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Kohanovski I, Pontz M, Vande Zande P, Selmecki A, Dahan O, Pilpel Y, Yona AH, Ram Y. Aneuploidy Can Be an Evolutionary Diversion on the Path to Adaptation. Mol Biol Evol 2024; 41:msae052. [PMID: 38427813 PMCID: PMC10951435 DOI: 10.1093/molbev/msae052] [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: 11/23/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024] Open
Abstract
Aneuploidy is common in eukaryotes, often leading to decreased fitness. However, evidence from fungi and human tumur cells suggests that specific aneuploidies can be beneficial under stressful conditions and facilitate adaptation. In a previous evolutionary experiment with yeast, populations evolving under heat stress became aneuploid, only to later revert to euploidy after beneficial mutations accumulated. It was therefore suggested that aneuploidy is a "stepping stone" on the path to adaptation. Here, we test this hypothesis. We use Bayesian inference to fit an evolutionary model with both aneuploidy and mutation to the experimental results. We then predict the genotype frequency dynamics during the experiment, demonstrating that most of the evolved euploid population likely did not descend from aneuploid cells, but rather from the euploid wild-type population. Our model shows how the beneficial mutation supply-the product of population size and beneficial mutation rate-determines the evolutionary dynamics: with low supply, much of the evolved population descends from aneuploid cells; but with high supply, beneficial mutations are generated fast enough to outcompete aneuploidy due to its inherent fitness cost. Our results suggest that despite its potential fitness benefits under stress, aneuploidy can be an evolutionary "diversion" rather than a "stepping stone": it can delay, rather than facilitate, the adaptation of the population, and cells that become aneuploid may leave less descendants compared to cells that remain diploid.
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Affiliation(s)
- Ilia Kohanovski
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science, Reichman University, Herzliya, Israel
| | - Martin Pontz
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avihu H Yona
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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2
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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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3
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Kawashima Y, Oda AH, Hikida Y, Ohta K. Chromosome-dependent aneuploid formation in Spo11-less meiosis. Genes Cells 2023; 28:129-148. [PMID: 36530025 PMCID: PMC10107155 DOI: 10.1111/gtc.12998] [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: 10/12/2022] [Revised: 11/21/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Deficiency in meiotic recombination leads to aberrant chromosome disjunction during meiosis, often resulting in the lethality of gametes or genetic disorders due to aneuploidy formation. Budding yeasts lacking Spo11, which is essential for initiation of meiotic recombination, produce many inviable spores in meiosis, while very rarely all sets of 16 chromosomes are coincidentally assorted into gametes to form viable spores. We induced meiosis in a spo11∆ diploid, in which homolog pairs can be distinguished by single nucleotide polymorphisms and determined whole-genome sequences of their exceptionally viable spores. We detected no homologous recombination in the viable spores of spo11∆ diploid. Point mutations were fewer in spo11∆ than in wild-type. We observed spo11∆ viable spores carrying a complete diploid set of homolog pairs or haploid spores with a complete haploid set of homologs but with aneuploidy in some chromosomes. In the latter, we found the chromosome-dependence in the aneuploid incidence, which was positively and negatively influenced by the chromosome length and the impact of dosage-sensitive genes, respectively. Selection of aneuploidy during meiosis II or mitosis after spore germination was also chromosome dependent. These results suggest a pathway by which specific chromosomes are more prone to cause aneuploidy, as observed in Down syndrome.
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Affiliation(s)
- Yuri Kawashima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Arisa H Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasushi Hikida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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4
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Genome-wide quantification of contributions to sexual fitness identifies genes required for spore viability and health in fission yeast. PLoS Genet 2022; 18:e1010462. [DOI: 10.1371/journal.pgen.1010462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/16/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
Numerous genes required for sexual reproduction remain to be identified even in simple model species like Schizosaccharomyces pombe. To address this, we developed an assay in S. pombe that couples transposon mutagenesis with high-throughput sequencing (TN-seq) to quantitatively measure the fitness contribution of nonessential genes across the genome to sexual reproduction. This approach identified 532 genes that contribute to sex, including more than 200 that were not previously annotated to be involved in the process, of which more than 150 have orthologs in vertebrates. Among our verified hits was an uncharacterized gene, ifs1 (important for sex), that is required for spore viability. In two other hits, plb1 and alg9, we observed a novel mutant phenotype of poor spore health wherein viable spores are produced, but the spores exhibit low fitness and are rapidly outcompeted by wild type. Finally, we fortuitously discovered that a gene previously thought to be essential, sdg1 (social distancing gene), is instead required for growth at low cell densities and can be rescued by conditioned medium. Our assay will be valuable in further studies of sexual reproduction in S. pombe and identifies multiple candidate genes that could contribute to sexual reproduction in other eukaryotes, including humans.
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5
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Yukawa M, Teratani Y, Toda T. Escape from mitotic catastrophe by actin-dependent nuclear displacement in fission yeast. iScience 2021; 24:102031. [PMID: 33506191 PMCID: PMC7814194 DOI: 10.1016/j.isci.2020.102031] [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] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/17/2020] [Accepted: 12/29/2020] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic cells position the nucleus within the proper intracellular space, thereby safeguarding a variety of cellular processes. In fission yeast, the interphase nucleus is placed in the cell middle in a microtubule-dependent manner. By contrast, how the mitotic nucleus is positioned remains elusive. Here we show that several cell-cycle mutants that arrest in mitosis all displace the nucleus toward one end of the cell. Intriguingly, the actin cytoskeleton is responsible for nuclear movement. Time-lapse live imaging indicates that mitosis-specific F-actin cables possibly push the nucleus through direct interaction with the nuclear envelope, and subsequently actomyosin ring constriction further shifts the nucleus away from the center. This nuclear movement is beneficial, because if the nuclei were retained in the center, unseparated chromosomes would be intersected by the contractile actin ring and the septum, imposing the lethal cut phenotype. Thus, fission yeast escapes from mitotic catastrophe by means of actin-dependent nuclear movement. Actin-dependent mitotic nuclear positioning in fission yeast Actin cables and ring closure drive nuclear displacement upon mitotic arrest Nuclear displacement evades cut-mediated cell death Survivors resume cell division as diploids
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Affiliation(s)
- Masashi Yukawa
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima 739-8530, Japan.,Laboratory of Molecular and Chemical Cell Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Yasuhiro Teratani
- Laboratory of Molecular and Chemical Cell Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Takashi Toda
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima 739-8530, Japan.,Laboratory of Molecular and Chemical Cell Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
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6
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Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers. eLife 2020; 9:57936. [PMID: 32790622 PMCID: PMC7426094 DOI: 10.7554/elife.57936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Killer meiotic drivers are genetic parasites that destroy ‘sibling’ gametes lacking the driver allele. The fitness costs of drive can lead to selection of unlinked suppressors. This suppression could involve evolutionary tradeoffs that compromise gametogenesis and contribute to infertility. Schizosaccharomyces pombe, an organism containing numerous gamete (spore)-killing wtf drivers, offers a tractable system to test this hypothesis. Here, we demonstrate that in scenarios analogous to outcrossing, wtf drivers generate a fitness landscape in which atypical spores, such as aneuploids and diploids, are advantageous. In this context, wtf drivers can decrease the fitness costs of mutations that disrupt meiotic fidelity and, in some circumstances, can even make such mutations beneficial. Moreover, we find that S. pombe isolates vary greatly in their ability to make haploid spores, with some isolates generating up to 46% aneuploid or diploid spores. This work empirically demonstrates the potential for meiotic drivers to shape the evolution of gametogenesis.
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Affiliation(s)
| | | | - Lauren E Eide
- Stowers Institute for Medical Research, Kansas City, United States.,University of Missouri-Kansas City, Kansas City, United States
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
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7
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Nawa N, Hirata K, Kawatani K, Nambara T, Omori S, Banno K, Kokubu C, Takeda J, Nishimura K, Ohtaka M, Nakanishi M, Okuzaki D, Taniguchi H, Arahori H, Wada K, Kitabatake Y, Ozono K. Elimination of protein aggregates prevents premature senescence in human trisomy 21 fibroblasts. PLoS One 2019; 14:e0219592. [PMID: 31356639 PMCID: PMC6663065 DOI: 10.1371/journal.pone.0219592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Chromosome abnormalities induces profound alterations in gene expression, leading to various disease phenotypes. Recent studies on yeast and mammalian cells have demonstrated that aneuploidy exerts detrimental effects on organismal growth and development, regardless of the karyotype, suggesting that aneuploidy-associated stress plays an important role in disease pathogenesis. However, whether and how this effect alters cellular homeostasis and long-term features of human disease are not fully understood. Here, we aimed to investigate cellular stress responses in human trisomy syndromes, using fibroblasts and induced pluripotent stem cells (iPSCs). Dermal fibroblasts derived from patients with trisomy 21, 18 and 13 showed a severe impairment of cell proliferation and enhanced premature senescence. These phenomena were accompanied by perturbation of protein homeostasis, leading to the accumulation of protein aggregates. We found that treatment with sodium 4-phenylbutyrate (4-PBA), a chemical chaperone, decreased the protein aggregates in trisomy fibroblasts. Notably, 4-PBA treatment successfully prevented the progression of premature senescence in secondary fibroblasts derived from trisomy 21 iPSCs. Our study reveals aneuploidy-associated stress as a potential therapeutic target for human trisomies, including Down syndrome.
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Affiliation(s)
- Nobutoshi Nawa
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Katsuya Hirata
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Neonatal Medicine, Osaka Women’s and Children’s Hospital, Izumi, Osaka, Japan
| | - Keiji Kawatani
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Toshihiko Nambara
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Sayaka Omori
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kimihiko Banno
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Chikara Kokubu
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Manami Ohtaka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hidetoshi Taniguchi
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hitomi Arahori
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kazuko Wada
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Neonatal Medicine, Osaka Women’s and Children’s Hospital, Izumi, Osaka, Japan
| | - Yasuji Kitabatake
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- * E-mail:
| | - Keiichi Ozono
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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8
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Chen Y, Chen S, Li K, Zhang Y, Huang X, Li T, Wu S, Wang Y, Carey LB, Qian W. Overdosage of Balanced Protein Complexes Reduces Proliferation Rate in Aneuploid Cells. Cell Syst 2019; 9:129-142.e5. [PMID: 31351919 DOI: 10.1016/j.cels.2019.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 02/27/2019] [Accepted: 06/17/2019] [Indexed: 11/26/2022]
Abstract
Cells with complex aneuploidies display a wide range of phenotypic abnormalities. However, the molecular basis for this has been mainly studied in trisomic (2n + 1) and disomic (n + 1) cells. To determine how karyotype affects proliferation in cells with complex aneuploidies, we generated 92 2n + x yeast strains in which each diploid cell has between 3 and 12 extra chromosomes. Genome-wide and, for individual protein complexes, proliferation defects are caused by the presence of protein complexes in which all subunits are balanced at the 3-copy level. Proteomics revealed that over 50% of 3-copy members of imbalanced complexes were expressed at only 2n protein levels, whereas members of complexes in which all subunits are stoichiometrically balanced at 3 copies per cell had 3n protein levels. We validated this finding using orthogonal datasets from yeast and from human cancers. Taken together, our study provides an explanation of how aneuploidy affects phenotype.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuliang Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shaohuan Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Dürrbaum M, Kruse C, Nieken KJ, Habermann B, Storchová Z. The deregulated microRNAome contributes to the cellular response to aneuploidy. BMC Genomics 2018; 19:197. [PMID: 29703144 PMCID: PMC6389165 DOI: 10.1186/s12864-018-4556-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/19/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Aneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has been demonstrated that aneuploidy per se impairs proliferation, leads to proteotoxic as well as replication stress and triggers conserved transcriptome and proteome changes. RESULTS In this study, we analysed for the first time miRNAs and demonstrate that their expression is altered in response to chromosome gain. The miRNA deregulation is independent of the identity of the extra chromosome and specific to individual cell lines. By cross-omics analysis we demonstrate that although the deregulated miRNAs differ among individual aneuploid cell lines, their known targets are predominantly associated with cell development, growth and proliferation, pathways known to be inhibited in response to chromosome gain. Indeed, we show that up to 72% of these targets are downregulated and the associated miRNAs are overexpressed in aneuploid cells, suggesting that the miRNA changes contribute to the global transcription changes triggered by aneuploidy. We identified hsa-miR-10a-5p to be overexpressed in majority of aneuploid cells. Hsa-miR-10a-5p enhances translation of a subset of mRNAs that contain so called 5'TOP motif and we show that its upregulation in aneuploids provides resistance to starvation-induced shut down of ribosomal protein translation. CONCLUSIONS Our work suggests that the changes of the microRNAome contribute on one hand to the adverse effects of aneuploidy on cell physiology, and on the other hand to the adaptation to aneuploidy by supporting translation under adverse conditions.
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Affiliation(s)
- Milena Dürrbaum
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center for Integrated Protein Sciences Munich, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Christine Kruse
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - K. Julia Nieken
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Bianca Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Computational Biology Group, Developmental Biology Institute of Marseille (IBDM) UMR 7288, CNRS, Aix Marseille Université, 13288 Marseille, France
| | - Zuzana Storchová
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center for Integrated Protein Sciences Munich, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
- Department of Molecular Genetics, TU Kaiserslautern, Paul Ehrlich Strasse 24, 67663 Kaiserslautern, Germany
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10
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López Hernández JF, Zanders SE. Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast. Yeast 2018; 35:447-453. [PMID: 29322557 PMCID: PMC6033644 DOI: 10.1002/yea.3305] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022] Open
Abstract
Meiotic drivers are selfish DNA loci that can bias their own transmission into gametes. Owing to their transmission advantages, meiotic drivers can spread in populations even if the drivers or linked variants decrease organismal fitness. Meiotic drive was first formally described in the 1950s and is thought to be a powerful force shaping eukaryotic genomes. Classic genetic analyses have detected the action of meiotic drivers in plants, filamentous fungi, insects and vertebrates. Several of these drive systems have limited experimental tractability and relatively little is known about the molecular mechanisms of meiotic drive. Recently, however, meiotic drivers were discovered in a yeast species. The Schizosaccharomyces pombe wtf gene family contains several active meiotic drive genes. This review summarizes what is known about the wtf family and highlights its potential as a highly tractable experimental model for molecular and evolutionary characterization of meiotic drive.
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Affiliation(s)
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
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11
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Zadesenets KS, Schärer L, Rubtsov NB. New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria). Sci Rep 2017; 7:6066. [PMID: 28729552 PMCID: PMC5519732 DOI: 10.1038/s41598-017-06498-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/13/2017] [Indexed: 01/02/2023] Open
Abstract
The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either ‘normal’ 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 — a sibling species of M. lignano — revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.
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Affiliation(s)
- Kira S Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk, 630090, Russian Federation.
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, CH-4051, Switzerland
| | - Nikolay B Rubtsov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, Pirogova str., 2, Novosibirsk, 630090, Russian Federation
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12
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Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. eLife 2017; 6:e26057. [PMID: 28631610 PMCID: PMC5478263 DOI: 10.7554/elife.26057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Affiliation(s)
- Wen Hu
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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13
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Santaguida S, Richardson A, Iyer DR, M'Saad O, Zasadil L, Knouse KA, Wong YL, Rhind N, Desai A, Amon A. Chromosome Mis-segregation Generates Cell-Cycle-Arrested Cells with Complex Karyotypes that Are Eliminated by the Immune System. Dev Cell 2017; 41:638-651.e5. [PMID: 28633018 PMCID: PMC5536848 DOI: 10.1016/j.devcel.2017.05.022] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 03/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023]
Abstract
Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways that limit the prevalence of such cells exist? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells. We find that chromosome mis-segregation leads to further genomic instability that ultimately causes cell-cycle arrest. We further show that cells with complex karyotypes exhibit features of senescence and produce pro-inflammatory signals that promote their clearance by the immune system. We propose that cells with abnormal karyotypes generate a signal for their own elimination that may serve as a means for cancer cell immunosurveillance.
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Affiliation(s)
- Stefano Santaguida
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
| | - Amelia Richardson
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Divya Ramalingam Iyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ons M'Saad
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Lauren Zasadil
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Kristin A Knouse
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA; Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Yao Liang Wong
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshad Desai
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelika Amon
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
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14
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Abstract
Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyces strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes.
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15
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Exploring the power of yeast to model aging and age-related neurodegenerative disorders. Biogerontology 2016; 18:3-34. [PMID: 27804052 DOI: 10.1007/s10522-016-9666-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
Abstract
Aging is a multifactorial process determined by molecular, cellular and systemic factors and it is well established that advancing age is a leading risk factor for several neurodegenerative diseases. In fact, the close association of aging and neurodegenerative disorders has placed aging as the greatest social and economic challenge of the 21st century, and age-related diseases have also become a key priority for countries worldwide. The growing need to better understand both aging and neurodegenerative processes has led to the development of simple eukaryotic models amenable for mechanistic studies. Saccharomyces cerevisiae has proven to be an unprecedented experimental model to study the fundamental aspects of aging and to decipher the intricacies of neurodegenerative disorders greatly because the molecular mechanisms underlying these processes are evolutionarily conserved from yeast to human. Moreover, yeast offers several methodological advantages allowing a rapid and relatively easy way of establishing gene-protein-function associations. Here we review different aging theories, common cellular pathways driving aging and neurodegenerative diseases and discuss the major contributions of yeast to the state-of-art knowledge in both research fields.
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16
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Passerini V, Storchová Z. Too much to handle - how gaining chromosomes destabilizes the genome. Cell Cycle 2016; 15:2867-2874. [PMID: 27636196 PMCID: PMC5105935 DOI: 10.1080/15384101.2016.1231285] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022] Open
Abstract
Most eukaryotic organisms are diploid, with 2 chromosome sets in their nuclei. Whole chromosomal aneuploidy, a deviation from multiples of the haploid chromosome number, arises from chromosome segregation errors and often has detrimental consequences for cells. In humans, numerical aneuploidy severely impairs embryonic development and the rare survivors develop disorders characterized by multiple pathologies. Moreover, as many as 75 % of malignant tumors display aneuploidy. Although the exact contribution of aneuploidy to tumorigenesis remains unclear, previous studies have suggested that aneuploidy may affect the maintenance of genome integrity. We found that human cells with extra chromosomes showed phenotypes suggestive of replication defects, a phenomenon which we went on to characterize as being due to the aneuploidy-driven downregulation of replication factors, in particular of the replicative helicase MCM2-7. Thus, missegregation of even a single chromosome can further promote genomic instability and thereby contribute to tumor development. In this review we will examine the possible causes of downregulation of replicative factors and discuss the consequences of genomic instability in aneuploid cells.
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Affiliation(s)
- Verena Passerini
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
- Center for Integrated Protein Science, Ludwig-Maximilian-University, Munich, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
- Center for Integrated Protein Science, Ludwig-Maximilian-University, Munich, Germany
- Technical University Kaiserslautern, Kaiserslautern, Germany
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17
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Zadesenets KS, Vizoso DB, Schlatter A, Konopatskaia ID, Berezikov E, Schärer L, Rubtsov NB. Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology. PLoS One 2016; 11:e0164915. [PMID: 27755577 PMCID: PMC5068713 DOI: 10.1371/journal.pone.0164915] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/03/2016] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and tools, makes it essential to have a detailed description of the chromosome organization of this species, previously suggested to have a karyotype with 2n = 8 and one pair of large and three pairs of small metacentric chromosomes. We performed cytogenetic analyses for chromosomes of one commonly used inbred line of M. lignano (called DV1) and uncovered unexpected chromosome number variation in the form of aneuploidies of the largest chromosomes. These results prompted us to perform karyotypic studies in individual specimens of this and other lines of M. lignano reared under laboratory conditions, as well as in freshly field-collected specimens from different natural populations. Our analyses revealed a high frequency of aneuploids and in some cases other numerical and structural chromosome abnormalities in laboratory-reared lines of M. lignano, and some cases of aneuploidy were also found in freshly field-collected specimens. Moreover, karyological analyses were performed in specimens of three further species: Macrostomum sp. 8 (a close relative of M. lignano), M. spirale and M. hystrix. Macrostomum sp. 8 showed a karyotype that was similar to that of M. lignano, with tetrasomy for its largest chromosome being the most common karyotype, while the other two species showed a simpler karyotype that is more typical of the genus Macrostomum. These findings suggest that M. lignano and Macrostomum sp. 8 can be used as new models for studying processes of partial genome duplication in genome evolution.
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Affiliation(s)
- Kira S. Zadesenets
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- * E-mail:
| | - Dita B. Vizoso
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Aline Schlatter
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Eugene Berezikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Nikolay B. Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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18
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Wang Y, Chang J, Shao L, Feng W, Luo Y, Chow M, Du W, Meng A, Zhou D. Hematopoietic Stem Cells from Ts65Dn Mice Are Deficient in the Repair of DNA Double-Strand Breaks. Radiat Res 2016; 185:630-7. [PMID: 27243896 DOI: 10.1667/rr14407.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Down syndrome (DS) is a genetic disorder caused by the presence of an extra partial or whole copy of chromosome 21. In addition to musculoskeletal and neurodevelopmental abnormalities, children with DS exhibit various hematologic disorders and have an increased risk of developing acute lymphoblastic leukemia and acute megakaryocytic leukemia. Using the Ts65Dn mouse model, we investigated bone marrow defects caused by trisomy for 132 orthologs of the genes on human chromosome 21. The results showed that, although the total bone marrow cellularity as well as the frequency of hematopoietic progenitor cells (HPCs) was comparable between Ts65Dn mice and their age-matched euploid wild-type (WT) control littermates, human chromosome 21 trisomy led to a significant reduction in hematopoietic stem cell (HSC) numbers and clonogenic function in Ts65Dn mice. We also found that spontaneous DNA double-strand breaks (DSBs) were significantly increased in HSCs from the Ts65Dn mice, which was correlated with the significant reduction in HSC clonogenic activity compared to those from WT controls. Moreover, analysis of the repair kinetics of radiation-induced DSBs revealed that HSCs from Ts65Dn mice were less proficient in DSB repair than the cells from WT controls. This deficiency was associated with a higher sensitivity of Ts65Dn HSCs to radiation-induced suppression of HSC clonogenic activity than that of euploid HSCs. These findings suggest that an additional copy of genes on human chromosome 21 may selectively impair the ability of HSCs to repair DSBs, which may contribute to DS-associated hematological abnormalities and malignancies.
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Affiliation(s)
- Yingying Wang
- a Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Tianjin 300192, China; and.,b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Jianhui Chang
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Lijian Shao
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Wei Feng
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Yi Luo
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Marie Chow
- c Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Wei Du
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
| | - Aimin Meng
- a Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Tianjin 300192, China; and
| | - Daohong Zhou
- b Division of Radiation Health, Department of Pharmaceutical Sciences and
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19
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Torres EM, Springer M, Amon A. No current evidence for widespread dosage compensation in S. cerevisiae. eLife 2016; 5:e10996. [PMID: 26949255 PMCID: PMC4798953 DOI: 10.7554/elife.10996] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/29/2015] [Indexed: 11/17/2022] Open
Abstract
Previous studies of laboratory strains of budding yeast had shown that when gene copy number is altered experimentally, RNA levels generally scale accordingly. This is true when the copy number of individual genes or entire chromosomes is altered. In a recent study, Hose et al. (2015) reported that this tight correlation between gene copy number and RNA levels is not observed in recently isolated wild Saccharomyces cerevisiae variants. To understand the origins of this proposed difference in gene expression regulation between natural variants and laboratory strains of S. cerevisiae, we evaluated the karyotype and gene expression studies performed by Hose et al. on wild S. cerevisiae strains. In contrast to the results of Hose et al., our reexamination of their data revealed a tight correlation between gene copy number and gene expression. We conclude that widespread dosage compensation occurs neither in laboratory strains nor in natural variants of S. cerevisiae. DOI:http://dx.doi.org/10.7554/eLife.10996.001 DNA inside cells is packaged into structures called chromosomes. Different species can have different numbers of chromosomes, but when any cell divides it must allocate the right number of chromosomes to each new cell. If this process goes wrong, cells end up with too many or too few chromosomes. The presence of extra copies of the genes on the additional chromosomes can cause the levels of the proteins encoded by those genes to rise abnormally, which can in turn lead to cell damage and disease. Proteins are produced using the information in genes via a two-step process. First, the gene’s DNA is copied to create molecules of RNA, and these molecules are then translated into proteins. In many organisms, the presence of extra chromosomes in a cell is matched by a corresponding increase in the RNA molecules encoded by the extra genes. Some organisms, however, counteract this effect through a process called dosage compensation. This process inactivates single genes or whole chromosomes by various means, and ensures that normal levels of RNA are produced, even in the presence of extra genes. In 2015, researchers from the University of Wisconsin-Madison reported that dosage compensation occurs in wild strains of budding yeast and effectively protects the yeast cells against the harmful effects of having extra chromosomes. However, these findings conflicted with earlier studies of laboratory strains of this yeast, which had reported that RNA levels increased along with gene number. Torres, Springer and Amon have re-analysed the data published in 2015, and now challenge the findings of the previous study involving the wild yeast strains. The new re-analysis instead showed that, like in laboratory yeast strains, gene number still correlates closely with RNA levels in the wild yeast. This led Torres, Springer and Amon to conclude that, in contrast with the previous report, there is currently no evidence that dosage compensation occurs in wild strains of yeast. So why do the results of these two studies disagree? Torres, Springer and Amon identified several issues concerning the original analysis made by the researchers from the University of Wisconsin-Madison. For example, some of the strains included in the 2015 study were unstable and were naturally losing the additional chromosomes that they’d acquired. Also, the thresholds set in the analysis to identify dosage compensated genes do not appear to have been stringent enough. Together, the new findings indicate that dosage compensation is a rare event in both wild and laboratory strains of yeast. DOI:http://dx.doi.org/10.7554/eLife.10996.002
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Affiliation(s)
- Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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20
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The presence of extra chromosomes leads to genomic instability. Nat Commun 2016; 7:10754. [PMID: 26876972 PMCID: PMC4756715 DOI: 10.1038/ncomms10754] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/15/2016] [Indexed: 12/14/2022] Open
Abstract
Aneuploidy is a hallmark of cancer and underlies genetic disorders characterized by severe developmental defects, yet the molecular mechanisms explaining its effects on cellular physiology remain elusive. Here we show, using a series of human cells with defined aneuploid karyotypes, that gain of a single chromosome increases genomic instability. Next-generation sequencing and SNP-array analysis reveal accumulation of chromosomal rearrangements in aneuploids, with break point junction patterns suggestive of replication defects. Trisomic and tetrasomic cells also show increased DNA damage and sensitivity to replication stress. Strikingly, we find that aneuploidy-induced genomic instability can be explained by the reduced expression of the replicative helicase MCM2-7. Accordingly, restoring near-wild-type levels of chromatin-bound MCM helicase partly rescues the genomic instability phenotypes. Thus, gain of chromosomes triggers replication stress, thereby promoting genomic instability and possibly contributing to tumorigenesis. One of the hallmarks of cancer cells is aneuploidy, however the molecular effects are poorly understood. Here the authors show that trisomic and tetrasomic cells display increased genomic instability and reduced levels of the helicase MCM2-7.
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21
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Kaboli S, Miyamoto T, Sunada K, Sasano Y, Sugiyama M, Harashima S. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:638-644. [PMID: 26690924 DOI: 10.1016/j.jbiosc.2015.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
Saccharomyces cerevisiae strains from industrial and natural geographical environments are reported to show great variation in copy number of chromosomal regions. Such variation contributes to the mechanisms underlying adaptation to different environments. Here, we created and phenotypically analyzed segmentally haploidized strains, each harboring a deletion of one copy of approximately 100-300 kb of the left or right terminal region of 16 chromosomes in a diploid strain by using a PCR-mediated chromosomal deletion method. No haploidized strain of the 158-kb deleted right terminal region of chromosome III or the 172-kb deleted right terminal region of chromosome VI was produced; however, segmentally haploidized strains of the remaining 30 terminal regions were obtained. Among these 30 strains, two exhibited higher lactic acid resistance and two displayed higher thermo-tolerance at 41°C versus the host diploid strain. By contrast, four and two segmentally haploidized strains showed sensitivity to 6% lactic acid and low temperature at 13°C, respectively. The effect of the decreased copy number of the chromosomal terminal regions on ethanol production was analyzed. As compared with the host diploid strain, a 3.8% and 4.3% improvement in ethanol production in 10% glucose medium was observed for two strains in which one of two copies of the 197-kb left terminal region of chromosome V and one of two copies of the 195-kb left terminal region of chromosome X was deleted, respectively. These results indicate that artificial segmental haploidization might contribute to improvement of industrially important phenotypes and provide a new approach to breeding superior yeast strains.
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Affiliation(s)
- Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Miyamoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Sunada
- 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.
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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22
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Genome-Wide Estimates of Mutation Rates and Spectrum in Schizosaccharomyces pombe Indicate CpG Sites are Highly Mutagenic Despite the Absence of DNA Methylation. G3-GENES GENOMES GENETICS 2015; 6:149-60. [PMID: 26564949 PMCID: PMC4704713 DOI: 10.1534/g3.115.022129] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We accumulated mutations for 1952 generations in 79 initially identical, haploid lines of the fission yeast Schizosaccharomyces pombe, and then performed whole-genome sequencing to determine the mutation rates and spectrum. We captured 696 spontaneous mutations across the 79 mutation accumulation (MA) lines. We compared the mutation spectrum and rate to a recently published equivalent experiment on the same species, and to another model ascomycetous yeast, the budding yeast Saccharomyces cerevisiae. While the two species are approximately 600 million years diverged from each other, they share similar life histories, genome size and genomic G/C content. We found that Sc. pombe and S. cerevisiae have similar mutation rates, but Sc. pombe exhibits a stronger insertion bias. Intriguingly, we observed an increased mutation rate at cytosine nucleotides, specifically CpG nucleotides, which is also seen in S. cerevisiae. However, the absence of methylation in Sc. pombe and the pattern of mutation at these sites, primarily C → A as opposed to C → T, strongly suggest that the increased mutation rate is not caused by deamination of methylated cytosines. This result implies that the high mutability of CpG dinucleotides in other species may be caused in part by a methylation-independent mechanism. Many of our findings mirror those seen in the recent study, despite the use of different passaging conditions, indicating that MA is a reliable method for estimating mutation rates and spectra.
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Abstract
Dividing cells that experience chromosome mis-segregation generate aneuploid daughter cells, which contain an incorrect number of chromosomes. Although aneuploidy interferes with the proliferation of untransformed cells, it is also, paradoxically, a hallmark of cancer, a disease defined by increased proliferative potential. These contradictory effects are also observed in mouse models of chromosome instability (CIN). CIN can inhibit and promote tumorigenesis. Recent work has provided insights into the cellular consequences of CIN and aneuploidy. Chromosome mis-segregation per se can alter the genome in many more ways than just causing the gain or loss of chromosomes. The short- and long-term effects of aneuploidy are caused by gene-specific effects and a stereotypic aneuploidy stress response. Importantly, these recent findings provide insights into the role of aneuploidy in tumorigenesis.
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24
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Protacio RU, Storey AJ, Davidson MK, Wahls WP. Nonsense codon suppression in fission yeast due to mutations of tRNA(Ser.11) and translation release factor Sup35 (eRF3). Curr Genet 2015; 61:165-73. [PMID: 25519804 PMCID: PMC4393767 DOI: 10.1007/s00294-014-0465-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 02/07/2023]
Abstract
In the fission yeast Schizosaccharomyces pombe, sup9 mutations can suppress the termination of translation at nonsense (stop) codons. We localized sup9 physically to the spctrnaser.11 locus and confirmed that one allele (sup9-UGA) alters the anticodon of a serine tRNA. We also found that another purported allele is not allelic. Instead, strains with that suppressor (renamed sup35-F592S) have a single base pair substitution (T1775C) that introduces an amino acid substitution in the Sup35 protein (Sup35-F592S). Reduced functionality of Sup35 (eRF3), the ubiquitous guanine nucleotide-responsive translation release factor of eukaryotes, increases read-through of stop codons. Tetrad dissection revealed that suppression is tightly linked to (inseparable from) the sup35-F592S mutation and that there are no additional extragenic modifiers. The Mendelian inheritance indicates that the Sup35-F592S protein does not adopt an infectious amyloid state ([PSI (+)] prion) to affect suppression, consistent with recent evidence that fission yeast Sup35 does not form prions. We also report that sup9-UGA and sup35-F592S exhibit different strengths of suppression for opal stop codons of ade6-M26 and ade6-M375. We discuss possible mechanisms for the variation in suppressibility exhibited by the two alleles.
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Affiliation(s)
- Reine U. Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Aaron J. Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Mari K. Davidson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Wayne P. Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
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25
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Veitia RA, Potier MC. Gene dosage imbalances: action, reaction, and models. Trends Biochem Sci 2015; 40:309-17. [PMID: 25937627 DOI: 10.1016/j.tibs.2015.03.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/17/2015] [Accepted: 03/27/2015] [Indexed: 12/29/2022]
Abstract
Single-gene deletions, duplications, and misregulation, as well as aneuploidy, can lead to stoichiometric imbalances within macromolecular complexes and cellular networks, causing their malfunction. Such alterations can be responsible for inherited or somatic genetic disorders including Mendelian diseases, aneuploid syndromes, and cancer. We review the effects of gene dosage alterations at the transcriptomic and proteomic levels, and the various responses of the cell to counteract their effects. Furthermore, we explore several biochemical models and ideas that can provide the rationale for treatments modulating the effects of gene dosage imbalances.
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Affiliation(s)
- Reiner A Veitia
- Institut Jacques Monod, Paris, France; Université Paris Diderot, Paris, France.
| | - Marie Claude Potier
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Université Paris 06, Institut National de la Santé et de la Recherche Médicale (INSERM) and Centre National de la Recherche Scientifique (CNRS) Unités de Recherche U75, U1127, U7225, and Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
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26
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Blank HM, Sheltzer JM, Meehl CM, Amon A. Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast. Mol Biol Cell 2015; 26:1440-51. [PMID: 25694455 PMCID: PMC4395125 DOI: 10.1091/mbc.e14-10-1442] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/11/2015] [Indexed: 11/11/2022] Open
Abstract
Aneuploidy causes DNA replication defects and premature adaptation to DNA damage, with profound consequences for genome stability. Such abnormalities provide the substrate for translocations and deletions that are a hallmark of cancer. Genetic instability is a hallmark of aneuploidy in budding and fission yeast. All aneuploid yeast strains analyzed to date harbor elevated levels of Rad52-GFP foci, a sign of DNA damage. Here we investigate how continuously elevated levels of DNA damage affect aneuploid cells. We show that Rad52-GFP foci form during S phase, consistent with the observation that DNA replication initiation and elongation are impaired in some aneuploid yeast strains. We furthermore find that although DNA damage is low in aneuploid cells, it nevertheless has dramatic consequences. Many aneuploid yeast strains adapt to DNA damage and undergo mitosis despite the presence of unrepaired DNA leading to cell death. Wild-type cells exposed to low levels of DNA damage exhibit a similar phenotype, indicating that adaptation to low levels of unrepaired DNA is a general property of the cell's response to DNA damage. Our results indicate that by causing low levels of DNA damage, whole-chromosome aneuploidies lead to DNA breaks that persist into mitosis. Such breaks provide the substrate for translocations and deletions that are a hallmark of cancer.
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Affiliation(s)
- Heidi M Blank
- Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jason M Sheltzer
- Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Colleen M Meehl
- Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Angelika Amon
- Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
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27
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Donnelly N, Passerini V, Dürrbaum M, Stingele S, Storchová Z. HSF1 deficiency and impaired HSP90-dependent protein folding are hallmarks of aneuploid human cells. EMBO J 2014; 33:2374-87. [PMID: 25205676 DOI: 10.15252/embj.201488648] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aneuploidy is a hallmark of cancer and is associated with malignancy and poor prognosis. Recent studies have revealed that aneuploidy inhibits proliferation, causes distinct alterations in the transcriptome and proteome and disturbs cellular proteostasis. However, the molecular mechanisms underlying the changes in gene expression and the impairment of proteostasis are not understood. Here, we report that human aneuploid cells are impaired in HSP90-mediated protein folding. We show that aneuploidy impairs induction of the heat shock response suggesting that the activity of the transcription factor heat shock factor 1 (HSF1) is compromised. Indeed, increased levels of HSF1 counteract the effects of aneuploidy on HSP90 expression and protein folding, identifying HSF1 overexpression as the first aneuploidy-tolerating mutation in human cells. Thus, impaired HSF1 activity emerges as a critical factor underlying the phenotypes linked to aneuploidy. Finally, we demonstrate that deficient protein folding capacity directly shapes gene expression in aneuploid cells. Our study provides mechanistic insight into the causes of the disturbed proteostasis in aneuploids and deepens our understanding of the role of HSF1 in cytoprotection and carcinogenesis.
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Affiliation(s)
- Neysan Donnelly
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Verena Passerini
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Milena Dürrbaum
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Silvia Stingele
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, Munich, Germany
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28
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Storchova Z. Ploidy changes and genome stability in yeast. Yeast 2014; 31:421-30. [DOI: 10.1002/yea.3037] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zuzana Storchova
- Group Maintenance of Genome Stability; Max Planck Institute of Biochemistry; Martinsried Germany
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29
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Zanders SE, Eickbush MT, Yu JS, Kang JW, Fowler KR, Smith GR, Malik HS. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. eLife 2014; 3:e02630. [PMID: 24963140 PMCID: PMC4066438 DOI: 10.7554/elife.02630] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. We find that chromosomal rearrangements and related recombination defects are major but not sole causes of hybrid infertility. At least three distinct meiotic drive alleles, one on each S. kambucha chromosome, independently contribute to hybrid infertility by causing nonrandom spore death. Two of these driving loci are linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. Our study reveals how quickly multiple barriers to fertility can arise. In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.001 It is widely thought that all of the billions of species on Earth are descended from a common ancestor. New species are created via a process called speciation, and nature employs various ‘barriers’ to keep closely related species distinct from one another. One of these barriers is called hybrid sterility. Horses and donkeys, for example, can mate to produce hybrids called mules, but mules cannot produce offspring of their own because they are infertile. Hybrid sterility can occur for a number of reasons. Mules are infertile because they inherit 32 chromosomes from their horse parent, but only 31 chromosomes from their donkey parent—and so have an odd chromosome that they cannot pair-off when they make sperm or egg cells. However, even if a hybrid inherits the same number of chromosomes from each parent, if the chromosomes from the two parents have different structures, the hybrid may still be infertile. Zanders et al. have now looked at two species of fission yeast—S. pombe and S. kambucha—that share 99.5% of their DNA sequence. Although hybrids of these two species inherit three chromosomes from each parent, the majority of spores (the yeast equivalent of sperm) that these hybrids produce fail to develop into new yeast cells. Zanders et al. identified two causes of this infertility: one of these was chromosomal rearrangement; the other was due to three different sites in the DNA of S. kambucha that interfere with the development of the spores that inherit S. pombe chromosomes. Since these two yeast species are so closely related, the findings of Zanders et al. reveal how quickly multiple barriers to fertility can arise. In addition, these findings provide further support for models in which conflicts between different genes in genomes can drive the process of speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.002
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Affiliation(s)
- Sarah E Zanders
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Michael T Eickbush
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jonathan S Yu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Ji-Won Kang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States University of Washington, Seattle, United States
| | - Kyle R Fowler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit Singh Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
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30
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Dürrbaum M, Kuznetsova AY, Passerini V, Stingele S, Stoehr G, Storchová Z. Unique features of the transcriptional response to model aneuploidy in human cells. BMC Genomics 2014; 15:139. [PMID: 24548329 PMCID: PMC3932016 DOI: 10.1186/1471-2164-15-139] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/14/2014] [Indexed: 02/08/2023] Open
Abstract
Background Aneuploidy, a karyotype deviating from multiples of a haploid chromosome set, affects the physiology of eukaryotes. In humans, aneuploidy is linked to pathological defects such as developmental abnormalities, mental retardation or cancer, but the underlying mechanisms remain elusive. There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far. Results Here we evaluate the transcription profiles of eleven trisomic and tetrasomic cell lines and two cell lines with complex aneuploid karyotypes. We identify a characteristic aneuploidy response pattern defined by upregulation of genes linked to endoplasmic reticulum, Golgi apparatus and lysosomes, and downregulation of DNA replication, transcription as well as ribosomes. Strikingly, complex aneuploidy elicits the same transcriptional changes as trisomy. To uncover the triggers of the response, we compared the profiles with transcription changes in human cells subjected to stress conditions. Interestingly, we found an overlap only with the response to treatment with the autophagy inhibitor bafilomycin A1. Finally, we identified 23 genes whose expression is significantly altered in all aneuploids and which may thus serve as aneuploidy markers. Conclusions Our analysis shows that despite the variability in chromosome content, aneuploidy triggers uniform transcriptional response in human cells. A common response independent of the type of aneuploidy might be exploited as a novel target for cancer therapy. Moreover, the potential aneuploidy markers identified in our analysis might represent novel biomarkers to assess the malignant potential of a tumor.
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Affiliation(s)
| | | | | | | | | | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.
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31
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Donnelly N, Storchová Z. Dynamic karyotype, dynamic proteome: buffering the effects of aneuploidy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:473-81. [DOI: 10.1016/j.bbamcr.2013.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 12/18/2022]
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32
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Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 2014; 111:1903-8. [PMID: 24449889 DOI: 10.1073/pnas.1216934111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochore assembly is unclear. Schizosaccharomyces pombe is an important experimental system for investigating centromere function, but all of the previous work with this species has exploited a single strain or its derivatives. The laboratory strain and most other S. pombe strains contain three chromosomes, but one recently discovered strain, CBS 2777, contains four. We show that the genome of CBS 2777 is related to that of the laboratory strain by a complex chromosome rearrangement. As a result, two of the kinetochores in CBS 2777 contain the central core sequences present in the laboratory strain centromeres, but lack adjacent heterochromatin. The closest block of heterochromatin to these rearranged kinetochores is ∼100 kb away at new telomeres. Despite lacking large amounts of adjacent heterochromatin, the rearranged kinetochores bind CENP-A(Cnp1) and CENP-C(Cnp3) in similar quantities and with similar specificities as those of the laboratory strain. The simplest interpretation of this result is that constitutive kinetochore assembly and heterochromatin formation occur autonomously.
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33
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Mulla W, Zhu J, Li R. Yeast: a simple model system to study complex phenomena of aneuploidy. FEMS Microbiol Rev 2013; 38:201-12. [PMID: 24118136 DOI: 10.1111/1574-6976.12048] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/29/2013] [Accepted: 09/30/2013] [Indexed: 12/29/2022] Open
Abstract
Aneuploidy, the state of having a chromosome number different from a multiple of the haploid number, has been associated with diseases and developmental disorders. The role of aneuploidy in human disease pathology, especially in cancer, has been a subject of much attention and debate over the last century due to the intrinsic complexity of the phenomena and experimental challenges. Over the last decade, yeast has been an invaluable model for driving discoveries about the genetic and molecular aspects of aneuploidy. The understanding of aneuploidy has been significantly improved owing to the methods for selectively generating aneuploid yeast strains without causing other genetic changes, techniques for detecting aneuploidy, and cutting-edge genetics and 'omics' approaches. In this review, we discuss the contribution of studies in yeast to current knowledge about aneuploidy. Special emphasis is placed on experimental features that make yeast a simpler and efficient model to investigate the complex questions in the field of aneuploidy.
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Affiliation(s)
- Wahid Mulla
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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34
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Kumaran R, Yang SY, Leu JY. Characterization of chromosome stability in diploid, polyploid and hybrid yeast cells. PLoS One 2013; 8:e68094. [PMID: 23874507 PMCID: PMC3707968 DOI: 10.1371/journal.pone.0068094] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/24/2013] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability is a key component of cancer progression and many heritable diseases. Understanding why some chromosomes are more unstable than others could provide insight into understanding genome integrity. Here we systematically investigate the spontaneous chromosome loss for all sixteen chromosomes in Saccharomyces cerevisiae in order to elucidate the mechanisms underlying chromosome instability. We observed that the stability of different chromosomes varied more than 100-fold. Consistent with previous studies on artificial chromosomes, chromosome loss frequency was negatively correlated to chromosome length in S. cerevisiae diploids, triploids and S. cerevisiae-S. bayanus hybrids. Chromosome III, an equivalent of sex chromosomes in budding yeast, was found to be the most unstable chromosome among all cases examined. Moreover, similar instability was observed in chromosome III of S. bayanus, a species that diverged from S. cerevisiae about 20 million years ago, suggesting that the instability is caused by a conserved mechanism. Chromosome III was found to have a highly relaxed spindle checkpoint response in the genome. Using a plasmid stability assay, we found that differences in the centromeric sequence may explain certain aspects of chromosome instability. Our results reveal that even under normal conditions, individual chromosomes in a genome are subject to different levels of pressure in chromosome loss (or gain).
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Affiliation(s)
- Rajaraman Kumaran
- Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shi-Yow Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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35
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Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A. Aneuploid yeast strains exhibit defects in cell growth and passage through START. Mol Biol Cell 2013; 24:1274-89. [PMID: 23468524 PMCID: PMC3639041 DOI: 10.1091/mbc.e12-07-0520] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aneuploidy causes cell proliferation defects in budding yeast, with many aneuploid strains exhibiting a G1 delay. This study shows that the G1 delay in aneuploid budding yeast is caused by a growth defect and delayed passage through START due to delayed G1 cyclin accumulation. Aneuploidy, a chromosome content that is not a multiple of the haploid karyotype, is associated with reduced fitness in all organisms analyzed to date. In budding yeast aneuploidy causes cell proliferation defects, with many different aneuploid strains exhibiting a delay in G1, a cell cycle stage governed by extracellular cues, growth rate, and cell cycle events. Here we characterize this G1 delay. We show that 10 of 14 aneuploid yeast strains exhibit a growth defect during G1. Furthermore, 10 of 14 aneuploid strains display a cell cycle entry delay that correlates with the size of the additional chromosome. This cell cycle entry delay is due to a delayed accumulation of G1 cyclins that can be suppressed by supplying cells with high levels of a G1 cyclin. Our results indicate that aneuploidy frequently interferes with the ability of cells to grow and, as with many other cellular stresses, entry into the cell cycle.
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Affiliation(s)
- Rebecca R Thorburn
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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36
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Rancati G, Pavelka N. Karyotypic changes as drivers and catalyzers of cellular evolvability: a perspective from non-pathogenic yeasts. Semin Cell Dev Biol 2013; 24:332-8. [PMID: 23403271 DOI: 10.1016/j.semcdb.2013.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/17/2013] [Accepted: 01/25/2013] [Indexed: 02/08/2023]
Abstract
In spite of the existence of multiple cellular mechanisms that ensure genome stability, thanks to the advent of quantitative genomic assays in the last decade, an unforeseen level of plasticity in cellular genomes has begun to emerge in many different fields of cell biology. Eukaryotic cells not only have a remarkable ability to change their karyotypes in response to various perturbations, but also these karyotypic changes impact cellular fitness and in some circumstances enable evolutionary adaptation. In this review, we focus on recent findings in non-pathogenic yeasts indicating that karyotypic changes generate selectable phenotypic variation and alter genomic instability. Based on these findings, we propose that in highly stressful and thus strongly selective environments karyotypic changes could act both as a driver and as a catalyzer of cellular adaptation, i.e. karyotypic changes drive large phenotypic leaps and at the same time catalyze the accumulation of even more genotypic and karyotypic changes.
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Affiliation(s)
- Giulia Rancati
- Institute of Medical Biology, Agency of Science, Technology and Research, 8A Biomedical Grove, Singapore 138648, Singapore.
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37
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Tang YC, Amon A. Gene copy-number alterations: a cost-benefit analysis. Cell 2013; 152:394-405. [PMID: 23374337 PMCID: PMC3641674 DOI: 10.1016/j.cell.2012.11.043] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/22/2012] [Accepted: 11/01/2012] [Indexed: 11/25/2022]
Abstract
Changes in DNA copy number, whether confined to specific genes or affecting whole chromosomes, have been identified as causes of diseases and developmental abnormalities and as sources of adaptive potential. Here, we discuss the costs and benefits of DNA copy-number alterations. Changes in DNA copy number are largely detrimental. Amplifications or deletions of specific genes can elicit discrete defects. Large-scale changes in DNA copy number can also cause detrimental phenotypes that are due to the cumulative effects of copy-number alterations of many genes simultaneously. On the other hand, studies in microorganisms show that DNA copy-number alterations can be beneficial, increasing survival under selective pressure. As DNA copy-number alterations underlie many human diseases, we will end with a discussion of gene copy-number changes as therapeutic targets.
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Affiliation(s)
- Yun-Chi Tang
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-561, 500 Main Street, Cambridge, MA 02139, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-561, 500 Main Street, Cambridge, MA 02139, USA
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38
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Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Mol Syst Biol 2013; 8:608. [PMID: 22968442 PMCID: PMC3472693 DOI: 10.1038/msb.2012.40] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/01/2012] [Indexed: 12/26/2022] Open
Abstract
Genomic, transcriptomic and proteomic profiles of human aneuploid cells reveal that mRNA levels increase with gene copy number, but protein levels are partially compensated. Aneuploid cells also exhibit common alterations in several pathways, including an activation of autophagy. ![]()
Comparative genomics, transcriptomics and proteomics of model human aneuploid cell lines reveal that whereas the mRNA levels increase proportionally to the chromosome copy numbers, the abundance of some proteins (e.g., subunits of complexes) is decreased to normal levels. The pattern of up- and downregulated pathways was similar in all analyzed aneuploids, indicating that it might be possible to use aneuploidy as a cancer treatment target regardless of the exact chromosome composition of cancer cells. Autophagy, in particular p62-dependent selective autophagy, is activated in aneuploid human cell lines.
Extra chromosome copies markedly alter the physiology of eukaryotic cells, but the underlying reasons are not well understood. We created human trisomic and tetrasomic cell lines and determined the quantitative changes in their transcriptome and proteome in comparison with their diploid counterparts. We found that whereas transcription levels reflect the chromosome copy number changes, the abundance of some proteins, such as subunits of protein complexes and protein kinases, is reduced toward diploid levels. Furthermore, using the quantitative data we investigated the changes of cellular pathways in response to aneuploidy. This analysis revealed specific and uniform alterations in pathway regulation in cells with extra chromosomes. For example, the DNA and RNA metabolism pathways were downregulated, whereas several pathways such as energy metabolism, membrane metabolism and lysosomal pathways were upregulated. In particular, we found that the p62-dependent selective autophagy is activated in the human trisomic and tetrasomic cells. Our data present the first broad proteomic analysis of human cells with abnormal karyotypes and suggest a uniform cellular response to the presence of an extra chromosome.
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39
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Abstract
Gains or losses of entire chromosomes lead to aneuploidy, a condition tolerated poorly in all eukaryotes analyzed to date. How aneuploidy affects organismal and cellular physiology is poorly understood. We found that aneuploid budding yeast cells are under proteotoxic stress. Aneuploid strains are prone to aggregation of endogenous proteins as well as of ectopically expressed hard-to-fold proteins such as those containing polyglutamine (polyQ) stretches. Protein aggregate formation in aneuploid yeast strains is likely due to limiting protein quality-control systems, since the proteasome and at least one chaperone family, Hsp90, are compromised in many aneuploid strains. The link between aneuploidy and the formation and persistence of protein aggregates could have important implications for diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Ana B Oromendia
- Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, USA
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40
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Lane AB, Clarke DJ. Genome instability: does genetic diversity amplification drive tumorigenesis? Bioessays 2012; 34:963-72. [PMID: 22948965 DOI: 10.1002/bies.201200082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent data show that catastrophic events during one cell cycle can cause massive genome damage producing viable clones with unstable genomes. This is in contrast with the traditional view that tumorigenesis requires a long-term process in which mutations gradually accumulate over decades. These sudden events are likely to result in a large increase in genomic diversity within a relatively short time, providing the opportunity for selective advantages to be gained by a subset of cells within a population. This genetic diversity amplification, arising from a single aberrant cell cycle, may drive a population conversion from benign to malignant. However, there is likely a period of relative genome stability during the clonal expansion of tumors - this may provide an opportunity for therapeutic intervention, especially if mechanisms that limit tolerance of aneuploidy are exploited.
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Affiliation(s)
- Andrew B Lane
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, USA
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41
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Ngamskulrungroj P, Chang Y, Hansen B, Bugge C, Fischer E, Kwon-Chung KJ. Cryptococcus neoformans Yop1 , an endoplasmic reticulum curvature-stabilizing protein, participates with Sey1 in influencing fluconazole-induced disomy formation. FEMS Yeast Res 2012; 12:748-54. [PMID: 22731401 DOI: 10.1111/j.1567-1364.2012.00824.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/07/2012] [Accepted: 06/19/2012] [Indexed: 11/28/2022] Open
Abstract
Cryptococcus neoformans, an opportunistic fungal pathogen, manifests an intrinsic adaptive mechanism of resistance toward fluconazole (FLC) termed heteroresistance. Heteroresistance is characterized by the emergence of minor resistant subpopulations at levels of FLC that are higher than the strain's minimum inhibitory concentration. The heteroresistant clones that tolerate high concentrations of FLC often contain disomic chromosome 4 (Chr4). SEY1 , GLO3 , and GCS2 on Chr4 are responsible for endoplasmic reticulum (ER) integrity and important for Chr4 disomy formation under FLC stress. We sought an evidence of a direct relationship between ER morphology and Chr4 disomy formation. Deletion of the YOP1 gene on Chr7, which encodes an ER curvature-stabilizing protein that interacts with Sey1 , perturbed ER morphology without affecting FLC susceptibility or the frequency of FLC-induced disomies. However, deletion of both YOP1 and SEY1 , not only perturbed ER morphology more severely than in sey1∆ or yop1∆ strains, but also abrogated the FLC-induced disomy. Although the heteroresistance phenotype was retained in the sey1∆yop1∆ strains, tolerance to FLC appeared to have resulted not from chromosome duplication but from gene amplification restricted to the region surrounding ERG11 on Chr1. These data support the importance of ER integrity in C. neoformans for the formation of disomy under FLC stress.
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Affiliation(s)
- Popchai Ngamskulrungroj
- Molecular Microbiology Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA
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42
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Abstract
Deviation from a balanced genome by either gain or loss of entire chromosomes is generally tolerated poorly in all eukaryotic systems studied to date. Errors in mitotic or meiotic cell division lead to aneuploidy, which places a burden of additional or insufficient gene products from the missegregated chromosomes on the daughter cells. The burden of aneuploidy often manifests itself as impaired fitness of individual cells and whole organisms, in which abnormal development is also characteristic. However, most human cancers, noted for their rapid growth, also display various levels of aneuploidy. Here we discuss the detrimental, potentially beneficial, and sometimes puzzling effects of aneuploidy on cellular and organismal fitness and tissue function as well as its role in diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Jake J Siegel
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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43
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Tange Y, Kurabayashi A, Goto B, Hoe KL, Kim DU, Park HO, Hayles J, Chikashige Y, Tsutumi C, Hiraoka Y, Yamao F, Nurse P, Niwa O. The CCR4-NOT complex is implicated in the viability of aneuploid yeasts. PLoS Genet 2012; 8:e1002776. [PMID: 22737087 PMCID: PMC3380822 DOI: 10.1371/journal.pgen.1002776] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/05/2012] [Indexed: 12/23/2022] Open
Abstract
To identify the genes required to sustain aneuploid viability, we screened a deletion library of non-essential genes in the fission yeast Schizosaccharomyces pombe, in which most types of aneuploidy are eventually lethal to the cell. Aneuploids remain viable for a period of time and can form colonies by reducing the extent of the aneuploidy. We hypothesized that a reduction in colony formation efficiency could be used to screen for gene deletions that compromise aneuploid viability. Deletion mutants were used to measure the effects on the viability of spores derived from triploid meiosis and from a chromosome instability mutant. We found that the CCR4-NOT complex, an evolutionarily conserved general regulator of mRNA turnover, and other related factors, including poly(A)-specific nuclease for mRNA decay, are involved in aneuploid viability. Defective mutations in CCR4-NOT complex components in the distantly related yeast Saccharomyces cerevisiae also affected the viability of spores produced from triploid cells, suggesting that this complex has a conserved role in aneuploids. In addition, our findings suggest that the genes required for homologous recombination repair are important for aneuploid viability.
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Affiliation(s)
- Yoshie Tange
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | | | - Bunshiro Goto
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Kwang-Lae Hoe
- Chungnam National University, Graduate School of New Drug Discovery and Development, Yusong-gu, Daejeon, Korea
| | - Dong-Uk Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong-gu, Daejeon, Korea
| | | | - Jacqueline Hayles
- Cancer Research UK, The London Research Institute, London, United Kingdom
| | - Yuji Chikashige
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Chihiro Tsutumi
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Fumiaki Yamao
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Paul Nurse
- Cancer Research UK, The London Research Institute, London, United Kingdom
- The Rockefeller University, New York, New York, United States of America
| | - Osami Niwa
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
- The Rockefeller University, New York, New York, United States of America
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44
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Losing balance: the origin and impact of aneuploidy in cancer. EMBO Rep 2012; 13:501-14. [PMID: 22565320 DOI: 10.1038/embor.2012.55] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/03/2012] [Indexed: 02/06/2023] Open
Abstract
Most solid human tumours are aneuploid, that is, they contain an abnormal number of chromosomes. Paradoxically, however, aneuploidy has been reported to induce a stress response that suppresses cellular proliferation in vitro. Here, we review the progress in our understanding of the causes and effects of aneuploidy in cancer and discuss how, in specific contexts, aneuploidy can provide a growth advantage and facilitate cellular transformation. We also explore the emerging possibilities for targeting the cause or consequences of aneuploidy therapeutically.
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45
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Gordon DJ, Resio B, Pellman D. Causes and consequences of aneuploidy in cancer. Nat Rev Genet 2012; 13:189-203. [PMID: 22269907 DOI: 10.1038/nrg3123] [Citation(s) in RCA: 611] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic instability, which includes both numerical and structural chromosomal abnormalities, is a hallmark of cancer. Whereas the structural chromosome rearrangements have received substantial attention, the role of whole-chromosome aneuploidy in cancer is much less well-understood. Here we review recent progress in understanding the roles of whole-chromosome aneuploidy in cancer, including the mechanistic causes of aneuploidy, the cellular responses to chromosome gains or losses and how cells might adapt to tolerate these usually detrimental alterations. We also explore the role of aneuploidy in cellular transformation and discuss the possibility of developing aneuploidy-specific therapies.
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Affiliation(s)
- David J Gordon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
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46
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Sheltzer JM, Amon A. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet 2011; 27:446-53. [PMID: 21872963 DOI: 10.1016/j.tig.2011.07.003] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/21/2011] [Accepted: 07/26/2011] [Indexed: 01/09/2023]
Abstract
Aneuploidy has a paradoxical effect on cell proliferation. In all normal cells analyzed to date, aneuploidy has been found to decrease the rate of cell proliferation. Yet, aneuploidy is also a hallmark of cancer, a disease of enhanced proliferative capacity, and aneuploid cells are frequently recovered following the experimental evolution of microorganisms. Thus, in certain contexts, aneuploidy might also have growth-advantageous properties. New models of aneuploidy and chromosomal instability have shed light on the diverse effects that karyotypic imbalances have on cellular phenotypes, and suggest novel ways of understanding the role of aneuploidy in development and disease.
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Affiliation(s)
- Jason M Sheltzer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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47
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Sheltzer JM, Blank HM, Pfau SJ, Tange Y, George BM, Humpton TJ, Brito IL, Hiraoka Y, Niwa O, Amon A. Aneuploidy drives genomic instability in yeast. Science 2011; 333:1026-30. [PMID: 21852501 PMCID: PMC3278960 DOI: 10.1126/science.1206412] [Citation(s) in RCA: 301] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Aneuploidy decreases cellular fitness, yet it is also associated with cancer, a disease of enhanced proliferative capacity. To investigate one mechanism by which aneuploidy could contribute to tumorigenesis, we examined the effects of aneuploidy on genomic stability. We analyzed 13 budding yeast strains that carry extra copies of single chromosomes and found that all aneuploid strains exhibited one or more forms of genomic instability. Most strains displayed increased chromosome loss and mitotic recombination, as well as defective DNA damage repair. Aneuploid fission yeast strains also exhibited defects in mitotic recombination. Aneuploidy-induced genomic instability could facilitate the development of genetic alterations that drive malignant growth in cancer.
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Affiliation(s)
- Jason M. Sheltzer
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heidi M. Blank
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah J. Pfau
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yoshie Tange
- Graduate School of Frontier Biosciences, Osaka University 1–3 Yamadaoka, Suita 565-0871, Japan
| | - Benson M. George
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Timothy J. Humpton
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ilana L. Brito
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University 1–3 Yamadaoka, Suita 565-0871, Japan
- Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Osami Niwa
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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48
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Aberrant genome size and instability of Phytophthora ramorum oospore progenies. Fungal Genet Biol 2011; 48:537-43. [DOI: 10.1016/j.fgb.2011.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 11/22/2022]
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49
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Tang YC, Williams BR, Siegel JJ, Amon A. Identification of aneuploidy-selective antiproliferation compounds. Cell 2011; 144:499-512. [PMID: 21315436 PMCID: PMC3532042 DOI: 10.1016/j.cell.2011.01.017] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 11/22/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
Abstract
Aneuploidy, an incorrect chromosome number, is a hallmark of cancer. Compounds that cause lethality in aneuploid, but not euploid, cells could therefore provide new cancer therapies. We have identified the energy stress-inducing agent AICAR, the protein folding inhibitor 17-AAG, and the autophagy inhibitor chloroquine as exhibiting this property. AICAR induces p53-mediated apoptosis in primary mouse embryonic fibroblasts (MEFs) trisomic for chromosome 1, 13, 16, or 19. AICAR and 17-AAG, especially when combined, also show efficacy against aneuploid human cancer cell lines. Our results suggest that compounds that interfere with pathways that are essential for the survival of aneuploid cells could serve as a new treatment strategy against a broad spectrum of human tumors.
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Affiliation(s)
- Yun-Chi Tang
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
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50
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Torres EM, Williams BR, Tang YC, Amon A. Thoughts on aneuploidy. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2011; 75:445-51. [PMID: 21289044 PMCID: PMC3293208 DOI: 10.1101/sqb.2010.75.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aneuploidy refers to karyotypic abnormalities characterized by gain or loss of individual chromosomes. This condition is associated with disease and death in all organisms in which it has been studied. We have characterized the effects of aneuploidy on yeast and primary mouse cells and found it to be detrimental at the cellular level. Furthermore, we find that aneuploid cells exhibit phenotypes consistent with increased energy need and proteotoxic stress. These observations, together with the finding that the additional chromosomes found in aneuploid cells are active, lead us to propose that aneuploidy causes an increased burden on protein synthesis and protein quality-control pathways and so induces an aneuploidy stress response.
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Affiliation(s)
- E M Torres
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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