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Wang J, Thomas HR, Chen Y, Percival SM, Waldrep SC, Ramaker RC, Thompson RG, Cooper SJ, Chong Z, Parant JM. Reduced sister chromatid cohesion acts as a tumor penetrance modifier. PLoS Genet 2022; 18:e1010341. [PMID: 35994499 PMCID: PMC9436123 DOI: 10.1371/journal.pgen.1010341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/01/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Sister chromatid cohesion (SCC) is an important process in chromosome segregation. ESCO2 is essential for establishment of SCC and is often deleted/altered in human cancers. We demonstrate that esco2 haploinsufficiency results in reduced SCC and accelerates the timing of tumor onset in both zebrafish and mouse p53 heterozygous null models, but not in p53 homozygous mutant or wild-type animals. These data indicate that esco2 haploinsufficiency accelerates tumor onset in a loss of heterozygosity (LOH) sensitive background. Analysis of The Cancer Genome Atlas (TCGA) confirmed ESCO2 deficient tumors have elevated number of LOH events throughout the genome. Further, we demonstrated heterozygous loss of sgo1, important in maintaining SCC, also results in reduced SCC and accelerated tumor formation in a p53 heterozygous background. Surprisingly, while we did observe elevated levels of chromosome missegregation and micronuclei formation in esco2 heterozygous mutant animals, this chromosomal instability did not contribute to the accelerated tumor onset in a p53 heterozygous background. Interestingly, SCC also plays a role in homologous recombination, and we did observe elevated levels of mitotic recombination derived p53 LOH in tumors from esco2 haploinsufficient animals; as well as elevated levels of mitotic recombination throughout the genome of human ESCO2 deficient tumors. Together these data suggest that reduced SCC contributes to accelerated tumor penetrance through elevated mitotic recombination. Tumorigenesis often involves the inactivation of tumor suppressor genes. This often encompasses an inactivation mutation in one allele and loss of the other wild-type allele, referred to as loss of heterozygosity (LOH). The rate at which the cells lose the wild-type allele can influence the timing of tumor onset, and therefore an indicator of a patient’s risk of cancer. Factors that influence this process could be used as a predictive indicator of cancer risk, however these factors are still unclear. We demonstrate that partial impairment of sister chromatid cohesion (SCC), a fundamental component of the chromosome segregation in mitosis and homologous recombination repair, enhanced tumorigenesis. Our data suggest this is through elevated levels of mitotic recombination derived p53 LOH. This study emphasizes the importance of understanding how impaired SCC, mitotic recombination rates, and LOH rates influence cancer risk.
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Yu Chen
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - Stefanie M. Percival
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Ryne C. Ramaker
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Sara J. Cooper
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Zechen Chong
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- * E-mail:
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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Kouprina N, Liskovykh M, Petrov N, Larionov V. Human artificial chromosome (HAC) for measuring chromosome instability (CIN) and identification of genes required for proper chromosome transmission. Exp Cell Res 2019; 387:111805. [PMID: 31877307 DOI: 10.1016/j.yexcr.2019.111805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 01/24/2023]
Abstract
Chromosomal instability (CIN) is one of the characteristics of cancer inherent for tumor initiation and progression, which is defined as a persistent, high rate of gain/loss of whole chromosomes. In the vast majority of human tumors the molecular basis of CIN remains unknown. The development of a conceptually simple colony color sectoring assay that measures yeast artificial chromosome (YAC) loss provided a powerful genetic tool to assess the rate of chromosome mis-segregation and also identified 937 yeast genes involved in this process. Similarly, a human artificial chromosome (HAC)-based assay has been recently developed and applied to quantify chromosome mis-segregation events in human cells. This assay allowed identification of novel human CIN genes in the library of protein kinases. Among them are PINK1, TRIO, IRAK1, PNCK, and TAOK1. The HAC-based assay may be applied to screen siRNA, shRNA and CRISPR-based libraries to identify the complete spectrum of CIN genes. This will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Nikolai Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
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4
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Tsai HJ, Nelliat A. A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation. Genes (Basel) 2019; 10:E787. [PMID: 31658789 PMCID: PMC6826469 DOI: 10.3390/genes10100787] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/28/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Aneuploidy, a deviation from a balanced genome by either gain or loss of chromosomes, is generally associated with impaired fitness and developmental defects in eukaryotic organisms. While the general physiological impact of aneuploidy remains largely elusive, many phenotypes associated with aneuploidy link to a common theme of stress adaptation. Here, we review previously identified mechanisms and observations related to aneuploidy, focusing on the highly diverse eukaryotes, fungi. Fungi, which have conquered virtually all environments, including several hostile ecological niches, exhibit widespread aneuploidy and employ it as an adaptive strategy under severe stress. Gambling with the balance between genome plasticity and stability has its cost and in fact, most aneuploidies have fitness defects. How can this fitness defect be reconciled with the prevalence of aneuploidy in fungi? It is likely that the fitness cost of the extra chromosomes is outweighed by the advantage they confer under life-threatening stresses. In fact, once the selective pressures are withdrawn, aneuploidy is often lost and replaced by less drastic mutations that possibly incur a lower fitness cost. We discuss representative examples across hostile environments, including medically and industrially relevant cases, to highlight potential adaptive mechanisms in aneuploid yeast.
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Affiliation(s)
- Hung-Ji Tsai
- Institute of Microbiology and Infection, and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Anjali Nelliat
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Liskovykh M, Goncharov NV, Petrov N, Aksenova V, Pegoraro G, Ozbun LL, Reinhold WC, Varma S, Dasso M, Kumeiko V, Masumoto H, Earnshaw WC, Larionov V, Kouprina N. A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission. Genome Res 2019; 29:1719-1732. [PMID: 31515286 PMCID: PMC6771407 DOI: 10.1101/gr.254276.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/21/2019] [Indexed: 12/30/2022]
Abstract
One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations, and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partly because not all genes controlling chromosome transmission have yet been identified. To address this question, we developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen an siRNA library of protein kinases, we identified PINK1, TRIO, IRAK1, PNCK, and TAOK1 as potential novel genes whose knockdown induces various mitotic abnormalities and results in chromosome loss. The HAC-based assay can be applied for screening different siRNA libraries (cell cycle regulation, DNA damage response, epigenetics, and transcription factors) to identify additional genes involved in CIN. Identification of the complete spectrum of CIN genes will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nikolay V. Goncharov
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;,School of Biomedicine, Far Eastern Federal University, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690000, Russia
| | - Nikolai Petrov
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Laurent L. Ozbun
- High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William C. Reinhold
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Vadim Kumeiko
- School of Biomedicine, Far Eastern Federal University, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690000, Russia
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818d, Japan
| | - William C. Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Xu H, Di Antonio M, McKinney S, Mathew V, Ho B, O'Neil NJ, Santos ND, Silvester J, Wei V, Garcia J, Kabeer F, Lai D, Soriano P, Banáth J, Chiu DS, Yap D, Le DD, Ye FB, Zhang A, Thu K, Soong J, Lin SC, Tsai AHC, Osako T, Algara T, Saunders DN, Wong J, Xian J, Bally MB, Brenton JD, Brown GW, Shah SP, Cescon D, Mak TW, Caldas C, Stirling PC, Hieter P, Balasubramanian S, Aparicio S. CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours. Nat Commun 2017; 8:14432. [PMID: 28211448 PMCID: PMC5321743 DOI: 10.1038/ncomms14432] [Citation(s) in RCA: 343] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 12/28/2016] [Indexed: 12/29/2022] Open
Abstract
G-quadruplex DNAs form four-stranded helical structures and are proposed to play key roles in different cellular processes. Targeting G-quadruplex DNAs for cancer treatment is a very promising prospect. Here, we show that CX-5461 is a G-quadruplex stabilizer, with specific toxicity against BRCA deficiencies in cancer cells and polyclonal patient-derived xenograft models, including tumours resistant to PARP inhibition. Exposure to CX-5461, and its related drug CX-3543, blocks replication forks and induces ssDNA gaps or breaks. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality. These data strengthen the concept of G4 targeting as a therapeutic approach, specifically for targeting HR and NHEJ deficient cancers and other tumours deficient for DNA damage repair. CX-5461 is now in advanced phase I clinical trial for patients with BRCA1/2 deficient tumours (Canadian trial, NCT02719977, opened May 2016).
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Affiliation(s)
- Hong Xu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Marco Di Antonio
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Veena Mathew
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
| | - Nigel J. O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Nancy Dos Santos
- Advanced Therapeutics, BC Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jennifer Silvester
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - Vivien Wei
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jessica Garcia
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Farhia Kabeer
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Priscilla Soriano
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Judit Banáth
- Department of Integrative Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Derek S. Chiu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Daniel D. Le
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Frank B. Ye
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Anni Zhang
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Kelsie Thu
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - John Soong
- Senhwa Biosciences, Inc., 9 F, No.205-1, Section 3, Peihsin Road, Hsintien District, New Taipei City 23143, Taiwan R.O.C
| | - Shu-chuan Lin
- Senhwa Biosciences, Inc., 9 F, No.205-1, Section 3, Peihsin Road, Hsintien District, New Taipei City 23143, Taiwan R.O.C
| | - Angela Hsin Chin Tsai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Tomo Osako
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Teresa Algara
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Darren N. Saunders
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jason Wong
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jian Xian
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Marcel B. Bally
- Advanced Therapeutics, BC Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - James D. Brenton
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
| | - Sohrab P. Shah
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - David Cescon
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Canada M5S 1A8
| | - Tak W. Mak
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - Carlos Caldas
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Peter C. Stirling
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Phil Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
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7
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Duffy S, Fam HK, Wang YK, Styles EB, Kim JH, Ang JS, Singh T, Larionov V, Shah SP, Andrews B, Boerkoel CF, Hieter P. Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. Proc Natl Acad Sci U S A 2016; 113:9967-76. [PMID: 27551064 PMCID: PMC5018746 DOI: 10.1073/pnas.1611839113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Rhabdomyosarcoma lines with elevated human Tdp1 levels also exhibit CIN that can be partially rescued by siRNA-mediated knockdown of TDP1 Overexpression of dCIN genes represents a genetic vulnerability that could be leveraged for selective killing of cancer cells through targeting of an unlinked synthetic dosage lethal (SDL) partner. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1. One gene was the histone deacetylase RPD3, for which there are known inhibitors. Both HT1080 cells overexpressing hTDP1 and rhabdomyosarcoma cells with elevated levels of hTdp1 were more sensitive to histone deacetylase inhibitors valproic acid (VPA) and trichostatin A (TSA), recapitulating the SDL interaction in human cells and suggesting VPA and TSA as potential therapeutic agents for tumors with elevated levels of hTdp1. The catalog of dCIN genes presented here provides a candidate list to identify genes that cause CIN when overexpressed in cancer, which can then be leveraged through SDL to selectively target tumors.
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Affiliation(s)
- Supipi Duffy
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Hok Khim Fam
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Yi Kan Wang
- BC Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Erin B Styles
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Jung-Hyun Kim
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - J Sidney Ang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Tejomayee Singh
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Vladimir Larionov
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | | | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Cornelius F Boerkoel
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
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8
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Dosage Mutator Genes in Saccharomyces cerevisiae: A Novel Mutator Mode-of-Action of the Mph1 DNA Helicase. Genetics 2016; 204:975-986. [PMID: 27585847 PMCID: PMC5105872 DOI: 10.1534/genetics.116.192211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/25/2016] [Indexed: 01/25/2023] Open
Abstract
Mutations that cause genome instability are considered important predisposing events that contribute to initiation and progression of cancer. Genome instability arises either due to defects in genes that cause an increased mutation rate (mutator phenotype), or defects in genes that cause chromosome instability (CIN). To extend the catalog of genome instability genes, we systematically explored the effects of gene overexpression on mutation rate, using a forward-mutation screen in budding yeast. We screened ∼5100 plasmids, each overexpressing a unique single gene, and characterized the five strongest mutators, MPH1 (mutator phenotype 1), RRM3, UBP12, PIF1, and DNA2 We show that, for MPH1, the yeast homolog of Fanconi Anemia complementation group M (FANCM), the overexpression mutator phenotype is distinct from that of mph1Δ. Moreover, while four of our top hits encode DNA helicases, the overexpression of 48 other DNA helicases did not cause a mutator phenotype, suggesting this is not a general property of helicases. For Mph1 overexpression, helicase activity was not required for the mutator phenotype; in contrast Mph1 DEAH-box function was required for hypermutation. Mutagenesis by MPH1 overexpression was independent of translesion synthesis (TLS), but was suppressed by overexpression of RAD27, a conserved flap endonuclease. We propose that binding of DNA flap structures by excess Mph1 may block Rad27 action, creating a mutator phenotype that phenocopies rad27Δ. We believe this represents a novel mutator mode-of-action and opens up new prospects to understand how upregulation of DNA repair proteins may contribute to mutagenesis.
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Abstract
Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer.
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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Covo S, Puccia CM, Argueso JL, Gordenin DA, Resnick MA. The sister chromatid cohesion pathway suppresses multiple chromosome gain and chromosome amplification. Genetics 2014; 196:373-84. [PMID: 24298060 PMCID: PMC3914611 DOI: 10.1534/genetics.113.159202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022] Open
Abstract
Gain or loss of chromosomes resulting in aneuploidy can be important factors in cancer and adaptive evolution. Although chromosome gain is a frequent event in eukaryotes, there is limited information on its genetic control. Here we measured the rates of chromosome gain in wild-type yeast and sister chromatid cohesion (SCC) compromised strains. SCC tethers the newly replicated chromatids until anaphase via the cohesin complex. Chromosome gain was measured by selecting and characterizing copper-resistant colonies that emerged due to increased copies of the metallothionein gene CUP1. Although all defective SCC diploid strains exhibited increased rates of chromosome gain, there were 15-fold differences between them. Of all mutants examined, a hypomorphic mutation at the cohesin complex caused the highest rate of chromosome gain while disruption of WPL1, an important regulator of SCC and chromosome condensation, resulted in the smallest increase in chromosome gain. In addition to defects in SCC, yeast cell type contributed significantly to chromosome gain, with the greatest rates observed for homozygous mating-type diploids, followed by heterozygous mating type, and smallest in haploids. In fact, wpl1-deficient haploids did not show any difference in chromosome gain rates compared to wild-type haploids. Genomic analysis of copper-resistant colonies revealed that the "driver" chromosome for which selection was applied could be amplified to over five copies per diploid cell. In addition, an increase in the expected driver chromosome was often accompanied by a gain of a small number of other chromosomes. We suggest that while chromosome gain due to SCC malfunction can have negative effects through gene imbalance, it could also facilitate opportunities for adaptive changes. In multicellular organisms, both factors could lead to somatic diseases including cancer.
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Affiliation(s)
- Shay Covo
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Christopher M. Puccia
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Dmitry A. Gordenin
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael A. Resnick
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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Kouprina N, Tomilin AN, Masumoto H, Earnshaw WC, Larionov V. Human artificial chromosome-based gene delivery vectors for biomedicine and biotechnology. Expert Opin Drug Deliv 2014; 11:517-35. [DOI: 10.1517/17425247.2014.882314] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FCP, Johnson JR, Bloom K, Krogan NJ. Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Cell Rep 2013; 3:2168-78. [PMID: 23746449 DOI: 10.1016/j.celrep.2013.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/27/2013] [Accepted: 05/06/2013] [Indexed: 01/08/2023] Open
Abstract
Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA). We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.
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Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Waltham, MA 02454, USA.
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O'Neil NJ, van Pel DM, Hieter P. Synthetic lethality and cancer: cohesin and PARP at the replication fork. Trends Genet 2013; 29:290-7. [PMID: 23333522 PMCID: PMC3868440 DOI: 10.1016/j.tig.2012.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/28/2012] [Accepted: 12/14/2012] [Indexed: 01/19/2023]
Abstract
Cohesins are mutated in a significant number of tumors of various types making them attractive targets for chemotherapeutic intervention. However, cohesins have a spectrum of cellular roles including sister chromatid cohesion, transcription, replication, and repair. Which of these roles are central to cancer biology and which roles can be exploited for therapeutic intervention? Genetic interaction networks in yeast have identified synthetic lethal interactions between mutations in cohesin and replication fork mediators. These interactions are conserved in worms and in human cells suggesting that inhibition of replication fork stability mediators such as poly (ADP-ribose) polymerase (PARP) could result in the specific killing of tumors with cohesin mutations. These findings also highlight the utility of genetic interaction networks in model organisms for the identification of clinically relevant interactions. Here, we review this type of approach, emphasizing the power of synthetic lethal interactions to reveal new avenues for developing cancer therapeutics.
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Affiliation(s)
- Nigel J O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Saccharomyces cerevisiae genetics predicts candidate therapeutic genetic interactions at the mammalian replication fork. G3-GENES GENOMES GENETICS 2013; 3:273-82. [PMID: 23390603 PMCID: PMC3564987 DOI: 10.1534/g3.112.004754] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/09/2012] [Indexed: 12/15/2022]
Abstract
The concept of synthetic lethality has gained popularity as a rational guide for predicting chemotherapeutic targets based on negative genetic interactions between tumor-specific somatic mutations and a second-site target gene. One hallmark of most cancers that can be exploited by chemotherapies is chromosome instability (CIN). Because chromosome replication, maintenance, and segregation represent conserved and cell-essential processes, they can be modeled effectively in simpler eukaryotes such as Saccharomyces cerevisiae. Here we analyze and extend genetic networks of CIN cancer gene orthologs in yeast, focusing on essential genes. This identifies hub genes and processes that are candidate targets for synthetic lethal killing of cancer cells with defined somatic mutations. One hub process in these networks is DNA replication. A nonessential, fork-associated scaffold, CTF4, is among the most highly connected genes. As Ctf4 lacks enzymatic activity, potentially limiting its development as a therapeutic target, we exploited its function as a physical interaction hub to rationally predict synthetic lethal interactions between essential Ctf4-binding proteins and CIN cancer gene orthologs. We then validated a subset of predicted genetic interactions in a human colorectal cancer cell line, showing that siRNA-mediated knockdown of MRE11A sensitizes cells to depletion of various replication fork-associated proteins. Overall, this work describes methods to identify, predict, and validate in cancer cells candidate therapeutic targets for tumors with known somatic mutations in CIN genes using data from yeast. We affirm not only replication stress but also the targeting of DNA replication fork proteins themselves as potential targets for anticancer therapeutic development.
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Biogenesis of RNA polymerases II and III requires the conserved GPN small GTPases in Saccharomyces cerevisiae. Genetics 2012; 193:853-64. [PMID: 23267056 PMCID: PMC3584002 DOI: 10.1534/genetics.112.148726] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The GPN proteins are a poorly characterized and deeply evolutionarily conserved family of three paralogous small GTPases, Gpn1, 2, and 3. The founding member, GPN1/NPA3/XAB1, is proposed to function in nuclear import of RNA polymerase II along with a recently described protein called Iwr1. Here we show that the previously uncharacterized protein Gpn2 binds both Gpn3 and Npa3/Gpn1 and that temperature-sensitive alleles of Saccharomyces cerevisiae GPN2 and GPN3 exhibit genetic interactions with RNA polymerase II mutants, hypersensitivity to transcription inhibition, and defects in RNA polymerase II nuclear localization. Importantly, we identify previously unrecognized RNA polymerase III localization defects in GPN2, GPN3, and IWR1 mutant backgrounds but find no localization defects of unrelated nuclear proteins or of RNA polymerase I. Previously, it was unclear whether the GPN proteins and Iwr1 had overlapping function in RNA polymerase II assembly or import. In this study, we show that the nuclear import defect of iwr1Δ, but not the GPN2 or GPN3 mutant defects, is partially suppressed by fusion of a nuclear localization signal to the RNA polymerase II subunit Rpb3. These data, combined with strong genetic interactions between GPN2 and IWR1, suggest that the GPN proteins function upstream of Iwr1 in RNA polymerase II and III biogenesis. We propose that the three GPN proteins execute a common, and likely essential, function in RNA polymerase assembly and transport.
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