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Fang X, Li J, Siegmund D. Segmentation and estimation of change-point models: False positive control and confidence regions. Ann Stat 2020. [DOI: 10.1214/19-aos1861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. G3-GENES GENOMES GENETICS 2017; 7:3295-3303. [PMID: 28801508 PMCID: PMC5633380 DOI: 10.1534/g3.117.300141] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.
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3
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Snijders AM, Mao JH. Multi-omics approach to infer cancer therapeutic targets on chromosome 20q across tumor types. ACTA ACUST UNITED AC 2016; 2:215-223. [PMID: 27642640 PMCID: PMC5025263 DOI: 10.18282/amor.v2.i4.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The identification of good targets is a critical step for the development of targeted therapies for cancer treatment. Here, we used a multi-omics approach to delineate potential targets on chromosome 20q, which frequently shows a complex pattern of DNA copy number amplification in many human cancers suggesting the presence of multiple driver genes. By comparing the amounts of individual mRNAs in cancer from 11 different human tissues with those in their corresponding normal tissues, we identified 18 genes that were robustly elevated across human cancers. Moreover, we found that higher expression levels of a majority of these genes were associated with poor prognosis in many human cancer types. Using DNA copy number and expression data for all 18 genes obtained from The Cancer Genome Atlas project, we discovered that amplification is a major mechanism driving overexpression of these 18 genes in the majority of human cancers. Our integrated analysis suggests that 18 genes on chromosome 20q might serve as novel potential molecular targets for targeted cancer therapy.
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Affiliation(s)
- Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States
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4
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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5
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Hanlon KE, Lozano-Ondoua AN, Umaretiya PJ, Symons-Liguori AM, Chandramouli A, Moy JK, Kwass WK, Mantyh PW, Nelson MA, Vanderah TW. Modulation of breast cancer cell viability by a cannabinoid receptor 2 agonist, JWH-015, is calcium dependent. BREAST CANCER-TARGETS AND THERAPY 2016; 8:59-71. [PMID: 27186076 PMCID: PMC4847606 DOI: 10.2147/bctt.s100393] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction Cannabinoid compounds, both nonspecific as well as agonists selective for either cannabinoid receptor 1 (CB1) or cannabinoid receptor 2 (CB2), have been shown to modulate the tumor microenvironment by inducing apoptosis in tumor cells in several model systems. The mechanism of this modulation remains only partially delineated, and activity induced via the CB1 and CB2 receptors may be distinct despite significant sequence homology and structural similarity of ligands. Methods The CB2-selective agonist JWH-015 was used to investigate mechanisms downstream of CB2 activation in mouse and human breast cancer cell lines in vitro and in a murine mammary tumor model. Results JWH-015 treatment significantly reduced primary tumor burden and metastasis of luciferase-tagged murine mammary carcinoma 4T1 cells in immunocompetent mice in vivo. Furthermore, JWH-015 reduced the viability of murine 4T1 and human MCF7 mammary carcinoma cells in vitro by inducing apoptosis. JWH-015-mediated reduction of breast cancer cell viability was not dependent on Gαi signaling in vitro or modified by classical pharmacological blockade of CB1, GPR55, TRPV1, or TRPA1 receptors. JWH-015 effects were calcium dependent and induced changes in MAPK/ERK signaling. Conclusion The results of this work characterize the actions of a CB2-selective agonist on breast cancer cells in a syngeneic murine model representing how a clinical presentation of cancer progression and metastasis may be significantly modulated by a G-protein-coupled receptor.
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Affiliation(s)
- Katherine E Hanlon
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA; Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, USA
| | | | - Puja J Umaretiya
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - Anupama Chandramouli
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jamie K Moy
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - William K Kwass
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Patrick W Mantyh
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Mark A Nelson
- Department of Pathology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Todd W Vanderah
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
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6
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Chen KB, Hardison R, Zhang Y. dCaP: detecting differential binding events in multiple conditions and proteins. BMC Genomics 2014; 15 Suppl 9:S12. [PMID: 25522020 PMCID: PMC4290593 DOI: 10.1186/1471-2164-15-s9-s12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than analyzing individual features and/or samples separately. Yet there are currently few tools can perform joint inference of constitutive and differential regulation in multi-feature-multi-condition contexts with statistical testing. Existing tools either test regulatory variation for one factor in multiple samples at a time, or for multiple factors in one or two samples. Many of them only identify binary rather than quantitative variation, which are sensitive to threshold choices. RESULTS We propose a novel and powerful method called dCaP for simultaneously detecting constitutive and differential regulation of multiple epigenetic factors in multiple samples. Using simulation, we demonstrate the superior power of dCaP compared to existing methods. We then apply dCaP to two datasets from human and mouse ENCODE projects to demonstrate its utility. We show in the human dataset that the cell-type specific regulatory loci detected by dCaP are significantly enriched near genes with cell-type specific functions and disease relevance. We further show in the mouse dataset that dCaP captures genomic regions showing significant signal variations for TAL1 occupancy between two mouse erythroid cell lines. The novel TAL1 occupancy loci detected only by dCaP are highly enriched with GATA1 occupancy and differential gene expression, while those detected only by other methods are not. CONCLUSIONS Here, we developed a novel approach to utilize the cooperative property of proteins to detect differential binding given multivariate ChIP-seq samples to provide better power, aiming for complementing existing approaches and providing new insights in the method development in this field.
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Affiliation(s)
- Kuan-Bei Chen
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ross Hardison
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
- Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yu Zhang
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Statistics, The Pennsylvania State University, 422A Thomas, University Park, PA 16802, USA
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7
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Magbanua MJM, Roy R, Sosa EV, Hauranieh L, Kablanian A, Eisenbud LE, Ryazantsev A, Au A, Scott JH, Melisko M, Park JW. Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors. GENOMICS DATA 2014; 2:60-2. [PMID: 26484071 PMCID: PMC4535622 DOI: 10.1016/j.gdata.2014.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/02/2014] [Indexed: 11/10/2022]
Abstract
A debilitating complication of breast cancer is the metastatic spread of tumor cells to the leptomeninges or cerebrospinal fluid (CSF). Patients diagnosed with this aggressive clinical syndrome, known as leptomeningeal carcinomatosis, have very poor prognosis. Despite improvements in detecting cerebrospinal fluid tumor cells (CSFTCs), information regarding their molecular biology is extremely limited. In our recent work, we utilized a protocol previously used for circulating tumor cell isolation to purify tumor cells from the CSF. We then performed genomic characterization of CSFTCs as well as archival tumors from the same patient. Here, we describe the microarray data and quality controls associated with our study published in the Cancer Research journal in 2013 [1]. We also provide an R script containing code for quality control of microarray data and assessment of copy number calls. The microarray data has been deposited into Gene Expression Omnibus under accession # GSE46068.
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Affiliation(s)
- Mark Jesus M Magbanua
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA ; Helen Diller Family Comprehensive Cancer Center Computational Biology Core, University of California San Francisco, San Francisco, California, USA
| | - Eduardo V Sosa
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Louai Hauranieh
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Andrea Kablanian
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Lauren E Eisenbud
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Artem Ryazantsev
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Alfred Au
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Janet H Scott
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Michelle Melisko
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - John W Park
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
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8
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Comparative genomic hybridization. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Detection of copy number variation and single nucleotide polymorphisms in genes involved in drug resistance and other phenotypic traits in P. falciparum clinical isolates collected from Uganda. Acta Trop 2013; 125:269-75. [PMID: 23220229 DOI: 10.1016/j.actatropica.2012.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 02/04/2023]
Abstract
There is an increasing interest in mapping the genes of pathogens which underlie important phenotypic traits such as virulence and drug resistance. The Plasmodium falciparum genome exhibits sequence variation that contributes to the pathogenic mechanisms of the parasite. Determining the prevalence of resistance markers could provide a prediction about drug efficacy. Copy number polymorphism (CNP) of genes has been shown to influence important parasite phenotypes. In this work, CNPs within genes involved in drug resistance and other phenotypic traits namely P. falciparum multidrug resistance 1 (pfmdr-1), GTP cyclo hydrolase (gch1), Ring infected erythrocyte surface antigen precursor (resa) and a hypothetical protein coding gene were analyzed by quantitative real time-polymerase reaction (qRT-PCR) among clinical isolates collected from Uganda. The pfmdr-1 codons 86 and 1246 and P. falciparum chloroquine resistance (pfcrt) codon 76 were genotyped for single nucleotide polymorphisms (SNPs) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and the proportion of resistance associated mutations were determined among mild and severe malaria cases using the chi-square test. Forty and 42 P. falciparum isolates collected from children with mild and severe malaria respectively were analyzed for CNPs. Seventy five and 81 P. falciparum isolates from children with mild or severe malaria were analyzed for SNPs. No pfmdr-1, gch1 or novel gene amplifications were identified among the P. falciparum clinical isolates. Although chloroquine was officially withdrawn from policy use since 7 years, all P. falciparum isolates presented the associated pfcrt K76T mutation, whatever the clinical status and no specific mutation in the pfmdr-1 gene was associated with disease type. In conclusion, this study provides baseline measures for continued surveillance for changes in copy number and SNP types among genes implicated in drug resistance and other important phenotypes that may have a potential role in parasite virulence mechanisms or drug treatment outcomes.
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Kumar P, Mukherjee M, Johnson JPS, Patel M, Huey B, Albertson DG, Simin K. Cooperativity of Rb, Brca1, and p53 in malignant breast cancer evolution. PLoS Genet 2012; 8:e1003027. [PMID: 23173005 PMCID: PMC3500050 DOI: 10.1371/journal.pgen.1003027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 08/23/2012] [Indexed: 12/11/2022] Open
Abstract
Breast cancers that are "triple-negative" for the clinical markers ESR1, PGR, and HER2 typically belong to the Basal-like molecular subtype. Defective Rb, p53, and Brca1 pathways are each associated with triple-negative and Basal-like subtypes. Our mouse genetic studies demonstrate that the combined inactivation of Rb and p53 pathways is sufficient to suppress the physiological cell death of mammary involution. Furthermore, concomitant inactivation of all three pathways in mammary epithelium has an additive effect on tumor latency and predisposes highly penetrant, metastatic adenocarcinomas. The tumors are poorly differentiated and have histologic features that are common among human Brca1-mutated tumors, including heterogeneous morphology, metaplasia, and necrosis. Gene expression analyses demonstrate that the tumors share attributes of both Basal-like and Claudin-low signatures, two molecular subtypes encompassed by the broader, triple-negative class defined by clinical markers.
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MESH Headings
- Animals
- Apoptosis
- BRCA1 Protein/genetics
- BRCA1 Protein/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Evolution, Molecular
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Metabolic Networks and Pathways
- Mice
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Retinoblastoma Protein/genetics
- Retinoblastoma Protein/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Prashant Kumar
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Malini Mukherjee
- Department of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jacob P. S. Johnson
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Milan Patel
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Bing Huey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Donna G. Albertson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Karl Simin
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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Rübben A, Nordhoff O. A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution. Biol Open 2012; 2:49-62. [PMID: 23336076 PMCID: PMC3545268 DOI: 10.1242/bio.20122543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/15/2012] [Indexed: 12/22/2022] Open
Abstract
Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages. Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients.
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Affiliation(s)
- Albert Rübben
- Independent Institute of Systems Sciences Aachen , 52064 Aachen , Germany ; Department of Dermatology, RWTH Aachen University , 52074 Aachen , Germany
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12
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George CM, Alani E. Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA. Crit Rev Biochem Mol Biol 2012; 47:297-313. [PMID: 22494239 PMCID: PMC3337352 DOI: 10.3109/10409238.2012.675644] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. In this review, we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences.
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Affiliation(s)
- Carolyn M George
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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13
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Fan B, Dachrut S, Coral H, Yuen ST, Chu KM, Law S, Zhang L, Ji J, Leung SY, Chen X. Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer. PLoS One 2012; 7:e29824. [PMID: 22539939 PMCID: PMC3335165 DOI: 10.1371/journal.pone.0029824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/03/2011] [Indexed: 12/16/2022] Open
Abstract
Background Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level. Principal Findings We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis. Conclusions This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic targets.
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Affiliation(s)
- Biao Fan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Somkid Dachrut
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ho Coral
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Kent Man Chu
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Lianhai Zhang
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Jiafu Ji
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
- * E-mail: (XC); (SYL); (JFJ)
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
- * E-mail: (XC); (SYL); (JFJ)
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (XC); (SYL); (JFJ)
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14
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Seifert M, Gohr A, Strickert M, Grosse I. Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana. PLoS Comput Biol 2012; 8:e1002286. [PMID: 22253580 PMCID: PMC3257270 DOI: 10.1371/journal.pcbi.1002286] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 10/11/2011] [Indexed: 12/19/2022] Open
Abstract
Array-based comparative genomic hybridization (Array-CGH) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs) are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM). Array-based comparative genomics is a standard approach for the identification of DNA copy number polymorphisms between closely related genomes. The huge amounts of data produced by these experiments require efficient and accurate bioinformatics tools for the identification of copy number polymorphisms. Hidden Markov Models (HMMs) are frequently used for analyzing such data sets, but current models are based on first-order HMMs only having limited capabilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. We develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling these dependencies to overcome this limitation. In an in-depth case study with Arabidopsis thaliana, we find that parsimonious higher-order HMMs clearly improve the identification of copy number polymorphisms in comparison to standard first-order HMMs and other frequently used methods. Functional analysis of identified polymorphisms revealed details of genomic differences between the accessions C24 and Col-0 of Arabidopsis thaliana. An additional study on human cell lines further indicates that parsimonious HMMs are well-suited for the analysis of Array-CGH data.
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Affiliation(s)
- Michael Seifert
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
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Rothenberg SM, Settleman J. Discovering tumor suppressor genes through genome-wide copy number analysis. Curr Genomics 2011; 11:297-310. [PMID: 21286308 PMCID: PMC2944996 DOI: 10.2174/138920210791616734] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/07/2010] [Accepted: 04/07/2010] [Indexed: 12/31/2022] Open
Abstract
Classical tumor suppressor gene discovery has largely involved linkage analysis and loss-of-heterozygosity (LOH) screens, followed by detailed mapping of relatively large chromosomal regions. Subsequent efforts made use of genome-wide PCR-based methods to detect rare homozygous deletions. More recently, high-resolution genomic arrays have been applied to cancer gene discovery. However, accurate characterization of regions of genomic loss is particularly challenging due to sample heterogeneity, the small size of deleted regions and the high frequency of germline copy number polymorphisms. Here, we review the application of genome-wide copy number analysis to the specific problem of identifying tumor suppressor genes.
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Affiliation(s)
- S Michael Rothenberg
- Massachusetts General Hospital Cancer Center and Harvard Medical School, 149, 13th Street, Charlestown, MA 02129, USA
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Souček K, Gajdušková P, Brázdová M, Hýžd'alová M, Kočí L, Vydra D, Trojanec R, Pernicová Z, Lentvorská L, Hajdúch M, Hofmanová J, Kozubík A. Fetal colon cell line FHC exhibits tumorigenic phenotype, complex karyotype, and TP53 gene mutation. ACTA ACUST UNITED AC 2010; 197:107-16. [DOI: 10.1016/j.cancergencyto.2009.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Revised: 11/02/2009] [Accepted: 11/13/2009] [Indexed: 11/29/2022]
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Horvai AE, DeVries S, Roy R, O'Donnell RJ, Waldman F. Similarity in genetic alterations between paired well-differentiated and dedifferentiated components of dedifferentiated liposarcoma. Mod Pathol 2009; 22:1477-88. [PMID: 19734852 DOI: 10.1038/modpathol.2009.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Liposarcoma represents a unique model insofar as some well-differentiated liposarcomas progress to non-lipogenic, so-called 'dedifferentiated,' forms. The well-differentiated and dedifferentiated family of liposarcomas demonstrates amplification of the chromosome subregion 12q13-q15 with resultant amplification of the MDM2 and CDK4 genes. However, the specific genetic changes that distinguish between well-differentiated and dedifferentiated liposarcomas are less well understood. To study the genetic changes in dedifferentiated liposarcomas, paired well-differentiated and dedifferentiated components of 29 tumors were analyzed separately by array-based comparative genomic hybridization. A bacterial artificial chromosome array at approximately 1-Mb resolution was used. The genetic changes were compared with clinical presentation, grade of the dedifferentiated component and overexpression of MDM2 and CDK4. Most tumors (n=21, 72%) were retroperitoneal, with both components present at initial diagnosis (n=25, 86%). Eight tumors (28%) were classified as low-grade dedifferentiation. In four cases (14%), a well-differentiated liposarcoma preceded the presentation of the dedifferentiated tumor by 1-5 years. 12q13-q15 was amplified in all tumors. Using unsupervised hierarchical clustering of copy-number changes, all but two tumors showed close similarities between well-differentiated and dedifferentiated components, and segregated as pairs. Dedifferentiated components had more total amplifications (P=0.008) and a trend for gain at 19q13.2, but no genetic changes were significant in distinguishing between the two components. High-level amplifications of 1p21-32 (n=7, 24%), 1q21-23 (n=9, 31%), 6q23-24 (n=6, 21%) and 12q24 (n=3, 10%) were common, but none significantly correlated with differentiation. Presentation and grade correlated with the frequency of changes at a number of genetic loci (P<0.001), whereas CDK4 immunostaining showed negative correlation with 12q13.13 amplification. The genotypic similarity, at the limit of the array's resolution, between components implies that most genetic changes precede phenotypic 'progression,' early in tumorigenesis. The relationship between genetic changes and presentation or grade may reflect differences in factors that control genomic instability or the background genotype of the tumor.
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Affiliation(s)
- Andrew E Horvai
- Department of Pathology, University of California, San Francisco, CA 94115-1656, USA.
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Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis. Oncogene 2009; 28:1892-903. [PMID: 19330026 PMCID: PMC2722962 DOI: 10.1038/onc.2009.34] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate oncogenes mapping to these regions were identified by combining copy number and RNA and protein expression analyses. These studies also suggested that CCND1 at 11q13 induced expression of ZNF703 mapping at 8p12, which was subsequently shown to be mediated via the Rb/E2F pathway. Nine candidate oncogenes from 8p12 and four from 11q13 were further evaluated for oncogenic function. None of the genes individually promoted colony formation in soft agar or collaborated with each other functionally. On the other hand, FGFR1 and DDHD2 at 8p12 cooperated functionally with MYC, while CCND1 and ZNF703 cooperated with a dominant negative form of TP53. These observations highlight the complexity and functional consequences of the genomic rearrangements that occur in these breast cancer amplicons, including transcriptional cross-talk between genes in the 8p and 11q amplicons, as well as their cooperation with major pathways of tumorigenesis.
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Morales C, García MJ, Ribas M, Miró R, Muñoz M, Caldas C, Peinado MA. Dihydrofolate reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells. Mol Cancer Ther 2009; 8:424-32. [DOI: 10.1158/1535-7163.mct-08-0759] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Stromal control of oncogenic traits expressed in response to the overexpression of GLI2, a pleiotropic oncogene. Oncogene 2008; 28:625-37. [PMID: 19015636 PMCID: PMC2643346 DOI: 10.1038/onc.2008.421] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hedgehog signaling is often activated in tumors, yet it remains unclear how GLI2, a transcription factor activated by this pathway, acts as an oncogene. We show that GLI2 is a pleiotropic oncogene. Overexpression induces genomic instability and blocks differentiation, likely mediated in part by enhanced expression of the stem cell gene SOX2. GLI2 also induces TGFβ dependent transdifferentiation of foreskin and tongue, but not gingival fibroblasts into myofibroblasts, creating an environment permissive for invasion by keratinocytes, which are in various stages of differentiation having down regulated GLI2. Thus, up-regulated GLI2 expression is sufficient to induce a number of the acquired characteristics of tumor cells; however the stroma, in a tissue specific manner, determines whether certain GLI2 oncogenic traits are expressed.
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Adaptive copy number evolution in malaria parasites. PLoS Genet 2008; 4:e1000243. [PMID: 18974876 PMCID: PMC2570623 DOI: 10.1371/journal.pgen.1000243] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/29/2008] [Indexed: 11/19/2022] Open
Abstract
Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2–11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation. Recent comparative genomic hybridization studies have revealed extensive copy number variation in eukaryotic genomes. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive copy number polymorphism (CNP). We provide compelling evidence that gch1 CNP is adaptive and most likely results from selection by antifolate drugs, which target enzymes downstream in this pathway. Gch1 CNP shows extreme geographical differentiation; hitchhiking reduces diversity and increases LD in flanking sequence, indicating recent rapid spread within Thailand, while amplicon structure reveals multiple origins and parallel evolution. Furthermore, strong association between elevated copy number and a critical mutation dhfr-I164L that underlies high-level antifolate resistance indicates functional linkage and fitness epistasis between genes on different chromosomes. These data reveal hidden complexity in the evolutionary response to antifolate treatment and demonstrate that analysis of structural variation can provide a fast-track to locating genes that underlie adaptation.
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Kitada K, Yamasaki T. The complicated copy number alterations in chromosome 7 of a lung cancer cell line is explained by a model based on repeated breakage-fusion-bridge cycles. ACTA ACUST UNITED AC 2008; 185:11-9. [PMID: 18656688 DOI: 10.1016/j.cancergencyto.2008.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/31/2008] [Accepted: 04/07/2008] [Indexed: 10/21/2022]
Abstract
The drug-resistant lung cancer cell line PTX250, which has been previously established by exposure to an anti-cancer drug paclitaxel, has an increased copy number in the MDR1/ABCB1 locus region. In addition, the flanking regions also exhibit aberrant copy numbers, making the copy number profile of chromosome 7 complicated. In this study, we tested whether the breakage-fusion-bridge (BFB) cycle model can explain such copy number alterations. An analysis using fluorescence in situ hybridization (FISH) with a painting probe demonstrated that the aberrant chromosome, designated chromosome 7(amp), was derived from an intact chromosome 7. Using high-density comparative genomic hybridization arrays, we examined the copy number profile in detail and divided chromosome 7(amp) into seven segments. Based on copy numbers of each segment, which were determined using interphase- and metaphase-FISH analysis, we constructed a formation model for the complicated copy number alteration. Six-time BFB cycles and the cycle-termination by healing of broken ends were presupposed in the model. Locations and orientations of the segments observed in chromosome 7(amp) agreed well with those predicted from the model. Telomere addition was also cytogenetically confirmed. In all, it could be concluded that the complicated copy number alteration found in chromosome 7(amp) is generated from the intact chromosome 7 by the repeated BFB cycles.
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Affiliation(s)
- Kunio Kitada
- Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., 200-Kajiwara, Kamakura, Kanagawa 247-8530, Japan.
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Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. Genome position and gene amplification. Genome Biol 2008; 8:R120. [PMID: 17584934 PMCID: PMC2394771 DOI: 10.1186/gb-2007-8-6-r120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 05/15/2007] [Accepted: 06/21/2007] [Indexed: 01/05/2023] Open
Abstract
Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
Background Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. Results We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. Conclusion These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
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Affiliation(s)
- Pavla Gajduskova
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská, Brno, 612 65, Czech Republic
| | - Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Serena Kwek
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Ritu Roydasgupta
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane Fridlyand
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Taku Tokuyasu
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Snijders AM, Hermsen MA, Baughman J, Buffart TE, Huey B, Gajduskova P, Roydasgupta R, Tokuyasu T, Meijer GA, Fridlyand J, Albertson DG. Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability. Genes Chromosomes Cancer 2008; 47:71-83. [PMID: 17943968 DOI: 10.1002/gcc.20509] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tumors vary widely in chromosomal level genome instability. To gain a better understanding of the underlying defects which foster specific types of aberrations, we investigated the response of cells of related genetic backgrounds to challenge with methotrexate. We studied mismatch repair deficient HCT116 cells, two derivatives also deficient in XRCC5 (HCT116 Ku86+/-) or BLM (HCT116 BLM-/-), and mismatch repair competent HCT116+chr3 cells. We show that colony formation occurred at a significantly higher frequency in HCT116 cells and HCT116 Ku86+/- cells compared to HCT116 BLM-/- and HCT116+chr3 cells. Visible colonies arose most rapidly in HCT116 Ku86+/- cells, whereas they formed most slowly in HCT116+chr3 cells. Copy number changes acquired by the methotrexate resistant HCT116 and HCT116 BLM-/- cells most often included whole chromosome gains or losses or no acquired copy number changes, whereas resistance in HCT116+chr3 and HCT116 Ku86+/- cells was associated with amplification of DHFR and copy number transitions leading to increased copy number of DHFR, respectively. The additional copies of DHFR were present on unstable chromosomes and organized as inverted repeats in HCT116+chr3 cells, while they were most often present as direct repeats in HCT116 Ku86+/- cells. These observations suggest that different mutational mechanisms promote drug resistance in these genetic backgrounds; mismatch repair deficiency in HCT116, high rates of chromosomal instability in HCT116 Ku86+/-, and low rates of chromosomal instability in HCT116+chr3. On the other hand, it appears that loss of BLM function suppresses the mismatch repair mutator mechanism in mismatch repair and BLM deficient HCT116 BLM-/- cells.
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Affiliation(s)
- Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
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Adélaïde J, Finetti P, Bekhouche I, Repellini L, Geneix J, Sircoulomb F, Charafe-Jauffret E, Cervera N, Desplans J, Parzy D, Schoenmakers E, Viens P, Jacquemier J, Birnbaum D, Bertucci F, Chaffanet M. Integrated profiling of basal and luminal breast cancers. Cancer Res 2008; 67:11565-75. [PMID: 18089785 DOI: 10.1158/0008-5472.can-07-2536] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Basal and luminal are two molecular subtypes of breast cancer with opposite histoclinical features. We report a combined, high-resolution analysis of genome copy number and gene expression in primary basal and luminal breast cancers. First, we identified and compared genomic alterations in 45 basal and 48 luminal tumors by using 244K oligonucleotide array comparative genomic hybridization (aCGH). We found various genome gains and losses and rare high-level gene amplifications that may provide therapeutic targets. We show that gain of 10p is a new alteration in basal breast cancer and that a subregion of the 8p12 amplification is specific of luminal tumors. Rare high-level amplifications contained BCL2L2, CCNE, EGFR, FGFR2, IGF1R, NOTCH2, and PIK3CA. Potential gene breaks involved ETV6 and FLT3. Second, we analyzed both aCGH and gene expression profiles for 42 basal and 32 luminal breast cancers. The results support the existence of specific oncogenic pathways in basal and luminal breast cancers, involving several potential oncogenes and tumor suppressor genes (TSG). In basal tumors, 73 candidate oncogenes were identified in chromosome regions 1q21-23, 10p14, and 12p13 and 28 candidate TSG in regions 4q32-34 and 5q11-23. In luminal breast cancers, 33 potential oncogenes were identified in 1q21-23, 8p12-q21, 11q13, and 16p12-13 and 61 candidate TSG in 16q12-13, 16q22-24, and 17p13. HORMAD1 (P = 6.5 x 10(-5)) and ZNF703 (P = 7 x 10(-4)) were the most significant basal and luminal potential oncogenes, respectively. Finally, among 10p candidate oncogenes associated with basal subtype, we validated CDC123/C10orf7 protein as a basal marker.
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Affiliation(s)
- José Adélaïde
- Marseille Cancer Research Center, Department of Molecular Oncology, Institut Paoli-Calmettes and UMR599 Institut National de la Santé et de la Recherche Médicale, Marseille, France
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Martin ES, Tonon G, Sinha R, Xiao Y, Feng B, Kimmelman AC, Protopopov A, Ivanova E, Brennan C, Montgomery K, Kucherlapati R, Bailey G, Redston M, Chin L, DePinho RA. Common and distinct genomic events in sporadic colorectal cancer and diverse cancer types. Cancer Res 2007; 67:10736-43. [PMID: 18006816 DOI: 10.1158/0008-5472.can-07-2742] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) is a major cause of cancer morbidity and mortality, and elucidation of its underlying genetics has advanced diagnostic screening, early detection, and treatment. Because CRC genomes are characterized by numerous non-random chromosomal structural alterations, we sought to delimit regions of recurrent amplifications and deletions in a collection of 42 primary specimens and 37 tumor cell lines derived from chromosomal instability neoplasia and microsatellite instability neoplasia CRC subtypes and to compare the pattern of genomic aberrations in CRC with those in other cancers. Application of oligomer-based array-comparative genome hybridization and custom analytic tools identified 50 minimal common regions (MCRs) of copy number alterations, 28 amplifications, and 22 deletions. Fifteen were highly recurrent and focal (<12 genes) MCRs, five of them harboring known CRC genes including EGFR and MYC with the remaining 10 containing a total of 65 resident genes with established links to cancer. Furthermore, comparisons of these delimited genomic profiles revealed that 22 of the 50 CRC MCRs are also present in lung cancer, glioblastoma, and/or multiple myeloma. Among 22 shared MCRs, nine do not contain genes previously shown genetically altered in cancer, whereas the remaining 13 harbor 35 known cancer genes, of which only 14 have been linked to CRC pathogenesis. Together, these observations point to the existence of many yet-to-be discovered cancer genes driving CRC development, as well as other human cancers, and show the utility of high-resolution copy number analysis in the identification of genetic events common and specific to the development of various tumor types.
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Affiliation(s)
- Eric S Martin
- Department of Medical Oncology, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Byrd KN, Huey B, Roydasgupta R, Fridlyand J, Snijders AM, Albertson DG. FBXW7 and DNA copy number instability. Breast Cancer Res Treat 2007; 109:47-54. [PMID: 17588203 DOI: 10.1007/s10549-007-9623-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 05/13/2007] [Indexed: 10/23/2022]
Abstract
SKP1-cullin-F-box protein (SCF) type ubiquitin ligases degrade proteins controlling the G1/S transition. Deficiency for FBXW7 (also known as hCDC4), which encodes the F-box protein of the SCF type ubiquitin ligase is associated with genomic instability. Here, we investigated the association of FBXW7 deficiency with chromosomal instability in breast cancer. We screened 49 tumors previously profiled by array CGH for mutations in conserved regions of FBXW7, but found no mutations. Copy number loss of FBXW7, however was associated with enhanced genomic instability in the Complex breast tumor subtype, but instability may not be due to FBXW7 haploinsufficiency, since transcript levels were not reduced in tumors with loss of the locus, whereas reduced expression was observed for other neighboring genes involved in maintenance of genome stability. We also investigated whether cells deficient for FBXW7 showed enhanced instability by challenging cells with methotrexate and assessing numbers of genomic alterations arising in resistant cells. Although methotrexate resistant colonies formed at high frequencies in HCT116 FBXW7+/- and HCT116 FBXW7-/- cells compared to parental HCT116, few copy number alterations were detected in the resistant cells. Taken together these studies suggest that FBXW7 deficiency is unlikely to contribute to the extensive copy number aberrations associated with breast and possibly other tumor types.
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Affiliation(s)
- Kristin N Byrd
- Cancer Research Institute, University of California San Francisco, Box 0808, San Francisco, CA 94143-0808, USA
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Li P, Maines-Bandiera S, Kuo WL, Guan Y, Sun Y, Hills M, Huang G, Collins CC, Leung PCK, Gray JW, Auersperg N. Multiple roles of the candidate oncogene ZNF217 in ovarian epithelial neoplastic progression. Int J Cancer 2007; 120:1863-73. [PMID: 17266044 DOI: 10.1002/ijc.22300] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The transcription factor ZNF217 is often amplified in ovarian cancer, but its role in neoplastic progression is unknown. We introduced ZNF217-HA by adenoviral and retroviral infection into normal human ovarian surface epithelial cells (OSE), i.e., the source of ovarian cancer, and into SV40 Tag/tag expressing, p53/pRB-deficient OSE with extended but finite life spans (IOSE). In OSE, ZNF217-HA reduced cell-substratum adhesion and accelerated loss of senescent cells, but caused no obvious proneoplastic changes. In contrast, ZNF217-HA transduction into IOSE yielded two permanent lines, I-80RZ and I-144RZ, which exhibited telomerase activity, stable telomere lengths, anchorage independence and reduced serum dependence, but were not tumorigenic in SCID mice. This immortalization required short-term EGF treatment near the time of crisis. The permanent lines were EGF-independent, but ZNF217-dependent since siRNA to ZNF217 inhibited anchorage independence and arrested growth. Array CGH revealed genomic changes resembling those of ovarian carcinomas, such as amplicons at 3q and 20q, and deletions at 4q and 18, associated with underexpressed annexin A10, N-cadherin, desmocollin 3 and PAI-2, which have been reported as tumor suppressors. The lines overexpressed EEF1A2, SMARA3 and STAT1 and underexpressed other oncogenes, tumor suppressors and extracellular matrix/adhesion genes. The results implicate ZNF217 as an ovarian oncogene, which is detrimental to senescing normal OSE cells but contributes to neoplastic progression in OSE with inactivated p53/RB. The resemblance of the genomic changes in the ZNF217-overexpressing lines to ovarian carcinomas provides a unique model to investigate interrelationships between these changes and ovarian neoplastic phenotypes.
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Affiliation(s)
- Peixiang Li
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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29
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Kuuselo R, Savinainen K, Azorsa DO, Basu GD, Karhu R, Tuzmen S, Mousses S, Kallioniemi A. Intersex-like (IXL) is a cell survival regulator in pancreatic cancer with 19q13 amplification. Cancer Res 2007; 67:1943-9. [PMID: 17332321 DOI: 10.1158/0008-5472.can-06-3387] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pancreatic cancer is a highly aggressive disease characterized by poor prognosis and vast genetic instability. Recent microarray-based, genome-wide surveys have identified multiple recurrent copy number aberrations in pancreatic cancer; however, the target genes are, for the most part, unknown. Here, we characterized the 19q13 amplicon in pancreatic cancer to identify putative new drug targets. Copy number increases at 19q13 were quantitated in 16 pancreatic cancer cell lines and 31 primary tumors by fluorescence in situ hybridization. Cell line copy number data delineated a 1.1 Mb amplicon, the presence of which was also validated in 10% of primary pancreatic tumors. Comprehensive expression analysis by quantitative real-time reverse transcription-PCR indicated that seven transcripts within this region had consistently elevated expression levels in the amplified versus nonamplified cell lines. High-throughput loss-of-function screen by RNA interference was applied across the amplicon to identify genes whose down-regulation affected cell viability. This screen revealed five genes whose down-regulation led to significantly decreased cell viability in the amplified PANC-1 cells but not in the nonamplified MiaPaca-2 cells, suggesting the presence of multiple biologically interesting genes in this region. Of these, the transcriptional regulator intersex-like (IXL) was consistently overexpressed in amplified cells and had the most dramatic effect on cell viability. IXL silencing also resulted in G(0)-G(1) cell cycle arrest and increased apoptosis in PANC-1 cells. These findings implicate IXL as a novel amplification target gene in pancreatic cancer and suggest that IXL is required for cancer cell survival in 19q13-amplified tumors.
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Affiliation(s)
- Riina Kuuselo
- Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
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30
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Hu J, Gao JB, Cao Y, Bottinger E, Zhang W. Exploiting noise in array CGH data to improve detection of DNA copy number change. Nucleic Acids Res 2007; 35:e35. [PMID: 17272296 PMCID: PMC1994778 DOI: 10.1093/nar/gkl730] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Developing effective methods for analyzing array-CGH data to detect chromosomal aberrations is very important for the diagnosis of pathogenesis of cancer and other diseases. Current analysis methods, being largely based on smoothing and/or segmentation, are not quite capable of detecting both the aberration regions and the boundary break points very accurately. Furthermore, when evaluating the accuracy of an algorithm for analyzing array-CGH data, it is commonly assumed that noise in the data follows normal distribution. A fundamental question is whether noise in array-CGH is indeed Gaussian, and if not, can one exploit the characteristics of noise to develop novel analysis methods that are capable of detecting accurately the aberration regions as well as the boundary break points simultaneously? By analyzing bacterial artificial chromosomes (BACs) arrays with an average 1 mb resolution, 19 k oligo arrays with the average probe spacing <100 kb and 385 k oligo arrays with the average probe spacing of about 6 kb, we show that when there are aberrations, noise in all three types of arrays is highly non-Gaussian and possesses long-range spatial correlations, and that such noise leads to worse performance of existing methods for detecting aberrations in array-CGH than the Gaussian noise case. We further develop a novel method, which has optimally exploited the character of the noise, and is capable of identifying both aberration regions as well as the boundary break points very accurately. Finally, we propose a new concept, posteriori signal-to-noise ratio (p-SNR), to assign certain confidence level to an aberration region and boundaries detected.
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Affiliation(s)
| | - Jian-Bo Gao
- *Correspondence may also be addressed to Jian-Bo Gao.
| | - Yinhe Cao
- Department of Electrical and Computer Engineering, University of Florida Gainesville, FL 32611, Biosieve 1026 Springfield Drive, Campbell, CA 95008 and Department of Medicine, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029, USA
| | - Erwin Bottinger
- Department of Electrical and Computer Engineering, University of Florida Gainesville, FL 32611, Biosieve 1026 Springfield Drive, Campbell, CA 95008 and Department of Medicine, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029, USA
| | - Weijia Zhang
- Department of Electrical and Computer Engineering, University of Florida Gainesville, FL 32611, Biosieve 1026 Springfield Drive, Campbell, CA 95008 and Department of Medicine, Mount Sinai School of Medicine One Gustave L. Levy Place, New York, NY 10029, USA
- *To whom correspondence should be addressed. +1 21224128831 2128492643
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31
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Trautmann K, Terdiman JP, French AJ, Roydasgupta R, Sein N, Kakar S, Fridlyand J, Snijders AM, Albertson DG, Thibodeau SN, Waldman FM. Chromosomal instability in microsatellite-unstable and stable colon cancer. Clin Cancer Res 2007; 12:6379-85. [PMID: 17085649 DOI: 10.1158/1078-0432.ccr-06-1248] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
PURPOSE The genomic instability in colon cancer can be divided into at least two major types, microsatellite instability (MSI) or chromosomal instability (CIN). Although initially felt to be mutually exclusive, recent evidence suggests that there may be overlap between the two. The aim of this study was to identify chromosomal alterations at high resolution in sporadic colon cancers with high-level microsatellite instability (MSI-H) and to compare them to those present in a set of matched microsatellite stable (MSS) tumors. EXPERIMENTAL DESIGN Array-based comparative genomic hybridization was used to analyze a set of 23 sporadic MSI-H and 23 MSS colon cancers matched for location, gender, stage, and age. The arrays consisted of 2,464 bacterial artificial chromosome clones. RESULTS MSI and MSS colon cancers differed significantly with respect to frequency and type of chromosomal alterations. The median fraction of genome altered was lower among MSI-H tumors than MSS tumors (2.8% versus 30.7%, P=0.00006). However, the MSI-H tumors displayed a range of genomic alterations, from the absence of detectable alterations to extensive alterations. Frequent alterations in MSI-H tumors included gains of chromosomes 8, 12, and 13, and loss of 15q14. In contrast, the most frequent alterations in MSS tumors were gains of 7, 13, 8q, and 20, and losses of 8p, 17p, and 18. A small, previously uncharacterized, genomic deletion on 16p13.2, found in 35% of MSI-H and 21% of MSS tumors, was confirmed by fluorescence in situ hybridization. CONCLUSION MSI and CIN are not mutually exclusive forms of genomic instability in sporadic colon cancer, with MSI tumors also showing varying degrees of CIN.
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Affiliation(s)
- Karolin Trautmann
- Comprehensive Cancer Center, Department of Medicine, University of California San Francisco, San Francisco, California 94143-0808, USA
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32
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Zanazzi C, Hersmus R, Veltman IM, Gillis AJM, van Drunen E, Beverloo HB, Hegmans JPJJ, Verweij M, Lambrecht BN, Oosterhuis JW, Looijenga LHJ. Gene expression profiling and gene copy-number changes in malignant mesothelioma cell lines. Genes Chromosomes Cancer 2007; 46:895-908. [PMID: 17620293 DOI: 10.1002/gcc.20475] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Malignant mesothelioma (MM) is an asbestos-induced tumor that acquires aneuploid DNA content during the tumorigenic process. We used instable MM cell lines as an in vitro model to study the impact of DNA copy-number changes on gene expression profiling, in the course of their chromosomal redistribution process. Two MM cell lines, PMR-MM2 (early passages of in vitro culture) and PMR-MM7 (both early and late passages of in vitro culture), were cytogenetically characterized. Genomic gains and losses were precisely defined using microarray-based comparative genomic hybridization (array-CGH), and minimal overlapping analysis led to the identification of the common unbalanced genomic regions. Using the U133Plus 2.0 Affymetrix gene chip array, we analyzed PMR-MM7 early and late passages for genome-wide gene expression, and correlated the differentially expressed genes with copy-number changes. The presence of a high number of genetic imbalances occurring from early to late culture steps reflected the tendency of MM cells toward genomic instability. The selection of specific chromosomal abnormalities observed during subsequent cultures demonstrated the spontaneous evolution of the cancer cells in an in vitro environment. MM cell lines were characterized by copy-number changes associated with the TP53 apoptotic pathway already present at the first steps of in vitro culture. Prolonged culture led to acquisition of additional chromosomal copy-number changes associated with dysregulation of genes involved in cell adhesion, regulation of mitotic cell cycle, signal transduction, carbohydrate metabolism, motor activity, glycosaminoglycan biosynthesis, protein binding activity, lipid transport, ATP synthesis, and methyltransferase activity.
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Affiliation(s)
- Claudia Zanazzi
- Department of Pathology, Erasmus Medical Center, Daniel den Hoed Cancer Center, Josephine Nefkens Institute, Rotterdam, The Netherlands
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Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006; 10:529-41. [PMID: 17157792 DOI: 10.1016/j.ccr.2006.10.009] [Citation(s) in RCA: 935] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 08/19/2006] [Accepted: 10/06/2006] [Indexed: 02/07/2023]
Abstract
This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.
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Affiliation(s)
- Koei Chin
- Comprehensive Cancer Center, 2340 Sutter Street, University of California, San Francisco, San Francisco, California 94143
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34
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Zhang NR, Siegmund DO. A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data. Biometrics 2006; 63:22-32. [PMID: 17447926 DOI: 10.1111/j.1541-0420.2006.00662.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In the analysis of data generated by change-point processes, one critical challenge is to determine the number of change-points. The classic Bayes information criterion (BIC) statistic does not work well here because of irregularities in the likelihood function. By asymptotic approximation of the Bayes factor, we derive a modified BIC for the model of Brownian motion with changing drift. The modified BIC is similar to the classic BIC in the sense that the first term consists of the log likelihood, but it differs in the terms that penalize for model dimension. As an example of application, this new statistic is used to analyze array-based comparative genomic hybridization (array-CGH) data. Array-CGH measures the number of chromosome copies at each genome location of a cell sample, and is useful for finding the regions of genome deletion and amplification in tumor cells. The modified BIC performs well compared to existing methods in accurately choosing the number of regions of changed copy number. Unlike existing methods, it does not rely on tuning parameters or intensive computing. Thus it is impartial and easier to understand and to use.
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Affiliation(s)
- Nancy R Zhang
- Department of Statistics, Stanford University, Stanford, California 94305, USA.
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35
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Benz CC, Fedele V, Xu F, Ylstra B, Ginzinger D, Yu M, Moore D, Hall RK, Wolff DJ, Disis ML, Eppenberger-Castori S, Eppenberger U, Schittulli F, Tommasi S, Paradiso A, Scott GK, Albertson DG. Altered promoter usage characterizes monoallelic transcription arising with ERBB2 amplification in human breast cancers. Genes Chromosomes Cancer 2006; 45:983-94. [PMID: 16883574 DOI: 10.1002/gcc.20364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Analysis of a collection of human breast cancers (n = 150), enriched in ERBB2-positive cases (n = 57) and involving tumor genotyping relative to population-matched blood genotyping (n = 749) for a common ERBB2 single nucleotide polymorphism Ala(G)1170Pro(C), revealed that ERBB2 amplification in breast cancer is invariably monoallelic. Analysis of paired breast cancer and blood samples from informative (G1170C heterozygotic) ERBB2-positive (n = 12) and ERBB2-negative (n = 17) cases not only confirmed monoallelic amplification and ERBB2 transcriptional overexpression but also revealed that most low ERBB2 expressing breast cancers (12/17) exhibit unbalanced allelic transcription, showing 3-fold to nearly 5,000-fold preferential expression from one of two inherited alleles. To explore cis-acting transcriptional mechanisms potentially selected during ERBB2 amplification, levels of four different ERBB2 transcript variants (5.2, 4.7, 2.1, and 1.4 kb) were correlated with total (4.6 kb) ERBB2 mRNA levels in ERBB2-positive (n = 14) versus ERBB2-negative (n = 43) primary breast cancers. Relative expression of only the 2.1 kb extracellular domain-encoding splice variant and a 4.7 kb mRNA variant that uses an alternative start site were significantly increased in association with ERBB2-positivity, implicating altered promoter usage and selective transcript regulation within the ERBB2 amplicon. Altogether, these findings provide new mechanistic insights into the development of ERBB2-positive breast cancer and strong rationale for delineating candidate cis-acting regulatory elements that may link allele-specific ERBB2 transcription in premalignant breast epithelia with subsequent development of breast cancers bearing monoallelic ERBB2 amplicons.
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36
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Jong K, Marchiori E, van der Vaart A, Chin SF, Carvalho B, Tijssen M, Eijk PP, van den Ijssel P, Grabsch H, Quirke P, Oudejans JJ, Meijer GA, Caldas C, Ylstra B. Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 2006; 26:1499-506. [PMID: 16936777 DOI: 10.1038/sj.onc.1209919] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array comparative genomic hybridization (array CGH); however, the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression, a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods, which performed noise reduction and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore, it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by meta-analysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number data sets for cancer subtype classification.
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Affiliation(s)
- K Jong
- Faculty of Sciences, Vrije Universiteit (VU), Amsterdam, The Netherlands
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37
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Curtin JA, Busam K, Pinkel D, Bastian BC. Somatic activation of KIT in distinct subtypes of melanoma. J Clin Oncol 2006; 24:4340-6. [PMID: 16908931 DOI: 10.1200/jco.2006.06.2984] [Citation(s) in RCA: 1095] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Melanomas on mucosal membranes, acral skin (soles, palms, and nail bed), and skin with chronic sun-induced damage have infrequent mutations in BRAF and NRAS, genes within the mitogen-activated protein (MAP) kinase pathway commonly mutated in melanomas on intermittently sun-exposed skin. This raises the question of whether other aberrations are occurring in the MAP kinase cascade in the melanoma types with infrequent mutations of BRAF and NRAS. PATIENTS AND METHODS We analyzed array comparative genomic hybridization data from 102 primary melanomas (38 from mucosa, 28 from acral skin, and 18 from skin with and 18 from skin without chronic sun-induced damage) for DNA copy number aberrations specific to melanoma subtypes where mutations in BRAF and NRAS are infrequent. A narrow amplification on 4q12 was found, and candidate genes within it were analyzed. RESULTS Oncogenic mutations in KIT were found in three of seven tumors with amplifications. Examination of all 102 primary melanomas found mutations and/or copy number increases of KIT in 39% of mucosal, 36% of acral, and 28% of melanomas on chronically sun-damaged skin, but not in any (0%) melanomas on skin without chronic sun damage. Seventy-nine percent of tumors with mutations and 53% of tumors with multiple copies of KIT demonstrated increased KIT protein levels. CONCLUSION KIT is an important oncogene in melanoma. Because the majority of the KIT mutations we found in melanoma also occur in imatinib-responsive cancers of other types, imatinib may offer an immediate therapeutic benefit for a significant proportion of the global melanoma burden.
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Affiliation(s)
- John A Curtin
- Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143-0808, USA
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38
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Heck JA, Gresham D, Botstein D, Alani E. Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics 2006; 174:519-23. [PMID: 16816424 PMCID: PMC1569777 DOI: 10.1534/genetics.106.059311] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examined mismatch repair (MMR)-defective diploid strains of budding yeast grown for approximately 160 generations to determine whether decreases in spore viability due to the uncovering of recessive lethal mutations correlated with an increase in gross chromosomal rearrangements (GCRs). No GCRs were detected despite dramatic decreases in spore viability, suggesting that frameshift and/or other unrepaired DNA replication lesions play a greater role than chromosomal instability in decreasing viability in MMR-defective strains.
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Affiliation(s)
- Julie Akiko Heck
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
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39
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Albertson DG. Gene amplification in cancer. Trends Genet 2006; 22:447-55. [PMID: 16787682 DOI: 10.1016/j.tig.2006.06.007] [Citation(s) in RCA: 364] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 04/26/2006] [Accepted: 06/08/2006] [Indexed: 02/07/2023]
Abstract
Gene amplification is a copy number increase of a restricted region of a chromosome arm. It is prevalent in some tumors and is associated with overexpression of the amplified gene(s). Amplified DNA can be organized as extrachromosomal elements, as repeated units at a single locus or scattered throughout the genome. Common chromosomal fragile sites, defects in DNA replication or telomere dysfunction might promote amplification. Some regions of amplification are complex, yet elements of the pattern are reproduced in different tumor types. A genetic basis for amplification is suggested by its relative frequency in some tumor subtypes, and its occurrence in "early" preneoplastic lesions. Clinically, amplification has prognostic and diagnostic usefulness, and is a mechanism of acquired drug resistance.
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Affiliation(s)
- Donna G Albertson
- Cancer Research Institute and Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA 94143, USA.
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40
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Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006; 6:96. [PMID: 16620391 PMCID: PMC1459181 DOI: 10.1186/1471-2407-6-96] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 04/18/2006] [Indexed: 01/24/2023] Open
Abstract
Background Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.
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Affiliation(s)
- Jane Fridlyand
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, San Francisco, CA 94143, USA
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Antoine M Snijders
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Bauke Ylstra
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Micro Array Core Facility, VUMC University Medical Center, 1081BT Amsterdam, The Netherlands
| | - Hua Li
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Adam Olshen
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York 20021, USA
| | - Richard Segraves
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Shanaz Dairkee
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Geraldine Brush Cancer Research Institute, California Pacific Medical Center, San Francisco, California 94115, USA
| | - Taku Tokuyasu
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Britt Marie Ljung
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Ajay N Jain
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane McLennan
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - John Ziegler
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Koei Chin
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Sandy Devries
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Heidi Feiler
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Division of Life Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joe W Gray
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Division of Life Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederic Waldman
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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41
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Han W, Han MR, Kang JJ, Bae JY, Lee JH, Bae YJ, Lee JE, Shin HJ, Hwang KT, Hwang SE, Kim SW, Noh DY. Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer. BMC Cancer 2006; 6:92. [PMID: 16608533 PMCID: PMC1459182 DOI: 10.1186/1471-2407-6-92] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 04/12/2006] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A considerable proportion of estrogen receptor (ER)-positive breast cancer recurs despite tamoxifen treatment, which is a serious problem commonly encountered in clinical practice. We tried to find novel prognostic markers in this subtype of breast cancer. METHODS We performed array comparative genomic hybridization (CGH) with 1,440 human bacterial artificial chromosome (BAC) clones to assess copy number changes in 28 fresh-frozen ER-positive breast cancer tissues. All of the patients included had received at least 1 year of tamoxifen treatment. Nine patients had distant recurrence within 5 years (Recurrence group) of diagnosis and 19 patients were alive without disease at least 5 years after diagnosis (Non-recurrence group). RESULTS Potential prognostic variables were comparable between the two groups. In an unsupervised clustering analysis, samples from each group were well separated. The most common regions of gain in all samples were 1q32.1, 17q23.3, 8q24.11, 17q12-q21.1, and 8p11.21, and the most common regions of loss were 6q14.1-q16.3, 11q21-q24.3, and 13q13.2-q14.3, as called by CGH-Explorer software. The average frequency of copy number changes was similar between the two groups. The most significant chromosomal alterations found more often in the Recurrence group using two different statistical methods were loss of 11p15.5-p15.4, 1p36.33, 11q13.1, and 11p11.2 (adjusted p values < 0.001). In subgroup analysis according to lymph node status, loss of 11p15 and 1p36 were found more often in Recurrence group with borderline significance within the lymph node positive patients (adjusted p = 0.052). CONCLUSION Our array CGH analysis with BAC clones could detect various genomic alterations in ER-positive breast cancers, and Recurrence group samples showed a significantly different pattern of DNA copy number changes than did Non-recurrence group samples.
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MESH Headings
- Adult
- Aged
- Antineoplastic Agents, Hormonal/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Breast Neoplasms/chemistry
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/radiotherapy
- Breast Neoplasms/surgery
- Carcinoma, Ductal, Breast/chemistry
- Carcinoma, Ductal, Breast/drug therapy
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/radiotherapy
- Carcinoma, Ductal, Breast/secondary
- Carcinoma, Ductal, Breast/surgery
- Chemotherapy, Adjuvant
- Chromosomes, Artificial, Bacterial
- Cluster Analysis
- Combined Modality Therapy
- Cyclophosphamide/administration & dosage
- DNA, Neoplasm/genetics
- Disease-Free Survival
- Estrogen Receptor Modulators/therapeutic use
- Estrogens
- Female
- Fluorouracil/administration & dosage
- Humans
- Life Tables
- Mastectomy
- Methotrexate/administration & dosage
- Middle Aged
- Neoplasm Metastasis
- Neoplasm Proteins/analysis
- Neoplasms, Hormone-Dependent/chemistry
- Neoplasms, Hormone-Dependent/drug therapy
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/radiotherapy
- Neoplasms, Hormone-Dependent/surgery
- Nucleic Acid Hybridization
- Oligonucleotide Array Sequence Analysis
- Prognosis
- Radiotherapy, Adjuvant
- Receptors, Estrogen/analysis
- Tamoxifen/therapeutic use
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Affiliation(s)
- Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Mi-Ryung Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | - Ji-Yeon Bae
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Jeong Eon Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk-Jae Shin
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Ki-Tae Hwang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Eun Hwang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Dong-Young Noh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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42
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Abstract
Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.
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Affiliation(s)
- Daniel Pinkel
- Comprehensive Cancer Center, Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA.
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43
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Baldocchi RA, Glynne RJ, Chin K, Kowbel D, Collins C, Mack DH, Gray JW. Design considerations for array CGH to oligonucleotide arrays. Cytometry A 2005; 67:129-36. [PMID: 16163695 DOI: 10.1002/cyto.a.20161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. METHODS In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. RESULTS In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. CONCLUSION Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.
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Affiliation(s)
- R A Baldocchi
- University of California at San Francisco Cancer Center, San Francisco, California, USA.
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44
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Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Bröcker EB, LeBoit PE, Pinkel D, Bastian BC. Distinct sets of genetic alterations in melanoma. N Engl J Med 2005; 353:2135-47. [PMID: 16291983 DOI: 10.1056/nejmoa050092] [Citation(s) in RCA: 1929] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Exposure to ultraviolet light is a major causative factor in melanoma, although the relationship between risk and exposure is complex. We hypothesized that the clinical heterogeneity is explained by genetically distinct types of melanoma with different susceptibility to ultraviolet light. METHODS We compared genome-wide alterations in the number of copies of DNA and mutational status of BRAF and N-RAS in 126 melanomas from four groups in which the degree of exposure to ultraviolet light differs: 30 melanomas from skin with chronic sun-induced damage and 40 melanomas from skin without such damage; 36 melanomas from palms, soles, and subungual (acral) sites; and 20 mucosal melanomas. RESULTS We found significant differences in the frequencies of regional changes in the number of copies of DNA and mutation frequencies in BRAF among the four groups of melanomas. Samples could be correctly classified into the four groups with 70 percent accuracy on the basis of the changes in the number of copies of genomic DNA. In two-way comparisons, melanomas arising on skin with signs of chronic sun-induced damage and skin without such signs could be correctly classified with 84 percent accuracy. Acral melanoma could be distinguished from mucosal melanoma with 89 percent accuracy. Eighty-one percent of melanomas on skin without chronic sun-induced damage had mutations in BRAF or N-RAS; the majority of melanomas in the other groups had mutations in neither gene. Melanomas with wild-type BRAF or N-RAS frequently had increases in the number of copies of the genes for cyclin-dependent kinase 4 (CDK4) and cyclin D1 (CCND1), downstream components of the RAS-BRAF pathway. CONCLUSIONS The genetic alterations identified in melanomas at different sites and with different levels of sun exposure indicate that there are distinct genetic pathways in the development of melanoma and implicate CDK4 and CCND1 as independent oncogenes in melanomas without mutations in BRAF or N-RAS.
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Affiliation(s)
- John A Curtin
- Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143-0808, USA
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45
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Gupta PB, Kuperwasser C, Brunet JP, Ramaswamy S, Kuo WL, Gray JW, Naber SP, Weinberg RA. The melanocyte differentiation program predisposes to metastasis after neoplastic transformation. Nat Genet 2005; 37:1047-54. [PMID: 16142232 PMCID: PMC1694635 DOI: 10.1038/ng1634] [Citation(s) in RCA: 339] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 07/12/2005] [Indexed: 11/09/2022]
Abstract
The aggressive clinical behavior of melanoma suggests that the developmental origins of melanocytes in the neural crest might be relevant to their metastatic propensity. Here we show that primary human melanocytes, transformed using a specific set of introduced genes, form melanomas that frequently metastasize to multiple secondary sites, whereas human fibroblasts and epithelial cells transformed using an identical set of genes generate primary tumors that rarely do so. Notably, these melanomas have a metastasis spectrum similar to that observed in humans with melanoma. These observations indicate that part of the metastatic proclivity of melanoma is attributable to lineage-specific factors expressed in melanocytes and not in other cell types analyzed. Analysis of microarray data from human nevi shows that the expression pattern of Slug, a master regulator of neural crest cell specification and migration, correlates with those of other genes that are important for neural crest cell migrations during development. Moreover, Slug is required for the metastasis of the transformed melanoma cells. These findings indicate that melanocyte-specific factors present before neoplastic transformation can have a pivotal role in governing melanoma progression.
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Affiliation(s)
- Piyush B Gupta
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
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46
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Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005; 21:3763-70. [PMID: 16081473 PMCID: PMC2819184 DOI: 10.1093/bioinformatics/bti611] [Citation(s) in RCA: 297] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Array Comparative Genomic Hybridization (CGH) can reveal chromosomal aberrations in the genomic DNA. These amplifications and deletions at the DNA level are important in the pathogenesis of cancer and other diseases. While a large number of approaches have been proposed for analyzing the large array CGH datasets, the relative merits of these methods in practice are not clear. RESULTS We compare 11 different algorithms for analyzing array CGH data. These include both segment detection methods and smoothing methods, based on diverse techniques such as mixture models, Hidden Markov Models, maximum likelihood, regression, wavelets and genetic algorithms. We compute the Receiver Operating Characteristic (ROC) curves using simulated data to quantify sensitivity and specificity for various levels of signal-to-noise ratio and different sizes of abnormalities. We also characterize their performance on chromosomal regions of interest in a real dataset obtained from patients with Glioblastoma Multiforme. While comparisons of this type are difficult due to possibly sub-optimal choice of parameters in the methods, they nevertheless reveal general characteristics that are helpful to the biological investigator.
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Affiliation(s)
- Weil R Lai
- Harvard-Partners Center for Genetics and Genomics 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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47
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Radisky DC, Levy DD, Littlepage LE, Liu H, Nelson CM, Fata JE, Leake D, Godden EL, Albertson DG, Nieto MA, Werb Z, Bissell MJ. Rac1b and reactive oxygen species mediate MMP-3-induced EMT and genomic instability. Nature 2005; 436:123-7. [PMID: 16001073 PMCID: PMC2784913 DOI: 10.1038/nature03688] [Citation(s) in RCA: 938] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/25/2005] [Indexed: 02/07/2023]
Abstract
The tumour microenvironment can be a potent carcinogen, not only by facilitating cancer progression and activating dormant cancer cells, but also by stimulating tumour formation. We have previously investigated stromelysin-1/matrix metalloproteinase-3 (MMP-3), a stromal enzyme upregulated in many breast tumours, and found that MMP-3 can cause epithelial-mesenchymal transition (EMT) and malignant transformation in cultured cells, and genomically unstable mammary carcinomas in transgenic mice. Here we explain the molecular pathways by which MMP-3 exerts these effects: exposure of mouse mammary epithelial cells to MMP-3 induces the expression of an alternatively spliced form of Rac1, which causes an increase in cellular reactive oxygen species (ROS). The ROS stimulate the expression of the transcription factor Snail and EMT, and cause oxidative damage to DNA and genomic instability. These findings identify a previously undescribed pathway in which a component of the breast tumour microenvironment alters cellular structure in culture and tissue structure in vivo, leading to malignant transformation.
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Affiliation(s)
- Derek C Radisky
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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48
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Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RCK, Albertson DG. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene 2005; 24:4232-42. [PMID: 15824737 DOI: 10.1038/sj.onc.1208601] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned <3 Mb. We found genes involved in integrin signaling (TLN1), survival (YAP1, BIRC2), and adhesion and migration (TLN1, LAMA3, MMP7), as well as members of the hedgehog (GLI2) and notch (JAG1, RBPSUH, FJX1) pathways to be amplified and overexpressed. Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development.
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Affiliation(s)
- Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, Box 0808, San Francisco, CA 94143-0808, USA
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49
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Morales C, Ribas M, Aiza G, Peinado MA. Genetic determinants of methotrexate responsiveness and resistance in colon cancer cells. Oncogene 2005; 24:6842-7. [PMID: 16007155 DOI: 10.1038/sj.onc.1208834] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative genetic pathways characterized by specific genetic profiles and exhibiting distinctive biological and clinical features have been proposed in colorectal carcinogenesis. Methotrexate (MTX) is a potent inhibitor of the dihydrofolate reductase (DHFR) enzyme, which is essential for DNA synthesis and cell growth. We have evaluated the association between different genetic features and the capacity to develop MTX resistance in colon cancer cell lines representative of alternative genetic pathways. Three aneuploid cell lines (HT-29, SW480, and SK-CO-1) showed pre-existing amplifications, but only one (HT-29) developed MTX resistance, showing amplification of the DHFR gene at 5q12-14 (>20-fold amplification and presence of extrachromosomal double minutes). Failure to develop resistance was attributed to the absence of two complete chromosomes 5 in SW480 and SK-CO-1 cells. Four near-diploid cell lines (LoVo, HCT116, DLD-1 and KM12C) and two aneuploid KM12C-derived metastases (KM12SM and KM12L4A) developed MTX resistance but none exhibited DHFR amplification. All resistant cells without DHFR gene amplification showed microsatellite instability. We conclude that chemoresistance capacity and the mechanism of chemoresistance are related with the genetic pathway and the karyotypic features of colon cancer cells.
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Affiliation(s)
- Cristina Morales
- IDIBELL-Institut de Recerca Oncològica, Granvia km 2,7, L'Hospitalet, 08907 Barcelona, Spain
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50
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Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005; 37 Suppl:S11-7. [PMID: 15920524 DOI: 10.1038/ng1569] [Citation(s) in RCA: 371] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alteration in DNA copy number is one of the many ways in which gene expression and function may be modified. Some variations are found among normal individuals, others occur in the course of normal processes in some species and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur before or shortly after fertilization, and DNA dosage-alteration changes occurring in somatic cells are frequent contributors to cancer. Detecting these aberrations and interpreting them in the context of broader knowledge facilitates the identification of crucial genes and pathways involved in biological processes and disease. Over the past several years, array comparative genomic hybridization has proven its value for analyzing DNA copy-number variations. Here, we discuss the state of the art of array comparative genomic hybridization and its applications in cancer, emphasizing general concepts rather than specific results.
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Affiliation(s)
- Daniel Pinkel
- Department of Laboratory Medicine and Comprehensive Cancer Center, University of California San Francisco, Box 0808, San Francisco, California 94143, USA.
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