Aneuploid Circulating Tumor Cells as a Predictor of Response to Neoadjuvant Chemotherapy in Non-Small Cell Lung Cancer. Int J Gen Med 2021; 14:6609-6620. [PMID: 34703281 PMCID: PMC8523810 DOI: 10.2147/ijgm.s330361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/02/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to explore the potential application of circulating tumor cells (CTCs) in predicting the therapeutic effect of neoadjuvant chemotherapy (NAC) in non-small-cell lung cancer (NSCLC). Methods Using integrated subtraction enrichment and immunostaining-fluorescence in situ hybridization, the serial CTCs of patients with NSCLC were detected in 7.5 mL of blood at baseline and after two cycles of cisplatin-based NAC, and all aneuploidies of chromosome 8 were examined in the enriched CTCs. Tumor responses were evaluated radiologically with serial chest computed tomography (CT) using the response evaluation criteria in solid tumors and microscopically using the tumor cell necrosis rate (TCNR) of the resected specimen after NAC. Results After two cycles of cisplatin-based NAC, 89% (8/9) of the patients with radiological partial response to NAC had reduced CTC numbers, while 73% (8/11) of the patients with stable disease exhibited increased CTC numbers (P = 0.0098). On pathological examination, 90% (9/10) of patients with a TCNR lower than 30% had >1 CTC post-NAC, while 80% (4/5) of patients with a TCNR higher than 30% had ≤1 CTC post-NAC (P = 0.017). In aneuploidy analysis, the positive rate (CTC > 0) of triploid CTCs was found to have increased after NAC, in contrast with the tetraploid and multiploid CTCs. Furthermore, tetraploid and multiploid CTCs were found to be significantly downregulated in the patients with partial response to NAC. Conclusion The correlations of aneuploid CTCs with both radiological and pathological responses in patients with NSCLC who received NAC were summarized, and the findings indicate that enumerating and karyotyping aneuploid CTCs can serve as a surrogate marker for disease monitoring in NSCLC.
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Affiliation(s)
- Miao Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Chao Lv
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Shaolei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Fangliang Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Shanyuan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | | | | | - Yue Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
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Bendixsen DP, Peris D, Stelkens R. Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:742894. [PMID: 37744091 PMCID: PMC10512264 DOI: 10.3389/ffunb.2021.742894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
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Affiliation(s)
- Devin P. Bendixsen
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Health, Valencian International University, Valencia, Spain
| | - Rike Stelkens
- Population Genetics Division, Department of Zoology, Stockholm University, Stockholm, Sweden
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9
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Pal S, Nixon BR, Glennon MS, Shridhar P, Satterfield SL, Su YR, Becker JR. Replication Stress Response Modifies Sarcomeric Cardiomyopathy Remodeling. J Am Heart Assoc 2021; 10:e021768. [PMID: 34323119 PMCID: PMC8475701 DOI: 10.1161/jaha.121.021768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Background Sarcomere gene mutations lead to cardiomyocyte hypertrophy and pathological myocardial remodeling. However, there is considerable phenotypic heterogeneity at both the cellular and the organ level, suggesting modifiers regulate the effects of these mutations. We hypothesized that sarcomere dysfunction leads to cardiomyocyte genotoxic stress, and this modifies pathological ventricular remodeling. Methods and Results Using a murine model deficient in the sarcomere protein, Mybpc3−/− (cardiac myosin‐binding protein 3), we discovered that there was a surge in cardiomyocyte nuclear DNA damage during the earliest stages of cardiomyopathy. This was accompanied by a selective increase in ataxia telangiectasia and rad3‐related phosphorylation and increased p53 protein accumulation. The cause of the DNA damage and DNA damage pathway activation was dysregulated cardiomyocyte DNA synthesis, leading to replication stress. We discovered that selective inhibition of ataxia telangiectasia and rad3 related or cardiomyocyte deletion of p53 reduced pathological left ventricular remodeling and cardiomyocyte hypertrophy in Mybpc3−/− animals. Mice and humans harboring other types of sarcomere gene mutations also had evidence of activation of the replication stress response, and this was associated with cardiomyocyte aneuploidy in all models studied. Conclusions Collectively, our results show that sarcomere mutations lead to activation of the cardiomyocyte replication stress response, which modifies pathological myocardial remodeling in sarcomeric cardiomyopathy.
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Affiliation(s)
- Soumojit Pal
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Benjamin R Nixon
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Michael S Glennon
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Puneeth Shridhar
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA.,Department of Bioengineering Swanson School of Engineering University of Pittsburgh PA
| | - Sidney L Satterfield
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
| | - Yan Ru Su
- Division of Cardiology Department of Medicine Vanderbilt University Medical Center Nashville TN
| | - Jason R Becker
- Division of Cardiology Department of Medicine Heart, Lung Blood and Vascular Medicine InstituteSchool of MedicineUniversity of PittsburghUniversity of Pittsburgh Medical Center PA
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10
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Ascencio D, Diss G, Gagnon-Arsenault I, Dubé AK, DeLuna A, Landry CR. Expression attenuation as a mechanism of robustness against gene duplication. Proc Natl Acad Sci U S A 2021; 118:e2014345118. [PMID: 33526669 PMCID: PMC7970654 DOI: 10.1073/pnas.2014345118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gene duplication is ubiquitous and a major driver of phenotypic diversity across the tree of life, but its immediate consequences are not fully understood. Deleterious effects would decrease the probability of retention of duplicates and prevent their contribution to long-term evolution. One possible detrimental effect of duplication is the perturbation of the stoichiometry of protein complexes. Here, we measured the fitness effects of the duplication of 899 essential genes in the budding yeast using high-resolution competition assays. At least 10% of genes caused a fitness disadvantage when duplicated. Intriguingly, the duplication of most protein complex subunits had small to nondetectable effects on fitness, with few exceptions. We selected four complexes with subunits that had an impact on fitness when duplicated and measured the impact of individual gene duplications on their protein-protein interactions. We found that very few duplications affect both fitness and interactions. Furthermore, large complexes such as the 26S proteasome are protected from gene duplication by attenuation of protein abundance. Regulatory mechanisms that maintain the stoichiometric balance of protein complexes may protect from the immediate effects of gene duplication. Our results show that a better understanding of protein regulation and assembly in complexes is required for the refinement of current models of gene duplication.
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Affiliation(s)
- Diana Ascencio
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, 36824 Irapuato, Guanajuato, Mexico
| | - Guillaume Diss
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexandre K Dubé
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, 36824 Irapuato, Guanajuato, Mexico
| | - Christian R Landry
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada;
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
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11
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Fu J, Guo W, Yan C, Lv Z, Wang Y, Wang Z, Fan Z, Lei T. Combining targeted sequencing and ultra-low-pass whole-genome sequencing for accurate somatic copy number alteration detection. Funct Integr Genomics 2021; 21:161-169. [PMID: 33543400 DOI: 10.1007/s10142-021-00767-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/14/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
This study investigated the feasibility of combining targeted sequencing and ultra-low-pass whole-genome sequencing (ULP-WGS) for improved somatic copy number alteration (SCNA) detection, due to its role in tumorigenesis and prognosis. Cerebrospinal fluid and matched blood samples were obtained from 29 patients with brain metastasis derived from lung cancer. Samples were subjected to targeted sequencing (genomic coverage: 300 kb) and 2×ULP-WGS. The SCNA was detected by the CTLW_CNV, Control-FreeC, and CNVkit methods and their accuracy was analyzed. Eighteen tumor samples showed consistent SCNA results between the three methods, while a small fraction of samples resulted in different SCNA estimations. Further analysis indicated that consistency of SCNA highly correlated with the difference of baseline depth (normalized depth of regions without SCNA events) estimation between methods. Conflict Index showed that CTLW_CNV significantly improved the accuracy of SCNA detection through precise baseline depth estimation. CTLW_CNV combines targeted sequencing and ULP-WGS for improved SCNA detection. The improvement in detection accuracy is mainly due to a refined baseline depth estimation, guided by single-nucleotide polymorphism allele frequencies within the deeply sequenced region (targeted sequencing). This method is especially suitable for tumor samples with biased aneuploidy, a previously under-estimated genomic characteristic across different cancer types.
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Affiliation(s)
- Junfeng Fu
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Weihua Guo
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Cheng Yan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Zhenyang Lv
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Yu Wang
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Ze Wang
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Zhe Fan
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China
| | - Ting Lei
- Department of Thoracic Surgery, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian, 116000, Liaoning Province, China.
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12
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Giam M, Wong CK, Low JS, Sinelli M, Dreesen O, Rancati G. P53 induces senescence in the unstable progeny of aneuploid cells. Cell Cycle 2020; 19:3508-3520. [PMID: 33305692 DOI: 10.1080/15384101.2020.1850968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aneuploidy is the condition of having an imbalanced karyotype, which is associated with tumor initiation, evolution, and acquisition of drug-resistant features, possibly by generating heterogeneous populations of cells with distinct genotypes and phenotypes. Multicellular eukaryotes have therefore evolved a range of extrinsic and cell-autonomous mechanisms for restraining proliferation of aneuploid cells, including activation of the tumor suppressor protein p53. However, accumulating evidence indicates that a subset of aneuploid cells can escape p53-mediated growth restriction and continue proliferating in vitro. Here we show that such aneuploid cell lines display a robust modal karyotype and low frequency of chromosomal aberrations despite ongoing chromosome instability. Indeed, while these aneuploid cells are able to survive for extended periods in vitro, their chromosomally unstable progeny remain subject to p53-induced senescence and growth restriction, leading to subsequent elimination from the aneuploid pool. This mechanism helps maintain low levels of heterogeneity in aneuploid populations and may prevent detrimental evolutionary processes such as cancer progression and development of drug resistance.
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Affiliation(s)
- Maybelline Giam
- nstitute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Cheng Kit Wong
- nstitute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Jun Siong Low
- nstitute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore.,Institute for Research in Biomedicine, Università Della Svizzera Italiana , Bellinzona, Switzerland
| | - Matteo Sinelli
- nstitute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Oliver Dreesen
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Giulia Rancati
- nstitute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore.,Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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13
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Ryu HY, Ahn SH, Hochstrasser M. SUMO and cellular adaptive mechanisms. Exp Mol Med 2020; 52:931-939. [PMID: 32591648 PMCID: PMC7338444 DOI: 10.1038/s12276-020-0457-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, which reverses SUMO-protein modifications, in the model eukaryote Saccharomyces cerevisiae is severely detrimental to cell fitness and has emerged as a useful model for studying how cells adapt to SUMO system dysfunction. Both short-term and long-term adaptive mechanisms are triggered depending on the length of time cells spend without this SUMO chain-cleaving enzyme. Such short-term adaptations include a highly specific multichromosome aneuploidy and large changes in ribosomal gene transcription. While aneuploid ulp2Δ cells survive, they suffer severe defects in growth and stress resistance. Over many generations, euploidy is restored, transcriptional programs are adjusted, and specific genetic changes that compensate for the loss of the SUMO protease are observed. These long-term adapted cells grow at normal rates with no detectable defects in stress resistance. In this review, we examine the connections between SUMO and cellular adaptive mechanisms more broadly. Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress responses by attaching to key proteins, results in some remarkable adaptations. Mark Hochstrasser at Yale University, New Haven, USA, and co-workers review how this “sumoylation” is reversed by protease enzymes, and how imbalances between sumoylation and desumoylation may be linked to diseases including cancer. When certain SUMO proteases are deliberately disrupted, the cells quickly become aneuploid, i.e., carry an abnormal number of chromosomes. These cells show severe growth defects, but over many generations they regain the normal number of chromosomes. They also undergo genetic changes that promote alternative mechanisms that compensate for losing the SUMO protease and facilitate the same efficient stress responses as the original cells.
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Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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14
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Yang F, Teoh F, Tan ASM, Cao Y, Pavelka N, Berman J. Aneuploidy Enables Cross-Adaptation to Unrelated Drugs. Mol Biol Evol 2020; 36:1768-1782. [PMID: 31028698 PMCID: PMC6657732 DOI: 10.1093/molbev/msz104] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aneuploidy is common both in tumor cells responding to chemotherapeutic agents and in fungal cells adapting to antifungal drugs. Because aneuploidy simultaneously affects many genes, it has the potential to confer multiple phenotypes to the same cells. Here, we analyzed the mechanisms by which Candida albicans, the most prevalent human fungal pathogen, acquires the ability to survive both chemotherapeutic agents and antifungal drugs. Strikingly, adaptation to both types of drugs was accompanied by the acquisition of specific whole-chromosome aneuploidies, with some aneuploid karyotypes recovered independently and repeatedly from very different drug conditions. Specifically, strains selected for survival in hydroxyurea, an anticancer drug, acquired cross-adaptation to caspofungin, a first-line antifungal drug, and both acquired traits were attributable to trisomy of the same chromosome: loss of trisomy was accompanied by loss of adaptation to both drugs. Mechanistically, aneuploidy simultaneously altered the copy number of most genes on chromosome 2, yet survival in hydroxyurea or caspofungin required different genes and stress response pathways. Similarly, chromosome 5 monosomy conferred increased tolerance to both fluconazole and to caspofungin, antifungals with different mechanisms of action. Thus, the potential for cross-adaptation is not a feature of aneuploidy per se; rather, it is dependent on specific genes harbored on given aneuploid chromosomes. Furthermore, pre-exposure to hydroxyurea increased the frequency of appearance of caspofungin survivors, and hydroxyurea-adapted C. albicans cells were refractory to antifungal drug treatment in a mouse model of systemic candidiasis. This highlights the potential clinical consequences for the management of cancer chemotherapy patients at risk of fungal infections.
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Affiliation(s)
- Feng Yang
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Flora Teoh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yongbing Cao
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Shanghai TCM-Integrated Institute of Vascular Disease, Shanghai, China
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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15
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Wu PH, Gilkes DM, Phillip JM, Narkar A, Cheng TWT, Marchand J, Lee MH, Li R, Wirtz D. Single-cell morphology encodes metastatic potential. SCIENCE ADVANCES 2020; 6:eaaw6938. [PMID: 32010778 PMCID: PMC6976289 DOI: 10.1126/sciadv.aaw6938] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 11/13/2019] [Indexed: 05/10/2023]
Abstract
A central goal of precision medicine is to predict disease outcomes and design treatments based on multidimensional information from afflicted cells and tissues. Cell morphology is an emergent readout of the molecular underpinnings of a cell's functions and, thus, can be used as a method to define the functional state of an individual cell. We measured 216 features derived from cell and nucleus morphology for more than 30,000 breast cancer cells. We find that single cell-derived clones (SCCs) established from the same parental cells exhibit distinct and heritable morphological traits associated with genomic (ploidy) and transcriptomic phenotypes. Using unsupervised clustering analysis, we find that the morphological classes of SCCs predict distinct tumorigenic and metastatic potentials in vivo using multiple mouse models of breast cancer. These findings lay the groundwork for using quantitative morpho-profiling in vitro as a potentially convenient and economical method for phenotyping function in cancer in vivo.
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Affiliation(s)
- Pei-Hsun Wu
- Johns Hopkins Physical Sciences–Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniele M. Gilkes
- Johns Hopkins Physical Sciences–Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jude M. Phillip
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akshay Narkar
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Thomas Wen-Tao Cheng
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Division of Vascular and Endovascular Surgery, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jorge Marchand
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Meng-Horng Lee
- Johns Hopkins Physical Sciences–Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rong Li
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Mechanobiology Institute National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Denis Wirtz
- Johns Hopkins Physical Sciences–Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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16
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Tsai HJ, Nelliat A. A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation. Genes (Basel) 2019; 10:E787. [PMID: 31658789 PMCID: PMC6826469 DOI: 10.3390/genes10100787] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/28/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Aneuploidy, a deviation from a balanced genome by either gain or loss of chromosomes, is generally associated with impaired fitness and developmental defects in eukaryotic organisms. While the general physiological impact of aneuploidy remains largely elusive, many phenotypes associated with aneuploidy link to a common theme of stress adaptation. Here, we review previously identified mechanisms and observations related to aneuploidy, focusing on the highly diverse eukaryotes, fungi. Fungi, which have conquered virtually all environments, including several hostile ecological niches, exhibit widespread aneuploidy and employ it as an adaptive strategy under severe stress. Gambling with the balance between genome plasticity and stability has its cost and in fact, most aneuploidies have fitness defects. How can this fitness defect be reconciled with the prevalence of aneuploidy in fungi? It is likely that the fitness cost of the extra chromosomes is outweighed by the advantage they confer under life-threatening stresses. In fact, once the selective pressures are withdrawn, aneuploidy is often lost and replaced by less drastic mutations that possibly incur a lower fitness cost. We discuss representative examples across hostile environments, including medically and industrially relevant cases, to highlight potential adaptive mechanisms in aneuploid yeast.
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Affiliation(s)
- Hung-Ji Tsai
- Institute of Microbiology and Infection, and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Anjali Nelliat
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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17
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Taheri F, Goudarzi H, Faghihloo E. Aneuploidy and oncoviruses. Rev Med Virol 2019; 29:e2076. [PMID: 31407416 DOI: 10.1002/rmv.2076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/01/2023]
Abstract
Seven oncogenic viruses are known for tumorigenesis and contribute to 12% of all human cancers. The oncogenic factors, the target tissue, and pathology of cancer vary among these viruses with several mechanisms proposed for the initiation and development of cancer. Aneuploidy in cells is associated with anomalies in chromosome number that can be a hallmark of cancer, a disease defined by expanded proliferative potential. In this review, we summarize the different mechanisms of aneuploidy and furthermore discuss recent findings of the role of viral oncoproteins in inducing cellular aneuploidy that might facilitate tumorigenesis. Improved understanding of viral oncogenesis may help to find new strategies for controlling virus-associated cancers.
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Affiliation(s)
- Fateme Taheri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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18
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Natali F, Rancati G. The Mutator Phenotype: Adapting Microbial Evolution to Cancer Biology. Front Genet 2019; 10:713. [PMID: 31447882 PMCID: PMC6691094 DOI: 10.3389/fgene.2019.00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
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Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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19
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Tsai HJ, Nelliat AR, Choudhury MI, Kucharavy A, Bradford WD, Cook ME, Kim J, Mair DB, Sun SX, Schatz MC, Li R. Hypo-osmotic-like stress underlies general cellular defects of aneuploidy. Nature 2019; 570:117-121. [PMID: 31068692 PMCID: PMC6583789 DOI: 10.1038/s41586-019-1187-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/10/2019] [Indexed: 01/06/2023]
Abstract
Aneuploidy, which refers to unbalanced chromosome numbers, represents a class of genetic variation that is associated with cancer, birth defects and eukaryotic micro-organisms1-4. Whereas it is known that each aneuploid chromosome stoichiometry can give rise to a distinct pattern of gene expression and phenotypic profile4,5, it remains a fundamental question as to whether there are common cellular defects that are associated with aneuploidy. Here we show the existence in budding yeast of a common aneuploidy gene-expression signature that is suggestive of hypo-osmotic stress, using a strategy that enables the observation of common transcriptome changes of aneuploidy by averaging out karyotype-specific dosage effects in aneuploid yeast-cell populations with random and diverse chromosome stoichiometry. Consistently, aneuploid yeast exhibited increased plasma-membrane stress that led to impaired endocytosis, and this defect was also observed in aneuploid human cells. Thermodynamic modelling showed that hypo-osmotic-like stress is a general outcome of the proteome imbalance that is caused by aneuploidy, and also predicted a relationship between ploidy and cell size that was observed in yeast and aneuploid cancer cells. A genome-wide screen uncovered a general dependency of aneuploid cells on a pathway of ubiquitin-mediated endocytic recycling of nutrient transporters. Loss of this pathway, coupled with the endocytic defect inherent to aneuploidy, leads to a marked alteration of intracellular nutrient homeostasis.
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Affiliation(s)
- Hung-Ji Tsai
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anjali R Nelliat
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mohammad Ikbal Choudhury
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Andrei Kucharavy
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Malcolm E Cook
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jisoo Kim
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Devin B Mair
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sean X Sun
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
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20
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Beh TT, Kalitsis P. The Role of Centromere Defects in Cancer. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:541-554. [PMID: 28840252 DOI: 10.1007/978-3-319-58592-5_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The accurate segregation of chromosomes to daughter cells is essential for healthy development to occur. Imbalances in chromosome number have long been associated with cancers amongst other medical disorders. Little is known whether abnormal chromosome numbers are an early contributor to the cancer progression pathway. Centromere DNA and protein defects are known to impact on the fidelity of chromosome segregation in cell and model systems. In this chapter we discuss recent developments in understanding the contribution of centromere abnormalities at the protein and DNA level and their role in cancer in human and mouse systems.
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Affiliation(s)
- Thian Thian Beh
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Melbourne, 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, 3052, Australia
| | - Paul Kalitsis
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Melbourne, 3052, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, 3052, Australia.
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21
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Detecting Chromosome Instability in Cancer: Approaches to Resolve Cell-to-Cell Heterogeneity. Cancers (Basel) 2019; 11:cancers11020226. [PMID: 30781398 PMCID: PMC6406658 DOI: 10.3390/cancers11020226] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability (CIN) is defined as an increased rate of chromosome gains and losses that manifests as cell-to-cell karyotypic heterogeneity and drives cancer initiation and evolution. Current research efforts are aimed at identifying the etiological origins of CIN, establishing its roles in cancer pathogenesis, understanding its implications for patient prognosis, and developing novel therapeutics that are capable of exploiting CIN. Thus, the ability to accurately identify and evaluate CIN is critical within both research and clinical settings. Here, we provide an overview of quantitative single cell approaches that evaluate and resolve cell-to-cell heterogeneity and CIN, and discuss considerations when selecting the most appropriate approach to suit both research and clinical contexts.
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22
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Ryu HY, López-Giráldez F, Knight J, Hwang SS, Renner C, Kreft SG, Hochstrasser M. Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nat Commun 2018; 9:5417. [PMID: 30575729 PMCID: PMC6303320 DOI: 10.1038/s41467-018-07836-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
In response to acute loss of the Ulp2 SUMO-specific protease, yeast become disomic for chromosome I (ChrI) and ChrXII. Here we report that ChrI disomy, which creates an adaptive advantage in part by increasing the dosage of the Ccr4 deadenylase, was eliminated by extended passaging. Loss of aneuploidy is often accompanied by mutations in essential SUMO-ligating enzymes, which reduced polySUMO-conjugate accumulation. The mRNA levels for almost all ribosomal proteins increase transiently upon initial loss of Ulp2, but elevated Ccr4 levels limit excess ribosome formation. Notably, extended passaging leads to increased levels of many small nucleolar RNAs (snoRNAs) involved in ribosome biogenesis, and higher dosage of three linked ChrXII snoRNA genes suppressed ChrXII disomy in ulp2Δ cells. Our data reveal that aneuploidy allows rapid adaptation to Ulp2 loss, but long-term adaptation restores euploidy. Cellular evolution restores homeostasis through countervailing mutations in SUMO-modification pathways and regulatory shifts in ribosome biogenesis.
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Affiliation(s)
- Hong-Yeoul Ryu
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06520, USA
| | - Soo Seok Hwang
- Department of Immunobiology, Yale University, New Haven, CT, 06520, USA
| | - Christina Renner
- Department of Biology, Molecular Microbiology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
| | - Stefan G Kreft
- Department of Biology, Molecular Microbiology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA.
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23
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Fouché S, Plissonneau C, McDonald BA, Croll D. Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici. Genome Biol Evol 2018; 10:1416-1429. [PMID: 29850789 PMCID: PMC6007412 DOI: 10.1093/gbe/evy100] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Meiosis is one of the most conserved molecular processes in eukaryotes. The fidelity of pairing and segregation of homologous chromosomes has a major impact on the proper transmission of genetic information. Aberrant chromosomal transmission can have major phenotypic consequences, yet the mechanisms are poorly understood. Fungi are excellent models to investigate processes of chromosomal transmission, because many species have highly polymorphic genomes that include accessory chromosomes. Inheritance of accessory chromosomes is often unstable and chromosomal losses have little impact on fitness. We analyzed chromosomal inheritance in 477 progeny coming from two crosses of the fungal wheat pathogen Zymoseptoria tritici. For this, we developed a high-throughput screening method based on restriction site-associated DNA sequencing that generated dense coverage of genetic markers along each chromosome. We identified rare instances of chromosomal duplications (disomy) in core chromosomes. Accessory chromosomes showed high overall frequencies of disomy. Chromosomal rearrangements were found exclusively on accessory chromosomes and were more frequent than disomy. Accessory chromosomes present in only one of the parents in an analyzed cross were inherited at significantly higher rates than the expected 1:1 segregation ratio. Both the chromosome and the parental background had significant impacts on the rates of disomy, losses, rearrangements, and distorted inheritance. We found that chromosomes with higher sequence similarity and lower repeat content were inherited more faithfully. The large number of rearranged progeny chromosomes identified in this species will enable detailed analyses of the mechanisms underlying chromosomal rearrangement.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
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Cancer: a CINful evolution. Curr Opin Cell Biol 2018; 52:136-144. [DOI: 10.1016/j.ceb.2018.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/06/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
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de Francisco P, Martín-González A, Turkewitz AP, Gutiérrez JC. Genome plasticity in response to stress in Tetrahymena thermophila: selective and reversible chromosome amplification and paralogous expansion of metallothionein genes. Environ Microbiol 2018; 20:2410-2421. [PMID: 29687579 DOI: 10.1111/1462-2920.14251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022]
Abstract
Extreme stress situations can induce genetic variations including genome reorganization. In ciliates like Tetrahymena thermophila, the approximately 45-fold ploidy of the somatic macronucleus may enable adaptive responses that depend on genome plasticity. To identify potential genome-level adaptations related to metal toxicity, we isolated three Tetrahymena thermophila strains after an extended adaptation period to extreme metal concentrations (Cd2+ , Cu2+ or Pb2+ ). In the Cd-adapted strain, we found a approximately five-fold copy number increase of three genes located in the same macronuclear chromosome, including two metallothionein genes, MTT1 and MTT3. The apparent amplification of this macronuclear chromosome was reversible and reproducible, depending on the presence of environmental metal. We also analysed three knockout (KO) and/or knockdown (KD) strains for MTT1 and/or MTT5. In the MTT5KD strain, we found at least two new genes arising from paralogous expansion of MTT1, which encode truncated variants of MTT1. The expansion can be explained by a model based on somatic recombination between MTT1 genes on pairs of macronuclear chromosomes. At least two of the new paralogs are transcribed and upregulated in response to Cd2+ . Altogether, we have thus identified two distinct mechanisms, both involving genomic plasticity in the polyploid macronucleus that may represent adaptive responses to metal-related stress.
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Affiliation(s)
- Patricia de Francisco
- Departamento Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid (UCM). C/. Jose Antonio Nováis, 12. 28040 Madrid, Spain
| | - Ana Martín-González
- Departamento Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid (UCM). C/. Jose Antonio Nováis, 12. 28040 Madrid, Spain
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, Cummings Life Science Center, University of Chicago. 920 East 58th Street, Chicago, IL 60637, USA
| | - Juan Carlos Gutiérrez
- Departamento Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid (UCM). C/. Jose Antonio Nováis, 12. 28040 Madrid, Spain
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26
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Ye CJ, Regan S, Liu G, Alemara S, Heng HH. Understanding aneuploidy in cancer through the lens of system inheritance, fuzzy inheritance and emergence of new genome systems. Mol Cytogenet 2018; 11:31. [PMID: 29760781 PMCID: PMC5946397 DOI: 10.1186/s13039-018-0376-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In the past 15 years, impressive progress has been made to understand the molecular mechanism behind aneuploidy, largely due to the effort of using various -omics approaches to study model systems (e.g. yeast and mouse models) and patient samples, as well as the new realization that chromosome alteration-mediated genome instability plays the key role in cancer. As the molecular characterization of the causes and effects of aneuploidy progresses, the search for the general mechanism of how aneuploidy contributes to cancer becomes increasingly challenging: since aneuploidy can be linked to diverse molecular pathways (in regards to both cause and effect), the chances of it being cancerous is highly context-dependent, making it more difficult to study than individual molecular mechanisms. When so many genomic and environmental factors can be linked to aneuploidy, and most of them not commonly shared among patients, the practical value of characterizing additional genetic/epigenetic factors contributing to aneuploidy decreases. RESULTS Based on the fact that cancer typically represents a complex adaptive system, where there is no linear relationship between lower-level agents (such as each individual gene mutation) and emergent properties (such as cancer phenotypes), we call for a new strategy based on the evolutionary mechanism of aneuploidy in cancer, rather than continuous analysis of various individual molecular mechanisms. To illustrate our viewpoint, we have briefly reviewed both the progress and challenges in this field, suggesting the incorporation of an evolutionary-based mechanism to unify diverse molecular mechanisms. To further clarify this rationale, we will discuss some key concepts of the genome theory of cancer evolution, including system inheritance, fuzzy inheritance, and cancer as a newly emergent cellular system. CONCLUSION Illustrating how aneuploidy impacts system inheritance, fuzzy inheritance and the emergence of new systems is of great importance. Such synthesis encourages efforts to apply the principles/approaches of complex adaptive systems to ultimately understand aneuploidy in cancer.
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Affiliation(s)
- Christine J. Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Sarah Regan
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Sarah Alemara
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Henry H. Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201 USA
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27
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Libouban MAA, de Roos JADM, Uitdehaag JCM, Willemsen-Seegers N, Mainardi S, Dylus J, de Man J, Tops B, Meijerink JPP, Storchová Z, Buijsman RC, Medema RH, Zaman GJR. Stable aneuploid tumors cells are more sensitive to TTK inhibition than chromosomally unstable cell lines. Oncotarget 2018; 8:38309-38325. [PMID: 28415765 PMCID: PMC5503534 DOI: 10.18632/oncotarget.16213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/03/2017] [Indexed: 01/26/2023] Open
Abstract
Inhibition of the spindle assembly checkpoint kinase TTK causes chromosome mis-segregation and tumor cell death. However, high levels of TTK correlate with chromosomal instability (CIN), which can lead to aneuploidy. We show that treatment of tumor cells with the selective small molecule TTK inhibitor NTRC 0066-0 overrides the mitotic checkpoint, irrespective of cell line sensitivity. In stable aneuploid cells NTRC 0066-0 induced acute CIN, whereas in cells with high levels of pre-existing CIN there was only a small additional fraction of cells mis-segregating their chromosomes. In proliferation assays stable aneuploid cells were more sensitive than cell lines with pre-existing CIN. Tetraploids are thought to be an intermediate between diploid and unstable aneuploid cells. TTK inhibitors had the same potency on post-tetraploid and parental diploid cells, which is remarkable because the post-tetraploids are more resistant to mitotic drugs. Finally, we confirm that the reference compound reversine is a TTK inhibitor and like NTRC 0066-0, inhibits the proliferation of patient-derived colorectal cancer organoids. In contrast, treatment with TTK inhibitor did not reduce the viability of non-proliferating T cell acute lymphoblastic leukemia cells samples. Consequently, TTK inhibitor therapy is expected to spare non-dividing cells, and may be used to target stable aneuploid tumors.
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Affiliation(s)
- Marion A A Libouban
- Netherlands Translational Research Center B.V., Oss, The Netherlands.,Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Sara Mainardi
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Dylus
- Netherlands Translational Research Center B.V., Oss, The Netherlands
| | - Jos de Man
- Netherlands Translational Research Center B.V., Oss, The Netherlands
| | - Bastiaan Tops
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Rogier C Buijsman
- Netherlands Translational Research Center B.V., Oss, The Netherlands
| | - René H Medema
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido J R Zaman
- Netherlands Translational Research Center B.V., Oss, The Netherlands
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28
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Koo DH, Jugulam M, Putta K, Cuvaca IB, Peterson DE, Currie RS, Friebe B, Gill BS. Gene Duplication and Aneuploidy Trigger Rapid Evolution of Herbicide Resistance in Common Waterhemp. PLANT PHYSIOLOGY 2018; 176:1932-1938. [PMID: 29295942 PMCID: PMC5841708 DOI: 10.1104/pp.17.01668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/27/2017] [Indexed: 05/25/2023]
Abstract
An increase in gene copy number is often associated with changes in the number and structure of chromosomes, as has been widely observed in yeast and eukaryotic tumors, yet little is known about stress-induced chromosomal changes in plants. Previously, we reported that the EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene, the molecular target of glyphosate, was amplified at the native locus and on an extra chromosome in glyphosate-resistant Amaranthus tuberculatus Here, we report that the extra chromosome is a ring chromosome termed extra circular chromosome carrying amplified EPSPS (ECCAE). The ECCAE is heterochromatic, harbors four major EPSPS amplified foci, and is sexually transmitted to 35% of the progeny. Two highly glyphosate resistant (HGR) A. tuberculatus plants with a chromosome constitution of 2n = 32+1 ECCAE displayed soma cell heterogeneity. Some cells had secondary ECCAEs, which displayed size polymorphisms and produced novel chromosomal variants with multiple gene amplification foci. We hypothesize that the ECCAE in the soma cells of HGR A. tuberculatus plants underwent breakage-fusion-bridge cycles to generate the observed soma cell heterogeneity, including de novo EPSPS gene integration into chromosomes. Resistant soma cells with stable EPSPS amplification events as de novo insertions into chromosomes may survive glyphosate selection pressure during the sporophytic phase and are plausibly transmitted to germ cells leading to durable glyphosate resistance in A. tuberculatus This is the first report of early events in aneuploidy-triggered de novo chromosome integration by an as yet unknown mechanism, which may drive rapid adaptive evolution of herbicide resistance in common waterhemp.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Mithila Jugulam
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Karthik Putta
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Ivan B Cuvaca
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Dallas E Peterson
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kansas 66506
| | - Randall S Currie
- Southwest Research and Extension Center, Garden City, Kansas State University, Manhattan, Kansas 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
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29
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Vargas-Rondón N, Villegas VE, Rondón-Lagos M. The Role of Chromosomal Instability in Cancer and Therapeutic Responses. Cancers (Basel) 2017; 10:cancers10010004. [PMID: 29283387 PMCID: PMC5789354 DOI: 10.3390/cancers10010004] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/22/2017] [Accepted: 12/25/2017] [Indexed: 12/31/2022] Open
Abstract
Cancer is one of the leading causes of death, and despite increased research in recent years, control of advanced-stage disease and optimal therapeutic responses remain elusive. Recent technological improvements have increased our understanding of human cancer as a heterogeneous disease. For instance, four hallmarks of cancer have recently been included, which in addition to being involved in cancer development, could be involved in therapeutic responses and resistance. One of these hallmarks is chromosome instability (CIN), a source of genetic variation in either altered chromosome number or structure. CIN has become a hot topic in recent years, not only for its implications in cancer diagnostics and prognostics, but also for its role in therapeutic responses. Chromosomal alterations are mainly used to determine genetic heterogeneity in tumors, but CIN could also reveal treatment efficacy, as many therapies are based on increasing CIN, which causes aberrant cells to undergo apoptosis. However, it should be noted that contradictory findings on the implications of CIN for the therapeutic response have been reported, with some studies associating high CIN with a better therapeutic response and others associating it with therapeutic resistance. Considering these observations, it is necessary to increase our understanding of the role CIN plays not only in tumor development, but also in therapeutic responses. This review focuses on recent studies that suggest possible mechanisms and consequences of CIN in different disease types, with a primary focus on cancer outcomes and therapeutic responses.
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Affiliation(s)
- Natalia Vargas-Rondón
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia.
| | - Victoria E Villegas
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá 111221, Colombia.
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia.
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30
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Wu P, Li T, Li R, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y, Li C. 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. Nat Commun 2017; 8:1937. [PMID: 29203764 PMCID: PMC5715138 DOI: 10.1038/s41467-017-01793-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 10/17/2017] [Indexed: 01/06/2023] Open
Abstract
The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the numbers of TADs increases by 25% in MM, the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid MM cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation. Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy number variations and changes in gene expression.
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Affiliation(s)
- Pengze Wu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lumeng Jia
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ping Zhu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yifang Liu
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qing Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Daiwei Tang
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuezhou Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China. .,Center for Statistical Science, Peking University, Beijing, 100871, China.
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31
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Wertheimer NB, Stone N, Berman J. Ploidy dynamics and evolvability in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0461. [PMID: 28080987 PMCID: PMC5095540 DOI: 10.1098/rstb.2015.0461] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Noa Blutraich Wertheimer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
| | - Neil Stone
- Institute of Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
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32
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Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin JC, Notredame C, Späth GF. Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani. Nat Ecol Evol 2017; 1:1961-1969. [DOI: 10.1038/s41559-017-0361-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/26/2017] [Indexed: 11/09/2022]
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Mating of natural Saccharomyces cerevisiae strains for improved glucose fermentation and lignocellulosic inhibitor tolerance. Folia Microbiol (Praha) 2017; 63:155-168. [PMID: 28887734 DOI: 10.1007/s12223-017-0546-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Natural Saccharomyces cerevisiae isolates from vineyards in the Western Cape, South Africa were evaluated for ethanol production in industrial conditions associated with the production of second-generation biofuels. The strains displayed high phenotypic diversity including the ability to grow at 45 °C and in the presence of 20% (v/v) ethanol, strain YI13. Strains HR4 and YI30 were inhibitor-tolerant under aerobic and oxygen-limited conditions, respectively. Spore-to-spore hybridization generated progeny that displayed heterosis, including increased ethanol productivity and improved growth in the presence of a synthetic inhibitor cocktail. Hybrid strains HR4/YI30#6 and V3/YI30#6 were able to grow at a high salt concentration (2 mol/L NaCl) with V3/YI30#6 also able to grow at a high temperature (45 °C). Strains HR4/YI30#1 and #3 were inhibitor-tolerant, with strain HR4/YI30#3 having similar productivity (0.36 ± 0.0036 g/L per h) as the superior parental strain, YI30 (0.35 ± 0.0058 g/L per h). This study indicates that natural S. cerevisiae strains display phenotypic variation and heterosis can be achieved through spore-to-spore hybridization. Several of the phenotypes (temperature-, osmo-, and inhibitor tolerance) displayed by both the natural strains and the generated progeny were at the maximum conditions reported for S. cerevisiae strains.
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34
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Zhu XF, Yi M, He J, Tang W, Lu MY, Li T, Feng ZB. Pathological significance of MAD2L1 in breast cancer: an immunohistochemical study and meta analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:9190-9201. [PMID: 31966791 PMCID: PMC6965997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/09/2017] [Indexed: 06/10/2023]
Abstract
The aberrant expression of mitotic arrest deficient 2-like 1 (MAD2L1) has been found to promote tumor formation by inducing chromosomal instability and aneuploidy in cells. In breast cancer (BRCA), limited studies have been focused on MAD2L1 expression and its impact on tumor progression. Thus, we conducted this study to comprehensively analyze MAD2L1 expression and its clinicopathological significance as well as diagnostic value for BRCA. Immunohistochemistry was performed with the 209 invasive ductal BRCA samples and the corresponding adjacent tissues to investigate MAD2L1 expression in BRCA and its relationship between clinicopathological features of BRCA. Then, the clinicopathological role of MAD2L1 was confirmed by RNA-sequencing or microarray data from the Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO). Particularly, summarized receiver operating characteristic (SROC) curve was plotted to explore the diagnostic capacity of MAD2L1 in BRCA. The results showed that MAD2L1 presented overexpression in BRCA and was significantly associated with higher clinical stage and histological grade of BRCA. A significant correlation was also found between MAD2L1 expression and several tumor indicators including ER, P53, HER-2 and Ki-67. Moreover, area under curve (AUC) value (0.9642) from SROC revealed potential diagnostic value of MAD2L1 for BRCA. In summary, MAD2L1 may be involved in the occurrence and development of BRCA and MAD2L1 detection could improve the diagnosis and prognostic evaluation of BRCA.
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Affiliation(s)
- Xiao-Fei Zhu
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Min Yi
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Juan He
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Wei Tang
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Mei-Ying Lu
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Ting Li
- Department of Pathology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Worker’s HospitalLiuzhou, Guangxi Zhuang Autonomous Region, China
| | - Zhen-Bo Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi Zhuang Autonomous Region, China
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35
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Borg NA, Dixit VM. Ubiquitin in Cell-Cycle Regulation and Dysregulation in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2017. [DOI: 10.1146/annurev-cancerbio-040716-075607] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uncontrolled cell proliferation and genomic instability are common features of cancer and can arise from, respectively, the loss of cell-cycle control and defective checkpoints. Ubiquitin-mediated proteolysis, ultimately executed by ubiquitin-ligating enzymes (E3s), plays a key part in cell-cycle regulation and is dominated by two multisubunit E3s, the anaphase-promoting complex (or cyclosome) (APC/C) and SKP1–cullin-1–F-box (SCF) complex. We highlight the role of APC/C and the SCF bound to F-box proteins, FBXW7, SKP2, and β-TrCP, in regulating the abundance of select fundamental proteins, primarily during the cell cycle, that are associated with human cancer. The clinical success of the first proteasome inhibitor, bortezomib, in treating multiple myeloma and mantle-cell lymphoma set the precedent for viewing the ubiquitin–proteasome system as a druggable target for cancer. Given that there are more E3s than kinases, selective, small-molecule E3 inhibitors have the potential of opening up another dimension in the therapeutic armamentarium for the treatment of cancer.
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Affiliation(s)
- Natalie A. Borg
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Vishva M. Dixit
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, California 94080
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Potapova T, Gorbsky GJ. The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis. BIOLOGY 2017; 6:biology6010012. [PMID: 28208750 PMCID: PMC5372005 DOI: 10.3390/biology6010012] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 12/21/2022]
Abstract
Mistakes during cell division frequently generate changes in chromosome content, producing aneuploid or polyploid progeny cells. Polyploid cells may then undergo abnormal division to generate aneuploid cells. Chromosome segregation errors may also involve fragments of whole chromosomes. A major consequence of segregation defects is change in the relative dosage of products from genes located on the missegregated chromosomes. Abnormal expression of transcriptional regulators can also impact genes on the properly segregated chromosomes. The consequences of these perturbations in gene expression depend on the specific chromosomes affected and on the interplay of the aneuploid phenotype with the environment. Most often, these novel chromosome distributions are detrimental to the health and survival of the organism. However, in a changed environment, alterations in gene copy number may generate a more highly adapted phenotype. Chromosome segregation errors also have important implications in human health. They may promote drug resistance in pathogenic microorganisms. In cancer cells, they are a source for genetic and phenotypic variability that may select for populations with increased malignance and resistance to therapy. Lastly, chromosome segregation errors during gamete formation in meiosis are a primary cause of human birth defects and infertility. This review describes the consequences of mitotic and meiotic errors focusing on novel concepts and human health.
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Affiliation(s)
- Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Ryu HY, Wilson NR, Mehta S, Hwang SS, Hochstrasser M. Loss of the SUMO protease Ulp2 triggers a specific multichromosome aneuploidy. Genes Dev 2016; 30:1881-94. [PMID: 27585592 PMCID: PMC5024685 DOI: 10.1101/gad.282194.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/02/2016] [Indexed: 01/15/2023]
Abstract
The SUMO protease Ulp2 modulates many of the SUMO-dependent processes in budding yeast. Ryu et al. discovered that cells lacking Ulp2 display a twofold increase in transcript levels across two particular chromosomes: chromosome I (ChrI) and ChrXII. Extra copies of ChrI and ChrXII can be eliminated following reintroduction of ULP2, suggesting that aneuploidy is a reversible adaptive mechanism to counteract loss of the SUMO protease. Post-translational protein modification by the small ubiquitin-related modifier (SUMO) regulates numerous cellular pathways, including transcription, cell division, and genome maintenance. The SUMO protease Ulp2 modulates many of these SUMO-dependent processes in budding yeast. From whole-genome RNA sequencing (RNA-seq), we unexpectedly discovered that cells lacking Ulp2 display a twofold increase in transcript levels across two particular chromosomes: chromosome I (ChrI) and ChrXII. This is due to the two chromosomes being present at twice their normal copy number. An abnormal number of chromosomes, termed aneuploidy, is usually deleterious. However, development of specific aneuploidies allows rapid adaptation to cellular stresses, and aneuploidy characterizes most human tumors. Extra copies of ChrI and ChrXII appear quickly following loss of active Ulp2 and can be eliminated following reintroduction of ULP2, suggesting that aneuploidy is a reversible adaptive mechanism to counteract loss of the SUMO protease. Importantly, increased dosage of two genes on ChrI—CLN3 and CCR4, encoding a G1-phase cyclin and a subunit of the Ccr4–Not deadenylase complex, respectively—suppresses ulp2Δ aneuploidy, suggesting that increased levels of these genes underlie the aneuploidy induced by Ulp2 loss. Our results reveal a complex aneuploidy mechanism that adapts cells to loss of the SUMO protease Ulp2.
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Affiliation(s)
- Hong-Yeoul Ryu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Nicole R Wilson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Sameet Mehta
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut 06520, USA
| | - Soo Seok Hwang
- Department of Immunobiology, Yale University, New Haven, Connecticut 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Borges A, Adega F, Chaves R. Establishment and characterization of a new feline mammary cancer cell line, FkMTp. Cytotechnology 2016; 68:1529-43. [PMID: 26883919 DOI: 10.1007/s10616-015-9912-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022] Open
Abstract
Studies on tumours in domestic animals are believed to greatly contribute to a better understanding of similar diseases in humans. Comparative studies have shown that feline mammary carcinomas share important features with human breast cancers, including a similar biological behaviour and histological appearance. In the present study we have established and characterized at different cellular levels one feline mammary cancer cell line, FkMTp, derived from a cat mammary carcinoma. The FkMTp cell line revealed to be a promising resource and tool to study tumour microevolution and all the mechanisms and processes involved in carcinogenesis from the tumour (primary culture) to the immortalized cell line. Several assays were conducted to assess the growth behaviour, differentiated morphology, anchorage independent growth in soft agar, wound-healing invasion and migration of the cell line across time (from the primary culture until the 160th passage). FkMTp revealed increased levels of anchorage independence, migration and invasion according to the course of time as well as different numbers of ploidy. These results demonstrate and validate the in vitro tumorigenicity of the FkMTp cell line. During the cell line establishment, it was cryopreserved approximately every six passages, including the tumour primary culture, allowing now the possibility to access almost any specific momento of the tumour progression.
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Affiliation(s)
- Ana Borges
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), Universityof Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), Universityof Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), Universityof Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
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Vicedo E, Gasik Z, Dong YA, Goldberg T, Rost B. Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. F1000Res 2015; 4:1222. [PMID: 26673203 PMCID: PMC4670006 DOI: 10.12688/f1000research.7178.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Recent experiments established that a culture of
Saccharomyces cerevisiae (baker’s yeast) survives sudden high temperatures by specifically duplicating the entire chromosome III and two chromosomal fragments (from IV and XII). Heat shock proteins (HSPs) are not significantly over-abundant in the duplication. In contrast, we suggest a simple algorithm to “
postdict” the experimental results: Find a small enough chromosome with minimal protein disorder and duplicate this region. This algorithm largely explains all observed duplications. In particular, all regions duplicated in the experiment reduced the overall content of protein disorder. The differential analysis of the functional makeup of the duplication remained inconclusive. Gene Ontology (GO) enrichment suggested over-representation in processes related to reproduction and nutrient uptake. Analyzing the protein-protein interaction network (PPI) revealed that few network-central proteins were duplicated. The predictive hypothesis hinges upon the concept of reducing proteins with long regions of disorder in order to become less sensitive to heat shock attack.
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Affiliation(s)
- Esmeralda Vicedo
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Experimental Physics, Division of Biophysics, University of Warsaw, Warsaw, Poland
| | - Zofia Gasik
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Graduate School of Information Science in Health, TUM, Munich, Germany
| | - Yu-An Dong
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Systems Biology, Shanghai University, Shanghai, China
| | - Tatyana Goldberg
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Advanced Study, TUM, Munich, Germany ; Institute for Food and Plant Sciences WZW, TUM, Freising, Germany
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Liu G, Yong MYJ, Yurieva M, Srinivasan KG, Liu J, Lim JSY, Poidinger M, Wright GD, Zolezzi F, Choi H, Pavelka N, Rancati G. Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability. Cell 2015; 163:1388-99. [PMID: 26627736 DOI: 10.1016/j.cell.2015.10.069] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 08/01/2015] [Accepted: 10/20/2015] [Indexed: 11/24/2022]
Abstract
Gene essentiality is typically determined by assessing the viability of the corresponding mutant cells, but this definition fails to account for the ability of cells to adaptively evolve to genetic perturbations. Here, we performed a stringent screen to assess the degree to which Saccharomyces cerevisiae cells can survive the deletion of ~1,000 individual "essential" genes and found that ~9% of these genetic perturbations could in fact be overcome by adaptive evolution. Our analyses uncovered a genome-wide gradient of gene essentiality, with certain essential cellular functions being more "evolvable" than others. Ploidy changes were prevalent among the evolved mutant strains, and aneuploidy of a specific chromosome was adaptive for a class of evolvable nucleoporin mutants. These data justify a quantitative redefinition of gene essentiality that incorporates both viability and evolvability of the corresponding mutant cells and will enable selection of therapeutic targets associated with lower risk of emergence of drug resistance.
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Affiliation(s)
- Gaowen Liu
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Mei Yun Jacy Yong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Marina Yurieva
- Singapore Immunology Network (SIgN), A(∗)STAR, Singapore 138648, Singapore
| | | | - Jaron Liu
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - John Soon Yew Lim
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A(∗)STAR, Singapore 138648, Singapore
| | - Graham Daniel Wright
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), A(∗)STAR, Singapore 138648, Singapore
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore (NUS) and National University Health System, Singapore 117549, Singapore
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), A(∗)STAR, Singapore 138648, Singapore.
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, Van Pee M, van der Zande E, Meert W, Yang Y, Zhu B, Marchal K, DeLuna A, Van Noort V, Jelier R, Verstrepen KJ. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PLoS Genet 2015; 11:e1005635. [PMID: 26545090 PMCID: PMC4636377 DOI: 10.1371/journal.pgen.1005635] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/08/2015] [Indexed: 11/19/2022] Open
Abstract
Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. Organisms can evolve resistance to specific stress factors, which allows them to thrive in environments where non-adapted organisms fail to grow. However, the molecular mechanisms that underlie adaptation to complex stress factors that interfere with basic cellular processes are poorly understood. In this study, we reveal how yeast populations adapt to high ethanol concentrations, an ecologically and industrially relevant stress that is still poorly understood. We exposed six independent populations of genetically identical yeast cells to gradually increasing ethanol levels, and we monitored the changes in their DNA sequence over a two-year period. Together with novel computational analyses, we could identify the mutational dynamics and molecular mechanisms underlying increased ethanol resistance. Our results show how adaptation to high ethanol is complex and can be reached through different mutational pathways. Together, our study offers a detailed picture of how populations adapt to a complex continuous stress and identifies several mutations that increase ethanol resistance, which opens new routes to obtain superior biofuel yeast strains.
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Affiliation(s)
- Karin Voordeckers
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Jacek Kominek
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Anupam Das
- CMPG Laboratory of Predictive Genetics and Multicellular Systems, KU Leuven, Leuven, Belgium
| | - Adriana Espinosa-Cantú
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Dries De Maeyer
- CMPG Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Information Technology (INTEC, iMINDS), University of Ghent, Ghent, Belgium
| | - Ahmed Arslan
- CMPG Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | - Michiel Van Pee
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Elisa van der Zande
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Wim Meert
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Yudi Yang
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Bo Zhu
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- CMPG Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Information Technology (INTEC, iMINDS), University of Ghent, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, University of Ghent, Ghent, Belgium
| | - Alexander DeLuna
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Vera Van Noort
- CMPG Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | - Rob Jelier
- CMPG Laboratory of Predictive Genetics and Multicellular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J. Verstrepen
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
- * E-mail:
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Abstract
Adaptation is the process in which organisms improve their fitness by changing their phenotype using genetic or non-genetic mechanisms. The adaptation toolbox consists of varied molecular and genetic means that we posit span an almost continuous "adaptation spectrum." Different adaptations are characterized by the time needed for organisms to attain them and by their duration. We suggest that organisms often adapt by progressing the adaptation spectrum, starting with rapidly attained physiological and epigenetic adaptations and culminating with slower long-lasting genetic ones. A tantalizing possibility is that earlier adaptations facilitate realization of later ones.
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43
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Abstract
UNLABELLED Cryptococcus neoformans is a major life-threatening fungal pathogen. In response to the stress of the host environment, C. neoformans produces large polyploid titan cells. Titan cell production enhances the virulence of C. neoformans, yet whether the polyploid aspect of titan cells is specifically influential remains unknown. We show that titan cells were more likely to survive and produce offspring under multiple stress conditions than typical cells and that even their normally sized daughters maintained an advantage over typical cells in continued exposure to stress. Although polyploid titan cells generated haploid daughter cell progeny upon in vitro replication under nutrient-replete conditions, titan cells treated with the antifungal drug fluconazole produced fluconazole-resistant diploid and aneuploid daughter cells. Interestingly, a single titan mother cell was capable of generating multiple types of aneuploid daughter cells. The increased survival and genomic diversity of titan cell progeny promote rapid adaptation to new or high-stress conditions. IMPORTANCE The ability to adapt to stress is a key element for survival of pathogenic microbes in the host and thus plays an important role in pathogenesis. Here we investigated the predominantly haploid human fungal pathogen Cryptococcus neoformans, which is capable of ploidy and cell size increases during infection through production of titan cells. The enlarged polyploid titan cells are then able to rapidly undergo ploidy reduction to generate progeny with reduced ploidy and/or aneuploidy. Under stressful conditions, titan cell progeny have a growth and survival advantage over typical cell progeny. Understanding how titan cells enhance the rate of cryptococcal adaptation under stress conditions may assist in the development of novel drugs aimed at blocking ploidy transitions.
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Natesuntorn W, Iwami K, Matsubara Y, Sasano Y, Sugiyama M, Kaneko Y, Harashima S. Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae. Sci Rep 2015. [PMID: 26224198 PMCID: PMC4519793 DOI: 10.1038/srep12510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Segmental aneuploidy can play an important role in environmental adaptation. However, study of segmental aneuploids is severely hampered by the difficulty of creating them in a designed fashion. Here, we describe a PCR-mediated chromosome duplication (PCDup) technology that enables the generation of segmental aneuploidy at any desired chromosomal region in Saccharomyces cerevisiae. We constructed multiple strains harboring 100 kb to 200 kb segmental duplications covering the whole of the S. cerevisiae genome. Interestingly, some segmental aneuploidies confer stress tolerance, such as to high temperature, ethanol and strong acids, while others induce cell lethality and stress sensitivity, presumably as result of the simultaneous increases in dosages of multiple genes. We suggest that our PCDup technology will accelerate studies into the phenotypic changes resulting from alteration of gene dosage balance of multiple genes and will provide new insights into the adaptive molecular mechanisms in the genome in segmental aneuploidy-derived human diseases.
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Affiliation(s)
- Waranya Natesuntorn
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kotaro Iwami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Matsubara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshinobu Kaneko
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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45
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Abstract
Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution.
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46
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Jamal-Hanjani M, A'Hern R, Birkbak NJ, Gorman P, Grönroos E, Ngang S, Nicola P, Rahman L, Thanopoulou E, Kelly G, Ellis P, Barrett-Lee P, Johnston SRD, Bliss J, Roylance R, Swanton C. Extreme chromosomal instability forecasts improved outcome in ER-negative breast cancer: a prospective validation cohort study from the TACT trial. Ann Oncol 2015; 26:1340-6. [PMID: 26003169 DOI: 10.1093/annonc/mdv178] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/28/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chromosomal instability (CIN) has been shown to be associated with drug resistance and poor clinical outcome in several cancer types. However, in oestrogen receptor (ER)-negative breast cancer we have previously demonstrated that extreme CIN is associated with improved clinical outcome, consistent with a negative impact of CIN on tumour fitness and growth. The aim of this current study was to validate this finding using previously defined CIN thresholds in a much larger prospective cohort from a randomised, controlled, clinical trial. PATIENTS AND METHODS As a surrogate measurement of CIN, dual centromeric fluorescence in situ hybridisation was performed for both chromosomes 2 and 15 on 1173 tumours from the breast cancer TACT trial (CRUK01/001). Each tumour was scored manually and the mean percentage of cells deviating from the modal centromere number was used to define four CIN groups (MCD1-4), where tumours in the MCD4 group were defined as having extreme CIN. RESULTS In a multivariate analysis of disease-free survival, with a median follow-up of 91 months, increasing CIN was associated with improved outcome in patients with ER-negative cancer (P trend = 0.03). A similar pattern was seen in ER-negative/HER2-negative cancers (Ptrend = 0.007). CONCLUSIONS This prospective validation cohort study further substantiated the association between extreme CIN and improved outcome in ER-negative breast cancers. Identifying such patients with extreme CIN may help distinguish good from poor prognostic groups, and therefore support treatment and risk stratification in this aggressive breast cancer subtype.
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Affiliation(s)
- M Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - R A'Hern
- ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London
| | - N J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - P Gorman
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - E Grönroos
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - S Ngang
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - P Nicola
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - L Rahman
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London
| | - E Thanopoulou
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - G Kelly
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London
| | - P Ellis
- Guy's and St Thomas' NHS Trust, London
| | | | | | - J Bliss
- ICR-CTSU, Division of Clinical Studies, The Institute of Cancer Research, London
| | - R Roylance
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - C Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London The Francis Crick Institute, 44 Lincoln's Inn Fields, London
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47
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Giam M, Rancati G. Aneuploidy and chromosomal instability in cancer: a jackpot to chaos. Cell Div 2015; 10:3. [PMID: 26015801 PMCID: PMC4443636 DOI: 10.1186/s13008-015-0009-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic instability (GIN) is a hallmark of cancer cells that facilitates the acquisition of mutations conferring aggressive or drug-resistant phenotypes during cancer evolution. Chromosomal instability (CIN) is a form of GIN that involves frequent cytogenetic changes leading to changes in chromosome copy number (aneuploidy). While both CIN and aneuploidy are common characteristics of cancer cells, their roles in tumor initiation and progression are unclear. On the one hand, CIN and aneuploidy are known to provide genetic variation to allow cells to adapt in changing environments such as nutrient fluctuations and hypoxia. Patients with constitutive aneuploidies are more susceptible to certain types of cancers, suggesting that changes in chromosome copy number could positively contribute to cancer evolution. On the other hand, chromosomal imbalances have been observed to have detrimental effects on cellular fitness and might trigger cell cycle arrest or apoptosis. Furthermore, mouse models for CIN have led to conflicting results. Taken together these findings suggest that the relationship between CIN, aneuploidy and cancer is more complex than what was previously anticipated. Here we review what is known about this complex ménage à trois, discuss recent evidence suggesting that aneuploidy, CIN and GIN together promote a vicious cycle of genome chaos. Lastly, we propose a working hypothesis to reconcile the conflicting observations regarding the role of aneuploidy and CIN in tumorigenesis.
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Affiliation(s)
- Maybelline Giam
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore
| | - Giulia Rancati
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore ; School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, 117597 Singapore
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Nicholson JM, Macedo JC, Mattingly AJ, Wangsa D, Camps J, Lima V, Gomes AM, Dória S, Ried T, Logarinho E, Cimini D. Chromosome mis-segregation and cytokinesis failure in trisomic human cells. eLife 2015; 4. [PMID: 25942454 PMCID: PMC4443816 DOI: 10.7554/elife.05068] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/01/2015] [Indexed: 12/11/2022] Open
Abstract
Cancer cells display aneuploid karyotypes and typically mis-segregate chromosomes at high rates, a phenotype referred to as chromosomal instability (CIN). To test the effects of aneuploidy on chromosome segregation and other mitotic phenotypes we used the colorectal cancer cell line DLD1 (2n = 46) and two variants with trisomy 7 or 13 (DLD1+7 and DLD1+13), as well as euploid and trisomy 13 amniocytes (AF and AF+13). We found that trisomic cells displayed higher rates of chromosome mis-segregation compared to their euploid counterparts. Furthermore, cells with trisomy 13 displayed a distinctive cytokinesis failure phenotype. We showed that up-regulation of SPG20 expression, brought about by trisomy 13 in DLD1+13 and AF+13 cells, is sufficient for the cytokinesis failure phenotype. Overall, our study shows that aneuploidy can induce chromosome mis-segregation. Moreover, we identified a trisomy 13-specific mitotic phenotype that is driven by up-regulation of a gene encoded on the aneuploid chromosome. DOI:http://dx.doi.org/10.7554/eLife.05068.001 The DNA in a human cell is divided between forty-six structures called chromosomes. Before a cell divides, it copies every chromosome so that each daughter cell will have the same DNA as the parent cell. These chromosomes align in the center of the cell and then the matching chromosomes are separated and pulled to opposite ends. However, in some cases the separation process does not work properly, which can produce cells that either have too many, or too few, chromosomes. Abnormal numbers of chromosomes within cells—called aneuploidy—is a leading cause of miscarriage and birth defects in humans. Aneuploidy is also a common feature of cancer cells. It is common for the chromosomes in cancer cells to be distributed unequally when the cell divides. This phenomenon is known as chromosomal instability, but the link between aneuploidy and chromosomal instability in cancer cells is not fully understood. Here, Nicholson et al. used live-cell imaging techniques to analyze healthy human cells and cancer cells that had either the normal forty-six chromosomes, or a defined extra chromosome. Nicholson et al. found that when the cells divided, the chromosomes in the cells that had an extra copy of chromosome 7 or 13 were more prone to distributing chromosomes unequally, compared to cells with a normal number of chromosomes. Nicholson et al. also observed that the cells with an extra chromosome 13 were unable to properly divide into two. These cells had increased levels of a protein called Spartin—which is important for the last stage in cell division—and this was responsible for the failure to produce two daughter cells. These findings show that aneuploidy can cause chromosomal instability in human cells. Furthermore, Nicholson et al. have identified a defect in cell division that is specifically caused by the presence of an extra chromosome 13 in human cells. A future challenge will be to determine how, and to what extent, different chromosomes can affect chromosome stability. This could be useful in the development of therapies against cancer cells with aneuploidy. DOI:http://dx.doi.org/10.7554/eLife.05068.002
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Affiliation(s)
- Joshua M Nicholson
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
| | - Joana C Macedo
- Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Aaron J Mattingly
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Jordi Camps
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Vera Lima
- Department of Genetics, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Ana M Gomes
- Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Sofia Dória
- Department of Genetics, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Elsa Logarinho
- Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Daniela Cimini
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
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Sunshine AB, Payen C, Ong GT, Liachko I, Tan KM, Dunham MJ. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol 2015; 13:e1002155. [PMID: 26011532 PMCID: PMC4444335 DOI: 10.1371/journal.pbio.1002155] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/15/2015] [Indexed: 11/30/2022] Open
Abstract
Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell's proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp's fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations.
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Affiliation(s)
- Anna B. Sunshine
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Giang T. Ong
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kean Ming Tan
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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50
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Nicholson JM, Cimini D. Link between aneuploidy and chromosome instability. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:299-317. [PMID: 25708466 DOI: 10.1016/bs.ircmb.2014.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aneuploidy is widely acknowledged as a leading cause of miscarriage and birth defects in humans, and is generally known to be deleterious to the survival of individual cells. However, aneuploidy is also ubiquitous in cancer and is found to arise as an adaptive response in certain contexts. This dichotomy of aneuploidy has attracted the interest of researchers for over a century, but many studies have reached conflicting conclusions. The emergence of new technology has allowed scientists to revisit the aneuploidy problem and has fueled a number of recent studies aimed at understanding the effects of aneuploidy on cell physiology. Here, we review these studies, in light of previous observations and knowledge, specifically focusing on the effects of aneuploidy on cellular homeostasis, chromosome stability, and adaptation.
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Affiliation(s)
- Joshua M Nicholson
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Daniela Cimini
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
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