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Zhang X, Kschischo M. Profiling Numerical and Structural Chromosomal Instability in Different Cancer Types. Methods Mol Biol 2024; 2825:345-360. [PMID: 38913320 DOI: 10.1007/978-1-0716-3946-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Many cancers display whole chromosome instability (W-CIN) and structural chromosomal instability (S-CIN), referring to increased rates of acquiring numerically and structurally abnormal chromosome changes. This protocol provides detailed steps to analyze the W-CIN and S-CIN across cancer types, intending to leverage large-scale bulk sequencing and SNP array data complemented with the computational models to gain a better understanding of W-CIN and S-CIN.
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Affiliation(s)
- Xiaoxiao Zhang
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Maik Kschischo
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany.
- Institute for Computer Science, University of Koblenz, Koblenz, Germany.
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2
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Kandala S, Ramos M, Voith von Voithenberg L, Diaz-Jimenez A, Chocarro S, Keding J, Brors B, Imbusch CD, Sotillo R. Chronic chromosome instability induced by Plk1 results in immune suppression in breast cancer. Cell Rep 2023; 42:113266. [PMID: 37979172 DOI: 10.1016/j.celrep.2023.113266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/28/2023] [Accepted: 09/28/2023] [Indexed: 11/20/2023] Open
Abstract
Chromosome instability (CIN) contributes to resistance to therapies and tumor evolution. Although natural killer (NK) cells can eliminate cells with complex karyotypes, high-CIN human tumors have an immunosuppressive phenotype. To understand which CIN-associated molecular features alter immune recognition during tumor evolution, we overexpress Polo-like kinase 1 (Plk1) in a Her2+ breast cancer model. These high-CIN tumors activate a senescence-associated secretory phenotype (SASP), upregulate PD-L1 and CD206, and induce non-cell-autonomous nuclear factor κB (NF-κβ) signaling, facilitating immune evasion. Single-cell RNA sequencing from pre-neoplastic mammary glands unveiled the presence of Arg1+ macrophages, NK cells with reduced effector functions, and increased resting regulatory T cell infiltration. We further show that high PLK1-expressing human breast tumors display gene expression patterns associated with SASP, NF-κβ signaling, and immune suppression. These findings underscore the need to understand the immune landscape in CIN tumors to identify more effective therapies, potentially combining immune checkpoint or NF-κβ inhibitors with current treatments.
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Affiliation(s)
- Sridhar Kandala
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lena Voith von Voithenberg
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Johanna Keding
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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3
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Distinct and Common Features of Numerical and Structural Chromosomal Instability across Different Cancer Types. Cancers (Basel) 2022; 14:cancers14061424. [PMID: 35326573 DOI: 10.3390/cancers14061424] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023] Open
Abstract
A large proportion of tumours is characterised by numerical or structural chromosomal instability (CIN), defined as an increased rate of gaining or losing whole chromosomes (W-CIN) or of accumulating structural aberrations (S-CIN). Both W-CIN and S-CIN are associated with tumourigenesis, cancer progression, treatment resistance and clinical outcome. Although W-CIN and S-CIN can co-occur, they are initiated by different molecular events. By analysing tumour genomic data from 33 cancer types, we show that the majority of tumours with high levels of W-CIN underwent whole genome doubling, whereas S-CIN levels are strongly associated with homologous recombination deficiency. Both CIN phenotypes are prognostic in several cancer types. Most drugs are less efficient in high-CIN cell lines, but we also report compounds and drugs which should be investigated as targets for W-CIN or S-CIN. By analysing associations between CIN and bio-molecular entities with pathway and gene expression levels, we complement gene signatures of CIN and report that the drug resistance gene CKS1B is strongly associated with S-CIN. Finally, we propose a potential copy number-dependent mechanism to activate the PI3K pathway in high-S-CIN tumours.
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4
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Piemonte KM, Anstine LJ, Keri RA. Centrosome Aberrations as Drivers of Chromosomal Instability in Breast Cancer. Endocrinology 2021; 162:6381103. [PMID: 34606589 PMCID: PMC8557634 DOI: 10.1210/endocr/bqab208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Chromosomal instability (CIN), or the dynamic change in chromosome number and composition, has been observed in cancer for decades. Recently, this phenomenon has been implicated as facilitating the acquisition of cancer hallmarks and enabling the formation of aggressive disease. Hence, CIN has the potential to serve as a therapeutic target for a wide range of cancers. CIN in cancer often occurs as a result of disrupting key regulators of mitotic fidelity and faithful chromosome segregation. As a consequence of their essential roles in mitosis, dysfunctional centrosomes can induce and maintain CIN. Centrosome defects are common in breast cancer, a heterogeneous disease characterized by high CIN. These defects include amplification, structural defects, and loss of primary cilium nucleation. Recent studies have begun to illuminate the ability of centrosome aberrations to instigate genomic flux in breast cancer cells and the tumor evolution associated with aggressive disease and poor patient outcomes. Here, we review the role of CIN in breast cancer, the processes by which centrosome defects contribute to CIN in this disease, and the emerging therapeutic approaches that are being developed to capitalize upon such aberrations.
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Affiliation(s)
- Katrina M Piemonte
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Lindsey J Anstine
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Correspondence: Ruth A. Keri, PhD, Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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5
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Genome instability in multiple myeloma. Leukemia 2020; 34:2887-2897. [PMID: 32651540 DOI: 10.1038/s41375-020-0921-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Multiple myeloma (MM) is an incurable plasma cell malignancy characterized by clonal proliferation of plasma cells and a heterogenous genomic landscape. Copy number and structural changes due to chromosomal instability (CIN) are common features of MM. In this review, we describe how primary and secondary genetic events caused by CIN can contribute to increased instability across the genome of malignant plasma cells; with a focus on specific driver genomic events, and how they interfere with cell-cycle checkpoints, to prompt accelerated proliferation. We also provide insight into other forms of CIN, such as chromothripsis and chromoplexy. We evaluate how the tumor microenvironment can contribute to a further increase in chromosomal instability in myeloma cells. Lastly, we highlight the role of certain mutational signatures in leading to high mutation rate and genome instability in certain MM patients. We suggest that assessing CIN in MM and its precursors states may help improve predicting the risk of progression to symptomatic disease and relapse and identifying future therapeutic targets.
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6
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Dalayed Effects of Antitumor Drug Paclitaxel on the Hereditary Material and Hemopoietic System of CBA Mice. Bull Exp Biol Med 2020; 169:43-47. [PMID: 32488780 DOI: 10.1007/s10517-020-04820-x] [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: 07/05/2019] [Indexed: 10/24/2022]
Abstract
Paclitaxel in a single MTD of 40 mg/kg caused chromosome aberrations and genome changes (polyploidy) in the bone marrow cells of mice early and 3 months after the injection. The quantity of early precursors of erythropoiesis in the bone marrow decreased, as did their proliferative potential irrespective of the animal gender. Injection of paclitaxel in the MTD caused the development of bone marrow hypoplasia during the early period of observation (up to 14 days) and 3 months after injection.
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7
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Zheng L, Chen Z, Kawakami M, Chen Y, Roszik J, Mustachio LM, Kurie JM, Villalobos P, Lu W, Behrens C, Mino B, Solis LM, Silvester J, Thu KL, Cescon DW, Rodriguez-Canales J, Wistuba II, Mak TW, Liu X, Dmitrovsky E. Tyrosine Threonine Kinase Inhibition Eliminates Lung Cancers by Augmenting Apoptosis and Polyploidy. Mol Cancer Ther 2019; 18:1775-1786. [PMID: 31358662 DOI: 10.1158/1535-7163.mct-18-0864] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/18/2018] [Accepted: 07/24/2019] [Indexed: 01/11/2023]
Abstract
The spindle assembly checkpoint maintains genomic integrity. A key component is tyrosine threonine kinase (TTK, also known as Mps1). TTK antagonism is hypothesized to cause genomic instability and cell death. Interrogating The Cancer Genome Atlas revealed high TTK expression in lung adenocarcinomas and squamous cell cancers versus the normal lung (P < 0.001). This correlated with an unfavorable prognosis in examined lung adenocarcinoma cases (P = 0.007). TTK expression profiles in lung tumors were independently assessed by RNA in situ hybridization. CFI-402257 is a highly selective TTK inhibitor. Its potent antineoplastic effects are reported here against a panel of well-characterized murine and human lung cancer cell lines. Significant antitumorigenic activity followed independent treatments of athymic mice bearing human lung cancer xenografts (6.5 mg/kg, P < 0.05; 8.5 mg/kg, P < 0.01) and immunocompetent mice with syngeneic lung cancers (P < 0.001). CFI-402257 antineoplastic mechanisms were explored. CFI-402257 triggered aneuploidy and apoptotic death of lung cancer cells without changing centrosome number. Reverse phase protein arrays (RPPA) of vehicle versus CFI-402257-treated lung cancers were examined using more than 300 critical growth-regulatory proteins. RPPA bioinformatic analyses discovered CFI-402257 enhanced MAPK signaling, implicating MAPK antagonism in augmenting TTK inhibitory effects. This was independently confirmed using genetic and pharmacologic repression of MAPK that promoted CFI-402257 anticancer actions. TTK antagonism exerted marked antineoplastic effects against lung cancers and MAPK inhibition cooperated. Future work should determine whether CFI-402257 treatment alone or with a MAPK inhibitor is active in the lung cancer clinic.
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Affiliation(s)
- Lin Zheng
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zibo Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Masanori Kawakami
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Yulong Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lisa Maria Mustachio
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer Silvester
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kelsie L Thu
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David W Cescon
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xi Liu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Ethan Dmitrovsky
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Frederick National Laboratory for Cancer Research, Frederick, Maryland.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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8
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Kennedy K, Thomas R, Durrant J, Jiang T, Motsinger-Reif A, Breen M. Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex. Chromosome Res 2019; 27:179-202. [PMID: 31011867 DOI: 10.1007/s10577-019-09606-0] [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: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/16/2022]
Abstract
Canine histiocytic malignancies (HM) are rare across the general dog population, but overrepresented in certain breeds, such as Bernese mountain dog and flat-coated retriever. Accurate diagnosis relies on immunohistochemical staining to rule out histologically similar cancers with different prognoses and treatment strategies (e.g., lymphoma and hemangiosarcoma). HM are generally treatment refractory with overall survival of less than 6 months. A lack of understanding regarding the mechanisms of disease development and progression hinders development of novel therapeutics. While the study of human tumors can benefit veterinary medicine, the rarity of the suggested orthologous disease (dendritic cell sarcoma) precludes this. This study aims to improve the understanding of underlying disease mechanisms using genome-wide DNA copy number and gene expression analysis of spontaneous HM across several dog breeds. Extensive DNA copy number disruption was evident, with losses of segments of chromosomes 16 and 31 detected in 93% and 72% of tumors, respectively. Droplet digital PCR (ddPCR) evaluation of these regions in numerous cancer specimens effectively discriminated HM from other common round cell tumors, including lymphoma and hemangiosarcoma, resulting in a novel, rapid diagnostic aid for veterinary medicine. Transcriptional analysis demonstrated disruption of the spindle assembly complex, which is linked to genomic instability and reduced therapeutic impact in humans. A key signature detected was up-regulation of Matrix Metalloproteinase 9 (MMP9), supported by an immunohistochemistry-based assessment of MMP9 protein levels. Since MMP9 has been linked with rapid metastasis and tumor aggression in humans, the data in this study offer a possible mechanism of aggression in HM.
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Affiliation(s)
- Katherine Kennedy
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Sentinel Biomedical Incorporated, Centennial Biomedical Campus, Raleigh, NC, 27607, USA
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jessica Durrant
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27607, USA
| | - Tao Jiang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA. .,Cancer Genetics Program, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA. .,Duke Cancer Institute, Duke University, Durham, NC, 27710, USA.
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9
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Jing A, Vizeacoumar FS, Parameswaran S, Haave B, Cunningham CE, Wu Y, Arnold R, Bonham K, Freywald A, Han J, Vizeacoumar FJ. Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability. NPJ Syst Biol Appl 2018; 4:38. [PMID: 30374409 PMCID: PMC6200725 DOI: 10.1038/s41540-018-0074-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Can transcriptomic alterations drive the evolution of tumors? We asked if changes in gene expression found in all patients arise earlier in tumor development and can be relevant to tumor progression. Our analyses of non-mutated genes from the non-amplified regions of the genome of 158 triple-negative breast cancer (TNBC) cases identified 219 exclusively expression-altered (EEA) genes that may play important role in TNBC. Phylogenetic analyses of these genes predict a "punctuated burst" of multiple gene upregulation events occurring at early stages of tumor development, followed by minimal subsequent changes later in tumor progression. Remarkably, this punctuated burst of expressional changes is instigated by hypoxia-related molecular events, predominantly in two groups of genes that control chromosomal instability (CIN) and those that remodel tumor microenvironment (TME). We conclude that alterations in the transcriptome are not stochastic and that early-stage hypoxia induces CIN and TME remodeling to permit further tumor evolution.
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Affiliation(s)
- Anqi Jing
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Chelsea E. Cunningham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Yuliang Wu
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Keith Bonham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Jie Han
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Franco J. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
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10
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Kim S, Park C, Jun Y, Lee S, Jung Y, Kim J. Integrative Profiling of Alternative Splicing Induced by U2AF1 S34F Mutation in Lung Adenocarcinoma Reveals a Mechanistic Link to Mitotic Stress. Mol Cells 2018; 41:733-741. [PMID: 29991672 PMCID: PMC6125417 DOI: 10.14348/molcells.2018.0176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/27/2022] Open
Abstract
Mutations in spliceosome components have been implicated in carcinogenesis of various types of cancer. One of the most frequently found is U2AF1 S34F missense mutation. Functional analyses of this mutation have been largely limited to hematological malignancies although the mutation is also frequently seen in other cancer types including lung adenocarcinoma (LUAD). We examined the impact of knockdown (KD) of wild type (wt) U2AF1 and ectopic expression of two splice variant S34F mutant proteins in terms of alternative splicing (AS) pattern and cell cycle progression in A549 lung cancer cells. We demonstrate that induction of distinct AS events and disruption of mitosis at distinct sub-stages result from KD and ectopic expression of the mutant proteins. Importantly, when compared with the splicing pattern seen in LUAD patients with U2AF1 S34F mutation, ectopic expression of S34F mutants but not KD was shown to result in common AS events in several genes involved in cell cycle progression. Our study thus points to an active role of U2AF1 S34F mutant protein in inducing cell cycle dysregulation and mitotic stress. In addition, alternatively spliced genes which we describe here may represent novel potential markers of lung cancer development.
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Affiliation(s)
- Suyeon Kim
- Ewha Research Center for Systems Biology (ERCSB), Seoul 03760,
Korea
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Charny Park
- Research Institute, National Cancer Center, Goyang 10408,
Korea
| | - Yukyung Jun
- Ewha Research Center for Systems Biology (ERCSB), Seoul 03760,
Korea
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Sanghyuk Lee
- Ewha Research Center for Systems Biology (ERCSB), Seoul 03760,
Korea
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Yeonjoo Jung
- Ewha Research Center for Systems Biology (ERCSB), Seoul 03760,
Korea
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Jaesang Kim
- Ewha Research Center for Systems Biology (ERCSB), Seoul 03760,
Korea
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
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11
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Liu D, Shaukat Z, Xu T, Denton D, Saint R, Gregory S. Autophagy regulates the survival of cells with chromosomal instability. Oncotarget 2018; 7:63913-63923. [PMID: 27590505 PMCID: PMC5325413 DOI: 10.18632/oncotarget.11736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 08/21/2016] [Indexed: 01/05/2023] Open
Abstract
Chromosomal instability (CIN) refers to genomic instability in which cells have gained or lost chromosomes or chromosomal fragments. A high level of CIN is common in solid tumours and is associated with cancer drug resistance and poor prognosis. The impact of CIN-induced stress and the resulting cellular responses are only just beginning to emerge. Using proliferating tissue in Drosophila as a model, we found that autophagy is activated in CIN cells and is necessary for their survival. Specifically, increasing the removal of defective mitochondria by mitophagy is able to lower levels of reactive oxygen species and the resultant cellular damage that is normally seen in CIN cells. In response to DNA damage, CIN is increased in a positive feedback loop, and we found that increasing autophagy by Tor depletion could decrease the level of CIN in proliferating cells. These findings underline the importance of autophagy control in the development of CIN tumours.
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Affiliation(s)
- Dawei Liu
- Department of Genetics, University of Adelaide, Adelaide, SA, Australia
| | - Zeeshan Shaukat
- Department of Genetics, University of Adelaide, Adelaide, SA, Australia
| | - Tianqi Xu
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | | | - Stephen Gregory
- Department of Genetics, University of Adelaide, Adelaide, SA, Australia
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12
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Cordeiro MH, Smith RJ, Saurin AT. A fine balancing act: A delicate kinase-phosphatase equilibrium that protects against chromosomal instability and cancer. Int J Biochem Cell Biol 2018; 96:148-156. [PMID: 29108876 DOI: 10.1016/j.biocel.2017.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/31/2022]
Abstract
Cancer cells rewire signalling networks to acquire specific hallmarks needed for their proliferation, survival, and dissemination throughout the body. Although this is often associated with the constitutive activation or inactivation of protein phosphorylation networks, there are other contexts when the dysregulation must be much milder. For example, chromosomal instability is a widespread cancer hallmark that relies on subtle defects in chromosome replication and/or division, such that these processes remain functional, but nevertheless error-prone. In this article, we will discuss how perturbations to the delicate kinase-phosphatase balance could lie at the heart of this type of dysregulation. In particular, we will explain how the two principle mechanisms that safeguard the chromosome segregation process rely on an equilibrium between at least two kinases and two phosphatases to function correctly. This balance is set during mitosis by a central complex that has also been implicated in chromosomal instability - the BUB1/BUBR1/BUB3 complex - and we will put forward a hypothesis that could link these two findings. This could be relevant for cancer treatment because most tumours have evolved by pushing the boundaries of chromosomal instability to the limit. If this involves subtle changes to the kinase-phosphatase equilibrium, then it may be possible to exacerbate these defects and tip tumour cells over the edge, whilst still maintaining the viability of healthy cells.
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Affiliation(s)
- Marilia Henriques Cordeiro
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Richard John Smith
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Adrian Thomas Saurin
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
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13
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Scharf I, Bierbaumer L, Huber H, Wittmann P, Haider C, Pirker C, Berger W, Mikulits W. Dynamics of CRISPR/Cas9-mediated genomic editing of the AXL locus in hepatocellular carcinoma cells. Oncol Lett 2018; 15:2441-2450. [PMID: 29434956 DOI: 10.3892/ol.2017.7605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Genomic editing using the CRISPR/Cas9 technology allows selective interference with gene expression. With this method, a multitude of haploid and diploid cells from different organisms have been employed to successfully generate knockouts of genes coding for proteins or small RNAs. Yet, cancer cells exhibiting an aberrant ploidy are considered to be less accessible to CRISPR/Cas9-mediated genomic editing, as amplifications of the targeted gene locus could hamper its effectiveness. Here we examined the suitability of CRISPR/Cas9 to knockout the receptor tyrosine kinase Axl in the human hepatoma cell lines HLF and SNU449. The genomic editing events were validated in two single cell clones each from putative HLF and SNU449 knockout cells (HLF-Axl--1, HLF-Axl--2, SNU449-Axl--1, SNU449-Axl--2). Sequence analysis of respective AXL loci revealed one to six editing events in each individual Axl- clone. The majority of insertions and deletions in the AXL gene at exon 7/8 resulted in a frameshift and thus a premature stop in the coding region. However, one genomic editing event led to an insertion of two amino acids resulting in an altered protein sequence rather than in a frameshift in the AXL locus of the SNU449-Axl--1 cells. Notably, while no Axl protein expression could be detected by immunoblotting in all four cell clones, both expression of total Axl as well as release of soluble Axl into the supernatant was observed by ELISA in incompletely edited SNU449-Axl--1 cells. Importantly, a comparative genomic hybridization array revealed comparable genomic changes in Axl knockout cells as well as in cells expressing Cas9 nickase without guide RNAs in SNU449 and HLF cells, indicating vast alterations in genomic DNA triggered by nickase. Together, these data show that the dynamics of CRISPR/Cas9 may cause incomplete editing events in cancer cell lines, as gene copy numbers vary based on genomic heterogeneity.
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Affiliation(s)
- Irene Scharf
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Lisa Bierbaumer
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Heidemarie Huber
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Philipp Wittmann
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christine Haider
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christine Pirker
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Wolfgang Mikulits
- Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
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14
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Bakhoum SF, Landau DA. Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029611. [PMID: 28213433 DOI: 10.1101/cshperspect.a029611] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Large-scale, massively parallel sequencing of human cancer samples has revealed tremendous genetic heterogeneity within individual tumors. Indeed, tumors are composed of an admixture of diverse subpopulations-subclones-that vary in space and time. Here, we discuss a principal driver of clonal diversification in cancer known as chromosomal instability (CIN), which complements other modes of genetic diversification creating the multilayered genomic instability often seen in human cancer. Cancer cells have evolved to fine-tune chromosome missegregation rates to balance the acquisition of heterogeneity while preserving favorable genotypes, a dependence that can be exploited for a therapeutic benefit. We discuss how whole-genome doubling events accelerate clonal evolution in a subset of tumors by providing a viable path toward favorable near-triploid karyotypes and present evidence for CIN-induced clonal speciation that can overcome the dependence on truncal initiating events.
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Affiliation(s)
- Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065
| | - Dan Avi Landau
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065.,Division of Hematology and Medical Oncology and the Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021.,Core member of the New York Genome Center, New York, New York 10013
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15
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Germini D, Bou Saada Y, Tsfasman T, Osina K, Robin C, Lomov N, Rubtsov M, Sjakste N, Lipinski M, Vassetzky Y. A One-Step PCR-Based Assay to Evaluate the Efficiency and Precision of Genomic DNA-Editing Tools. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 5:43-50. [PMID: 28480303 PMCID: PMC5415314 DOI: 10.1016/j.omtm.2017.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/03/2017] [Indexed: 12/16/2022]
Abstract
Despite rapid progress, many problems and limitations persist and limit the applicability of gene-editing techniques. Making use of meganucleases, TALENs, or CRISPR/Cas9-based tools requires an initial step of pre-screening to determine the efficiency and specificity of the designed tools. This step remains time consuming and material consuming. Here we propose a simple, cheap, reliable, time-saving, and highly sensitive method to evaluate a given gene-editing tool based on its capacity to induce chromosomal translocations when combined with a reference engineered nuclease. In the proposed technique, designated engineered nuclease-induced translocations (ENIT), a plasmid coding for the DNA-editing tool to be tested is co-transfected into carefully chosen target cells along with that for an engineered nuclease of known specificity and efficiency. If the new enzyme efficiently cuts within the desired region, then specific chromosomal translocations will be generated between the two targeted genomic regions and be readily detectable by a one-step PCR or qPCR assay. The PCR product thus obtained can be directly sequenced, thereby determining the exact position of the double-strand breaks induced by the gene-editing tools. As a proof of concept, ENIT was successfully tested in different cell types and with different meganucleases, TALENs, and CRISPR/Cas9-based editing tools.
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Affiliation(s)
- Diego Germini
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,Department of Biophysics, Institute of Physics, Nanotechnology, and Telecommunications, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Yara Bou Saada
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Tatiana Tsfasman
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Kristina Osina
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,University of Latvia, 1586 Riga, Latvia
| | - Chloé Robin
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France
| | - Nikolay Lomov
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail Rubtsov
- LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Department of Biochemistry and Strategic Management Department, I.M. Sechenov First Moscow State Medical University, Moscow 119048, Russia
| | | | - Mar Lipinski
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Yegor Vassetzky
- UMR8126, Université Paris Sud - Paris Saclay, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.,LIA 1066, French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.,M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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16
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Wang GF, Dong Q, Bai Y, Yuan J, Xu Q, Cao C, Liu X. Oxidative stress induces mitotic arrest by inhibiting Aurora A-involved mitotic spindle formation. Free Radic Biol Med 2017; 103:177-187. [PMID: 28017898 DOI: 10.1016/j.freeradbiomed.2016.12.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/11/2023]
Abstract
Oxidative stress contributes to the oxidative modification of cellular components, including lipids, proteins and DNA, and results in DNA damage, cell cycle arrest, cellular dysfunction and apoptosis. However, the mechanism underlying oxidative stress-induced mitotic abnormalities is not fully understood. In this study, we demonstrated that exogenous and endogenous reactive oxygen species (ROS) promoted mitotic arrest. Delayed formation and abnormal function of the mitotic spindle, which directly impeded mitosis and promoted abnormal chromosome separation, was responsible for ROS-induced mitotic arrest. As a key regulator of mitotic spindle assembly, Aurora A kinase was hyperphosphorylated in early mitosis under oxidative stress, which may disturb the function of Aurora A in mitotic spindle formation. Our findings identified a mechanism by which ROS regulate mitotic progression and indicated a potential molecular target for the treatment of oxidative stress-related diseases.
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Affiliation(s)
- Guang-Fei Wang
- Key Laboratory of Cell Proliferation and Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Qincai Dong
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Yuanyuan Bai
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Jing Yuan
- Beijing Institute of Disease Control and Prevention, Beijing 100071, China
| | - Quanbin Xu
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, 27 Taiping Rd, Haidian District, Beijing 100850, China.
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17
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Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
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Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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18
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Augustin I, Dewi DL, Hundshammer J, Erdmann G, Kerr G, Boutros M. Autocrine Wnt regulates the survival and genomic stability of embryonic stem cells. Sci Signal 2017; 10:10/461/eaah6829. [PMID: 28074006 DOI: 10.1126/scisignal.aah6829] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Wnt signaling plays an important role in the self-renewal and differentiation of stem cells. The secretion of Wnt ligands requires Evi (also known as Wls). Genetically ablating Evi provides an experimental approach to studying the consequence of depleting all redundant Wnt proteins, and overexpressing Evi enables a nonspecific means of increasing Wnt signaling. We generated Evi-deficient and Evi-overexpressing mouse embryonic stem cells (ESCs) to analyze the role of autocrine Wnt production in self-renewal and differentiation. Self-renewal was reduced in Evi-deficient ESCs and increased in Evi-overexpressing ESCs in the absence of leukemia inhibitory factor, which supports the self-renewal of ESCs. The differentiation of ESCs into cardiomyocytes was enhanced when Evi was overexpressed and teratoma formation and growth of Evi-deficient ESCs in vivo were impaired, indicating that autocrine Wnt ligands were necessary for ESC differentiation and survival. ESCs lacking autocrine Wnt signaling had mitotic defects and showed genomic instability. Together, our study demonstrates that autocrine Wnt secretion is important for the survival, chromosomal stability, differentiation, and tumorigenic potential of ESCs.
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Affiliation(s)
- Iris Augustin
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg 69120, Germany.
| | - Dyah L Dewi
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg 69120, Germany
| | - Jennifer Hundshammer
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg 69120, Germany
| | - Gerrit Erdmann
- NMI TT Naturwissenschaftliches und Medizinisches Institut Technologie Transfer GmbH Pharmaservices, Berlin 13353, Germany
| | - Grainne Kerr
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg 69120, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics, and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg 69120, Germany.
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19
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Biomarkers of genome instability and cancer epigenetics. Tumour Biol 2016; 37:13029-13038. [DOI: 10.1007/s13277-016-5278-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/15/2016] [Indexed: 02/06/2023] Open
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20
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Li H, Lv X. Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer. Oncol Lett 2016; 12:222-230. [PMID: 27347129 DOI: 10.3892/ol.2016.4604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/01/2016] [Indexed: 11/05/2022] Open
Abstract
Multiple computational tools have been widely applied to the detection of coding driver mutations in cancer; however, the prioritization of pathogenic non-coding variants remains a difficult and demanding task. The present study was performed to distinguish non-coding disease-causing mutations from neutral ones, and to prioritize potential cancer-associated long non-coding RNAs (lncRNAs) with a logistic regression model in lung cancer. A logistic regression model was constructed, combining 19,153 disease-associated ClinVar and Human Gene Mutation Database pathogenic variants as the response variable and non-coding features as the predictor variable. Validation of the model was conducted with genome-wide association study (GWAS) disease- or trait-associated single nucleotide polymorphisms (SNPs) and recurrent somatic mutations. High scoring regions were characterized with respect to their distribution in various features and gene classes; potential cancer-associated lncRNA candidates were prioritized, combining the fraction of high-scoring regions and average score predicted by the logistic regression model. H3K79me2 was the most negative factor that contributed to the model, while conserved regions were most positively informative to the model. The area under the receiver operating characteristic curve of the model was 0.89. The model assigned a significantly higher score to GWAS SNPs and recurrent somatic mutations compared with neutral SNPs (mean, 5.9012 vs. 5.5238; P<0.001, Mann-Whitney U test) and non-recurrent mutations (mean, 5.4677 vs. 5.2277, P<0.001, Mann-Whitney U test), respectively. It was observed that regions, including splicing sites and untranslated regions, and gene classes, including cancer genes and cancer-associated lncRNAs, had an increased enrichment of high-scoring regions. In total, 2,679 cancer-associated lncRNAs were determined and characterized. A total of 104 of these lncRNAs were differentially expressed between lung cancer and normal specimens. The logistic regression model is a useful and efficient scoring system to prioritize non-coding pathogenic variants and lncRNAs, and may provide the basis for detecting non-coding driver lncRNAs in lung cancer.
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Affiliation(s)
- Hua Li
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
| | - Xin Lv
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200072, P.R. China
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21
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Giam M, Rancati G. Aneuploidy and chromosomal instability in cancer: a jackpot to chaos. Cell Div 2015; 10:3. [PMID: 26015801 PMCID: PMC4443636 DOI: 10.1186/s13008-015-0009-7] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic instability (GIN) is a hallmark of cancer cells that facilitates the acquisition of mutations conferring aggressive or drug-resistant phenotypes during cancer evolution. Chromosomal instability (CIN) is a form of GIN that involves frequent cytogenetic changes leading to changes in chromosome copy number (aneuploidy). While both CIN and aneuploidy are common characteristics of cancer cells, their roles in tumor initiation and progression are unclear. On the one hand, CIN and aneuploidy are known to provide genetic variation to allow cells to adapt in changing environments such as nutrient fluctuations and hypoxia. Patients with constitutive aneuploidies are more susceptible to certain types of cancers, suggesting that changes in chromosome copy number could positively contribute to cancer evolution. On the other hand, chromosomal imbalances have been observed to have detrimental effects on cellular fitness and might trigger cell cycle arrest or apoptosis. Furthermore, mouse models for CIN have led to conflicting results. Taken together these findings suggest that the relationship between CIN, aneuploidy and cancer is more complex than what was previously anticipated. Here we review what is known about this complex ménage à trois, discuss recent evidence suggesting that aneuploidy, CIN and GIN together promote a vicious cycle of genome chaos. Lastly, we propose a working hypothesis to reconcile the conflicting observations regarding the role of aneuploidy and CIN in tumorigenesis.
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Affiliation(s)
- Maybelline Giam
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore
| | - Giulia Rancati
- Institute for Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, 138648 Singapore ; School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, 117597 Singapore
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22
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Re-replication of a centromere induces chromosomal instability and aneuploidy. PLoS Genet 2015; 11:e1005039. [PMID: 25901968 PMCID: PMC4406714 DOI: 10.1371/journal.pgen.1005039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022] Open
Abstract
The faithful inheritance of chromosomes during cell division requires their precise replication and segregation. Numerous mechanisms ensure that each of these fundamental cell cycle events is performed with a high degree of fidelity. The fidelity of chromosomal replication is maintained in part by re-replication controls that ensure there are no more than two copies of every genomic segment to distribute to the two daughter cells. This control is enforced by inhibiting replication initiation proteins from reinitiating replication origins within a single cell cycle. Here we show in Saccharomyces cerevisiae that re-replication control is important for the fidelity of chromosome segregation. In particular, we demonstrate that transient re-replication of centromeric DNA due to disruption of re-replication control greatly induces aneuploidy of the re-replicated chromosome. Some of this aneuploidy arises from missegregation of both sister chromatids to one daughter cell. Aneuploidy can also arise from the generation of an extra sister chromatid via homologous recombination, suggesting that centromeric re-replication can trigger breakage and repair events that expand chromosome number without causing chromosomal rearrangements. Thus, we have identified a potential new non-mitotic source of aneuploidy that can arise from a defect in re-replication control. Given the emerging connections between the deregulation of replication initiation proteins and oncogenesis, this finding may be relevant to the aneuploidy that is prevalent in cancer. The stable inheritance of genetic information requires an elaborate mitotic machinery that acts on the centromeres of chromosomes to ensure their precise segregation. Errors in this segregation can lead to aneuploidy, an unbalanced chromosomal state in which some chromosomes have different copy number than others. Because aneuploidy is associated with developmental abnormalities and diseases such as cancer, there is considerable interest in understanding how these segregation errors arise. Much of this interest has focused on identifying defects in proteins that make up the mitotic machinery. Here, we show that defects in a completely separate process, the control of DNA replication initiation, can lead to chromosome segregation errors as a result of inappropriate re-replication of centromeres. Similar deregulation of replication initiation proteins has been observed in primary human tumors and shown to promote oncogenesis in mouse models. Together, these results raise the possibility that centromeric re-replication may be an additional source of aneuploidy in cancer. In combination with our previous work showing that re-replication is a potent inducer of gene amplification, these results also highlight the versatility of re-replication as a source of genomic instability.
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23
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New insight into cancer aneuploidy in zebrafish. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 314:149-70. [PMID: 25619717 DOI: 10.1016/bs.ircmb.2014.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Aneuploidy is one of the most common genetic alterations in cancer cell genomes. It greatly contributes to the heterogeneity of cancer cell genomes, and its roles in tumorigenesis are attracting more and more attentions. Zebrafish is emerging as a new genetic model for many human diseases including cancer. The zebrafish cancer model has shown an equivalent degree of aneuploidy as found in corresponding human cancers, thus it provides a great tool for us to study cancer aneuploidy and, in general, cancer biology. Here, we discuss some new advances of aneuploidy and the potential usages of this cancer model system.
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Endesfelder D, Burrell R, Kanu N, McGranahan N, Howell M, Parker PJ, Downward J, Swanton C, Kschischo M. Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. Cancer Res 2014; 74:4853-4863. [PMID: 24970479 PMCID: PMC4167338 DOI: 10.1158/0008-5472.can-13-2664] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal instability (CIN) is associated with poor outcome in epithelial malignancies, including breast carcinomas. Evidence suggests that prognostic signatures in estrogen receptor-positive (ER(+)) breast cancer define tumors with CIN and high proliferative potential. Intriguingly, CIN induction in lower eukaryotic cells and human cells is context dependent, typically resulting in a proliferation disadvantage but conferring a fitness benefit under strong selection pressures. We hypothesized that CIN permits accelerated genomic evolution through the generation of diverse DNA copy-number events that may be selected during disease development. In support of this hypothesis, we found evidence for selection of gene amplification of core regulators of proliferation in CIN-associated cancer genomes. Stable DNA copy-number amplifications of the core regulators TPX2 and UBE2C were associated with expression of a gene module involved in proliferation. The module genes were enriched within prognostic signature gene sets for ER(+) breast cancer, providing a logical connection between CIN and prognostic signature expression. Our results provide a framework to decipher the impact of intratumor heterogeneity on key cancer phenotypes, and they suggest that CIN provides a permissive landscape for selection of copy-number alterations that drive cancer proliferation.
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Affiliation(s)
- David Endesfelder
- Department of Mathematics and Technology, RheinAhrCampus, University of Applied Sciences Koblenz, 53424 Remagen, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Institute of Biomathematics and Biometry, Scientific Computing Research Unit, Neuherberg, Germany
| | - Rebecca Burrell
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Nnennaya Kanu
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley Street, WC1E 6BT London
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Mike Howell
- High Throughput Screening Laboratory,Cancer Research UK London Research Institute, London, United Kingdom
| | - Peter J. Parker
- Protein Phosphorylation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
- Division of Cancer Studies, King’s College London, London SE1 1UL
| | - Julian Downward
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Maik Kschischo
- Department of Mathematics and Technology, RheinAhrCampus, University of Applied Sciences Koblenz, 53424 Remagen, Germany
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Herman JA, Toledo CM, Olson JM, DeLuca JG, Paddison PJ. Molecular pathways: regulation and targeting of kinetochore-microtubule attachment in cancer. Clin Cancer Res 2014; 21:233-9. [PMID: 25104085 DOI: 10.1158/1078-0432.ccr-13-0645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Kinetochores are large protein structures assembled on centromeric DNA during mitosis that bind to microtubules of the mitotic spindle to orchestrate and power chromosome movements. Deregulation of kinetochore-microtubule (KT-MT) attachments has been implicated in driving chromosome instability and cancer evolution; however, the nature and source of KT-MT attachment defects in cancer cells remain largely unknown. Here, we highlight recent findings suggesting that oncogene-driven changes in kinetochore regulation occur in glioblastoma multiforme (GBM) and possibly other cancers exhibiting chromosome instability, giving rise to novel therapeutic opportunities. In particular, we consider the GLE2p-binding sequence domains of BubR1 and the newly discovered BuGZ, two kinetochore-associated proteins, as candidate therapeutic targets for GBM.
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Affiliation(s)
- Jacob A Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
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Bakhoum SF, Swanton C. Chromosomal instability, aneuploidy, and cancer. Front Oncol 2014; 4:161. [PMID: 24995162 PMCID: PMC4062911 DOI: 10.3389/fonc.2014.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/06/2014] [Indexed: 12/18/2022] Open
Affiliation(s)
- Samuel F. Bakhoum
- Department of Internal Medicine, Mount Auburn Hospital, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Charles Swanton
- Cancer Research UK London Research Institute, London, UK
- University College London Cancer Institute, London, UK
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