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Zheng S, Yao L, Li F, Huang L, Yu Y, Lin Z, Li H, Xia J, Lanuti M, Zhou H. Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma. PeerJ 2021; 9:e10680. [PMID: 33628633 PMCID: PMC7894105 DOI: 10.7717/peerj.10680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/09/2020] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE The current study aims to identify the dysregulated pathway involved in carcinogenesis and the essential survival-related dysregulated genes among this pathway in the early stage of lung adenocarcinoma (LUAD). PATIENTS AND METHODS Data from The Cancer Genome Atlas (TCGA) including 526 tumor tissues of LUAD and 59 healthy lung tissues were analyzed to gain differentially expressed genes (DEGs). Gene ontology (GO) analysis was conducted with DAVID, while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs was performed, followed by gene set enrichment analysis (GSEA) methods. Survival analysis was implemented in TCGA dataset and validated in Gene Expression Omnibus (GEO) cohort GSE50081, which includes 127 patients with stage I LUAD. RESULTS GSEA enrichment analysis suggested that homologous recombination repair (HRR) pathway was significantly enriched. Subsequent KEGG pathway enrichment analysis indicated the significant up-regulation of HRR pathway in patients with T1 stage LUAD. Retrieved in Gene database, RAD54L is involved in HRR pathway and were recognized to be significantly differentially expressed in T1 stage LUAD in our study. The survival analysis indicated that high expression of RAD54L was significantly related to worse overall survival in patients with T1 stage LUAD (TCGA cohort: HR=2.10, 95% CI [1.47-2.98], P = 0.001; GSE50081 validation cohort: HR = 2.61, 95% CI [1.51-4.52], P = 0.002). Multivariate cox regression analysis indicated that RAD54L is an independent prognostic factor in the early-stage LUAD. CONCLUSION HRR pathway is up-regulated in LUAD, among which the expression of RAD54L was found to be significantly differentially expressed in T1 stage tumor tissue. Patients with high expression of RAD54L were associated with worse overall survival in the TCGA cohort and validation cohort. This study suggests a potential mechanism of lung cancer progression and provide a budding prognostic factor and treatment target in early-stage LUAD.
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Affiliation(s)
- Shaopeng Zheng
- Department of Thoracic Surgery, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China
- Shantou University Medical College, Shantou, P.R. China
| | - Lintong Yao
- Division of Thoracic Surgery, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, P.R. China
- Shantou University Medical College, Shantou, P.R. China
| | - Fasheng Li
- Division of Thoracic Surgery, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, P.R. China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, P.R. China
| | - Luyu Huang
- Division of Thoracic Surgery, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, P.R. China
- Shantou University Medical College, Shantou, P.R. China
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zenan Lin
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Hao Li
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Jin Xia
- Division of Thoracic Surgery, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, P.R. China
| | - Michael Lanuti
- Department of Surgery, Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Haiyu Zhou
- Division of Thoracic Surgery, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, P.R. China
- Shantou University Medical College, Shantou, P.R. China
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Sinha D, Nag P, Nanayakkara D, Duijf PHG, Burgess A, Raninga P, Smits VAJ, Bain AL, Subramanian G, Wall M, Finnie JW, Kalimutho M, Khanna KK. Cep55 overexpression promotes genomic instability and tumorigenesis in mice. Commun Biol 2020; 3:593. [PMID: 33087841 PMCID: PMC7578791 DOI: 10.1038/s42003-020-01304-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
High expression of centrosomal protein CEP55 has been correlated with clinico-pathological parameters across multiple human cancers. Despite significant in vitro studies and association of aberrantly overexpressed CEP55 with worse prognosis, its causal role in vivo tumorigenesis remains elusive. Here, using a ubiquitously overexpressing transgenic mouse model, we show that Cep55 overexpression causes spontaneous tumorigenesis and accelerates Trp53+/− induced tumours in vivo. At the cellular level, using mouse embryonic fibroblasts (MEFs), we demonstrate that Cep55 overexpression induces proliferation advantage by modulating multiple cellular signalling networks including the hyperactivation of the Pi3k/Akt pathway. Notably, Cep55 overexpressing MEFs have a compromised Chk1-dependent S-phase checkpoint, causing increased replication speed and DNA damage, resulting in a prolonged aberrant mitotic division. Importantly, this phenotype was rescued by pharmacological inhibition of Pi3k/Akt or expression of mutant Chk1 (S280A) protein, which is insensitive to regulation by active Akt, in Cep55 overexpressing MEFs. Moreover, we report that Cep55 overexpression causes stabilized microtubules. Collectively, our data demonstrates causative effects of deregulated Cep55 on genome stability and tumorigenesis which have potential implications for tumour initiation and therapy development. Sinha et al. demonstrate that overexpression of centrosomal protein Cep55 in mice is sufficient to cause a wide-spectrum of cancer via multiple mechanisms including hyperactivation of the Pi3k/Akt pathway, stabilized microtubules and a defective replication checkpoint response. These findings are relevant to human cancers as high CEP55 expression is associated with worse prognosis across multiple cancer types.
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Affiliation(s)
- Debottam Sinha
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia.,School of Environment and Sciences, Griffith University, Nathan, 4111, QLD, Australia
| | - Purba Nag
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia.,School of Environment and Sciences, Griffith University, Nathan, 4111, QLD, Australia.,Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland and Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, 4029, QLD, Australia
| | - Devathri Nanayakkara
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia.,Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew Burgess
- ANZAC Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Prahlad Raninga
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia
| | - Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias, Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Tenerife, Spain.,Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Amanda L Bain
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia
| | - Goutham Subramanian
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, Fitzroy, Melbourne, Australia
| | - John W Finnie
- Discipline of Anatomy and Pathology, Adelaide Medical School, University of Adelaide and SA Pathology, Adelaide, Australia
| | - Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4006, QLD, Australia.
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Li M, Wang H, Liao H, Shen J, Wu Y, Wu Y, Weng Q, Zhu C, Geng X, Lan F, Xia Y, Zhang B, Zou H, Zhang N, Zhou Y, Chen Z, Shen H, Ying S, Li W. SETD8C302R Mutation Revealed from Myofibroblastoma-Discordant Monozygotic Twins Leads to p53/p21 Deficit and WEE1 Inhibitor Sensitivity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001041. [PMID: 33042742 PMCID: PMC7539211 DOI: 10.1002/advs.202001041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/21/2020] [Indexed: 06/11/2023]
Abstract
High-throughput gene sequencing has identified various genetic variants as the culprits for some common hereditary cancers. However, the heritability of a substantial proportion of cancers remains unexplained, which may result from rare deleterious mutations hidden in a myriad of nonsense genetic variations. This poses a great challenge to the understanding of the pathology and thus the rational design of effective treatments for affected patients. Here, whole genome sequencing is employed in a representative case in which one monozygotic twin is discordant for lung inflammatory myofibroblastoma to disclose rare tumor-related mutations. A missense single nucleotide variation rs61955126 T>C in the lysine methyltransferase SETD8 (accession: NM_020382, SETD8C302R ) is exposed. It is shown that SETD8 is vital for genomic integrity by promoting faithful DNA replication, and its C302R mutation downregulates the p53/p21 pathway. Importantly, the SETD8C302R mutation significantly increases the sensitivity of cancer cells to WEE1 inhibition. Given that WEE1 inhibitors have shown great promise for clinical approval, these results impart a potential therapeutic approach using WEE1 inhibitor for cancer patients carrying the same mutation, and indicate that genome sequencing and genetic functional studies can be integrated into individualized therapies.
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Affiliation(s)
- Miao Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Hongwu Wang
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Hongwei Liao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Jiaxin Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yinfang Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yanping Wu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Qingyu Weng
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Chen Zhu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Xinwei Geng
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Fen Lan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Yang Xia
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Bin Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Hang Zou
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Nan Zhang
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Yunzhi Zhou
- Department of Respiratory and Critical Care MedicineEmergency General HospitalBeijing100028China
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Songmin Ying
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care MedicineSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310009China
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Implications of CLSPN Variants in Cellular Function and Susceptibility to Cancer. Cancers (Basel) 2020; 12:cancers12092396. [PMID: 32847043 PMCID: PMC7565888 DOI: 10.3390/cancers12092396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 11/28/2022] Open
Abstract
Claspin is a multifunctional protein that participates in physiological processes essential for cell homeostasis that are often defective in cancer, namely due to genetic changes. It is conceivable that Claspin gene (CLSPN) alterations may contribute to cancer development. Therefore, CLSPN germline alterations were characterized in sporadic and familial breast cancer and glioma samples, as well as in six cancer cell lines. Their association to cancer susceptibility and functional impact were investigated. Eight variants were identified (c.-68C>T, c.17G>A, c.1574A>G, c.2230T>C, c.2028+16G>A, c.3595-3597del, and c.3839C>T). CLSPN c.1574A>G (p.Asn525Ser) was significantly associated with breast cancer and was shown to cause partial exon skipping and decreased Claspin expression and Chk1 activation in a minigene splicing assay and in signalling experiments, respectively. CLSPN c.2028+16G>A was significantly associated with familial breast cancer and glioma, whereas c.2230T>C (p.Ser744Pro), was exclusively detected in breast cancer and glioma patients, but not in healthy controls. The remaining variants lacked a significant association with cancer. Nevertheless, the c.-68C>T promoter variant increased transcriptional activity in a luciferase assay. In conclusion, some of the CLSPN variants identified in the present study appear to modulate Claspin’s function by altering CLSPN transcription and RNA processing, as well as Chk1 activation.
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55
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Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer. Proc Natl Acad Sci U S A 2020; 117:18880-18890. [PMID: 32694208 DOI: 10.1073/pnas.1920870117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.
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56
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Burgess JT, Rose M, Boucher D, Plowman J, Molloy C, Fisher M, O'Leary C, Richard DJ, O'Byrne KJ, Bolderson E. The Therapeutic Potential of DNA Damage Repair Pathways and Genomic Stability in Lung Cancer. Front Oncol 2020; 10:1256. [PMID: 32850380 PMCID: PMC7399071 DOI: 10.3389/fonc.2020.01256] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
Despite advances in our understanding of the molecular biology of the disease and improved therapeutics, lung cancer remains the most common cause of cancer-related deaths worldwide. Therefore, an unmet need remains for improved treatments, especially in advanced stage disease. Genomic instability is a universal hallmark of all cancers. Many of the most commonly prescribed chemotherapeutics, including platinum-based compounds such as cisplatin, target the characteristic genomic instability of tumors by directly damaging the DNA. Chemotherapies are designed to selectively target rapidly dividing cells, where they cause critical DNA damage and subsequent cell death (1, 2). Despite the initial efficacy of these drugs, the development of chemotherapy resistant tumors remains the primary concern for treatment of all lung cancer patients. The correct functioning of the DNA damage repair machinery is essential to ensure the maintenance of normal cycling cells. Dysregulation of these pathways promotes the accumulation of mutations which increase the potential of malignancy. Following the development of the initial malignancy, the continued disruption of the DNA repair machinery may result in the further progression of metastatic disease. Lung cancer is recognized as one of the most genomically unstable cancers (3). In this review, we present an overview of the DNA damage repair pathways and their contributions to lung cancer disease occurrence and progression. We conclude with an overview of current targeted lung cancer treatments and their evolution toward combination therapies, including chemotherapy with immunotherapies and antibody-drug conjugates and the mechanisms by which they target DNA damage repair pathways.
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Affiliation(s)
- Joshua T Burgess
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Maddison Rose
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Didier Boucher
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jennifer Plowman
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Christopher Molloy
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Mark Fisher
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Connor O'Leary
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer & Ageing Research Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
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57
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Zhang M, Xiao R, Liu G, Huang Y. Genotoxins exaggerate the stressed state of aneuploid embryonic stem cells via activation of autophagy. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1026-1036. [PMID: 31872377 DOI: 10.1007/s11427-019-9666-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/01/2019] [Indexed: 01/19/2023]
Abstract
The cellular consequences of aneuploidy are largely dependent on the cell types examined. Aneuploid yeasts and mouse embryonic fibroblasts exhibit cell proliferation defects and can be selectively inhibited by compounds that cause proteotoxic or energy stress. By contrast, most aneuploid pluripotent stem cells proliferate rapidly and reach higher saturation densities. The responses of aneuploid pluripotent stem cells to the stress-inducing compounds remain uncharacterized. Here, we tested the response of aneuploid embryonic stem cells to several compounds that caused proteotoxic, energy and genotoxic stress using previously established mouse embryonic stem cell lines trisomic for chromosome 6, 8, 11, or 15. Not all trisomic embryonic stem cells were selectively inhibited by compounds that cause proteotoxic or energy stress. However, most of these cells exhibited increased sensitivity to genotoxins. They displayed elevated DNA damage response as characterized by increased γH2A.X foci under genotoxic stress. Further investigations indicated that elevated autophagy levels might contribute to the increased cytotoxic effects of genotoxins on trisomic embryonic stem cells. Our study laid the foundation for eliminating aneuploidy that might be an effective approach for controlling cancer progression.
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Affiliation(s)
- Meili Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China. .,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| | - Rong Xiao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China. .,Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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58
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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59
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Samii A, Razmkhah F. Transformation of Hematopoietic Stem and Progenitor Cells by Leukemia Extracellular Vesicles: A Step Toward Leukemogenesis. Stem Cell Rev Rep 2020; 16:1081-1091. [DOI: 10.1007/s12015-020-09975-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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60
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Alagpulinsa DA, Szalat RE, Poznansky MC, Shmookler Reis RJ. Genomic Instability in Multiple Myeloma. Trends Cancer 2020; 6:858-873. [PMID: 32487486 DOI: 10.1016/j.trecan.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Genomic instability (GIN), an increased tendency to acquire genomic alterations, is a cancer hallmark. However, its frequency, underlying causes, and disease relevance vary across different cancers. Multiple myeloma (MM), a plasma cell malignancy, evolves through premalignant phases characterized by genomic abnormalities. Next-generation sequencing (NGS) methods are deconstructing the genomic landscape of MM across the continuum of its development, inextricably linking malignant transformation and disease progression with increasing acquisition of genomic alterations, and illuminating the mechanisms that generate these alterations. Although GIN drives disease evolution, it also creates vulnerabilities such as dependencies on 'superfluous' repair mechanisms and the induction of tumor-specific antigens that can be targeted. We review the mechanisms of GIN in MM, the associated vulnerabilities, and therapeutic targeting strategies.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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61
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Kaplan HG, Calip GS, Malmgren JA. Maximizing Breast Cancer Therapy with Awareness of Potential Treatment-Related Blood Disorders. Oncologist 2020; 25:391-397. [PMID: 32073195 PMCID: PMC7216464 DOI: 10.1634/theoncologist.2019-0099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 01/29/2020] [Indexed: 01/18/2023] Open
Abstract
In this review we summarize the impact of the various modalities of breast cancer therapy coupled with intrinsic patient factors on incidence of subsequent treatment-induced myelodysplasia and acute myelogenous leukemia (t-MDS/AML). It is clear that risk is increased for patients treated with radiation and chemotherapy at younger ages. Radiation is associated with modest risk, whereas chemotherapy, particularly the combination of an alkylating agent and an anthracycline, carries higher risk and radiation and chemotherapy combined increase the risk markedly. Recently, treatment with granulocyte colony-stimulating factor (G-CSF), but not pegylated G-CSF, has been identified as a factor associated with increased t-MDS/AML risk. Two newly identified associations may link homologous DNA repair gene deficiency and poly (ADP-ribose) polymerase inhibitor treatment to increased t-MDS/AML risk. When predisposing factors, such as young age, are combined with an increasing number of potentially leukemogenic treatments that may not confer large risk singly, the risk of t-MDS/AML appears to increase. Patient and treatment factors combine to form a biological cascade that can trigger a myelodysplastic event. Patients with breast cancer are often exposed to many of these risk factors in the course of their treatment, and triple-negative patients, who are often younger and/or BRCA positive, are often exposed to all of them. It is important going forward to identify effective therapies without these adverse associated effects and choose existing therapies that minimize the risk of t-MDS/AML without sacrificing therapeutic gain. IMPLICATIONS FOR PRACTICE: Breast cancer is far more curable than in the past but requires multimodality treatment. Great care must be taken to use the least leukemogenic treatment programs that do not sacrifice efficacy. Elimination of radiation and anthracycline/alkylating agent regimens will be helpful where possible, particularly in younger patients and possibly those with homologous repair deficiency (HRD). Use of colony-stimulating factors should be limited to those who truly require them for safe chemotherapy administration. Further study of a possible leukemogenic association with HRD and the various forms of colony-stimulating factors is badly needed.
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Affiliation(s)
| | - Gregory S. Calip
- Center for Pharmacoepidemiology and Pharmacoeconomic Research, University of Illinois at ChicagoChicagoIllinoisUSA
| | - Judith A. Malmgren
- Healthstat Consulting Inc.SeattleWashingtonUSA
- Department of Epidemiology, University of WashingtonSeattleWashingtonUSA
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62
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Dragomir MP, Kopetz S, Ajani JA, Calin GA. Non-coding RNAs in GI cancers: from cancer hallmarks to clinical utility. Gut 2020; 69:748-763. [PMID: 32034004 DOI: 10.1136/gutjnl-2019-318279] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/11/2022]
Abstract
One of the most unexpected discoveries in molecular oncology, in the last decades, was the identification of a new layer of protein coding gene regulation by transcripts that do not codify for proteins, the non-coding RNAs. These represent a heterogeneous category of transcripts that interact with many types of genetic elements, including regulatory DNAs, coding and other non-coding transcripts and directly to proteins. The final outcome, in the malignant context, is the regulation of any of the cancer hallmarks. Non-coding RNAs represent the most abundant type of hormones that contribute significantly to cell-to cell communication, revealing a complex interplay between tumour cells, tumour microenvironment cells and immune cells. Consequently, profiling their abundance in bodily fluids became a mainstream of biomarker identification. Therapeutic targeting of non-coding RNAs represents a new option for clinicians that is currently under development. This review will present the biology and translational value of three of the most studied categories on non-coding RNAs, the microRNAs, the long non-coding RNAs and the circular RNAs. We will also focus on some aspirational concepts that can help in the development of clinical applications related to non-coding RNAs, including using pyknons to discover new non-coding RNAs, targeting human-specific transcripts which are expressed specifically in the tumour cell and using non-coding RNAs to increase the efficiency of immunotherapy.
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Affiliation(s)
- Mihnea Paul Dragomir
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George Adrian Calin
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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63
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Vishwakarma R, McManus KJ. Chromosome Instability; Implications in Cancer Development, Progression, and Clinical Outcomes. Cancers (Basel) 2020; 12:cancers12040824. [PMID: 32235397 PMCID: PMC7226245 DOI: 10.3390/cancers12040824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN) refers to an ongoing rate of chromosomal changes and is a driver of genetic, cell-to-cell heterogeneity. It is an aberrant phenotype that is intimately associated with cancer development and progression. The presence, extent, and level of CIN has tremendous implications for the clinical management and outcomes of those living with cancer. Despite its relevance in cancer, there is still extensive misuse of the term CIN, and this has adversely impacted our ability to identify and characterize the molecular determinants of CIN. Though several decades of genetic research have provided insight into CIN, the molecular determinants remain largely unknown, which severely limits its clinical potential. In this review, we provide a definition of CIN, describe the two main types, and discuss how it differs from aneuploidy. We subsequently detail its impact on cancer development and progression, and describe how it influences metastatic potential with reference to cancer prognosis and outcomes. Finally, we end with a discussion of how CIN induces genetic heterogeneity to influence the use and efficacy of several precision medicine strategies, including patient and risk stratification, as well as its impact on the acquisition of drug resistance and disease recurrence.
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Affiliation(s)
- Raghvendra Vishwakarma
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Kirk J. McManus
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-787-2833
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64
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Li N, Yang J, Zhu W, Liang Y. MVSC: A Multi-variation Simulator of Cancer Genome. Comb Chem High Throughput Screen 2020; 23:326-333. [PMID: 32183666 DOI: 10.2174/1386207323666200317121136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/29/2019] [Accepted: 02/27/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Many forms of variations exist in the genome, which are the main causes of individual phenotypic differences. The detection of variants, especially those located in the tumor genome, still faces many challenges due to the complexity of the genome structure. Thus, the performance assessment of variation detection tools using next-generation sequencing platforms is urgently needed. METHOD We have created a software package called the Multi-Variation Simulator of Cancer genomes (MVSC) to simulate common genomic variants, including single nucleotide polymorphisms, small insertion and deletion polymorphisms, and structural variations (SVs), which are analogous to human somatically acquired variations. Three sets of variations embedded in genomic sequences in different periods were dynamically and sequentially simulated one by one. RESULTS In cancer genome simulation, complex SVs are important because this type of variation is characteristic of the tumor genome structure. Overlapping variations of different sizes can also coexist in the same genome regions, adding to the complexity of cancer genome architecture. Our results show that MVSC can efficiently simulate a variety of genomic variants that cannot be simulated by existing software packages. CONCLUSION The MVSC-simulated variants can be used to assess the performance of existing tools designed to detect SVs in next-generation sequencing data, and we also find that MVSC is memory and time-efficient compared with similar software packages.
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Affiliation(s)
- Ning Li
- School of Information and Electronic Engineering, Wuzhou University, Wuzhou, China
| | - Jialiang Yang
- Department of Mathematics and Statistics, Hainan Normal University, Haikou, Hainan 571158, China
| | - Wen Zhu
- Department of Mathematics and Statistics, Hainan Normal University, Haikou, Hainan 571158, China.,College of Computer Science and Electronic Engineering, Hunan University, Hunan, China
| | - Ying Liang
- College of Computer Science and Electronic Engineering, Hunan University, Hunan, China.,College of Computer and Information Engineering, Jiangxi Agricultural University, Nanchang 330000, China
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65
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Meliala ITS, Hosea R, Kasim V, Wu S. The biological implications of Yin Yang 1 in the hallmarks of cancer. Theranostics 2020; 10:4183-4200. [PMID: 32226547 PMCID: PMC7086370 DOI: 10.7150/thno.43481] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/09/2020] [Indexed: 12/24/2022] Open
Abstract
Tumorigenesis is a multistep process characterized by the acquisition of genetic and epigenetic alterations. During the course of malignancy development, tumor cells acquire several features that allow them to survive and adapt to the stress-related conditions of the tumor microenvironment. These properties, which are known as hallmarks of cancer, include uncontrolled cell proliferation, metabolic reprogramming, tumor angiogenesis, metastasis, and immune system evasion. Zinc-finger protein Yin Yang 1 (YY1) regulates numerous genes involved in cell death, cell cycle, cellular metabolism, and inflammatory response. YY1 is highly expressed in many cancers, whereby it is associated with cell proliferation, survival, and metabolic reprogramming. Furthermore, recent studies also have demonstrated the important role of YY1-related non-coding RNAs in acquiring cancer-specific characteristics. Therefore, these YY1-related non-coding RNAs are also crucial for YY1-mediated tumorigenesis. Herein, we summarize recent progress with respect to YY1 and its biological implications in the context of hallmarks of cancer.
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66
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Li L, Rao X, Wen Z, Ding X, Wang X, Xu W, Meng C, Yi Y, Guan Y, Chen Y, Wang J, Jun L. Implications of driver genes associated with a high tumor mutation burden identified using next-generation sequencing on immunotherapy in hepatocellular carcinoma. Oncol Lett 2020; 19:2739-2748. [PMID: 32218826 PMCID: PMC7068659 DOI: 10.3892/ol.2020.11372] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Immune checkpoint blockade (ICB) therapy is a treatment strategy for hepatocellular carcinoma (HCC); however, its clinical efficacy is limited to a select subset of patients. Next-generation sequencing has identified the value of tumor mutation burden (TMB) as a predictor for ICB efficacy in multiple types of tumor, including HCC. Specific driver gene mutations may be indicative of a high TMB (TMB-H) and analysis of such mutations may provide novel insights into the underlying mechanisms of TMB-H and potential therapeutic strategies. In the present study, a hybridization-capture method was used to target 1.45 Mb of the genomic sequence (coding sequence, 1 Mb), analyzing the somatic mutation landscape of 81 HCC tumor samples. Mutations in five genes were significantly associated with TMB-H, including mutations in tumor protein 53 (TP53), Catenin®1 (CTNNB1), AT-rich interactive domain-containing protein 1A (ARID1A), myeloid/lymphoid or mixed-lineage leukemia (MLL) and nuclear receptor co-repressor 1 (NCOR1). Further analysis using The Cancer Genome Atlas Liver Hepatocellular Carcinoma database showed that TP53, CTNNB1 and MLL mutations were positively correlated with TMB-H. Meanwhile, mutations in ARID1A, TP53 and MLL were associated with poor overall survival of patients with HCC. Overall, TMB-H and associated driver gene mutations may have potential as predictive biomarkers of ICB therapy efficacy for treatment of patients with HCC.
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Affiliation(s)
- Li Li
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xiaosong Rao
- Department of Pathology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Zhaohong Wen
- Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Xiaosheng Ding
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xiangyi Wang
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Weiran Xu
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Chao Meng
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing 102206, P.R. China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Yongshen Chen
- Geneplus-Beijing Institute, Beijing 102206, P.R. China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Liang Jun
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
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Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery. Nat Rev Mol Cell Biol 2020; 21:123-136. [PMID: 32020081 DOI: 10.1038/s41580-019-0209-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2019] [Indexed: 02/07/2023]
Abstract
Much of the mammalian genome is transcribed, generating long non-coding RNAs (lncRNAs) that can undergo post-transcriptional surveillance whereby only a subset of the non-coding transcripts is allowed to attain sufficient stability to persist in the cellular milieu and control various cellular functions. Paralleling protein turnover by the proteasome complex, lncRNAs are also likely to exist in a dynamic equilibrium that is maintained through constant monitoring by the RNA surveillance machinery. In this Review, we describe the RNA surveillance factors and discuss the vital role of lncRNA surveillance in orchestrating various biological processes, including the protection of genome integrity, maintenance of pluripotency of embryonic stem cells, antibody-gene diversification, coordination of immune cell activation and regulation of heterochromatin formation. We also discuss examples of human diseases and developmental defects associated with the failure of RNA surveillance mechanisms, further highlighting the importance of lncRNA surveillance in maintaining cell and organism functions and health.
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68
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Kim YJ, Park SJ, Maeng KJ, Lee SC, Lee CS. Multi-Platform Omics Analysis for Identification of Molecular Characteristics and Therapeutic Targets of Uveal Melanoma. Sci Rep 2019; 9:19235. [PMID: 31848373 PMCID: PMC6917695 DOI: 10.1038/s41598-019-55513-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/27/2019] [Indexed: 01/22/2023] Open
Abstract
Currently, there is no effective treatment for metastatic uveal melanoma (UVM). Here, we aimed to identify the mechanism involving intrinsic chemoresistance of metastatic UVM and the relevant therapeutic targets for UVM. We analyzed cohorts of 80 and 67 patients with primary UVM and skin cutaneous melanoma (SKCM), respectively, using The Cancer Genome Atlas dataset. Mutational burdens identified by whole exome sequencing were significantly lower in UVM than in SKCM patients. COSMIC mutational signature analysis identified that most of the mutations in UVM patients (>90%) were associated with spontaneous deamination of 5-methylcytosine or defective mismatch repair. Transcriptome analysis revealed that the MYC signature was more enriched in UVM patients, as compared to SKCM patients. Fifty-nine (73.8%) of 80 UVM patients showed gains in MYC copy number, and a high MYC copy number was associated with aggressive clinicopathological features of tumors and poor survival. Kinome-wide siRNA library screening identified several therapeutic targets, reported as synthetic lethal targets for MYC-addicted cancers. Notably, UVM cell lines showed high susceptibility to a WEE1 inhibitor (MK-1775; adavosertib) at a clinically tolerable dose. Overall, our study identified high MYC activity in UVM, and suggested G2/M checkpoint inhibitors as effective therapeutic targets for UVM.
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Affiliation(s)
- Yong Joon Kim
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seo Jin Park
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung Joo Maeng
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung Chul Lee
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Ophthalmology, Institute of Vision Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
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69
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Lama-Sherpa TD, Shevde LA. An Emerging Regulatory Role for the Tumor Microenvironment in the DNA Damage Response to Double-Strand Breaks. Mol Cancer Res 2019; 18:185-193. [PMID: 31676722 DOI: 10.1158/1541-7786.mcr-19-0665] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/23/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
Radiation, alkylating agents, and platinum-based chemotherapy treatments eliminate cancer cells through the induction of excessive DNA damage. The resultant DNA damage challenges the cancer cell's DNA repair capacity. Among the different types of DNA damage induced in cells, double-strand breaks (DSB) are the most lethal if left unrepaired. Unrepaired DSBs in tumor cells exacerbate existing gene deletions, chromosome losses and rearrangements, and aberrant features that characteristically enable tumor progression, metastasis, and drug resistance. Tumor microenvironmental factors like hypoxia, inflammation, cellular metabolism, and the immune system profoundly influence DSB repair mechanisms. Here, we put into context the role of the microenvironment in governing DSB repair mechanisms.
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Affiliation(s)
| | - Lalita A Shevde
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama. .,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama
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70
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Mechanisms of Genomic Instability in Breast Cancer. Trends Mol Med 2019; 25:595-611. [DOI: 10.1016/j.molmed.2019.04.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
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Abstract
The complexity of human cancer underlies its devastating clinical consequences. Drugs designed to target the genetic alterations that drive cancer have improved the outcome for many patients, but not the majority of them. Here, we review the genomic landscape of cancer, how genomic data can provide much more than a sum of its parts, and the approaches developed to identify and validate genomic alterations with potential therapeutic value. We highlight notable successes and pitfalls in predicting the value of potential therapeutic targets and discuss the use of multi-omic data to better understand cancer dependencies and drug sensitivity. We discuss how integrated approaches to collecting, curating, and sharing these large data sets might improve the identification and prioritization of cancer vulnerabilities as well as patient stratification within clinical trials. Finally, we outline how future approaches might improve the efficiency and speed of translating genomic data into clinically effective therapies and how the use of unbiased genome-wide information can identify novel predictive biomarkers that can be either simple or complex.
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Affiliation(s)
- Gary J Doherty
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
| | - Michele Petruzzelli
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom
| | - Emma Beddowes
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Saif S Ahmad
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Carlos Caldas
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Richard J Gilbertson
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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Liu X, Liu L, Ji Y, Li C, Wei T, Yang X, Zhang Y, Cai X, Gao Y, Xu W, Rao S, Jin D, Lou W, Qiu Z, Wang X. Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer. EBioMedicine 2019; 41:345-356. [PMID: 30857943 PMCID: PMC6442234 DOI: 10.1016/j.ebiom.2019.02.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 02/08/2023] Open
Abstract
Background Analysis of cell-free DNA (cfDNA) is promising for broad applications in clinical settings, but with significant bias towards late-stage cancers. Although recent studies have discussed the diverse and degraded nature of cfDNA molecules, little is known about its impact on the practice of cfDNA analysis. Methods We developed single-strand library preparation and hybrid-capture-based cfDNA sequencing (SLHC-seq) to analysis degraded cfDNA fragments. Next we used SLHC-seq to perform cfDNA profiling in 112 pancreatic cancer patients, and the results were compared with 13 previous reports. Extensive analysis was performed in terms of cfDNA fragments to explore the reasons for higher detection rate of KRAS mutations in the circulation of pancreatic cancers. Findings By applying the new approach, we achieved higher efficiency in analysis of mutations than previously reported using other detection assays. 791 cancer-specific mutations were detected in plasma of 88% patients with KRAS hotspots detected in 70% of all patients. Only 8 mutations were detected in 28 healthy controls without any known oncogenic or truncating alleles. cfDNA profiling by SLHC-seq was largely consistent with results of tissue-based sequencing. SLHC-seq rescued short or damaged cfDNA fragments along to increase the sensitivity and accuracy of circulating-tumour DNA detection. Interpretation We found that the small mutant fragments are prevalent in early-stage patients, which provides strong evidence for fragment size-based detection of pancreatic cancer. The new pipeline enhanced our understanding of cfDNA biology and provide new insights for liquid biopsy.
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Affiliation(s)
- Xiaoyu Liu
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China; Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Lingxiao Liu
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Changyu Li
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Xuerong Yang
- Department of Radiology, Shuguang Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuefang Zhang
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xuyu Cai
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Weihong Xu
- Stanford Genome Technology Center, Palo Alto, CA, USA
| | - Shengxiang Rao
- Department of Radiology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Dayong Jin
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai, China; Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Zhongshan Hospital Fudan University, Shanghai, China; Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai, China.
| | - Zilong Qiu
- Institute of Neuroscience, State Kay Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiaolin Wang
- Department of Interventional Radiology, Zhongshan Hospital Fudan University, Shanghai, China; Shanghai Institute of Medical Imaging, Shanghai, China.
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73
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Kalimutho M, Nones K, Srihari S, Duijf PHG, Waddell N, Khanna KK. Patterns of Genomic Instability in Breast Cancer. Trends Pharmacol Sci 2019; 40:198-211. [PMID: 30736983 DOI: 10.1016/j.tips.2019.01.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 01/02/2023]
Abstract
Breast cancer is one of the most common cancers affecting women. Despite significant improvements in overall survival, it remains a significant cause of death worldwide. Genomic instability (GI) is a hallmark of cancer and plays a pivotal role in breast cancer development and progression. In the past decade, high-throughput technologies have provided a wealth of information that has facilitated the identification of a diverse repertoire of mutated genes and mutational processes operative across cancers. Here, we review recent findings on genomic alterations and mutational processes in breast cancer pathogenesis. Most importantly, we summarize the clinical challenges and opportunities to utilize omics-based signatures for better management of breast cancer patients and treatment decision-making.
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Affiliation(s)
- Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia.
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, 37 Kent Street, Brisbane, QLD 4102, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia.
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74
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Sinha D, Duijf PH, Khanna KK. Mitotic slippage: an old tale with a new twist. Cell Cycle 2019; 18:7-15. [PMID: 30601084 PMCID: PMC6343733 DOI: 10.1080/15384101.2018.1559557] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Targeting the mitotic machinery using anti-mitotic drugs for elimination of cancer cells is a century-old concept, which continues to be routinely used as a first line of treatment in the clinic. However, patient response remains unpredictable and drug resistance limits effectiveness of these drugs. Cancer cells exit from drug-induced mitotic arrest (mitotic slippage) to avoid subsequent cell death which is thought to be a major mechanism contributing to this resistance. The tumor cells that acquire resistance to anti-mitotic drugs have chromosomal instability (CIN) and are often aneuploid. In this review, we outline the key mechanisms involved in dictating the cell fate during perturbed mitosis and how these processes impede the efficacy of anti-mitotic therapies. Further, we emphasize the recent work from our laboratory, which highlights the functional role of CEP55 in protecting aneuploid cells from death. We also discuss the rationale of targeting CEP55 in vivo, which could prove to be a novel and effective therapeutic strategy for sensitizing cells to microtubule inhibitors and might offer significantly improved patient outcome. Abbreviations: APC/C: Anaphase-Promoting Complex/Cyclosome; BAD: BCL2-Associated agonist of cell Death; BAK1: BCL2 Antagonist Kinase1; BAX: BCL2-Associated X; BCL2: B-cell Chronic Lymphocytic Leukaemia (CLL)/Lymphoma 2; BH: BCL2 Homology Domain; BID: BH3-Interacting domain Death agonist; BIM: BCL2-Interacting Mediator of cell death; BUB: Budding Uninhibited by Benzimidazoles; CDC: Cell Division Cycle; CDH1: Cadherin-1; CDK1: Cyclin-Dependent Kinase 1; CEP55: Centrosomal Protein (55 KDa): CIN: Chromosomal Instability; CTA: Cancer Testis Antigen; EGR1: Early Growth Response protein 1; ERK: Extracellular Signal-Regulated Kinase; ESCRT: Endosomal Sorting Complexes Required for Transport; GIN: Genomic Instability; MAD2: Mitotic Arrest Deficient 2; MCL1: Myeloid Cell Leukemia sequence 1; MPS1: Monopolar Spindle 1 Kinase; MYT1: MYelin Transcription factor 1; PLK1: Polo Like Kinase 1; PUMA: p53-Upregulated Mediator of Apoptosis; SAC: Spindle Assembly Checkpoint; TAA: Tumor-Associated Antigen.
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Affiliation(s)
- Debottam Sinha
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Pascal H.G. Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
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75
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Krol K, Antoniuk-Majchrzak J, Skoneczny M, Sienko M, Jendrysek J, Rumienczyk I, Halas A, Kurlandzka A, Skoneczna A. Lack of G1/S control destabilizes the yeast genome via replication stress-induced DSBs and illegitimate recombination. J Cell Sci 2018; 131:jcs.226480. [PMID: 30463853 DOI: 10.1242/jcs.226480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022] Open
Abstract
The protein Swi6 in Saccharomyces cerevisiae is a cofactor in two complexes that regulate the transcription of the genes controlling the G1/S transition. It also ensures proper oxidative and cell wall stress responses. Previously, we found that Swi6 was crucial for the survival of genotoxic stress. Here, we show that a lack of Swi6 causes replication stress leading to double-strand break (DSB) formation, inefficient DNA repair and DNA content alterations, resulting in high cell mortality. Comparative genome hybridization experiments revealed that there was a random genome rearrangement in swi6Δ cells, whereas in diploid swi6Δ/swi6Δ cells, chromosome V is duplicated. SWI4 and PAB1, which are located on chromosome V and are known multicopy suppressors of swi6Δ phenotypes, partially reverse swi6Δ genome instability when overexpressed. Another gene on chromosome V, RAD51, also supports swi6Δ survival, but at a high cost; Rad51-dependent illegitimate recombination in swi6Δ cells appears to connect DSBs, leading to genome rearrangement and preventing cell death.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kamil Krol
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Marzena Sienko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Justyna Jendrysek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Izabela Rumienczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Halas
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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76
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Abstract
Somatic structural variants undoubtedly play important roles in driving tumourigenesis. This is evident despite the substantial technical challenges that remain in accurately detecting structural variants and their breakpoints in tumours and in spite of our incomplete understanding of the impact of structural variants on cellular function. Developments in these areas of research contribute to the ongoing discovery of structural variation with a clear impact on the evolution of the tumour and on the clinical importance to the patient. Recent large whole genome sequencing studies have reinforced our impression of each tumour as a unique combination of mutations but paradoxically have also discovered similar genome-wide patterns of single-nucleotide and structural variation between tumours. Statistical methods have been developed to deconvolute mutation patterns, or signatures, that recur across samples, providing information about the mutagens and repair processes that may be active in a given tumour. These signatures can guide treatment by, for example, highlighting vulnerabilities in a particular tumour to a particular chemotherapy. Thus, although the complete reconstruction of the full evolutionary trajectory of a tumour genome remains currently out of reach, valuable data are already emerging to improve the treatment of cancer.
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Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
| | - Colin Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
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77
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Boisselier B, Dugay F, Belaud-Rotureau MA, Coutolleau A, Garcion E, Menei P, Guardiola P, Rousseau A. Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma. Oncotarget 2018; 9:36017-36028. [PMID: 30542515 PMCID: PMC6267593 DOI: 10.18632/oncotarget.26330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/24/2018] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma, the most frequent and lethal form of glioma, displays chromosome instability and recurrent somatic copy number alterations (SCNA). Chromothripsis and whole genome duplication (WGD) have been recently identified in cancer. In the present study, we analyzed SCNA and determine the ploidy pattern in 123 IDH-wild-type glioblastomas, using SNP array data. WGD and chromothripsis events were validated using, respectively, FISH and CTLPScanner. WGD was detected in 11.4% glioblastomas (14/123) and was associated with TP53 mutation (p = 0.0068). It was an early event occurring after the recurrent SCNA observed in diffuse high-grade gliomas. Glioblastomas with WGD were more aneuploid compared to glioblastomas without WGD (p < 0.0001). Chromothripsis occurred in 29.3% glioblastomas (36/123) and mostly affected chromosomes 7, 9 and 12, with amplification of oncogenes (EGFR, MDM2/CDK4), and homozygous deletion of tumor suppressor genes (CDKN2A). There was a significant association between chromothripsis and gene rearrangement at a given locus. WGD is an early genetic event significantly associated to TP53 mutation and leading to chromosome instability and aneuploidy in IDH-wild-type glioblastoma. Chromothripsis recurrently targets oncogenes and tumor suppressor genes that are key players in gliomagenesis and tumor progression. The occurrence of chromothripsis points to underlying gene rearrangements (including gene fusions), potential therapeutic targets in glioblastoma.
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Affiliation(s)
- Blandine Boisselier
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Frédéric Dugay
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | | | | | - Emmanuel Garcion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Philippe Menei
- Département de Neurochirurgie, CHU Angers, Angers, France
| | | | - Audrey Rousseau
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
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78
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Ahmad SS, Ahmed K, Venkitaraman AR. Science in Focus: Genomic Instability and its Implications for Clinical Cancer Care. Clin Oncol (R Coll Radiol) 2018; 30:751-755. [PMID: 30269933 DOI: 10.1016/j.clon.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/13/2018] [Accepted: 08/15/2018] [Indexed: 12/22/2022]
Affiliation(s)
- S S Ahmad
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, UK.
| | - K Ahmed
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, UK
| | - A R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, UK
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79
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Litwin I, Bakowski T, Szakal B, Pilarczyk E, Maciaszczyk-Dziubinska E, Branzei D, Wysocki R. Error-free DNA damage tolerance pathway is facilitated by the Irc5 translocase through cohesin. EMBO J 2018; 37:e98732. [PMID: 30111537 PMCID: PMC6138436 DOI: 10.15252/embj.201798732] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage tolerance (DDT) mechanisms facilitate replication resumption and completion when DNA replication is blocked by bulky DNA lesions. In budding yeast, template switching (TS) via the Rad18/Rad5 pathway is a favored DDT pathway that involves usage of the sister chromatid as a template to bypass DNA lesions in an error-free recombination-like process. Here, we establish that the Snf2 family translocase Irc5 is a novel factor that promotes TS and averts single-stranded DNA persistence during replication. We demonstrate that, during replication stress, Irc5 enables replication progression by assisting enrichment of cohesin complexes, recruited in an Scc2/Scc4-dependent fashion, near blocked replication forks. This allows efficient formation of sister chromatid junctions that are crucial for error-free DNA lesion bypass. Our results support the notion of a key role of cohesin in the completion of DNA synthesis under replication stress and reveal that the Rad18/Rad5-mediated DDT pathway is linked to cohesin enrichment at sites of perturbed replication via the Snf2 family translocase Irc5.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Tomasz Bakowski
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Barnabas Szakal
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Ewa Pilarczyk
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | | | - Dana Branzei
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
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80
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Wang Z, Zhao J, Wang G, Zhang F, Zhang Z, Zhang F, Zhang Y, Dong H, Zhao X, Duan J, Bai H, Tian Y, Wan R, Han M, Cao Y, Xiong L, Liu L, Wang S, Cai S, Mok TSK, Wang J. Comutations in DNA Damage Response Pathways Serve as Potential Biomarkers for Immune Checkpoint Blockade. Cancer Res 2018; 78:6486-6496. [PMID: 30171052 DOI: 10.1158/0008-5472.can-18-1814] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
Abstract
Biomarkers such as programmed death receptor 1 ligand (PD-L1) expression, tumor mutational burden (TMB), and high microsatellite instability are potentially applicable to predict the efficacy of immune checkpoint blockade (ICB). However, several challenges such as defining the cut-off value, test platform uniformity, and low frequencies limit their broad clinical application. Here we identify comutations in the DNA damage response (DDR) pathways of homologous recombination repair and mismatch repair (HRR-MMR) or HRR and base excision repair (HRR-BER; defined as co-mut+) that are associated with increased TMB and neoantigen load and increased levels of immune gene expression signatures. In four public clinical cohorts, co-mut+ patients presented a higher objective response rate and a longer progression-free survival or overall survival than co-mut- patients. Overall, identification of DDR comutations in HRR-MMR or HRR-BER as predictors of response to ICB provides a potentially convenient approach for future clinical practice.Significance: Identification of comutations in specific DDR pathways as predictors of superior survival outcomes in response to immune checkpoint blockade provide a clinically convenient approach for estimation of tumor mutational burden and delivery of ICB therapy. Cancer Res; 78(22); 6486-96. ©2018 AACR.
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Affiliation(s)
- Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China.
| | - Jing Zhao
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Guoqiang Wang
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Fan Zhang
- Department of Oncology, Chinese PLA General Hospital, Beijing, P.R. China
| | - Zemin Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Fan Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Yuzi Zhang
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Hua Dong
- The Bioinformatics Department, R&D Center of Precision Medicine, 3D Medicines Inc., Shanghai, P.R. China
| | - Xiaochen Zhao
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Yanhua Tian
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Miao Han
- The Bioinformatics Department, R&D Center of Precision Medicine, 3D Medicines Inc., Shanghai, P.R. China
| | - Yan Cao
- The Bioinformatics Department, R&D Center of Precision Medicine, 3D Medicines Inc., Shanghai, P.R. China
| | - Lei Xiong
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Shuhang Wang
- Clinical Trial Center of National Cancer Center, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Shangli Cai
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Tony S K Mok
- Department of Clinical Oncology, State Key Laboratory of South China, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, P.R. China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
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81
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Joseph C, Papadaki A, Althobiti M, Alsaleem M, Aleskandarany MA, Rakha EA. Breast cancer intratumour heterogeneity: current status and clinical implications. Histopathology 2018; 73:717-731. [PMID: 29722058 DOI: 10.1111/his.13642] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Breast cancer (BC) is a heterogeneous disease that varies in presentation, morphological features, behaviour, and response to therapy. High-throughput molecular profiling studies have revolutionised our understanding of BC heterogeneity, and have demonstrated that molecular profiles of tumours are variable not only between tumours, but also within individual tumours. Current evidence indicates that spatial and temporal intratumour heterogeneity of BC exists at levels beyond what are commonly expected. Intratumour heterogeneity poses critical challenges in the diagnosis, prediction of behaviour and management of BC. For instance, heterogeneous expression of oestrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 can be seen not only in primary tumours between different regions, but also between primary tumours and their corresponding metastatic/recurrent lesions. The demonstration of molecularly distinct subclones within individual tumours may explain, at least in part, the mechanisms controlling the variable behaviour of BC, and may change our approach to BC sampling and treatment. In this review, BC intratumour heterogeneity is highlighted, with a special emphasis on the current knowledge pertaining to the relationship between intratumour heterogeneity and BC pathogenesis, evolution, and progression, with consideration of its impact on disease diagnosis, management, and the emergence of novel therapeutic targets. The key role of high-throughput molecular and imaging techniques is also addressed.
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Affiliation(s)
- Chitra Joseph
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Athanasia Papadaki
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Maryam Althobiti
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mansour Alsaleem
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mohammed A Aleskandarany
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Emad A Rakha
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
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82
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Liu Y, Xu H, Van der Jeught K, Li Y, Liu S, Zhang L, Fang Y, Zhang X, Radovich M, Schneider BP, He X, Huang C, Zhang C, Wan J, Ji G, Lu X. Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer. J Clin Invest 2018; 128:2951-2965. [PMID: 29649003 PMCID: PMC6025969 DOI: 10.1172/jci98727] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022] Open
Abstract
A synthetic lethality-based strategy has been developed to identify therapeutic targets in cancer harboring tumor-suppressor gene mutations, as exemplified by the effectiveness of poly ADP-ribose polymerase (PARP) inhibitors in BRCA1/2-mutated tumors. However, many synthetic lethal interactors are less reliable due to the fact that such genes usually do not perform fundamental or indispensable functions in the cell. Here, we developed an approach to identifying the "essential lethality" arising from these mutated/deleted essential genes, which are largely tolerated in cancer cells due to genetic redundancy. We uncovered the cohesion subunit SA1 as a putative synthetic-essential target in cancers carrying inactivating mutations of its paralog, SA2. In SA2-deficient Ewing sarcoma and bladder cancer, further depletion of SA1 profoundly and specifically suppressed cancer cell proliferation, survival, and tumorigenic potential. Mechanistically, inhibition of SA1 in the SA2-mutated cells led to premature chromatid separation, dramatic extension of mitotic duration, and consequently, lethal failure of cell division. More importantly, depletion of SA1 rendered those SA2-mutated cells more susceptible to DNA damage, especially double-strand breaks (DSBs), due to reduced functionality of DNA repair. Furthermore, inhibition of SA1 sensitized the SA2-deficient cancer cells to PARP inhibitors in vitro and in vivo, providing a potential therapeutic strategy for patients with SA2-deficient tumors.
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MESH Headings
- Animals
- Antigens, Nuclear/chemistry
- Antigens, Nuclear/genetics
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/genetics
- Cell Line, Tumor
- Chromosomal Proteins, Non-Histone/antagonists & inhibitors
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- DNA Breaks, Double-Stranded
- Female
- Gene Knockdown Techniques
- Genes, Essential
- Humans
- Mice
- Mice, Nude
- Mutation
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/pathology
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Phthalazines/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Protein Subunits/antagonists & inhibitors
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Sarcoma, Ewing/drug therapy
- Sarcoma, Ewing/genetics
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/genetics
- Xenograft Model Antitumor Assays
- Cohesins
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Affiliation(s)
- Yunhua Liu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Kevin Van der Jeught
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Yujing Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Sheng Liu
- Department of Medical and Molecular Genetics
| | - Lu Zhang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Yuanzhang Fang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
| | - Xinna Zhang
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
| | - Milan Radovich
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
- Department of Surgery, and
| | - Bryan P. Schneider
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Xiaoming He
- Department of Biomedical Engineering, Ohio State University, Columbus, Ohio, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
- Martha and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, USA
| | - Cheng Huang
- Drug Discovery Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chi Zhang
- Department of Medical and Molecular Genetics
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Medical and Molecular Genetics
- Indiana University Melvin and Bren Simon Cancer Center
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83
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Vodák D, Lorenz S, Nakken S, Aasheim LB, Holte H, Bai B, Myklebost O, Meza-Zepeda LA, Hovig E. Sample-Index Misassignment Impacts Tumour Exome Sequencing. Sci Rep 2018; 8:5307. [PMID: 29593270 PMCID: PMC5871786 DOI: 10.1038/s41598-018-23563-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/15/2018] [Indexed: 12/11/2022] Open
Abstract
Sample pooling enabled by dedicated indexes is a common strategy for cost-effective and robust high-throughput sequencing. Index misassignment leading to mutual contamination between pooled samples has however been described as a general problem of the latest Illumina sequencing instruments utilizing exclusion amplification. Using real-life data from multiple tumour sequencing projects, we demonstrate that index misassignment can induce artefactual variant calls closely resembling true, high-quality somatic variants. These artefactual calls potentially impact cancer applications utilizing low allelic frequencies, such as in clonal analysis of tumours. We discuss the available countermeasures with an emphasis on improved library indexing methods, and provide software that can assist in the identification of variants that may be consequences of index misassignment.
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Affiliation(s)
- Daniel Vodák
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Sigve Nakken
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Lars Birger Aasheim
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Harald Holte
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Oncology, Cancer Clinic, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Baoyan Bai
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway.,Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway. .,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway. .,Department of Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway. .,Department of Informatics, University of Oslo, Oslo, Norway.
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84
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Litwin I, Wysocki R. New insights into cohesin loading. Curr Genet 2018; 64:53-61. [PMID: 28631016 DOI: 10.1007/s00294-017-0723-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/13/2023]
Abstract
Cohesin is a conserved, ring-shaped protein complex that encircles sister chromatids and ensures correct chromosome segregation during mitosis and meiosis. It also plays a crucial role in the regulation of gene expression, DNA condensation, and DNA repair through both non-homologous end joining and homologous recombination. Cohesins are spatiotemporally regulated by the Scc2-Scc4 complex which facilitates cohesin loading onto chromatin at specific chromosomal sites. Over the last few years, much attention has been paid to cohesin and cohesin loader as it became clear that even minor disruptions of these complexes may lead to developmental disorders and cancers. Here we summarize recent developments in the structure of Scc2-Scc4 complex, cohesin loading process, and mediators that determine the Scc2-Scc4 binding patterns to chromatin.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland
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85
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McGinty RJ, Rubinstein RG, Neil AJ, Dominska M, Kiktev D, Petes TD, Mirkin SM. Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. Genome Res 2017; 27:2072-2082. [PMID: 29113982 PMCID: PMC5741057 DOI: 10.1101/gr.228148.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/26/2017] [Indexed: 01/25/2023]
Abstract
Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy, and (CGG)n repeats in fragile X syndrome, are also subject to double-strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects. However, high-resolution mapping of CGRs has traditionally been a laborious and highly skilled process. Recent advances in long-read DNA sequencing technologies, specifically Nanopore sequencing, have made possible the rapid identification of CGRs with single base pair resolution. Here, we have used whole-genome Nanopore sequencing to characterize several CGRs that originated from naturally occurring DSBs at (GAA)n microsatellites in Saccharomyces cerevisiae. These data gave us important insights into the mechanisms of DSB repair leading to CGRs.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | | | - Alexander J Neil
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Denis Kiktev
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
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86
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Genome Instability and γH2AX. Int J Mol Sci 2017; 18:ijms18091979. [PMID: 28914798 PMCID: PMC5618628 DOI: 10.3390/ijms18091979] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
γH2AX has emerged in the last 20 years as a central player in the DDR (DNA damage response), with specificity for DSBs (double-strand breaks). Upon the generation of DSBs, γ-phosphorylation extends along megabase-long domains in chromatin, both sides of the damage. The significance of this mechanism is of great importance; it depicts a biological amplification mechanism where one DSB induces the γ-phosphorylation of thousands of H2AX molecules along megabaselong domains of chromatin, that are adjusted to the sites of DSBs. A sequential recruitment of signal transduction factors that interact to each other and become activated to further amplify the signal that will travel to the cytoplasm take place on the γ-phosphorylated chromatin. γ-phosphorylation is an early event in the DSB damage response, induced in all phases of the cell cycle, and participates in both DSB repair pathways, the HR (homologous recombination) and NHEJ (non-homologous end joining). Today, numerous studies support the notion that γH2AX functions as a guardian of the genome by preventing misrepaired DSB that increase the mutation load of the cells and may further lead to genome instability and carcinogenesis.
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87
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Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme. Sci Rep 2017; 7:6968. [PMID: 28761058 PMCID: PMC5537248 DOI: 10.1038/s41598-017-05538-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/18/2017] [Indexed: 11/08/2022] Open
Abstract
Hypothetically, intratumoral genomic heterogeneity has the potential to foster tumor-infiltrating lymphocyte (TIL) diversity; however, no study has directly tested this hypothesis by simultaneously investigating somatic mutations, TIL diversity, and immune response activity. Thus, we performed whole-exome sequencing, immune repertoire sequencing and gene expression on ten spatially separated tumor samples obtained from two tumor masses excised from a glioblastoma multiforme (GBM) patient, and we included peripheral blood as control. We found that although the multi-region samples from one tumor shared more common mutations than those from different tumors, the TIL populations did not. TIL repertoire diversity did not significantly correlate with the number of non-synonymous mutations; however, TIL diversity was highly correlated with local immune activity, as the pathways were all immune-related pathways that highly positive correlated with local TIL diversity. Twenty-three genes with expression largely unaffected by the intratumor heterogeneity were extracted from these pathways. Fifty GBM patients were stratified into two clusters by the expression of these genes with significant difference in prognosis. This finding was validated by The Cancer Genome Atlas (TCGA) GBM dataset, which indicated that despite the heterogeneity of intra-tumor immune status, the overall level of the immune response in GBM could be connected with prognosis.
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88
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Forsberg J, Zhivotovsky B, Olsson M. Caspase-2: an orphan enzyme out of the shadows. Oncogene 2017; 36:5441-5444. [PMID: 28581521 DOI: 10.1038/onc.2017.169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/18/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Caspase-2 has been embodied as an initiator or executioner protease in diverse apoptotic scenarios. However, accumulating evidence is challenging this view, pertaining to its true role. The enzyme's catalytic activity is currently implicated in various functions required for correct cell proliferation, such as counteracting genomic instability, as well as suppressing tumorigenesis. Here, apart from summarizing the latest observations in caspase-2-related research, we make an attempt to reconcile these findings and discuss their implications for future directions.
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Affiliation(s)
- J Forsberg
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - B Zhivotovsky
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - M Olsson
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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89
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Balani S, Nguyen LV, Eaves CJ. Modeling the process of human tumorigenesis. Nat Commun 2017; 8:15422. [PMID: 28541307 PMCID: PMC5458507 DOI: 10.1038/ncomms15422] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Modelling the genesis of human cancers is at a scientific turning point. Starting from primary sources of normal human cells, it is now possible to reproducibly generate several types of malignant cell populations. Powerful methods for clonally tracking and manipulating their appearance and progression in serially transplanted immunodeficient mice are also in place. These developments circumvent historic drawbacks inherent in analyses of cancers produced in model organisms, established human malignant cell lines, or highly heterogeneous patient samples. In this review, we survey the advantages, contributions and limitations of current de novo human tumorigenesis strategies and note several exciting prospects on the horizon. A better understanding of the earliest stages of human cancer formation can enable future improvements in early detection, diagnosis and treatment. In this review, the authors summarize the methods enabling de novo tumorigenesis protocols to be applied to human cells and the insights derived from them to date, as well as the exciting and relevant technical developments anticipated to extend even further the utility of these strategies.
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Affiliation(s)
- Sneha Balani
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Long V. Nguyen
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Connie J. Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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90
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Maleki SS, Röcken C. Chromosomal Instability in Gastric Cancer Biology. Neoplasia 2017; 19:412-420. [PMID: 28431273 PMCID: PMC5397576 DOI: 10.1016/j.neo.2017.02.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/21/2017] [Indexed: 02/08/2023] Open
Abstract
Gastric cancer (GC) is the fifth most common cancer in the world and accounts for 7% of the total cancer incidence. The prognosis of GC is dismal in Western countries due to late diagnosis: approximately 70% of the patients die within 5 years following initial diagnosis. Recently, integrative genomic analyses led to the proposal of a molecular classification of GC into four subtypes, i.e.,microsatellite-instable, Epstein-Barr virus–positive, chromosomal-instable (CIN), and genomically stable GCs. Molecular classification of GC advances our knowledge of the biology of GC and may have implications for diagnostics and patient treatment. Diagnosis of microsatellite-instable GC and Epstein-Barr virus–positive GC is more or less straightforward. Microsatellite instability can be tested by immunohistochemistry (MLH1, PMS2, MSH2, and MSH6) and/or molecular-biological analysis. Epstein-Barr virus–positive GC can be tested by in situ hybridization (Epstein-Barr virus encoded small RNA). However, with regard to CIN, testing may be more complicated and may require a more in-depth knowledge of the underlying mechanism leading to CIN. In addition, CIN GC may not constitute a distinct subgroup but may rather be a compilation of a more heterogeneous group of tumors. In this review, we aim to clarify the definition of CIN and to point out the molecular mechanisms leading to this molecular phenotype and the challenges faced in characterizing this type of cancer.
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Affiliation(s)
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, Kiel, Germany.
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91
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Abstract
Tumor-growth-factor-beta signaling helps cancer cells to evolve and become resistant to drugs by down-regulating accurate DNA repair.
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Affiliation(s)
- Devon M Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, United States.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, United States
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, United States.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, United States
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92
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Hu Z, Sun R, Curtis C. A population genetics perspective on the determinants of intra-tumor heterogeneity. Biochim Biophys Acta Rev Cancer 2017; 1867:109-126. [PMID: 28274726 DOI: 10.1016/j.bbcan.2017.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
Cancer results from the acquisition of somatic alterations in a microevolutionary process that typically occurs over many years, much of which is occult. Understanding the evolutionary dynamics that are operative at different stages of progression in individual tumors might inform the earlier detection, diagnosis, and treatment of cancer. Although these processes cannot be directly observed, the resultant spatiotemporal patterns of genetic variation amongst tumor cells encode their evolutionary histories. Such intra-tumor heterogeneity is pervasive not only at the genomic level, but also at the transcriptomic, phenotypic, and cellular levels. Given the implications for precision medicine, the accurate quantification of heterogeneity within and between tumors has become a major focus of current research. In this review, we provide a population genetics perspective on the determinants of intra-tumor heterogeneity and approaches to quantify genetic diversity. We summarize evidence for different modes of evolution based on recent cancer genome sequencing studies and discuss emerging evolutionary strategies to therapeutically exploit tumor heterogeneity. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- Zheng Hu
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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93
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Fitzgerald DM, Hastings PJ, Rosenberg SM. Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance. ANNUAL REVIEW OF CANCER BIOLOGY 2017; 1:119-140. [PMID: 29399660 PMCID: PMC5794033 DOI: 10.1146/annurev-cancerbio-050216-121919] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genomic instability underlies many cancers and generates genetic variation that drives cancer initiation, progression, and therapy resistance. In contrast with classical assumptions that mutations occur purely stochastically at constant, gradual rates, microbes, plants, flies, and human cancer cells possess mechanisms of mutagenesis that are upregulated by stress responses. These generate transient, genetic-diversity bursts that can propel evolution, specifically when cells are poorly adapted to their environments-that is, when stressed. We review molecular mechanisms of stress-response-dependent (stress-induced) mutagenesis that occur from bacteria to cancer, and are activated by starvation, drugs, hypoxia, and other stressors. We discuss mutagenic DNA break repair in Escherichia coli as a model for mechanisms in cancers. The temporal regulation of mutagenesis by stress responses and spatial restriction in genomes are common themes across the tree of life. Both can accelerate evolution, including the evolution of cancers. We discuss possible anti-evolvability drugs, aimed at targeting mutagenesis and other variation generators, that could be used to delay the evolution of cancer progression and therapy resistance.
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Affiliation(s)
- Devon M Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
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94
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Potapova T, Gorbsky GJ. The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis. BIOLOGY 2017; 6:biology6010012. [PMID: 28208750 PMCID: PMC5372005 DOI: 10.3390/biology6010012] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 12/21/2022]
Abstract
Mistakes during cell division frequently generate changes in chromosome content, producing aneuploid or polyploid progeny cells. Polyploid cells may then undergo abnormal division to generate aneuploid cells. Chromosome segregation errors may also involve fragments of whole chromosomes. A major consequence of segregation defects is change in the relative dosage of products from genes located on the missegregated chromosomes. Abnormal expression of transcriptional regulators can also impact genes on the properly segregated chromosomes. The consequences of these perturbations in gene expression depend on the specific chromosomes affected and on the interplay of the aneuploid phenotype with the environment. Most often, these novel chromosome distributions are detrimental to the health and survival of the organism. However, in a changed environment, alterations in gene copy number may generate a more highly adapted phenotype. Chromosome segregation errors also have important implications in human health. They may promote drug resistance in pathogenic microorganisms. In cancer cells, they are a source for genetic and phenotypic variability that may select for populations with increased malignance and resistance to therapy. Lastly, chromosome segregation errors during gamete formation in meiosis are a primary cause of human birth defects and infertility. This review describes the consequences of mitotic and meiotic errors focusing on novel concepts and human health.
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Affiliation(s)
- Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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95
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Comaills V, Kabeche L, Morris R, Buisson R, Yu M, Madden MW, LiCausi JA, Boukhali M, Tajima K, Pan S, Aceto N, Sil S, Zheng Y, Sundaresan T, Yae T, Jordan NV, Miyamoto DT, Ting DT, Ramaswamy S, Haas W, Zou L, Haber DA, Maheswaran S. Genomic Instability Is Induced by Persistent Proliferation of Cells Undergoing Epithelial-to-Mesenchymal Transition. Cell Rep 2016; 17:2632-2647. [PMID: 27926867 PMCID: PMC5320932 DOI: 10.1016/j.celrep.2016.11.022] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/16/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
TGF-β secreted by tumor stroma induces epithelial-to-mesenchymal transition (EMT) in cancer cells, a reversible phenotype linked to cancer progression and drug resistance. However, exposure to stromal signals may also lead to heritable changes in cancer cells, which are poorly understood. We show that epithelial cells failing to undergo proliferation arrest during TGF-β-induced EMT sustain mitotic abnormalities due to failed cytokinesis, resulting in aneuploidy. This genomic instability is associated with the suppression of multiple nuclear envelope proteins implicated in mitotic regulation and is phenocopied by modulating the expression of LaminB1. While TGF-β-induced mitotic defects in proliferating cells are reversible upon its withdrawal, the acquired genomic abnormalities persist, leading to increased tumorigenic phenotypes. In metastatic breast cancer patients, increased mesenchymal marker expression within single circulating tumor cells is correlated with genomic instability. These observations identify a mechanism whereby microenvironment-derived signals trigger heritable genetic changes within cancer cells, contributing to tumor evolution.
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Affiliation(s)
- Valentine Comaills
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lilian Kabeche
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Rémi Buisson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Min Yu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marissa Wells Madden
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Joseph A LiCausi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ken Tajima
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA
| | - Shiwei Pan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicola Aceto
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Srinjoy Sil
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yu Zheng
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Tilak Sundaresan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Toshifumi Yae
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicole Vincent Jordan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - David T Miyamoto
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Harvard Medical School, Charlestown, MA 02129, USA.
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96
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Niu ZS, Niu XJ, Wang WH. Genetic alterations in hepatocellular carcinoma: An update. World J Gastroenterol 2016; 22:9069-9095. [PMID: 27895396 PMCID: PMC5107590 DOI: 10.3748/wjg.v22.i41.9069] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although recent advances in therapeutic approaches for treating HCC have improved the prognoses of patients with HCC, this cancer is still associated with a poor survival rate mainly due to late diagnosis. Therefore, a diagnosis must be made sufficiently early to perform curative and effective treatments. There is a need for a deeper understanding of the molecular mechanisms underlying the initiation and progression of HCC because these mechanisms are critical for making early diagnoses and developing novel therapeutic strategies. Over the past decade, much progress has been made in elucidating the molecular mechanisms underlying hepatocarcinogenesis. In particular, recent advances in next-generation sequencing technologies have revealed numerous genetic alterations, including recurrently mutated genes and dysregulated signaling pathways in HCC. A better understanding of the genetic alterations in HCC could contribute to identifying potential driver mutations and discovering novel therapeutic targets in the future. In this article, we summarize the current advances in research on the genetic alterations, including genomic instability, single-nucleotide polymorphisms, somatic mutations and deregulated signaling pathways, implicated in the initiation and progression of HCC. We also attempt to elucidate some of the genetic mechanisms that contribute to making early diagnoses of and developing molecularly targeted therapies for HCC.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Molecular Diagnostic Techniques
- Molecular Targeted Therapy
- Mutation
- Patient Selection
- Phenotype
- Polymorphism, Single Nucleotide
- Precision Medicine
- Predictive Value of Tests
- Signal Transduction
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