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Chen G, Mulla WA, Kucharavy A, Tsai HJ, Rubinstein B, Conkright J, McCroskey S, Bradford WD, Weems L, Haug JS, Seidel CW, Berman J, Li R. Targeting the adaptability of heterogeneous aneuploids. Cell 2015; 160:771-784. [PMID: 25679766 DOI: 10.1016/j.cell.2015.01.026] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/17/2014] [Accepted: 12/31/2014] [Indexed: 02/08/2023]
Abstract
Aneuploid genomes, characterized by unbalanced chromosome stoichiometry (karyotype), are associated with cancer malignancy and drug resistance of pathogenic fungi. The phenotypic diversity resulting from karyotypic diversity endows the cell population with superior adaptability. We show here, using a combination of experimental data and a general stochastic model, that the degree of phenotypic variation, thus evolvability, escalates with the degree of overall growth suppression. Such scaling likely explains the challenge of treating aneuploidy diseases with a single stress-inducing agent. Instead, we propose the design of an "evolutionary trap" (ET) targeting both karyotypic diversity and fitness. This strategy entails a selective condition "channeling" a karyotypically divergent population into one with a predominant and predictably drugable karyotypic feature. We provide a proof-of-principle case in budding yeast and demonstrate the potential efficacy of this strategy toward aneuploidy-based azole resistance in Candida albicans. By analyzing existing pharmacogenomics data, we propose the potential design of an ET against glioblastoma.
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Affiliation(s)
- Guangbo Chen
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Wahid A Mulla
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Andrei Kucharavy
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Biologie Computationnelle et Quantitative, F-75005 Paris, France
| | - Hung-Ji Tsai
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Boris Rubinstein
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Juliana Conkright
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Scott McCroskey
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - William D Bradford
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Lauren Weems
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Jeff S Haug
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Rong Li
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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252
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Pailler E, Auger N, Lindsay CR, Vielh P, Islas-Morris-Hernandez A, Borget I, Ngo-Camus M, Planchard D, Soria JC, Besse B, Farace F. High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer. Ann Oncol 2015; 26:1408-15. [PMID: 25846554 PMCID: PMC4478971 DOI: 10.1093/annonc/mdv165] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/16/2015] [Indexed: 12/02/2022] Open
Abstract
ROS1-rearrangement can be detected in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer patients, offering perspectives for diagnosing patients eligible for ROS1-inhibitor therapy. ROS1-rearranged CTCs show considerable heterogeneity of ROS1-gene abnormalities and elevated numerical chromosomal instability, a potential mechanism of resistance to ROS1-inhibitor. Background Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Patients and methods Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. Results ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24–55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7–11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. Conclusion We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged patients show considerable heterogeneity of ROS1-gene abnormalities and elevated numerical CIN, a potential mechanism to escape ROS1-inhibitor therapy in ROS1-rearranged NSCLC tumors.
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Affiliation(s)
- E Pailler
- INSERM U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", University of Paris-Sud XI, Gustave Roussy, Villejuif Translational Research Laboratory, Gustave Roussy, Villejuif
| | - N Auger
- Departments of Biopathology, Gustave Roussy, Villejuif, France
| | - C R Lindsay
- INSERM U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", University of Paris-Sud XI, Gustave Roussy, Villejuif Translational Research Laboratory, Gustave Roussy, Villejuif
| | - P Vielh
- INSERM U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", University of Paris-Sud XI, Gustave Roussy, Villejuif Translational Research Laboratory, Gustave Roussy, Villejuif Departments of Biopathology, Gustave Roussy, Villejuif, France
| | | | - I Borget
- Biostatistics and Epidemiology, Gustave Roussy, Villejuif, France
| | | | | | - J-C Soria
- INSERM U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", University of Paris-Sud XI, Gustave Roussy, Villejuif Medicine, Gustave Roussy, Villejuif, France
| | - B Besse
- Medicine, Gustave Roussy, Villejuif, France
| | - F Farace
- INSERM U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", University of Paris-Sud XI, Gustave Roussy, Villejuif Translational Research Laboratory, Gustave Roussy, Villejuif
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253
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Cheng W, Li M, Cai J, Wang K, Zhang C, Bao Z, Liu Y, Wu A. HDAC4, a prognostic and chromosomal instability marker, refines the predictive value of MGMT promoter methylation. J Neurooncol 2015; 122:303-12. [PMID: 25557107 PMCID: PMC4368847 DOI: 10.1007/s11060-014-1709-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/24/2014] [Indexed: 01/23/2023]
Abstract
Chromosomal instability is a hallmark of human cancers and is closely linked to tumorigenesis. The prognostic value of molecular signatures of chromosomal instability (CIN) has been validated in various cancers. However, few studies have examined the relationship between CIN and glioma. Histone deacetylases (HDACs) regulate chromosome structure and are linked to the loss of genomic integrity in cancer cells. In this study, the prognostic value of HDAC4 expression and its association with markers of CIN were investigated by analyzing data from our own and four other large sample databases. The results showed that HDAC4 expression is downregulated in high- as compared to low-grade glioma and is associated with a favorable clinical outcome. HDAC4 expression and CIN were closely related in glioma from both functional and statistical standpoints. Moreover, the predictive value of the O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status-a widely used glioma marker-was refined by HDAC4 expression level, which was significantly related to CIN in our study. In conclusion, we propose that HDAC4 expression, a prognostic and CIN marker, enhances the predictive value of MGMT promoter methylation status for identifying patients who will most benefit from radiochemotherapy.
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Affiliation(s)
- Wen Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Nanjing Street 155, Heping District, Shenyang, 110001 China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Mingyang Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Kuanyu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Chuanbao Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Yanwei Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Nanjing Street 155, Heping District, Shenyang, 110001 China
- Chinese Glioma Cooperative Group (CGCG), Beijing, China
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254
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Cojoc M, Mäbert K, Muders MH, Dubrovska A. A role for cancer stem cells in therapy resistance: Cellular and molecular mechanisms. Semin Cancer Biol 2015; 31:16-27. [DOI: 10.1016/j.semcancer.2014.06.004] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 12/11/2022]
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255
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Chen C, Qi XJ, Cao YW, Wang YH, Yang XC, Shao SX, Niu HT. Bladder Tumor Heterogeneity: The Impact on Clinical Treatment. Urol Int 2015; 95:1-8. [DOI: 10.1159/000370165] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bladder cancer relapse and treatment failure in most patients have often been attributed to chemoresistance in tumor cells and metastasis. Emerging evidence indicates that tumor heterogeneity may play an equally important role and extends to virtually all measurable properties of cancer cells. Although the idea of tumor heterogeneity is not new, little attention has been paid to applying it to understand and control bladder cancer progression. With the development of biotechnology, such as Gene sequencing, recent advances in understanding its generation model, original basis, consequent problems, and derived therapies provide great potential for tumor heterogeneity to be considered a new insight in the treatment of bladder cancers.
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256
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Novel R pipeline for analyzing Biolog Phenotypic MicroArray data. PLoS One 2015; 10:e0118392. [PMID: 25786143 PMCID: PMC4365023 DOI: 10.1371/journal.pone.0118392] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/15/2015] [Indexed: 01/02/2023] Open
Abstract
Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells’ respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes.
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257
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Rahmutulla B, Matsushita K, Satoh M, Seimiya M, Tsuchida S, Kubo S, Shimada H, Ohtsuka M, Miyazaki M, Nomura F. Alternative splicing of FBP-interacting repressor coordinates c-Myc, P27Kip1/cyclinE and Ku86/XRCC5 expression as a molecular sensor for bleomycin-induced DNA damage pathway. Oncotarget 2015; 5:2404-17. [PMID: 24811221 PMCID: PMC4058014 DOI: 10.18632/oncotarget.1650] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The far-upstream element-binding protein-interacting repressor (FIR) is a c-myc transcriptional suppressor. FIR is alternatively spliced to lack the transcriptional repression domain within exon 2 (FIRΔexon2) in colorectal cancers. FIR and FIRΔexon2 form homo- or heterodimers that complex with SAP155. SAP155, a subunit of the essential splicing factor 3b subcomplex in the spliceosome, is required for proper P27Kip1 pre-mRNA splicing, and P27Kip1 arrests cells at G1. In contrast, FIR was co-immunoprecipitated with Ku86 and DNA-PKcs. siRNA against Ku86/Ku70 decreased FIR and P27Kip1 expression, whereas siRNA against FIR decreased Ku86/XRCC5 and P27Kip1 expression. Thus the mechanical interaction of FIR/FIRΔexon2/SAP155 bridges c-myc and P27Kip1 expression, potentially integrates cell-cycle progression and c-myc transcription in cell. Bleomycin (BLM) is an anticancer agent that introduces DNA breaks. Because DNA breaks generate the recruitment of Ku86/Ku70 to bind to the broken DNA ends, the possible involvement of FIR and Ku86/Ku70 interaction in the BLM-induced DNA damage repair response was investigated in this study. First, BLM treatment reduced SAP155 expression and increased FIR and FIRΔexon2 mRNA expression as well as the ratio of FIRΔexon2:FIR in hepatoblastoma cells (HLE and HLF). Second, FIR or FIRΔexon2 adenovirus vectors (Ad-FIR or Ad-FIRΔexon2) increased Ku86/Ku70 and P27Kip1 expression in vitro. Third, BLM decreased P27Kip1 protein expression, whereas increased P27Kip1 and γH2AX expression with Ad-FIRΔexon2. Together, the interaction of FIR/SAP155 modulates FIR splicing and involves in cell-cycle control or cell fate via P27Kip1 and c-myc in BLM-induced DNA damage pathway. This novel function of FIR splicing will contribute to clinical studies of cancer management through elucidating the mechanical interaction of FIR/FIRΔexon2/SAP155 as a potential target for cancer treatment.
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Affiliation(s)
- Bahityar Rahmutulla
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba, Japan
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Nicholson JM, Cimini D. Link between aneuploidy and chromosome instability. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:299-317. [PMID: 25708466 DOI: 10.1016/bs.ircmb.2014.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aneuploidy is widely acknowledged as a leading cause of miscarriage and birth defects in humans, and is generally known to be deleterious to the survival of individual cells. However, aneuploidy is also ubiquitous in cancer and is found to arise as an adaptive response in certain contexts. This dichotomy of aneuploidy has attracted the interest of researchers for over a century, but many studies have reached conflicting conclusions. The emergence of new technology has allowed scientists to revisit the aneuploidy problem and has fueled a number of recent studies aimed at understanding the effects of aneuploidy on cell physiology. Here, we review these studies, in light of previous observations and knowledge, specifically focusing on the effects of aneuploidy on cellular homeostasis, chromosome stability, and adaptation.
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Affiliation(s)
- Joshua M Nicholson
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Daniela Cimini
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
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Abstract
Cancer cells differ from normal healthy cells in multiple aspects ranging from altered cellular signaling through metabolic changes to aberrant chromosome content, so called aneuploidy. The large-scale changes in copy numbers of chromosomes or large chromosomal regions due to aneuploidy alter significantly the gene expression, as several hundreds of genes are gained or lost. Comparison of quantitative genome, transcriptome and proteome data enables dissection of the molecular causes that underlie the gene expression changes observed in cancer cells and provides a new perspective on the molecular consequences of aneuploidy. Here, we will map to what degree aneuploidy affects the expression of genes located on the affected chromosomes. We will also address the effects of aneuploidy on global gene expression in cancer cells as well as whether and how it may contribute to the physiology of cancer cells.
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Affiliation(s)
- Milena Dürrbaum
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Center for Integrated Protein Science Munich, Ludwig-Maximilian-University Munich, 80336, Munich, Germany.
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260
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Stepanenko A, Andreieva S, Korets K, Mykytenko D, Huleyuk N, Vassetzky Y, Kavsan V. Step-wise and punctuated genome evolution drive phenotype changes of tumor cells. Mutat Res 2015; 771:56-69. [PMID: 25771981 DOI: 10.1016/j.mrfmmm.2014.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
The pattern of genome evolution can be divided into two phases: the step-wise continuous phase (step-wise clonal evolution, stable dominant clonal chromosome aberrations (CCAs), and low frequency of non-CCAs, NCCAs) and punctuated phase (marked by elevated NCCAs and transitional CCAs). Depending on the phase, system stresses (the diverse CIN promoting factors) may lead to the very different phenotype responses. To address the contribution of chromosome instability (CIN) to phenotype changes of tumor cells, we characterized CCAs/NCCAs of HeLa and HEK293 cells, and their derivatives after genotoxic stresses (a stable plasmid transfection, ectopic expression of cancer-associated CHI3L1 gene or treatment with temozolomide) by conventional cytogenetics, copy number alterations (CNAs) by array comparative genome hybridization, and phenotype changes by cell viability and soft agar assays. Transfection of either the empty vector pcDNA3.1 or pcDNA3.1_CHI3L1 into 293 cells initiated the punctuated genome changes. In contrast, HeLa_CHI3L1 cells demonstrated the step-wise genome changes. Increased CIN correlated with lower viability of 293_pcDNA3.1 cells but higher colony formation efficiency (CFE). Artificial CHI3L1 production in 293_CHI3L1 cells increased viability and further contributed to CFE. The opposite growth characteristics of 293_CHI3L1 and HeLa_CHI3L1 cells were revealed. The effect and function of a (trans)gene can be opposite and versatile in cells with different genetic network, which is defined by genome context. Temozolomide treatment of 293_pcDNA3.1 cells intensified the stochastic punctuated genome changes and CNAs, and significantly reduced viability and CFE. In contrast, temozolomide treatment of HeLa_CHI3L1 cells promoted the step-wise genome changes, CNAs, and increased viability and CFE, which did not correlate with the ectopic CHI3L1 production. Thus, consistent coevolution of karyotypes and phenotypes was observed. CIN as a driving force of genome evolution significantly influences growth characteristics of tumor cells and should be always taken into consideration during the different experimental manipulations.
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Affiliation(s)
- Aleksei Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine.
| | - Svitlana Andreieva
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Kateryna Korets
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Dmytro Mykytenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Nataliya Huleyuk
- Institute of Hereditary Pathology, National Academy of Medical Sciences of Ukraine, Lviv 79008, Ukraine
| | - Yegor Vassetzky
- CNRS UMR8126, Université Paris-Sud 11, Institut de Cancérologie Gustave Roussy, Villejuif 94805, France
| | - Vadym Kavsan
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
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261
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Blighe K, Kenny L, Patel N, Guttery DS, Page K, Gronau JH, Golshani C, Stebbing J, Coombes RC, Shaw JA. Whole genome sequence analysis suggests intratumoral heterogeneity in dissemination of breast cancer to lymph nodes. PLoS One 2014; 9:e115346. [PMID: 25546409 PMCID: PMC4278903 DOI: 10.1371/journal.pone.0115346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/22/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Intratumoral heterogeneity may help drive resistance to targeted therapies in cancer. In breast cancer, the presence of nodal metastases is a key indicator of poorer overall survival. The aim of this study was to identify somatic genetic alterations in early dissemination of breast cancer by whole genome next generation sequencing (NGS) of a primary breast tumor, a matched locally-involved axillary lymph node and healthy normal DNA from blood. METHODS Whole genome NGS was performed on 12 µg (range 11.1-13.3 µg) of DNA isolated from fresh-frozen primary breast tumor, axillary lymph node and peripheral blood following the DNA nanoball sequencing protocol. Single nucleotide variants, insertions, deletions, and substitutions were identified through a bioinformatic pipeline and compared to CIN25, a key set of genes associated with tumor metastasis. RESULTS Whole genome sequencing revealed overlapping variants between the tumor and node, but also variants that were unique to each. Novel mutations unique to the node included those found in two CIN25 targets, TGIF2 and CCNB2, which are related to transcription cyclin activity and chromosomal stability, respectively, and a unique frameshift in PDS5B, which is required for accurate sister chromatid segregation during cell division. We also identified dominant clonal variants that progressed from tumor to node, including SNVs in TP53 and ARAP3, which mediates rearrangements to the cytoskeleton and cell shape, and an insertion in TOP2A, the expression of which is significantly associated with tumor proliferation and can segregate breast cancers by outcome. CONCLUSION This case study provides preliminary evidence that primary tumor and early nodal metastasis have largely overlapping somatic genetic alterations. There were very few mutations unique to the involved node. However, significant conclusions regarding early dissemination needs analysis of a larger number of patient samples.
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Affiliation(s)
- Kevin Blighe
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Laura Kenny
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Naina Patel
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - David S. Guttery
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Karen Page
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
| | - Julian H. Gronau
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Cyrus Golshani
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - R. Charles Coombes
- Division of Cancer, Imperial College, Hammersmith Hospital Campus, London, W12 0NN, United Kingdom
| | - Jacqueline A. Shaw
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, United Kingdom
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Mitotic accumulation of dimethylated lysine 79 of histone H3 is important for maintaining genome integrity during mitosis in human cells. Genetics 2014; 199:423-33. [PMID: 25533199 PMCID: PMC4317652 DOI: 10.1534/genetics.114.172874] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The loss of genome stability is an early event that drives the development and progression of virtually all tumor types. Recent studies have revealed that certain histone post-translational modifications exhibit dynamic and global increases in abundance that coincide with mitosis and exhibit essential roles in maintaining genomic stability. Histone H2B ubiquitination at lysine 120 (H2Bub1) is regulated by RNF20, an E3 ubiquitin ligase that is altered in many tumor types. Through an evolutionarily conserved trans-histone pathway, H2Bub1 is an essential prerequisite for subsequent downstream dimethylation events at lysines 4 (H3K4me2) and 79 (H3K79me2) of histone H3. Although the role that RNF20 plays in tumorigenesis has garnered much attention, the downstream components of the trans-histone pathway, H3K4me2 and H3K79me2, and their potential contributions to genome stability remain largely overlooked. In this study, we employ single-cell imaging and biochemical approaches to investigate the spatial and temporal patterning of RNF20, H2Bub1, H3K4me2, and H3K79me2 throughout the cell cycle, with a particular focus on mitosis. We show that H2Bub1, H3K4me2, and H3K79me2 exhibit distinct temporal progression patterns throughout the cell cycle. Most notably, we demonstrate that H3K79me2 is a highly dynamic histone post-translational modification that reaches maximal abundance during mitosis in an H2Bub1-independent manner. Using RNAi and chemical genetic approaches, we identify DOT1L as a histone methyltransferase required for the mitotic-associated increases in H3K79me2. We also demonstrate that the loss of mitotic H3K79me2 levels correlates with increases in chromosome numbers and increases in mitotic defects. Collectively, these data suggest that H3K79me2 dynamics during mitosis are normally required to maintain genome stability and further implicate the loss of H3K79me2 during mitosis as a pathogenic event that contributes to the development and progression of tumors.
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Rahmutulla B, Matsushita K, Nomura F. Alternative splicing of DNA damage response genes and gastrointestinal cancers. World J Gastroenterol 2014; 20:17305-17313. [PMID: 25516641 PMCID: PMC4265588 DOI: 10.3748/wjg.v20.i46.17305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/18/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing, which is a common phenomenon in mammalian genomes, is a fundamental process of gene regulation and contributes to great protein diversity. Alternative splicing events not only occur in the normal gene regulation process but are also closely related to certain diseases including cancer. In this review, we briefly demonstrate the concept of alternative splicing and DNA damage and describe the association of alternative splicing and cancer pathogenesis, focusing on the potential relationship of alternative splicing, DNA damage, and gastrointestinal cancers. We will also discuss whether alternative splicing leads to genetic instability, which is considered to be a driving force for tumorigenesis. Better understanding of the role and mechanism of alternative splicing in tumorigenesis may provide new directions for future cancer studies.
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264
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Zhao YF, Zhao JY, Yue H, Hu KS, Shen H, Guo ZG, Su XJ. FOXD1 promotes breast cancer proliferation and chemotherapeutic drug resistance by targeting p27. Biochem Biophys Res Commun 2014; 456:232-7. [PMID: 25462566 DOI: 10.1016/j.bbrc.2014.11.064] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 12/27/2022]
Abstract
Forkhead transcription factors are essential for diverse processes in early embryonic development and organogenesis. As a member of the forkhead family, FOXD1 is required during kidney development and its inactivation results in failure of nephron progenitor cells. However, the role of FOXD1 in carcinogenesis and progression is still limited. Here, we reported that FOXD1 is a potential oncogene in breast cancer. We found that FOXD1 is up-regulated in breast cancer tissues. Depletion of FOXD1 expression decreases the ability of cell proliferation and chemoresistance in MDA-MB-231 cells, whereas overexpression of FOXD1 increases the ability of cell proliferation and chemoresistance in MCF-7 cells. Furthermore, we observed that FOXD1 induces G1 to S phase transition by targeting p27 expression. Our results suggest that FOXD1 may be a potential therapy target for patients with breast cancer.
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Affiliation(s)
- Yi-Fan Zhao
- Department of Anesthesiology, The First Affiliated Hospital of the General Hospital of CPLA, Beijing 100048, China
| | - Jing-Yu Zhao
- Department of Anesthesiology, The First Affiliated Hospital of the General Hospital of CPLA, Beijing 100048, China
| | - Hong Yue
- Department of Anesthesiology, The First Affiliated Hospital of the General Hospital of CPLA, Beijing 100048, China
| | - Ke-Shi Hu
- Department of Anesthesiology, The General Hospital of CPLA, Beijing 100853, China
| | - Hao Shen
- Department of Anesthesiology, The General Hospital of CPLA, Beijing 100853, China
| | - Zheng-Gang Guo
- Department of Anesthesiology, The First Affiliated Hospital of the General Hospital of CPLA, Beijing 100048, China.
| | - Xiao-Jun Su
- Department of Anesthesiology, The First Affiliated Hospital of the General Hospital of CPLA, Beijing 100048, China.
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265
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Abstract
Genomic instability is a hallmark of cancer that leads to an increase in genetic alterations, thus enabling the acquisition of additional capabilities required for tumorigenesis and progression. Substantial heterogeneity in the amount and type of instability (nucleotide, microsatellite, or chromosomal) exists both within and between cancer types, with epithelial tumors typically displaying a greater degree of instability than hematological cancers. While high-throughput sequencing studies offer a comprehensive record of the genetic alterations within a tumor, detecting the rate of instability or cell-to-cell viability using this and most other available methods remains a challenge. Here, we discuss the different levels of genomic instability occurring in human cancers and touch on the current methods and limitations of detecting instability. We have applied one such approach to the surveying of public tumor data to provide a cursory view of genome instability across numerous tumor types.
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Affiliation(s)
- Larissa Pikor
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, Canada, V5Z 1L3,
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266
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Hunakova L, Gronesova P, Horvathova E, Chalupa I, Cholujova D, Duraj J, Sedlak J. Modulation of cisplatin sensitivity in human ovarian carcinoma A2780 and SKOV3 cell lines by sulforaphane. Toxicol Lett 2014; 230:479-86. [DOI: 10.1016/j.toxlet.2014.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 02/04/2023]
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267
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Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M. Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers. Eur Urol 2014; 66:936-48. [PMID: 25047176 PMCID: PMC4410302 DOI: 10.1016/j.eururo.2014.06.053] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/30/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND Candidate biomarkers have been identified for clear cell renal cell carcinoma (ccRCC) patients, but most have not been validated. OBJECTIVE To validate published ccRCC prognostic biomarkers in an independent patient cohort and to assess intratumour heterogeneity (ITH) of the most promising markers to guide biomarker optimisation. DESIGN, SETTING, AND PARTICIPANTS Cancer-specific survival (CSS) for each of 28 identified genetic or transcriptomic biomarkers was assessed in 350 ccRCC patients. ITH was interrogated in a multiregion biopsy data set of 10 ccRCCs. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Biomarker association with CSS was analysed by univariate and multivariate analyses. RESULTS AND LIMITATIONS A total of 17 of 28 biomarkers (TP53 mutations; amplifications of chromosomes 8q, 12, 20q11.21q13.32, and 20 and deletions of 4p, 9p, 9p21.3p24.1, and 22q; low EDNRB and TSPAN7 expression and six gene expression signatures) were validated as predictors of poor CSS in univariate analysis. Tumour stage and the ccB expression signature were the only independent predictors in multivariate analysis. ITH of the ccB signature was identified in 8 of 10 tumours. Several genetic alterations that were significant in univariate analysis were enriched, and chromosomal instability indices were increased in samples expressing the ccB signature. The study may be underpowered to validate low-prevalence biomarkers. CONCLUSIONS The ccB signature was the only independent prognostic biomarker. Enrichment of multiple poor prognosis genetic alterations in ccB samples indicated that several events may be required to establish this aggressive phenotype, catalysed in some tumours by chromosomal instability. Multiregion assessment may improve the precision of this biomarker. PATIENT SUMMARY We evaluated the ability of published biomarkers to predict the survival of patients with clear cell kidney cancer in an independent patient cohort. Only one molecular test adds prognostic information to routine clinical assessments. This marker showed good and poor prognosis results within most individual cancers. Future biomarkers need to consider variation within tumours to improve accuracy.
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Affiliation(s)
- Sakshi Gulati
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Pierre Martinez
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Tejal Joshi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Nicolai Juul Birkbak
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Claudio R Santos
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | | | | | | | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; UCL Cancer Institute, London, UK.
| | - Marco Gerlinger
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; Present address: Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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268
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Cirkel GA, Gadellaa-van Hooijdonk CG, Koudijs MJ, Willems SM, Voest EE. Tumor heterogeneity and personalized cancer medicine: are we being outnumbered? Future Oncol 2014; 10:417-28. [PMID: 24559448 DOI: 10.2217/fon.13.214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor heterogeneity is regarded as a major obstacle to successful personalized cancer medicine. The lack of reliable response assays reflective of in vivo tumor heterogeneity and associated resistance mechanisms hampers identification of reliable biomarkers. By contrast, oncogene addiction and paracrine signaling enable systemic responses despite tumor heterogeneity. This strengthens researchers in their efforts towards personalized cancer medicine. Given the fact that tumor heterogeneity is an integral part of cancer evolution, diagnostic tools need to be developed in order to better understand the dynamics within a tumor. Ultra-deep sequencing may reveal future resistant clones within a (liquid) tumor biopsy. On-treatment biopsies may provide insight into intrinsic or acquired drug resistance. Subsequently, upfront combinatorial treatment or sequential therapy strategies may forestall drug resistance and improve patient outcome. Finally, innovative response assays, such as organoid cultures or patient-derived tumor xenografts, provide an extra dimension to correlate molecular profiles with drug efficacy and control cancer growth.
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Affiliation(s)
- Geert A Cirkel
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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269
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de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee SM, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen SC, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014; 346:251-6. [PMID: 25301630 PMCID: PMC4636050 DOI: 10.1126/science.1253462] [Citation(s) in RCA: 839] [Impact Index Per Article: 83.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial and temporal dissection of the genomic changes occurring during the evolution of human non-small cell lung cancer (NSCLC) may help elucidate the basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs and found evidence of branched evolution, with driver mutations arising before and after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, and mutations associated with APOBEC cytidine deaminase activity. Despite maintained carcinogen exposure, tumors from smokers showed a relative decrease in smoking-related mutations over time, accompanied by an increase in APOBEC-associated mutations. In tumors from former smokers, genome-doubling occurred within a smoking-signature context before subclonal diversification, which suggested that a long period of tumor latency had preceded clinical detection. The regionally separated driver mutations, coupled with the relentless and heterogeneous nature of the genome instability processes, are likely to confound treatment success in NSCLC.
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Affiliation(s)
- Elza C de Bruin
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Nicholas McGranahan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Science and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - Richard Mitter
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Max Salm
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Lucy Yates
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. University of Cambridge, Cambridge CB2 1TN, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Nirupa Murugaesu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Andrew J Rowan
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Eva Grönroos
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Madiha A Muhammad
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK
| | - Stuart Horswell
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Marco Gerlinger
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - David Jones
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - John Marshall
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Doris M Rassl
- Papworth Hospital NHS Foundation Trust, Cambridge CB23 3RE, UK
| | | | - Sam M Janes
- Lungs for Living Research Centre, University College London, London WC1E 6BT, UK
| | - Siow-Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. University College London Hospitals, London NW1 2BU, UK
| | - Martin Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. University College London Hospitals, London NW1 2BU, UK
| | - Tanya Ahmad
- University College London Hospitals, London NW1 2BU, UK
| | | | - Mary Falzon
- University College London Hospitals, London NW1 2BU, UK
| | | | | | | | - Warren Tom
- Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Enock Teefe
- Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | | | - Sharmin Begum
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Adam Rabinowitz
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | | | | | - Gordon Stamp
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Zoltan Szallasi
- Technical University of Denmark, 2800 Kongens Lyngby, Denmark. Children's Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nik Matthews
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Aengus Stewart
- Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK. Cancer Research UK London Research Institute, London WC2A 3LY, UK.
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270
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Lönnstedt IM, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, Salm M, Kanu N, Savas P, Horswell S, Gade S, Loibl S, Neven P, Sotiriou C, Swanton C, Loi S, Speed TP. Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol 2014; 15:470. [PMID: 25270265 PMCID: PMC4220069 DOI: 10.1186/s13059-014-0470-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022] Open
Abstract
Intra-tumor heterogeneity concerns the existence of genetically different subclones within the same tumor. Single sample quantification of heterogeneity relies on precise determination of chromosomal copy numbers throughout the genome, and an assessment of whether identified mutation variant allele fractions match clonal or subclonal copy numbers. We discuss these issues using data from SNP arrays, whole exome sequencing and pathologist purity estimates on several breast cancers characterized by ERBB2 amplification. We show that chromosomal copy numbers can only be estimated from SNP array signals or sequencing depths for subclonal tumor samples with simple subclonal architectures under certain assumptions.
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Affiliation(s)
- Ingrid M Lönnstedt
- />Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia
- />University of Melbourne, Melbourne, VIC 3010 Australia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Franco Caramia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Jason Li
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Debora Fumagalli
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Roberto Salgado
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Andrew Rowan
- />Cancer Research UK, London Research Institute, Translational Cancer Therapeutics Laboratory, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
| | - Max Salm
- />Bioinformatics and BioStatistics, Cancer Research UK, Lincoln’s Inn Fields, Holborn, London WC2A 3LY UK
| | - Nnennaya Kanu
- />Translational Cancer Therapeutics Laboratory, UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street, London, WC1E 6DD UK
| | - Peter Savas
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Stuart Horswell
- />Bioinformatics and BioStatistics, Cancer Research UK, Lincoln’s Inn Fields, Holborn, London WC2A 3LY UK
| | - Stephan Gade
- />German Breast Group (GBG), Neu Isenburg, Germany
| | | | - Patrick Neven
- />Multidisciplinary Breast Centre and Gynaecological Oncology, KU Leuven, University of Leuven, Department of Oncology, B-3000 Leuven, Belgium
| | - Christos Sotiriou
- />Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - Charles Swanton
- />Cancer Research UK, London Research Institute, Translational Cancer Therapeutics Laboratory, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
- />UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street, London, WC1E 6DD UK
| | - Sherene Loi
- />University of Melbourne, Melbourne, VIC 3010 Australia
- />Division of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002 Australia
| | - Terence P Speed
- />Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia
- />Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
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271
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Establishing a biological profile for interval colorectal cancers. Dig Dis Sci 2014; 59:2390-402. [PMID: 24839919 DOI: 10.1007/s10620-014-3210-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/07/2014] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) remains the second leading cause of cancer-related deaths in North America. Screening for CRC and its precursor lesions is highly effective in reducing the incidence and deaths due to the disease. However, there remain a substantial number of individuals who are diagnosed with CRC soon after a negative/clearing colonoscopy with no documented evidence of CRC. The occurrence of these interval CRCs (I-CRCs) reduces the effectiveness of CRC screening and detection tests and has only recently attracted wide spread attention. I-CRCs can be subdivided into those that occur most likely due to the failure of the colonoscopy examination (missed CRC and CRC that developed from missed or incompletely resected precursor lesions) and those that develop rapidly after the colonoscopy (de novo I-CRCs). In this review, we discuss the current literature and present both the clinical and biological factors that have been identified to account for I-CRCs, with a particular focus on the aberrant molecular features that are candidate causative agents for I-CRCs. We conclude additional studies are required to fully understand the molecular features that lead to the development of I-CRCs, which in turn is essential to develop measures to prevent the occurrence of this group of CRCs and thereby improve CRC screening and detection strategies.
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272
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Abstract
Subclonal cancer populations change spatially and temporally during the disease course. Studies are revealing branched evolutionary cancer growth with low-frequency driver events present in subpopulations of cells, providing escape mechanisms for targeted therapeutic approaches. Despite such complexity, evidence is emerging for parallel evolution of subclones, mediated through distinct somatic events converging on the same gene, signal transduction pathway, or protein complex in different subclones within the same tumor. Tumors may follow gradualist paths (microevolution) as well as major shifts in evolutionary trajectories (macroevolution). Although macroevolution has been subject to considerable controversy in post-Darwinian evolutionary theory, we review evidence that such nongradual, saltatory leaps, driven through chromosomal rearrangements or genome doubling, may be particularly relevant to tumor evolution. Adapting cancer care to the challenges imposed by tumor micro- and macroevolution and developing deeper insight into parallel evolutionary events may prove central to improving outcome and reducing drug development costs.
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Affiliation(s)
- Marco Gerlinger
- Cancer Research UK London Research Institute, London, United Kingdom WC2A 3LY;
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273
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Cheng X, Chen H. Tumor heterogeneity and resistance to EGFR-targeted therapy in advanced nonsmall cell lung cancer: challenges and perspectives. Onco Targets Ther 2014; 7:1689-704. [PMID: 25285017 PMCID: PMC4181629 DOI: 10.2147/ott.s66502] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Lung cancer, mostly nonsmall cell lung cancer, continues to be the leading cause of cancer-related death worldwide. With the development of tyrosine kinase inhibitors that selectively target lung cancer-related epidermal growth factor receptor mutations, management of advanced nonsmall cell lung cancer has been greatly transformed. Improvements in progression-free survival and life quality of the patients were observed in numerous clinical studies. However, overall survival is not prolonged because of later-acquired drug resistance. Recent studies reveal a heterogeneous subclonal architecture of lung cancer, so it is speculated that the tumor may rapidly adapt to environmental changes via a Darwinian selection mechanism. In this review, we aim to provide an overview of both spatial and temporal tumor heterogeneity as potential mechanisms underlying epidermal growth factor receptor tyrosine kinase inhibitor resistance in nonsmall cell lung cancer and summarize the possible origins of tumor heterogeneity covering theories of cancer stem cells and clonal evolution, as well as genomic instability and epigenetic aberrations in lung cancer. Moreover, investigational measures that overcome heterogeneity-associated drug resistance and new assays to improve tumor assessment are also discussed.
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Affiliation(s)
- Xinghua Cheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
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274
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Burrell RA, Swanton C. Tumour heterogeneity and the evolution of polyclonal drug resistance. Mol Oncol 2014; 8:1095-111. [PMID: 25087573 PMCID: PMC5528620 DOI: 10.1016/j.molonc.2014.06.005] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 12/15/2022] Open
Abstract
Cancer drug resistance is a major problem, with the majority of patients with metastatic disease ultimately developing multidrug resistance and succumbing to their disease. Our understanding of molecular events underpinning treatment failure has been enhanced by new genomic technologies and pre-clinical studies. Intratumour genetic heterogeneity (ITH) is a prominent contributor to therapeutic failure, and it is becoming increasingly apparent that individual tumours may achieve resistance via multiple routes simultaneously - termed polyclonal resistance. Efforts to target single resistance mechanisms to overcome therapeutic failure may therefore yield only limited success. Clinical studies with sequential analysis of tumour material are needed to enhance our understanding of inter-clonal functional relationships and tumour evolution during therapy, and to improve drug development strategies in cancer medicine.
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Affiliation(s)
- Rebecca A Burrell
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3L7, UK; UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6DD, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3L7, UK; UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6DD, UK.
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275
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Endesfelder D, Burrell R, Kanu N, McGranahan N, Howell M, Parker PJ, Downward J, Swanton C, Kschischo M. Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. Cancer Res 2014; 74:4853-4863. [PMID: 24970479 PMCID: PMC4167338 DOI: 10.1158/0008-5472.can-13-2664] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal instability (CIN) is associated with poor outcome in epithelial malignancies, including breast carcinomas. Evidence suggests that prognostic signatures in estrogen receptor-positive (ER(+)) breast cancer define tumors with CIN and high proliferative potential. Intriguingly, CIN induction in lower eukaryotic cells and human cells is context dependent, typically resulting in a proliferation disadvantage but conferring a fitness benefit under strong selection pressures. We hypothesized that CIN permits accelerated genomic evolution through the generation of diverse DNA copy-number events that may be selected during disease development. In support of this hypothesis, we found evidence for selection of gene amplification of core regulators of proliferation in CIN-associated cancer genomes. Stable DNA copy-number amplifications of the core regulators TPX2 and UBE2C were associated with expression of a gene module involved in proliferation. The module genes were enriched within prognostic signature gene sets for ER(+) breast cancer, providing a logical connection between CIN and prognostic signature expression. Our results provide a framework to decipher the impact of intratumor heterogeneity on key cancer phenotypes, and they suggest that CIN provides a permissive landscape for selection of copy-number alterations that drive cancer proliferation.
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Affiliation(s)
- David Endesfelder
- Department of Mathematics and Technology, RheinAhrCampus, University of Applied Sciences Koblenz, 53424 Remagen, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Institute of Biomathematics and Biometry, Scientific Computing Research Unit, Neuherberg, Germany
| | - Rebecca Burrell
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Nnennaya Kanu
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley Street, WC1E 6BT London
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Mike Howell
- High Throughput Screening Laboratory,Cancer Research UK London Research Institute, London, United Kingdom
| | - Peter J. Parker
- Protein Phosphorylation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
- Division of Cancer Studies, King’s College London, London SE1 1UL
| | - Julian Downward
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Maik Kschischo
- Department of Mathematics and Technology, RheinAhrCampus, University of Applied Sciences Koblenz, 53424 Remagen, Germany
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276
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Panczyk M. Pharmacogenetics research on chemotherapy resistance in colorectal cancer over the last 20 years. World J Gastroenterol 2014; 20:9775-827. [PMID: 25110414 PMCID: PMC4123365 DOI: 10.3748/wjg.v20.i29.9775] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/17/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023] Open
Abstract
During the past two decades the first sequencing of the human genome was performed showing its high degree of inter-individual differentiation, as a result of large international research projects (Human Genome Project, the 1000 Genomes Project International HapMap Project, and Programs for Genomic Applications NHLBI-PGA). This period was also a time of intensive development of molecular biology techniques and enormous knowledge growth in the biology of cancer. For clinical use in the treatment of patients with colorectal cancer (CRC), in addition to fluoropyrimidines, another two new cytostatic drugs were allowed: irinotecan and oxaliplatin. Intensive research into new treatment regimens and a new generation of drugs used in targeted therapy has also been conducted. The last 20 years was a time of numerous in vitro and in vivo studies on the molecular basis of drug resistance. One of the most important factors limiting the effectiveness of chemotherapy is the primary and secondary resistance of cancer cells. Understanding the genetic factors and mechanisms that contribute to the lack of or low sensitivity of tumour tissue to cytostatics is a key element in the currently developing trend of personalized medicine. Scientists hope to increase the percentage of positive treatment response in CRC patients due to practical applications of pharmacogenetics/pharmacogenomics. Over the past 20 years the clinical usability of different predictive markers has been tested among which only a few have been confirmed to have high application potential. This review is a synthetic presentation of drug resistance in the context of CRC patient chemotherapy. The multifactorial nature and volume of the issues involved do not allow the author to present a comprehensive study on this subject in one review.
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277
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Kleyman M, Kabeche L, Compton DA. STAG2 promotes error correction in mitosis by regulating kinetochore-microtubule attachments. J Cell Sci 2014; 127:4225-33. [PMID: 25074805 DOI: 10.1242/jcs.151613] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mutations in the STAG2 gene are present in ∼20% of tumors from different tissues of origin. STAG2 encodes a subunit of the cohesin complex, and tumors with loss-of-function mutations are usually aneuploid and display elevated frequencies of lagging chromosomes during anaphase. Lagging chromosomes are a hallmark of chromosomal instability (CIN) arising from persistent errors in kinetochore-microtubule (kMT) attachment. To determine whether the loss of STAG2 increases the rate of formation of kMT attachment errors or decreases the rate of their correction, we examined mitosis in STAG2-deficient cells. STAG2 depletion does not impair bipolar spindle formation or delay mitotic progression. Instead, loss of STAG2 permits excessive centromere stretch along with hyperstabilization of kMT attachments. STAG2-deficient cells display mislocalization of Bub1 kinase, Bub3 and the chromosome passenger complex. Importantly, strategically destabilizing kMT attachments in tumor cells harboring STAG2 mutations by overexpression of the microtubule-destabilizing enzymes MCAK (also known as KIF2C) and Kif2B decreased the rate of lagging chromosomes and reduced the rate of chromosome missegregation. These data demonstrate that STAG2 promotes the correction of kMT attachment errors to ensure faithful chromosome segregation during mitosis.
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Affiliation(s)
- Marianna Kleyman
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Lilian Kabeche
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Duane A Compton
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Lebanon, NH 03766, USA
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278
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Jamal-Hanjani M, Hackshaw A, Ngai Y, Shaw J, Dive C, Quezada S, Middleton G, de Bruin E, Le Quesne J, Shafi S, Falzon M, Horswell S, Blackhall F, Khan I, Janes S, Nicolson M, Lawrence D, Forster M, Fennell D, Lee SM, Lester J, Kerr K, Muller S, Iles N, Smith S, Murugaesu N, Mitter R, Salm M, Stuart A, Matthews N, Adams H, Ahmad T, Attanoos R, Bennett J, Birkbak NJ, Booton R, Brady G, Buchan K, Capitano A, Chetty M, Cobbold M, Crosbie P, Davies H, Denison A, Djearman M, Goldman J, Haswell T, Joseph L, Kornaszewska M, Krebs M, Langman G, MacKenzie M, Millar J, Morgan B, Naidu B, Nonaka D, Peggs K, Pritchard C, Remmen H, Rowan A, Shah R, Smith E, Summers Y, Taylor M, Veeriah S, Waller D, Wilcox B, Wilcox M, Woolhouse I, McGranahan N, Swanton C. Tracking genomic cancer evolution for precision medicine: the lung TRACERx study. PLoS Biol 2014; 12:e1001906. [PMID: 25003521 PMCID: PMC4086714 DOI: 10.1371/journal.pbio.1001906] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The importance of intratumour genetic and functional heterogeneity is increasingly recognised as a driver of cancer progression and survival outcome. Understanding how tumour clonal heterogeneity impacts upon therapeutic outcome, however, is still an area of unmet clinical and scientific need. TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy [Rx]), a prospective study of patients with primary non-small cell lung cancer (NSCLC), aims to define the evolutionary trajectories of lung cancer in both space and time through multiregion and longitudinal tumour sampling and genetic analysis. By following cancers from diagnosis to relapse, tracking the evolutionary trajectories of tumours in relation to therapeutic interventions, and determining the impact of clonal heterogeneity on clinical outcomes, TRACERx may help to identify novel therapeutic targets for NSCLC and may also serve as a model applicable to other cancer types.
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Affiliation(s)
- Mariam Jamal-Hanjani
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Alan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom
| | - Yenting Ngai
- Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom
| | - Jacqueline Shaw
- Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Sergio Quezada
- Immune Regulation and Tumour Immunotherapy Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Gary Middleton
- Department of Medical Oncology, Birmingham Heartlands Hospital, Birmingham, United Kingdom
| | - Elza de Bruin
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
| | - John Le Quesne
- Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Seema Shafi
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, London, United Kingdom
| | - Stuart Horswell
- Department of Bioinformatics and BioStatistics, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester and The Christie Hospital, Manchester, United Kingdom
| | - Iftekhar Khan
- Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom
| | - Sam Janes
- Department of Respiratory Medicine, University College London Hospitals, London, United Kingdom
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, Scotland, United Kingdom
| | - David Lawrence
- Department of Cardiothoracic Surgery, Heart Hospital, London, United Kingdom
| | - Martin Forster
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Dean Fennell
- Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
- Department of Medical Oncology, University of Leicester & Leicester University Hospitals, Leicester, United Kingdom
| | - Siow-Ming Lee
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Jason Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff, Wales, United Kingdom
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, Scotland, United Kingdom
| | - Salli Muller
- Department of Pathology, University of Leicester & Leicester University Hospitals, Leicester, United Kingdom
| | - Natasha Iles
- Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom
| | - Sean Smith
- Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom
| | - Nirupa Murugaesu
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Richard Mitter
- Department of Bioinformatics and BioStatistics, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Max Salm
- Department of Bioinformatics and BioStatistics, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Aengus Stuart
- Department of Bioinformatics and BioStatistics, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Nik Matthews
- The Advanced Sequencing Facility, London Research Institute, London, United Kingdom
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff, Wales, United Kingdom
| | - Tanya Ahmad
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Richard Attanoos
- Department of Pathology, University Hospital Llandough, Cardiff, Wales, United Kingdom
| | - Jonathan Bennett
- Department of Respiratory Medicine, University of Leicester & Leicester University Hospitals, Leicester, United Kingdom
| | - Nicolai Juul Birkbak
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Richard Booton
- Department of Respiratory Medicine, University Hospital of South Manchester, Manchester, United Kingdom
| | - Ged Brady
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Keith Buchan
- Department of Cardiothoracic Surgery, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Arrigo Capitano
- Department of Pathology, University College London Hospitals, London, United Kingdom
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Mark Cobbold
- Department of Clinical Immunology, University of Birmingham, Birmingham, B15 2TT
| | - Philip Crosbie
- North West Lung Centre, University Hospital of South Manchester, Manchester, United Kingdom
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff, Wales, United Kingdom
| | - Alan Denison
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United kingdom
| | - Madhav Djearman
- Department of Radiology, Birmingham Heartlands Hospital, Birmingham, United Kingdom
| | - Jacki Goldman
- Department of IT, London Research Institute, London, United Kingdom
| | - Tom Haswell
- Independent Cancer Patient's Voice, London, united Kingdom
| | - Leena Joseph
- Department of Pathology, University Hospitals of South Manchester, Manchester
| | - Malgorzata Kornaszewska
- Department of Cardiothoracic Surgery, University Hospital Llandough, Cardiff, Wales, United Kingdom
| | - Matthew Krebs
- Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham, United Kingdom
| | | | - Joy Millar
- Department of Respiratory Medicine, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Bruno Morgan
- Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham, United Kingdom
| | - Daisuke Nonaka
- Department of Pathology, University Hospitals of South Manchester, Manchester
- The Christie Hospital, Manchester, United Kingdom
| | - Karl Peggs
- Immune Regulation and Tumour Immunotherapy Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Catrin Pritchard
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School & Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, London Research Institute, London, United Kingdom
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospitals of South Manchester, Manchester, United Kingdom
| | - Elaine Smith
- Department of Radiology, University Hospitals of South Manchester, Manchester, United Kingdom
| | - Yvonne Summers
- The Christie Hospital, Manchester, United Kingdom
- Department of Medical Oncology, University Hospital of South Manchester, Manchester, United Kingdom
| | - Magali Taylor
- Department of Radiology, University College London Hospitals, London, United Kingdom
| | - Selvaraju Veeriah
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
| | - David Waller
- Department of Cardiothoracic Surgery, University of Leicester & Leicester University Hospitals, Leicester, United Kingdom
| | - Ben Wilcox
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maggie Wilcox
- Independent Cancer Patient's Voice, London, united Kingdom
| | - Ian Woolhouse
- Department of Respiratory Medicine, Birmingham University Hospital, Birmingham, United Kingdom
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, London Research Institute, London, United Kingdom
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
- Translational Cancer Therapeutics Laboratory, London Research Institute, London, United Kingdom
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279
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Bakhoum SF, Swanton C. Chromosomal instability, aneuploidy, and cancer. Front Oncol 2014; 4:161. [PMID: 24995162 PMCID: PMC4062911 DOI: 10.3389/fonc.2014.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/06/2014] [Indexed: 12/18/2022] Open
Affiliation(s)
- Samuel F. Bakhoum
- Department of Internal Medicine, Mount Auburn Hospital, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Charles Swanton
- Cancer Research UK London Research Institute, London, UK
- University College London Cancer Institute, London, UK
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280
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Tetraspanin-enriched microdomains and hepatocellular carcinoma progression. Cancer Lett 2014; 351:23-9. [PMID: 24858024 DOI: 10.1016/j.canlet.2014.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 02/06/2023]
Abstract
As in many tumors, heterogeneity within the cell population is one of the main features of hepatocellular carcinoma (HCC). Heterogeneity results from the ability of tumor to produce multiple subpopulations of cells with diverse genetic, biochemical and immunological characteristics. Little is known about how heterogeneity emerges and how it is maintained. Fluctuations in single cells can be masked or completely misrepresented when cell populations are analyzed. It has become exceedingly apparent that the utility of measurement based on the analysis of bulk specimens is limited by intra-tumor genetic and epigenetic heterogeneity, as characteristics of the most abundant cell type might not necessarily predict the properties of cell populations. Yet, such non-uniformities often unveil molecular patterns that can represent mechanisms of tumor progression. Interestingly, variability among single cells in a population may arise from different responses to intrinsic and extrinsic perturbations mainly mediated by the plasma membrane. The association of certain proteins, including tetraspanins, and lipids in specific location on the plasma membrane constitutes specialized structure called tetraspanin-enriched microdomains (TEMs). TEMs organization in cancer may reveal essential clues for understanding pathogenic mechanisms underlying cancer progression. Along these lines, TEMs and HCC progression represent a valuable paradigm for gaining a deeper understanding of such mechanisms.
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281
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Emerson RO, Sherwood AM, Rieder MJ, Guenthoer J, Williamson DW, Carlson CS, Drescher CW, Tewari M, Bielas JH, Robins HS. High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer. J Pathol 2014; 231:433-440. [PMID: 24027095 DOI: 10.1002/path.4260] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/20/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
The cellular adaptive immune system mounts a response to many solid tumours mediated by tumour-infiltrating T lymphocytes (TILs). Basic measurements of these TILs, including total count, show promise as prognostic markers for a variety of cancers, including ovarian and colorectal. In addition, recent therapeutic advances are thought to exploit this immune response to effectively fight melanoma, with promising studies showing efficacy in additional cancers. However, many of the basic properties of TILs are poorly understood, including specificity, clonality, and spatial heterogeneity of the T-cell response. We utilize deep sequencing of rearranged T-cell receptor beta (TCRB) genes to characterize the basic properties of TILs in ovarian carcinoma. Due to somatic rearrangement during T-cell development, the TCR beta chain sequence serves as a molecular tag for each T-cell clone. Using these sequence tags, we assess similarities and differences between infiltrating T cells in discretely sampled sections of large tumours and compare to T cells from peripheral blood. Within the limits of sensitivity of our assay, the TIL repertoires show strong similarity throughout each tumour and are distinct from the circulating T-cell repertoire. We conclude that the cellular adaptive immune response within ovarian carcinomas is spatially homogeneous and distinct from the T-cell compartment of peripheral blood.
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Affiliation(s)
| | | | | | | | | | | | - Charles W Drescher
- Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington School of Medicine, Seattle, WA
| | - Muneesh Tewari
- Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington School of Medicine, Seattle, WA
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282
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Chromosome translocation may lead to PRK1-dependent anticancer drug resistance in yeast via endocytic actin network deregulation. Eur J Cell Biol 2014; 93:145-56. [DOI: 10.1016/j.ejcb.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/24/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
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283
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Rasool S, Rasool V, Naqvi T, Ganai BA, Shah BA. Genetic unraveling of colorectal cancer. Tumour Biol 2014; 35:5067-82. [PMID: 24573608 DOI: 10.1007/s13277-014-1713-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/29/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is a common disease in both men and women (being the third most common cancer in men and the second most common among women) and thus represents an important and serious public health issue, especially in the western world. Although it is a well-established fact that cancers of the large intestine produce symptoms relatively earlier at a stage that can be easily cured by resection, a large number of people lose their lives to this deadly disease each year. Recent times have seen an important change in the incidence of colorectal cancer in different parts of the world. The etiology of colorectal cancer is multifactorial and is likely to involve the actions of genes at multiple levels along the multistage carcinogenesis process. Exhaustive efforts have been made out in the direction of unraveling the role of various environmental factors, gene mutations, and polymorphisms worldwide (as well as in Kashmir-"a valley of gastrointestinal cancers") that have got a role to play in the development of this disease so that antitumor drugs could be developed against this cancer, first, and, finally, the responsiveness or resistance to these agents could be understood for combating this global issue.
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Affiliation(s)
- Sabha Rasool
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, 190006, Kashmir, India
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284
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Stepanenko AA, Kavsan VM. Karyotypically distinct U251, U373, and SNB19 glioma cell lines are of the same origin but have different drug treatment sensitivities. Gene 2014; 540:263-5. [PMID: 24583163 DOI: 10.1016/j.gene.2014.02.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Alexey A Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Kyiv 03680, Ukraine.
| | - Vadym M Kavsan
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Kyiv 03680, Ukraine
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285
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Donnelly N, Storchová Z. Dynamic karyotype, dynamic proteome: buffering the effects of aneuploidy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:473-81. [DOI: 10.1016/j.bbamcr.2013.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 12/18/2022]
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286
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Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov 2014; 4:175-185. [PMID: 24436049 DOI: 10.1158/2159-8290.cd-13-0285] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear. We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time. Rare cells that survive genome doubling demonstrate increased tolerance to chromosome aberrations. Tetraploid cells do not exhibit increased frequencies of structural or numerical CIN per chromosome. However, the tolerant phenotype in tetraploid cells, coupled with a doubling of chromosome aberrations per cell, allows chromosome abnormalities to evolve specifically in tetraploids, recapitulating chromosomal changes in genomically complex colorectal tumors. Finally, a genome-doubling event is independently predictive of poor relapse-free survival in early-stage disease in two independent cohorts in multivariate analyses [discovery data: hazard ratio (HR), 4.70, 95% confidence interval (CI), 1.04-21.37; validation data: HR, 1.59, 95% CI, 1.05-2.42]. These data highlight an important role for the tolerance of genome doubling in driving cancer genome evolution. SIGNIFICANCE Our work sheds light on the importance of whole-genome–doubling events in colorectal cancer evolution. We show that tetraploid cells undergo rapid genomic changes and recapitulate the genetic alterations seen in chromosomally unstable tumors. Furthermore, we demonstrate that a genome-doubling event is prognostic of poor relapse-free survival in this disease type.
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Affiliation(s)
- Sally M Dewhurst
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Nicholas McGranahan
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.,Centre for Mathematics & Physics in the Life Sciences & Experimental Biology (CoMPLEX), University College London, Physics Building, Gower Street, London WC1E 6BT, UK
| | - Rebecca A Burrell
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Andrew J Rowan
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Eva Grönroos
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - David Endesfelder
- University of Applied Sciences Koblenz, RheinAhrCampus, Department of Mathematics and Technology, Joseph-Rovan-Allee 2, 53424 Remagen, Germany
| | - Tejal Joshi
- Technical University of Denmark (DTU), Anker Engelunds Vej 1, 2800 Lyngby, Denmark
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Peter Gibbs
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Medical Oncology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Robyn L Ward
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas J Hawkins
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Zoltan Szallasi
- Technical University of Denmark (DTU), Anker Engelunds Vej 1, 2800 Lyngby, Denmark.,Harvard Medical School, 250 Longwood Ave, Boston, MA 02115, United States
| | - Oliver M Sieber
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Charles Swanton
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.,UCL Cancer Institute, Paul O'Gorman Building, Huntley Street, London WC1E 6BT, UK
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287
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The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma. PLoS One 2014; 9:e79079. [PMID: 24454681 PMCID: PMC3894223 DOI: 10.1371/journal.pone.0079079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/26/2013] [Indexed: 01/23/2023] Open
Abstract
Background Prognostic biomarkers are needed for superficial gastroesophageal adenocarcinoma (EAC) to predict clinical outcomes and select therapy. Although recurrent mutations have been characterized in EAC, little is known about their clinical and prognostic significance. Aneuploidy is predictive of clinical outcome in many malignancies but has not been evaluated in superficial EAC. Methods We quantified copy number changes in 41 superficial EAC using Affymetrix SNP 6.0 arrays. We identified recurrent chromosomal gains and losses and calculated the total copy number abnormality (CNA) count for each tumor as a measure of aneuploidy. We correlated CNA count with overall survival and time to first recurrence in univariate and multivariate analyses. Results Recurrent segmental gains and losses involved multiple genes, including: HER2, EGFR, MET, CDK6, KRAS (recurrent gains); and FHIT, WWOX, CDKN2A/B, SMAD4, RUNX1 (recurrent losses). There was a 40-fold variation in CNA count across all cases. Tumors with the lowest and highest quartile CNA count had significantly better overall survival (p = 0.032) and time to first recurrence (p = 0.010) compared to those with intermediate CNA counts. These associations persisted when controlling for other prognostic variables. Significance SNP arrays facilitate the assessment of recurrent chromosomal gain and loss and allow high resolution, quantitative assessment of segmental aneuploidy (total CNA count). The non-monotonic association of segmental aneuploidy with survival has been described in other tumors. The degree of aneuploidy is a promising prognostic biomarker in a potentially curable form of EAC.
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288
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Raynes Y, Halstead AL, Sniegowski PD. The effect of population bottlenecks on mutation rate evolution in asexual populations. J Evol Biol 2013; 27:161-9. [PMID: 24330404 DOI: 10.1111/jeb.12284] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 01/20/2023]
Abstract
In the absence of recombination, a mutator allele can spread through a population by hitchhiking with beneficial mutations that appear in its genetic background. Theoretical studies over the past decade have shown that the survival and fixation probability of beneficial mutations can be severely reduced by population size bottlenecks. Here, we use computational modelling and evolution experiments with the yeast S. cerevisiae to examine whether population bottlenecks can affect mutator dynamics in adapting asexual populations. In simulation, we show that population bottlenecks can inhibit mutator hitchhiking with beneficial mutations and are most effective at lower beneficial mutation supply rates. We then subjected experimental populations of yeast propagated at the same effective population size to three different bottleneck regimes and observed that the speed of mutator hitchhiking was significantly slower at smaller bottlenecks, consistent with our theoretical expectations. Our results, thus, suggest that bottlenecks can be an important factor in mutation rate evolution and can in certain circumstances act to stabilize or, at least, delay the progressive elevation of mutation rates in asexual populations. Additionally, our findings provide the first experimental support for the theoretically postulated effect of population bottlenecks on beneficial mutations and demonstrate the usefulness of studying mutator frequency dynamics for understanding the underlying dynamics of fitness-affecting mutations.
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Affiliation(s)
- Y Raynes
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - A L Halstead
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - P D Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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289
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Wong HWS, Shaukat Z, Wang J, Saint R, Gregory SL. JNK signaling is needed to tolerate chromosomal instability. Cell Cycle 2013; 13:622-31. [PMID: 24335260 DOI: 10.4161/cc.27484] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromosomal instability (CIN), as a common feature of tumors, represents a potential therapeutic target if ways can be found to specifically cause apoptosis in unstably dividing cells. We have previously shown that if signaling through the JNK pathway is reduced, apoptosis is triggered in models of chromosomal instability induced by loss of the spindle checkpoint. Here we identify components upstream and downstream of JNK that are able to mediate this effect, and test the involvement of p53 and DNA damage in causing apoptosis when JNK signaling is reduced in CIN cells. We show that cell cycle progression timing has a strong effect on the apoptosis seen when JNK signaling is reduced in genetically unstable cells: a shortened G 2 phase enhances the apoptosis, while lengthening G 2 rescues the JNK-deficient CIN cell death phenotype. Our findings suggest that chromosomal instability represents a significant stress to dividing cells, and that without JNK signaling, cells undergo apoptosis because they lack a timely and effective response to DNA damage.
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Affiliation(s)
- Heidi W-S Wong
- Department of Genetics; University of Melbourne; Melbourne, VIC, Australia
| | - Zeeshan Shaukat
- School of Molecular and Biomedical Sciences; University of Adelaide; Adelaide, SA, Australia
| | - Jianbin Wang
- Department of Genetics; University of Melbourne; Melbourne, VIC, Australia
| | - Robert Saint
- Department of Genetics; University of Melbourne; Melbourne, VIC, Australia; School of Molecular and Biomedical Sciences; University of Adelaide; Adelaide, SA, Australia
| | - Stephen L Gregory
- School of Molecular and Biomedical Sciences; University of Adelaide; Adelaide, SA, Australia
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290
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Roschke AV, Rozenblum E. Multi-layered cancer chromosomal instability phenotype. Front Oncol 2013; 3:302. [PMID: 24377086 PMCID: PMC3858786 DOI: 10.3389/fonc.2013.00302] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/27/2013] [Indexed: 01/13/2023] Open
Abstract
Whole-chromosomal instability (W-CIN) – unequal chromosome distribution during cell division – is a characteristic feature of a majority of cancer cells distinguishing them from their normal counterparts. The precise molecular mechanisms that may cause mis-segregation of chromosomes in tumor cells just recently became more evident. The consequences of W-CIN are numerous and play a critical role in carcinogenesis. W-CIN mediates evolution of cancer cell population under selective pressure and can facilitate the accumulation of genetic changes that promote malignancy. It has both tumor-promoting and tumor-suppressive effects, and their balance could be beneficial or detrimental for carcinogenesis. The characterization of W-CIN as a complex multi-layered adaptive phenotype highlights the intra- and extracellular adaptations to the consequences of genome reshuffling. It also provides a framework for targeting aggressive chromosomally unstable cancers.
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Affiliation(s)
- Anna V Roschke
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, MD , USA
| | - Ester Rozenblum
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, MD , USA
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291
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Abstract
In this paper we develop a theoretical frame to understand self-regulation of aneuploidy rate in cancer and stem cells. This is accomplished building upon quasispecies theory, by leaving its formal mathematical structure intact, but by drastically changing the meaning of its objects. In particular, we propose a novel definition of chromosomal master sequence, as a sequence of physically distinct whole or fragmented chromosomes, whose length is taken to be the sum of the copy numbers of each whole or fragmented chromosome. This fundamental change in the functional objects of quasispecies theory allows us to show that previously measured aneuploidy rates in cancer populations are already close to a formally derived aneuploid error threshold, and that any value of aneuploidy rate larger than the aneuploid error threshold would lead to a loss of fitness of a tumor population. Finally, we make a phenomenological analysis of existing experimental evidence to argue that single clone cancer cells, derived from an aneuploid cancer subpopulation, are capable of self-regulating their aneuploidy rate and of adapting it to distinct environments, namely primary and metastatic microenvironments. We also discuss the potential origin of this self-regulatory ability in the wider context of developmental and comparative biology and we hypothesize the existence of a diversification factor, i.e. a cellular mechanism that regulates adaptation of aneuploidy rates, active in all embryo, adult and cancer stem cells.
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Affiliation(s)
| | - Michele Signore
- Department of Hematology, Oncology and Molecular Medicine, Tumor Stem Cell Biobank, Istituto Superiore di Sanita, 00161, Rome, Italy
| | - Daniele C Struppa
- Schmid College of Science and Technology, Chapman University Chapman University, Orange, CA, 92866, USA
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292
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Slee RB, Grimes BR, Bansal R, Gore J, Blackburn C, Brown L, Gasaway R, Jeong J, Victorino J, March KL, Colombo R, Herbert BS, Korc M. Selective inhibition of pancreatic ductal adenocarcinoma cell growth by the mitotic MPS1 kinase inhibitor NMS-P715. Mol Cancer Ther 2013; 13:307-315. [PMID: 24282275 DOI: 10.1158/1535-7163.mct-13-0324] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most solid tumors, including pancreatic ductal adenocarcinoma (PDAC), exhibit structural and numerical chromosome instability (CIN). Although often implicated as a driver of tumor progression and drug resistance, CIN also reduces cell fitness and poses a vulnerability that can be exploited therapeutically. The spindle assembly checkpoint (SAC) ensures correct chromosome-microtubule attachment, thereby minimizing chromosome segregation errors. Many tumors exhibit upregulation of SAC components such as MPS1, which may help contain CIN within survivable limits. Prior studies showed that MPS1 inhibition with the small molecule NMS-P715 limits tumor growth in xenograft models. In cancer cell lines, NMS-P715 causes cell death associated with impaired SAC function and increased chromosome missegregation. Although normal cells appeared more resistant, effects on stem cells, which are the dose-limiting toxicity of most chemotherapeutics, were not examined. Elevated expression of 70 genes (CIN70), including MPS1, provides a surrogate measure of CIN and predicts poor patient survival in multiple tumor types. Our new findings show that the degree of CIN70 upregulation varies considerably among PDAC tumors, with higher CIN70 gene expression predictive of poor outcome. We identified a 25 gene subset (PDAC CIN25) whose overexpression was most strongly correlated with poor survival and included MPS1. In vitro, growth of human and murine PDAC cells is inhibited by NMS-P715 treatment, whereas adipose-derived human mesenchymal stem cells are relatively resistant and maintain chromosome stability upon exposure to NMS-P715. These studies suggest that NMS-P715 could have a favorable therapeutic index and warrant further investigation of MPS1 inhibition as a new PDAC treatment strategy.
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Affiliation(s)
- Roger B Slee
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy.,IU Melvin and Bren Simon Cancer Center (IUSCC), Nerviano Medical Sciences, Nerviano, Italy
| | - Brenda R Grimes
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy.,IU Melvin and Bren Simon Cancer Center (IUSCC), Nerviano Medical Sciences, Nerviano, Italy.,IUSCC Center for Pancreatic Cancer Research, Nerviano Medical Sciences, Nerviano, Italy
| | - Ruchi Bansal
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy
| | - Jesse Gore
- IUSM Department of Medicine, Nerviano Medical Sciences, Nerviano, Italy
| | - Corinne Blackburn
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy
| | - Lyndsey Brown
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy
| | - Rachel Gasaway
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy
| | - Jaesik Jeong
- IUSM Department of Biostatistics, Nerviano Medical Sciences, Nerviano, Italy
| | - Jose Victorino
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy.,California State University Dominguez Hills, Nerviano Medical Sciences, Nerviano, Italy
| | - Keith L March
- IUSM Department of Medicine, Nerviano Medical Sciences, Nerviano, Italy.,IUSM Department of Biochemistry and Molecular Biology, Nerviano Medical Sciences, Nerviano, Italy.,Krannert Institute of Cardiology, Nerviano Medical Sciences, Nerviano, Italy.,Indiana Center for Vascular Biology, Nerviano Medical Sciences, Nerviano, Italy.,R.L. Roudebush Veterans Affairs Medical Center, Nerviano Medical Sciences, Nerviano, Italy
| | - Riccardo Colombo
- Indianapolis, Indiana. Nerviano Medical Sciences, Nerviano, Italy
| | - Brittney-Shea Herbert
- Indiana University School of Medicine (IUSM) Department of Medical and Molecular Genetics,Indiana. Nerviano Medical Sciences, Nerviano, Italy.,IU Melvin and Bren Simon Cancer Center (IUSCC), Nerviano Medical Sciences, Nerviano, Italy
| | - Murray Korc
- IU Melvin and Bren Simon Cancer Center (IUSCC), Nerviano Medical Sciences, Nerviano, Italy.,IUSCC Center for Pancreatic Cancer Research, Nerviano Medical Sciences, Nerviano, Italy.,IUSM Department of Medicine, Nerviano Medical Sciences, Nerviano, Italy.,IUSM Department of Biochemistry and Molecular Biology, Nerviano Medical Sciences, Nerviano, Italy
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293
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Abstract
Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome.
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294
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Boardman LA, Johnson RA, Viker KB, Hafner KA, Jenkins RB, Riegert-Johnson DL, Smyrk TC, Litzelman K, Seo S, Gangnon RE, Engelman CD, Rider DN, Vanderboom RJ, Thibodeau SN, Petersen GM, Skinner HG. Correlation of chromosomal instability, telomere length and telomere maintenance in microsatellite stable rectal cancer: a molecular subclass of rectal cancer. PLoS One 2013; 8:e80015. [PMID: 24278232 PMCID: PMC3836975 DOI: 10.1371/journal.pone.0080015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/27/2013] [Indexed: 12/17/2022] Open
Abstract
Introduction Colorectal cancer (CRC) tumor DNA is characterized by chromosomal damage termed chromosomal instability (CIN) and excessively shortened telomeres. Up to 80% of CRC is microsatellite stable (MSS) and is historically considered to be chromosomally unstable (CIN+). However, tumor phenotyping depicts some MSS CRC with little or no genetic changes, thus being chromosomally stable (CIN-). MSS CIN- tumors have not been assessed for telomere attrition. Experimental Design MSS rectal cancers from patients ≤50 years old with Stage II (B2 or higher) or Stage III disease were assessed for CIN, telomere length and telomere maintenance mechanism (telomerase activation [TA]; alternative lengthening of telomeres [ALT]). Relative telomere length was measured by qPCR in somatic epithelial and cancer DNA. TA was measured with the TRAPeze assay, and tumors were evaluated for the presence of C-circles indicative of ALT. p53 mutation status was assessed in all available samples. DNA copy number changes were evaluated with Spectral Genomics aCGH. Results Tumors were classified as chromosomally stable (CIN-) and chromosomally instable (CIN+) by degree of DNA copy number changes. CIN- tumors (35%; n=6) had fewer copy number changes (<17% of their clones with DNA copy number changes) than CIN+ tumors (65%; n=13) which had high levels of copy number changes in 20% to 49% of clones. Telomere lengths were longer in CIN- compared to CIN+ tumors (p=0.0066) and in those in which telomerase was not activated (p=0.004). Tumors exhibiting activation of telomerase had shorter tumor telomeres (p=0.0040); and tended to be CIN+ (p=0.0949). Conclusions MSS rectal cancer appears to represent a heterogeneous group of tumors that may be categorized both on the basis of CIN status and telomere maintenance mechanism. MSS CIN- rectal cancers appear to have longer telomeres than those of MSS CIN+ rectal cancers and to utilize ALT rather than activation of telomerase.
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Affiliation(s)
- Lisa A. Boardman
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
| | - Ruth A. Johnson
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kimberly B. Viker
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kari A. Hafner
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Robert B. Jenkins
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Douglas L. Riegert-Johnson
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Thomas C. Smyrk
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kristin Litzelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Songwon Seo
- Department of Biostatistics and Medical Informatics, UW Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ronald E. Gangnon
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, UW Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - David N. Rider
- Biostatistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Russell J. Vanderboom
- Mayo Clinic Cancer Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gloria M. Petersen
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Halcyon G. Skinner
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, UW Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
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295
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Murugaesu N, Chew SK, Swanton C. Adapting clinical paradigms to the challenges of cancer clonal evolution. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 182:1962-71. [PMID: 23708210 DOI: 10.1016/j.ajpath.2013.02.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/05/2013] [Indexed: 02/08/2023]
Abstract
Emerging evidence suggests that cancer branched evolution may affect biomarker validation, clinical outcome, and emergence of drug resistance. The changing spatial and temporal nature of cancer subclonal architecture during the disease course suggests the need for longitudinal prospective studies of cancer evolution and robust and clinically implementable pathologic definitions of intratumor heterogeneity, genetic diversity, and chromosomal instability. Furthermore, subclonal heterogeneous events in tumors may evade detection through conventional biomarker strategies and influence clinical outcome. Minimally invasive methods for the study of cancer evolution and new approaches to clinical study design, incorporating understanding of the dynamics of tumor clonal architectures through treatment and during acquisition of drug resistance, have been suggested as important areas for development. Coordinated efforts will be required by the scientific and clinical trial communities to adapt to the challenges of detecting infrequently occurring somatic events that may influence clinical outcome and to understand the dynamics of cancer evolution and the waxing and waning of tumor subclones over time in advanced metastatic epithelial malignancies.
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Affiliation(s)
- Nirupa Murugaesu
- University College London Cancer Institute, London, United Kingdom
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296
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The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013; 501:338-45. [PMID: 24048066 DOI: 10.1038/nature12625] [Citation(s) in RCA: 1571] [Impact Index Per Article: 142.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/13/2013] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed extensive genetic diversity both between and within tumours. This heterogeneity affects key cancer pathways, driving phenotypic variation, and poses a significant challenge to personalized cancer medicine. A major cause of genetic heterogeneity in cancer is genomic instability. This instability leads to an increased mutation rate and can shape the evolution of the cancer genome through a plethora of mechanisms. By understanding these mechanisms we can gain insight into the common pathways of tumour evolution that could support the development of future therapeutic strategies.
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297
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Sheltzer JM. A transcriptional and metabolic signature of primary aneuploidy is present in chromosomally unstable cancer cells and informs clinical prognosis. Cancer Res 2013; 73:6401-12. [PMID: 24041940 PMCID: PMC3901577 DOI: 10.1158/0008-5472.can-13-0749] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aneuploidy is invariably associated with poor proliferation of primary cells, but the specific contributions of abnormal karyotypes to cancer, a disease characterized by aneuploidy and dysregulated proliferation, remain unclear. In this study, I demonstrate that the transcriptional alterations caused by aneuploidy in primary cells are also present in chromosomally unstable cancer cell lines, but the same alterations are not common to all aneuploid cancers. Chromosomally unstable cancer lines and aneuploid primary cells also share an increase in glycolytic and TCA cycle flux. The biological response to aneuploidy is associated with cellular stress and slow proliferation, and a 70-gene signature derived from primary aneuploid cells was defined as a strong predictor of increased survival in several cancers. Inversely, a transcriptional signature derived from clonal aneuploidy in tumors correlated with high mitotic activity and poor prognosis. Together, these findings suggested that there are two types of aneuploidy in cancer: one is clonal aneuploidy, which is selected during tumor evolution and associated with robust growth, and the other is subclonal aneuploidy caused by chromosomal instability (CIN). Subclonal aneuploidy more closely resembles the stressed state of primary aneuploid cells, yet CIN is not benign; a subset of genes upregulated in high-CIN cancers predict aggressive disease in human patients in a proliferation-independent manner.
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Affiliation(s)
- Jason M. Sheltzer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
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298
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Tang X, Hu G, Xu C, Ouyang K, Fang W, Huang W, Zhang J, Li F, Wang K, Qin X, Li Y. HZ08 reverse the aneuploidy-induced cisplatin-resistance in Gastric cancer by modulating the p53 pathway. Eur J Pharmacol 2013; 720:84-97. [PMID: 24183976 DOI: 10.1016/j.ejphar.2013.10.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/17/2013] [Accepted: 10/23/2013] [Indexed: 11/29/2022]
Abstract
We evaluated the influence of DNA aneuploidy on chemotherapy-resistance in human Gastric cancer cell MKN45; we also evaluated the reversal effects of HZ08 on these cells and then preliminary investigated the possible involved pathway. We made use of a pair of human Gastric cancer cell dip-MKN45 (diploid MKN45) and aneu-MKN45 (aneuploid MKN45). Growth inhibition in response to chemotherapeutic drugs was evaluated by CellTiter-Glo Luminescent Cell Viability assay and clone formation assay. Flow cytometry and immuno-assay were applied to evaluate apoptosis and the expression of relative signaling molecules. MKN45 xenograft was generated to evaluate in vivo action. Aneu-MKN45 developed a resistance to cisplatin which could be reversed by HZ08; Flow cytometry and western-blot indicates that HZ08-combination could induce apoptosis and increase the expression of apoptosis-related biomarkers on aneu-MKN45; in vivo study also reflect the same correlation between aneuploidy and cisplatin-resistance, which could be antagonized by HZ08 combination; When investigating the involved pathway, in anue-MKN45, the expression of molecules in p53 pathway was decreased; HZ08 could increase the expression of p53 down-stream molecules as well as elevate the activity of p53, while inhibiting Mdm2, the major negative regulator of p53; p53 inhibitor Pifithrin-α could completely abrogate HZ08's synergism effects, and mimic cisplatin-resistance on dip-MKN45.Lower p53 pathway expression that attenuates cisplatin-induced apoptosis might be at least partly the reason of cisplatin-resistance occurred in aneuploid MKN45 both in vitro and in vivo; Combination of HZ08 could sensitize cisplatin-induced apoptosis through the activation of the p53 pathway, therefore represented a synergism effect on aneuploid MKN45 cells.
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Affiliation(s)
- Xuzhen Tang
- Department of Physiology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China; Shanghai ChemPartner Co., Ltd., No. 6 Building, 998 Halei Road, Zhangjiang Hi-Tech Park Pudong New Area, Shanghai 201203, China
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299
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Salmela AL, Kallio MJ. Mitosis as an anti-cancer drug target. Chromosoma 2013; 122:431-49. [PMID: 23775312 DOI: 10.1007/s00412-013-0419-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/23/2013] [Accepted: 05/27/2013] [Indexed: 12/15/2022]
Abstract
Suppression of cell proliferation by targeting mitosis is one potential cancer intervention. A number of existing chemotherapy drugs disrupt mitosis by targeting microtubule dynamics. While efficacious, these drugs have limitations, i.e. neuropathy, unpredictability and development of resistance. In order to overcome these issues, a great deal of effort has been spent exploring novel mitotic targets including Polo-like kinase 1, Aurora kinases, Mps1, Cenp-E and KSP/Eg5. Here we summarize the latest developments in the discovery and clinical evaluation of new mitotic drug targets.
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Affiliation(s)
- Anna-Leena Salmela
- VTT Biotechnology for Health and Wellbeing, VTT Technical Research Centre of Finland, Itäinen Pitkäkatu 4C, Pharmacity Bldg, 4th Floor, P.O. Box 106, 20521, Turku, Finland
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300
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Du L, Borkowski R, Zhao Z, Ma X, Yu X, Xie XJ, Pertsemlidis A. A high-throughput screen identifies miRNA inhibitors regulating lung cancer cell survival and response to paclitaxel. RNA Biol 2013; 10:1700-13. [PMID: 24157646 DOI: 10.4161/rna.26541] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
microRNAs (miRNAs) are small RNAs endogenously expressed in multiple organisms that regulate gene expression largely by decreasing levels of target messenger RNAs (mRNAs). Over the past few years, numerous studies have demonstrated critical roles for miRNAs in the pathogenesis of many cancers, including lung cancer. Cellular miRNA levels can be easily manipulated, showing the promise of developing miRNA-targeted oligos as next-generation therapeutic agents. In a comprehensive effort to identify novel miRNA-based therapeutic agents for lung cancer treatment, we combined a high-throughput screening platform with a library of chemically synthesized miRNA inhibitors to systematically identify miRNA inhibitors that reduce lung cancer cell survival and those that sensitize cells to paclitaxel. By screening three lung cancer cell lines with different genetic backgrounds, we identified miRNA inhibitors that potentially have a universal cytotoxic effect on lung cancer cells and miRNA inhibitors that sensitize cells to paclitaxel treatment, suggesting the potential of developing these miRNA inhibitors as therapeutic agents for lung cancer. We then focused on characterizing the inhibitors of three miRNAs (miR-133a/b, miR-361-3p, and miR-346) that have the most potent effect on cell survival. We demonstrated that two of the miRNA inhibitors (miR-133a/b and miR-361-3p) decrease cell survival by activating caspase-3/7-dependent apoptotic pathways and inducing cell cycle arrest in S phase. Future studies are certainly needed to define the mechanisms by which the identified miRNA inhibitors regulate cell survival and drug response, and to explore the potential of translating the current findings into clinical applications.
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Affiliation(s)
- Liqin Du
- Greehey Children's Cancer Research Institute; Department of Cellular and Structural Biology; UT Health Science Center at San Antonio; San Antonio, TX USA
| | - Robert Borkowski
- Division of Basic Sciences; Southwestern Graduate School of Biomedical Sciences; UT Southwestern Medical Center; Dallas, TX USA
| | - Zhenze Zhao
- Greehey Children's Cancer Research Institute; Department of Cellular and Structural Biology; UT Health Science Center at San Antonio; San Antonio, TX USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute; Department of Cellular and Structural Biology; UT Health Science Center at San Antonio; San Antonio, TX USA
| | - Xiaojie Yu
- Graduate School of Biomedical Sciences; UT Health Science Center at San Antonio; San Antonio, TX USA
| | - Xian-Jin Xie
- Department of Clinical Sciences; UT Southwestern Medical Center; Dallas, TX USA
| | - Alexander Pertsemlidis
- Greehey Children's Cancer Research Institute; Department of Cellular and Structural Biology; UT Health Science Center at San Antonio; San Antonio, TX USA; Greehey Children's Cancer Research Institute; Department of Pediatrics; UT Health Science Center at San Antonio; San Antonio, TX USA
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