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N. Kachouie N, Deebani W, Shutaywi M, Christiani DC. Lung cancer clustering by identification of similarities and discrepancies of DNA copy numbers using maximal information coefficient. PLoS One 2024; 19:e0301131. [PMID: 38739669 PMCID: PMC11090345 DOI: 10.1371/journal.pone.0301131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 05/16/2024] Open
Abstract
Lung cancer is the second most diagnosed cancer and the first cause of cancer related death for men and women in the United States. Early detection is essential as patient survival is not optimal and recurrence rate is high. Copy number (CN) changes in cancer populations have been broadly investigated to identify CN gains and deletions associated with the cancer. In this research, the similarities between cancer and paired peripheral blood samples are identified using maximal information coefficient (MIC) and the spatial locations with substantially high MIC scores in each chromosome are used for clustering analysis. The results showed that a sizable reduction of feature set can be obtained using only a subset of locations with high MIC values. The clustering performance was evaluated using both true rate and normalized mutual information (NMI). Clustering results using the reduced feature set outperformed the performance of clustering using entire feature set in several chromosomes that are highly associated with lung cancer with several identified oncogenes.
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Affiliation(s)
- Nezamoddin N. Kachouie
- Department of Mathematics and Systems Engineering, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Wejdan Deebani
- Mathematics Department, College of Science and Arts, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Meshal Shutaywi
- Mathematics Department, College of Science and Arts, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America
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2
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Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
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Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
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3
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Hong C, Thiele R, Feuerbach L. GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis. Bioinformatics 2022; 38:2036-2038. [PMID: 35099519 PMCID: PMC8963283 DOI: 10.1093/bioinformatics/btac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/21/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Analysis of focal copy number variations (CNVs) is highly relevant for cancer research, as they pinpoint driver genes. More specifically, due to selective pressure oncogenes and tumor suppressor genes are more often affected by these events than neighboring passengers. In cases where multiple candidates co-reside in a genomic locus, careful comparison is required to either identify multigenic minimally deleted regions of synergistic co-mutations, or the true single driver gene. The study of focal CNVs in large cancer genome cohorts requires specialized visualization and statistical analysis. RESULTS We developed the GenomeTornadoPlot R-package which generates gene-centric visualizations of CNV types, locations and lengths from cohortwise NGS data. Furthermore, the software enables the pairwise comparison of proximate genes to identify co-mutation patterns or driver-passenger hierarchies. The visual examination provided by GenomeTornadoPlot is further supported by adaptable local and global focality scoring. Integrated into the GenomeTornadoPlot R-Package is the comprehensive PCAWG database of CNVs, comprising 2976 cancer genome entities from 46 cohorts of the Pan-cancer Analysis of Whole Genomes project. The GenomeTornadoPlot R-package can be used to perform exploratory or hypothesis-driven analyses on the basis of the PCAWG data or in combination with data provided by the user. AVAILABILITY AND IMPLEMENTATION GenomeTornadoPlot is written in R script and released via github: <https://github.com/chenhong-dkfz/GenomeTornadoPlot/>. The package is under the license of GPL-3.0.
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Affiliation(s)
- Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Robin Thiele
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
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4
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Landa I, Pozdeyev N, Korch C, Marlow LA, Smallridge RC, Copland JA, Henderson YC, Lai SY, Clayman GL, Onoda N, Tan AC, Garcia-Rendueles MER, Knauf JA, Haugen BR, Fagin JA, Schweppe RE. Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies. Clin Cancer Res 2019; 25:3141-3151. [PMID: 30737244 DOI: 10.1158/1078-0432.ccr-18-2953] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/26/2018] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE Thyroid cancer cell lines are valuable models but have been neglected in pancancer genomic studies. Moreover, their misidentification has been a significant problem. We aim to provide a validated dataset for thyroid cancer researchers. EXPERIMENTAL DESIGN We performed next-generation sequencing (NGS) and analyzed the transcriptome of 60 authenticated thyroid cell lines and compared our findings with the known genomic defects in human thyroid cancers. RESULTS Unsupervised transcriptomic analysis showed that 94% of thyroid cell lines clustered distinctly from other lineages. Thyroid cancer cell line mutations recapitulate those found in primary tumors (e.g., BRAF, RAS, or gene fusions). Mutations in the TERT promoter (83%) and TP53 (71%) were highly prevalent. There were frequent alterations in PTEN, PIK3CA, and of members of the SWI/SNF chromatin remodeling complex, mismatch repair, cell-cycle checkpoint, and histone methyl- and acetyltransferase functional groups. Copy number alterations (CNA) were more prevalent in cell lines derived from advanced versus differentiated cancers, as reported in primary tumors, although the precise CNAs were only partially recapitulated. Transcriptomic analysis showed that all cell lines were profoundly dedifferentiated, regardless of their derivation, making them good models for advanced disease. However, they maintained the BRAFV600E versus RAS-dependent consequences on MAPK transcriptional output, which correlated with differential sensitivity to MEK inhibitors. Paired primary tumor-cell line samples showed high concordance of mutations. Complete loss of p53 function in TP53 heterozygous tumors was the most prominent event selected during in vitro immortalization. CONCLUSIONS This cell line resource will help inform future preclinical studies exploring tumor-specific dependencies.
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Affiliation(s)
- Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikita Pozdeyev
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Laura A Marlow
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Robert C Smallridge
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida.,Division of Endocrinology, Internal Medicine Department, Mayo Clinic, Jacksonville, Florida
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Naoyoshi Onoda
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Aik Choon Tan
- University of Colorado Cancer Center, Aurora, Colorado
| | | | - Jeffrey A Knauf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan R Haugen
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rebecca E Schweppe
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado. .,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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5
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Cheng Z, Cheng N, Shi D, Ren X, Gan T, Bai Y, Yang K. The Relationship between Nkx2.1 and DNA Oxidative Damage Repair in Nickel Smelting Workers: Jinchang Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16010120. [PMID: 30621196 PMCID: PMC6339211 DOI: 10.3390/ijerph16010120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 01/24/2023]
Abstract
Background: Occupational nickel exposure can cause DNA oxidative damage and influence DNA repair. However, the underlying mechanism of nickel-induced high-risk of lung cancer has not been fully understood. Our study aims to evaluate whether the nickel-induced oxidative damage and DNA repair were correlated with the alterations in Smad2 phosphorylation status and Nkx2.1 expression levels, which has been considered as the lung cancer initiation gene. Methods: 140 nickel smelters and 140 age-matched administrative officers were randomly stratified by service length from Jinchang Cohort. Canonical regression, χ2 test, Spearman correlation etc. were used to evaluate the association among service length, MDA, 8-OHdG, hOGG1, PARP, pSmad2, and Nkx2.1. Results: The concentrations of MDA, PARP, pSmad2, and Nkx2.1 significantly increased. Nkx2.1 (rs = 0.312, p < 0.001) and Smad2 phosphorylation levels (rs = 0.232, p = 0.006) were positively correlated with the employment length in nickel smelters, which was not observed in the administrative officer group. Also, elevation of Nkx2.1 expression was positively correlated with service length, 8-OHdG, PARP, hOGG1 and pSmad2 levels in nickel smelters. Conclusions: Occupational nickel exposure could increase the expression of Nkx2.1 and pSmad2, which correlated with the nickel-induced oxidative damage and DNA repair change.
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Affiliation(s)
- Zhiyuan Cheng
- Evidence-Based Medicine Centre, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
- School of Public Health, Department of Epidemiology and Statistics, Lanzhou University, Lanzhou 730000, China.
| | - Ning Cheng
- Centre of Medical Laboratory, School of Basic Medical Science, Lanzhou University, Lanzhou 730000, China.
| | - Dian Shi
- School of Public Health, Department of Epidemiology and Statistics, Lanzhou University, Lanzhou 730000, China.
| | - Xiaoyu Ren
- School of Public Health, Department of Epidemiology and Statistics, Lanzhou University, Lanzhou 730000, China.
| | - Ting Gan
- School of Public Health, Department of Epidemiology and Statistics, Lanzhou University, Lanzhou 730000, China.
| | - Yana Bai
- School of Public Health, Department of Epidemiology and Statistics, Lanzhou University, Lanzhou 730000, China.
| | - Kehu Yang
- Evidence-Based Medicine Centre, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
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6
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Chari R, Lockwood WW, Lam WL. Computational Methods for the Analysis of Array Comparative Genomic Hybridization. Cancer Inform 2017. [DOI: 10.1177/117693510600200007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
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Affiliation(s)
- Raj Chari
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - William W. Lockwood
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - Wan L. Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
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7
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Xu C, Wang W, Wu M, Zhu Y, Zhuang W, Lin G, Du K, Huang Y, Chen Y, Chen G, Fang M. Comparison of the c-MET gene amplification between primary tumor and metastatic lymph nodes in non-small cell lung cancer. Thorac Cancer 2017; 8:417-422. [PMID: 28590585 PMCID: PMC5582467 DOI: 10.1111/1759-7714.12455] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND c-MET has recently been identified as a promising novel target in non-small cell lung cancer (NSCLC). We detected the consistency of c-MET gene amplification in metastatic lymph nodes and tumor tissues of NSCLC patients and discuss the clinical application value of c-MET gene amplification in metastatic lymph nodes. METHODS Real-time fluorescent quantitative PCR was used to test tumor tissues in 368 NSCLC patients and 178 paired metastatic lymph node samples. The amplification consistency in metastatic lymph nodes and tissue samples were compared and the correlation between c-MET gene amplification and the clinical characteristics of patients was analyzed. RESULTS The c-MET gene amplification rate was 8.97% (33/368) in tumor tissues. Of the 178 paired cases, c-MET gene amplification was positive in 7.95% (15/178) of cancerous tissues and 18.54% (33/178) of metastatic lymph nodes. c-MET gene amplification was detected more frequently in metastatic lymph nodes than in primary cancerous tissue. When metastatic lymph nodes were used as surrogate samples of primary cancerous tissues, the sensitivity was 86.67% (13/15) and the specificity was 87.69% (143/163). CONCLUSIONS Screening for c-MET gene amplification in lymph node metastases could determine which patients are eligible for tyrosine kinase inhibitor therapy. Lymph node metastasis can predict c-MET gene amplification in a primary tumor and guide the clinical use of c-MET gene targeted drugs.
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Affiliation(s)
- Chun‐wei Xu
- Department of Pathology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Wen‐xian Wang
- Department of ChemotherapyZhejiang Cancer HospitalHangzhouChina
| | - Mei‐juan Wu
- Department of PathologyZhejiang Cancer HospitalHangzhouChina
| | - You‐cai Zhu
- Department of Thoracic Disease CenterZhejiang Rongjun HospitalJiaxingChina
| | - Wu Zhuang
- Department of Medical Thoracic Oncology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Gen Lin
- Department of Medical Thoracic Oncology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Kai‐qi Du
- Department of Thoracic Disease CenterZhejiang Rongjun HospitalJiaxingChina
| | - Yun‐jian Huang
- Department of Medical Thoracic Oncology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Yan‐ping Chen
- Department of Pathology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Gang Chen
- Department of Pathology, Fujian Provincial Cancer HospitalFujian Medical University Cancer HospitalFuzhouChina
| | - Mei‐yu Fang
- Department of Comprehensive Medical OncologyZhejiang Cancer HospitalHangzhouChina
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8
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Qiu ZW, Bi JH, Gazdar AF, Song K. Genome-wide copy number variation pattern analysis and a classification signature for non-small cell lung cancer. Genes Chromosomes Cancer 2017; 56:559-569. [PMID: 28379620 DOI: 10.1002/gcc.22460] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/25/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
The accurate classification of non-small cell lung carcinoma (NSCLC) into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is essential for both clinical practice and lung cancer research. Although the standard WHO diagnosis of NSCLC on biopsy material is rapid and economic, more than 13% of NSCLC tumors in the USA are not further classified. The purpose of this study was to analyze the genome-wide pattern differences in copy number variations (CNVs) and to develop a CNV signature as an adjunct test for the routine histopathologic classification of NSCLCs. We investigated the genome-wide CNV differences between these two tumor types using three independent patient datasets. Approximately half of the genes examined exhibited significant differences between LUAD and LUSC tumors and the corresponding non-malignant tissues. A new classifier was developed to identify signature genes out of 20 000 genes. Thirty-three genes were identified as a CNV signature of NSCLC. Using only their CNV values, the classification model separated the LUADs from the LUSCs with an accuracy of 0.88 and 0.84, respectively, in the training and validation datasets. The same signature also classified NSCLC tumors from their corresponding non-malignant samples with an accuracy of 0.96 and 0.98, respectively. We also compared the CNV patterns of NSCLC tumors with those of histologically similar tumors arising at other sites, such as the breast, head, and neck, and four additional tumors. Of greater importance, the significant differences between these tumors may offer the possibility of identifying the origin of tumors whose origin is unknown.
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Affiliation(s)
- Zhe-Wei Qiu
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Jia-Hao Bi
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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9
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Niwa O, Barcellos-Hoff MH, Globus RK, Harrison JD, Hendry JH, Jacob P, Martin MT, Seed TM, Shay JW, Story MD, Suzuki K, Yamashita S. ICRP Publication 131: Stem Cell Biology with Respect to Carcinogenesis Aspects of Radiological Protection. Ann ICRP 2016; 44:7-357. [PMID: 26637346 DOI: 10.1177/0146645315595585] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This report provides a review of stem cells/progenitor cells and their responses to ionising radiation in relation to issues relevant to stochastic effects of radiation that form a major part of the International Commission on Radiological Protection's system of radiological protection. Current information on stem cell characteristics, maintenance and renewal, evolution with age, location in stem cell 'niches', and radiosensitivity to acute and protracted exposures is presented in a series of substantial reviews as annexes concerning haematopoietic tissue, mammary gland, thyroid, digestive tract, lung, skin, and bone. This foundation of knowledge of stem cells is used in the main text of the report to provide a biological insight into issues such as the linear-no-threshold (LNT) model, cancer risk among tissues, dose-rate effects, and changes in the risk of radiation carcinogenesis by age at exposure and attained age. Knowledge of the biology and associated radiation biology of stem cells and progenitor cells is more developed in tissues that renew fairly rapidly, such as haematopoietic tissue, intestinal mucosa, and epidermis, although all the tissues considered here possess stem cell populations. Important features of stem cell maintenance, renewal, and response are the microenvironmental signals operating in the niche residence, for which a well-defined spatial location has been identified in some tissues. The identity of the target cell for carcinogenesis continues to point to the more primitive stem cell population that is mostly quiescent, and hence able to accumulate the protracted sequence of mutations necessary to result in malignancy. In addition, there is some potential for daughter progenitor cells to be target cells in particular cases, such as in haematopoietic tissue and in skin. Several biological processes could contribute to protecting stem cells from mutation accumulation: (a) accurate DNA repair; (b) rapidly induced death of injured stem cells; (c) retention of the DNA parental template strand during divisions in some tissue systems, so that mutations are passed to the daughter differentiating cells and not retained in the parental cell; and (d) stem cell competition, whereby undamaged stem cells outcompete damaged stem cells for residence in the niche. DNA repair mainly occurs within a few days of irradiation, while stem cell competition requires weeks or many months depending on the tissue type. The aforementioned processes may contribute to the differences in carcinogenic radiation risk values between tissues, and may help to explain why a rapidly replicating tissue such as small intestine is less prone to such risk. The processes also provide a mechanistic insight relevant to the LNT model, and the relative and absolute risk models. The radiobiological knowledge also provides a scientific insight into discussions of the dose and dose-rate effectiveness factor currently used in radiological protection guidelines. In addition, the biological information contributes potential reasons for the age-dependent sensitivity to radiation carcinogenesis, including the effects of in-utero exposure.
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10
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Sasaki H, Maekawa M, Tatematsu T, Okuda K, Moriyama S, Yano M, Fujii Y. Increased BRAF copy number in lung adenocarcinoma. Oncol Lett 2014; 9:709-712. [PMID: 25621040 PMCID: PMC4301492 DOI: 10.3892/ol.2014.2719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022] Open
Abstract
Point mutation of the BRAF gene is a genetic event that occurs in a subset of lung adenocarcinoma cases. For example, BRAF V600E is a driver mutation that can be effectively targeted using selective BRAF and/or MEK inhibitors. The present study hypothesized that an increase in BRAF copy number may be correlated with certain clinicopathological features of lung adenocarcinoma in Japanese patients. The BRAF gene copy number was analyzed using quantitative polymerase chain reaction amplifications in 29 surgically treated lung adenocarcinoma cases without EGFR or Kras mutations from Nagoya City University Hospital (Nagoya, Japan). Seven BRAF-mutant cases were included. Increased BRAF gene copy number was identified in three lung adenocarcinoma patients (10.3%), all of which exhibited the V600E mutation. Using fluorescence in situ hybridization with BRAF-specific and chromosome 7 centromeric probes, increased copy number status was associated with gene amplification or gain of chromosome 7. Although increased BRAF copy number was correlated with BRAF V600E mutations, numerical changes in BRAF copy number were rare and mild in lung adenocarcinoma, resulting in no significant difference in pathological tumor status or tumor stage.
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Affiliation(s)
- Hidefumi Sasaki
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | | | - Tsutomu Tatematsu
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Katsuhiro Okuda
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Satoru Moriyama
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Motoki Yano
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Yoshitaka Fujii
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
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11
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Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2698-2704. [DOI: 10.1016/j.bbamcr.2014.08.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/22/2022]
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12
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Wright CM, Yang IA, Bowman RV, Fong KM. The potential of genome-wide analyses to improve non-small-cell lung cancer care. Lung Cancer Manag 2014. [DOI: 10.2217/lmt.14.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Genomic technologies have revolutionized the way we study and understand cancer. The advent of next-generation sequencing technology in particular is now starting to change the clinical management of non-small-cell lung cancer. These technologies have helped us to refine prognostication and identify new driver mutations that can allow subselection of patients for therapeutic intervention. However, several limitations and challenges must be overcome before these technologies are widely accepted in diagnostic laboratories. It will be important for clinicians and diagnostic laboratories to consider sample type, analytical platform, cost, data security and ethics, and the bioinformatics challenges associated with 'big data', before widespread integration to the clinic. If these challenges can be overcome, then genomics has the potential to change clinical management of lung cancer.
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Affiliation(s)
- Casey M Wright
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
| | - Ian A Yang
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rayleen V Bowman
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Kwun M Fong
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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13
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Yang YL, Hung MS, Wang Y, Ni J, Mao JH, Hsieh D, Au A, Kumar A, Quigley D, Fang LT, Yeh CC, Xu Z, Jablons DM, You L. Lung tumourigenesis in a conditional Cul4A transgenic mouse model. J Pathol 2014; 233:113-23. [PMID: 24648314 DOI: 10.1002/path.4352] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/15/2014] [Accepted: 03/10/2014] [Indexed: 12/29/2022]
Abstract
Cullin4A (Cul4A) is a scaffold protein that assembles cullin-RING ubiquitin ligase (E3) complexes and regulates many cellular events, including cell survival, development, growth and cell cycle control. Our previous study suggested that Cul4A is oncogenic in vitro, but its oncogenic role in vivo has not been studied. Here, we used a Cul4A transgenic mouse model to study the potential oncogenic role of Cul4A in lung tumour development. After Cul4A over-expression was induced in the lungs for 32 weeks, atypical epithelial cells were observed. After 40 weeks, lung tumours were visible and were characterized as grade I or II adenocarcinomas. Immunohistochemistry (IHC) revealed decreased levels of Cul4A-associated proteins p21(CIP1) and tumour suppressor p19(ARF) in the lung tumours, suggesting that Cul4A regulated their expression in these tumours. Increased levels of p27(KIP1) and p16(INK4a) were also detected in these tumours. Moreover, the protein level of DNA replication licensing factor CDT1 was decreased. Genomic instability in the lung tumours was further analysed by the results from pericentrin protein expression and array comparative genomic hybridization analysis. Furthermore, knocking down Cul4A expression in lung cancer H2170 cells increased their sensitivity to the chemotherapy drug cisplatin in vitro, suggesting that Cul4A over-expression is associated with cisplatin resistance in the cancer cells. Our findings indicate that Cul4A is oncogenic in vivo, and this Cul4A mouse model is a tool in understanding the mechanisms of Cul4A in human cancers and for testing experimental therapies targeting Cul4A.
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Affiliation(s)
- Yi-Lin Yang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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14
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Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP. Microarray-based ultra-high resolution discovery of genomic deletion mutations. BMC Genomics 2014; 15:224. [PMID: 24655320 PMCID: PMC3998191 DOI: 10.1186/1471-2164-15-224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/28/2014] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nicholas P Harberd
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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15
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Caffarel MM, Coleman N. Oncostatin M receptor is a novel therapeutic target in cervical squamous cell carcinoma. J Pathol 2014; 232:386-90. [PMID: 24659184 PMCID: PMC4260121 DOI: 10.1002/path.4305] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/13/2013] [Accepted: 11/14/2013] [Indexed: 12/25/2022]
Abstract
Cervical carcinoma is the second most common cause of cancer deaths in women worldwide. Treatments have not changed for decades and survival rates for advanced disease remain low. An exciting new molecular target for the treatment of cervical squamous cell carcinoma (SCC), and possibly for SCCs at other anatomical sites, is the oncostatin M receptor (OSMR). This cell surface cytokine receptor is commonly copy number gained and overexpressed in advanced cervical SCC, changes that are associated with significantly worse clinical outcomes. OSMR overexpression in cervical SCC cells results in enhanced responsiveness to the major ligand oncostatin M (OSM), which induces several pro-malignant effects, including a pro-angiogenic phenotype and increased cell migration and invasiveness. OSMR is a strong candidate for antibody-mediated inhibition, a strategy that has had a major impact on haematological malignancies and various solid tumours such as HER2-positive breast cancers.
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16
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17
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Lung cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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18
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Chen MC, Chen CH, Wang JC, Tsai AC, Liou JP, Pan SL, Teng CM. The HDAC inhibitor, MPT0E028, enhances erlotinib-induced cell death in EGFR-TKI-resistant NSCLC cells. Cell Death Dis 2013; 4:e810. [PMID: 24052078 PMCID: PMC3789188 DOI: 10.1038/cddis.2013.330] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/28/2013] [Accepted: 07/31/2013] [Indexed: 12/19/2022]
Abstract
Epidermal growth factor receptor (EGFR), which promotes cell survival and division, is found at abnormally high levels on the surface of many cancer cell types, including many cases of non-small cell lung cancer. Erlotinib (Tarceva), an oral small-molecule tyrosine kinase inhibitor, is a so-called targeted drug that inhibits the tyrosine kinase domain of EGFR, and thus targets cancer cells with some specificity while doing less damage to normal cells. However, erlotinib resistance can occur, reducing the efficacy of this treatment. To develop more effective therapeutic interventions by overcoming this resistance problem, we combined the histone deacetylase inhibitor, MPT0E028, with erlotinib in an effort to increase their antitumor effects in erlotinib-resistant lung adenocarcinoma cells. This combined treatment yielded significant growth inhibition, induced the expression of apoptotic proteins (PARP, γH2AX, and caspase-3), increased the levels of acetylated histone H3, and showed synergistic effects in vitro and in vivo. These effects were independent of the mutation status of the genes encoding EGFR or K-Ras. MPT0E028 synergistically blocked key regulators of the EGFR/HER2 signaling pathways, attenuating multiple compensatory pathways (e.g., AKT, extracellular signal-regulated kinase, and c-MET). Our results indicate that this combination therapy might be a promising strategy for facilitating the effects of erlotinib monotherapy by activating various networks. Taken together, our data provide compelling evidence that MPT0E028 has the potential to improve the treatment of heterogeneous and drug-resistant tumors that cannot be controlled with single-target agents.
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Affiliation(s)
- M-C Chen
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - C-H Chen
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - J-C Wang
- The PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - A-C Tsai
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - J-P Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - S-L Pan
- The PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - C-M Teng
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei, Taiwan
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19
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Mu D. The complexity of thyroid transcription factor 1 with both pro- and anti-oncogenic activities. J Biol Chem 2013; 288:24992-25000. [PMID: 23818522 PMCID: PMC3757165 DOI: 10.1074/jbc.r113.491647] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
After the original identification of thyroid transcription factor 1 (TTF-1 or NKX2-1) biochemical activity as a transcriptional regulator of thyroglobulin in 1989, the bulk of the ensuing research has concentrated on elucidating the roles of NKX2-1 in the development of lung and thyroid tissues. Motivated by its specific expression pattern, pathologists adopted the NKX2-1 immunoreactivity to distinguish pulmonary from nonpulmonary nonthyroid adenocarcinomas. Interestingly, the concept of NKX2-1 as an active participant in lung tumorigenesis did not take hold until 2007. This minireview contrasts the recent advancements of NKX2-1-related observations primarily in the realm of pulmonary malignancies.
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Affiliation(s)
- David Mu
- From the Leroy T. Canoles Jr. Cancer Research Center and the Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501.
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20
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Genetic alterations defining NSCLC subtypes and their therapeutic implications. Lung Cancer 2013; 82:179-89. [PMID: 24011633 DOI: 10.1016/j.lungcan.2013.07.025] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/20/2013] [Accepted: 07/29/2013] [Indexed: 01/03/2023]
Abstract
Lung cancer is the leading cause of cancer death worldwide, accounting for more deaths than breast, prostate and colon cancer combined. While treatment decisions are determined primarily by stage, therapeutically non small cell lung cancer (NSCLC) has traditionally been treated as a single disease. However, recent findings have led to the recognition of histology and molecular subtypes as important determinants in treatment selection. Identifying the genetic differences that define these molecular and histological subtypes has the potential to impact treatment and as such is currently the focus of much research. Microarray and genomic sequencing efforts have provided unparalleled insight into the genomes of lung cancer subtypes, specifically adenocarcinoma (AC) and squamous cell carcinoma (SqCC), revealing subtype specific genomic alterations and molecular subtypes as well as differences in cell signaling pathways. In this review, we discuss the recurrent genomic alterations characteristic of AC and SqCC (including molecular subtypes), their therapeutic implications and emerging clinical practices aimed at tailoring treatments based on a tumor's molecular alterations with the hope of improving patient response and survival.
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Abstract
INTRODUCTION Phospatidylinositol-3-kinases (PI3K) play an important role in various cell processes. Oncogenic mutations in the PIK3CA gene, which codes for the catalytic subunit, have been identified in various malignancies and activate the PI3K/AKT/mTOR pathway, which is a critical driver of tumorigenesis. METHODS We tested 41 tumor samples with known KRAS, BRAF, and EGFR mutation status for the occurrence of mutations in the PIK3CA gene, using a pyrosequencing assay. RESULTS Pyrosequencing revealed 2 mutations (4.9%) in the PIK3CA gene, one in exon 9 and the other in exon 20. Both mutations have not been identified yet in lung tumor tissue. DISCUSSION The screening of our small patient cohort by pyrosequencing identified 2 mutations (4.9%) in PIK3CA, one in exon 9 (Q546H) and the other in exon 20 (M1043T). Both mutations have not been described in lung tumors yet and seem to be rather uncommon mutations. Future screening of large patient cohorts with pyrosequencing may contribute to the detection of more mutations in lung cancer because of the low limit of detections of this method and may contribute to a better understanding of the interaction of mutations and tumorigenesis.
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The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. Neoplasia 2013; 14:1075-86. [PMID: 23226101 DOI: 10.1593/neo.121380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/25/2012] [Accepted: 09/28/2012] [Indexed: 12/16/2022] Open
Abstract
Lung cancer causes more deaths, worldwide, than any other cancer. Several histologic subtypes exist. Currently, there is a dearth of targeted therapies for treating one of the main subtypes: squamous cell carcinoma (SCC). As for many cancers, lung SCC karyotypes are often highly anomalous owing to large somatic structural variants, some of which are seen repeatedly in lung SCC, indicating a potential causal association for genes therein. We chose to characterize a lung SCC genome to unprecedented detail and integrate our findings with the concurrently characterized transcriptome. We aimed to ascertain how somatic structural changes affected gene expression within the cell in ways that could confer a pathogenic phenotype. We sequenced the genomes of a lung SCC cell line (LUDLU-1) and its matched lymphocyte cell line (AGLCL) to more than 50x coverage. We also sequenced the transcriptomes of LUDLU-1 and a normal bronchial epithelium cell line (LIMM-NBE1), resulting in more than 600 million aligned reads per sample, including both coding and non-coding RNA (ncRNA), in a strand-directional manner. We also captured small RNA (<30 bp). We discovered significant, but weak, correlations between copy number and expression for protein-coding genes, antisense transcripts, long intergenic ncRNA, and microRNA (miRNA). We found that miRNA undergo the largest change in overall expression pattern between the normal bronchial epithelium and the tumor cell line. We found evidence of transcription across the novel genomic sequence created from six somatic structural variants. For each part of our integrated analysis, we highlight candidate genes that have undergone the largest expression changes.
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Gevaert O, De Moor B. Prediction of cancer outcome using DNA microarray technology: past, present and future. ACTA ACUST UNITED AC 2013; 3:157-65. [PMID: 23485162 DOI: 10.1517/17530050802680172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The use of DNA microarray technology to predict cancer outcome already has a history of almost a decade. Although many breakthroughs have been made, the promise of individualized therapy is still not fulfilled. In addition, new technologies are emerging that also show promise in outcome prediction of cancer patients. OBJECTIVE The impact of DNA microarray and other 'omics' technologies on the outcome prediction of cancer patients was investigated. Whether integration of omics data results in better predictions was also examined. METHODS DNA microarray technology was focused on as a starting point because this technology is considered to be the most mature technology from all omics technologies. Next, emerging technologies that may accomplish the same goals but have been less extensively studied are described. CONCLUSION Besides DNA microarray technology, other omics technologies have shown promise in predicting the cancer outcome or have potential to replace microarray technology in the near future. Moreover, it is shown that integration of multiple omics data can result in better predictions of cancer outcome; but, owing to the lack of comprehensive studies, validation studies are required to verify which omics has the most information and whether a combination of multiple omics data improves predictive performance.
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Affiliation(s)
- Olivier Gevaert
- Katholieke Universiteit Leuven, Department of Electrical Engineering ESAT-SCD-Sista, Kasteelpark Arenberg 10, 3001 Leuven, Belgium +32 16 328646 ; +32 16 32 ;
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24
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Banerjee D. Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. Methods Mol Biol 2013; 973:1-13. [PMID: 23412780 DOI: 10.1007/978-1-62703-281-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and correspondingly the size of the datasets generated has grown exponentially such that computational methods required to handle massive datasets have had to be devised. This chapter provides a brief synopsis of the evolution of such techniques as an introduction to the subsequent chapters that provide methods and applications, relevant to research, and clinical diagnostics.
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Affiliation(s)
- Diponkar Banerjee
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, BC, Canada.
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25
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Abstract
This chapter summarizes the current knowledge on gene copy number changes found in lung tumors, and their application in the diagnosis, prognostication, and prediction of response to chemotherapy. Examples of the identification of specific "driver" oncogenes within amplified DNA segments are described. A model of how array-CGH could be integrated clinically into the routine workup of lung cancers in clinical laboratory is proposed.
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Affiliation(s)
- Kenneth J Craddock
- Department of Pathology, Toronto General Hospital University Health Network, Toronto, ON, Canada.
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26
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Abstract
Identifying specific somatic mutations that drive tumor growth has transformed the treatment of lung cancer. For example, cancers with sensitizing epidermal growth factor receptor mutations and echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase translocations can have remarkable responses to epidermal growth factor receptor and ALK inhibitors respectively, leading to significant clinical benefit. However, effective molecularly targeted therapies have disproportionately impacted adenocarcinomas compared to squamous cell carcinomas, and never or light smokers compared to heavy smokers. Further progress in non-small-cell lung cancer will require the identification and effective targeting of molecular alterations in all subtypes of lung cancer. Here, we review the current knowledge about the molecular alterations found in squamous cell carcinoma of the lung. First, we will discuss the ongoing efforts to comprehensively assess the squamous cell carcinoma genome. We will then discuss the evidence supporting the role of specific genes in driving squamous cell carcinomas. By describing the landscape of somatic targets in squamous cell lung cancer, we hope to crystallize the current understanding of potential targets, spur development of therapies that can have clinical impact, and underscore the importance of new discoveries in this field.
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27
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Genetic and biochemical alterations in non-small cell lung cancer. Biochem Res Int 2012; 2012:940405. [PMID: 22928112 PMCID: PMC3426175 DOI: 10.1155/2012/940405] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/09/2012] [Indexed: 11/17/2022] Open
Abstract
Despite significant advances in the detection and treatment of lung cancer, it causes the highest number of cancer-related mortality. Recent advances in the detection of genetic alterations in patient samples along with physiologically relevant animal models has yielded a new understanding of the molecular etiology of lung cancer. This has facilitated the development of potent and specific targeted therapies, based on the genetic and biochemical alterations present in the tumor, especially non-small-cell lung cancer (NSCLC). It is now clear that heterogeneous cell signaling pathways are disrupted to promote NSCLC, including mutations in critical growth regulatory proteins (K-Ras, EGFR, B-RAF, MEK-1, HER2, MET, EML-4-ALK, KIF5B-RET, and NKX2.1) and inactivation of growth inhibitory pathways (TP53, PTEN, p16, and LKB-1). How these pathways differ between smokers and non-smokers is also important for clinical treatment strategies and development of targeted therapies. This paper describes these molecular targets in NSCLC, and describes the biological significance of each mutation and their potential to act as a therapeutic target.
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28
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Smida M, Nijman SMB. Functional drug-gene interactions in lung cancer. Expert Rev Mol Diagn 2012; 12:291-302. [PMID: 22468819 DOI: 10.1586/erm.12.16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the dawn of the genomic information era, the challenges of cancer treatment remain formidable. Particularly for the most prevalent cancer types, including lung cancer, successful treatment of metastatic disease is rare and escalating costs for modern targeted drugs place an increasing strain on healthcare systems. Although powerful diagnostic tools to characterize individual tumor samples in great molecular detail are becoming rapidly available, the transformation of this information into therapy provides a major challenge. A fundamental difficulty is the molecular complexity of cancer cells that often causes drug resistance, but can also render tumors exquisitely sensitive to targeted agents. By using lung cancer as an example, we outline the principles that govern drug sensitivity and resistance from a genetic perspective and discuss how in vitro chemical-genetic screens can impact on patient stratification in the clinic.
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Affiliation(s)
- Michal Smida
- CeMM Research Center for Molecular Medicine of Austrian Academy of Sciences, Vienna, Austria
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29
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Scrima M, De Marco C, Fabiani F, Franco R, Pirozzi G, Rocco G, Ravo M, Weisz A, Zoppoli P, Ceccarelli M, Botti G, Malanga D, Viglietto G. Signaling networks associated with AKT activation in non-small cell lung cancer (NSCLC): new insights on the role of phosphatydil-inositol-3 kinase. PLoS One 2012; 7:e30427. [PMID: 22363436 PMCID: PMC3281846 DOI: 10.1371/journal.pone.0030427] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/16/2011] [Indexed: 11/19/2022] Open
Abstract
Aberrant activation of PI3K/AKT signalling represents one of the most common molecular alterations in lung cancer, though the relative contribution of the single components of the cascade to the NSCLC development is still poorly defined. In this manuscript we have investigated the relationship between expression and genetic alterations of the components of the PI3K/AKT pathway [KRAS, the catalytic subunit of PI3K (p110α), PTEN, AKT1 and AKT2] and the activation of AKT in 107 surgically resected NSCLCs and have analyzed the existing relationships with clinico-pathologic features. Expression analysis was performed by immunohistochemistry on Tissue Micro Arrays (TMA); mutation analysis was performed by DNA sequencing; copy number variation was determined by FISH. We report that activation of PI3K/AKT pathway in Italian NSCLC patients is associated with high grade (G3–G4 compared with G1–G2; n = 83; p<0.05) and more advanced disease (TNM stage III vs. stages I and II; n = 26; p<0.05). In addition, we found that PTEN loss (41/104, 39%) and the overexpression of p110α (27/92, 29%) represent the most frequent aberration observed in NSCLCs. Less frequent molecular lesions comprised the overexpression of AKT2 (18/83, 22%) or AKT1 (17/96, 18%), and KRAS mutation (7/63, 11%). Our results indicate that, among all genes, only p110α overexpression was significantly associated to AKT activation in NSCLCs (p = 0.02). Manipulation of p110α expression in lung cancer cells carrying an active PI3K allele (NCI-H460) efficiently reduced proliferation of NSCLC cells in vitro and tumour growth in vivo. Finally, RNA profiling of lung epithelial cells (BEAS-2B) expressing a mutant allele of PIK3 (E545K) identified a network of transcription factors such as MYC, FOS and HMGA1, not previously recognised to be associated with aberrant PI3K signalling in lung cancer.
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Affiliation(s)
- Marianna Scrima
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
| | - Carmela De Marco
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
- Department of Experimental and Clinical Medicine, University Magna Graecia Catanzaro, Italy
| | - Fernanda Fabiani
- Department of Experimental and Clinical Medicine, University Magna Graecia Catanzaro, Italy
| | - Renato Franco
- Fondazione “G Pascale”, National Cancer Institute, Naples, Italy
| | - Giuseppe Pirozzi
- Fondazione “G Pascale”, National Cancer Institute, Naples, Italy
| | - Gaetano Rocco
- Fondazione “G Pascale”, National Cancer Institute, Naples, Italy
| | - Maria Ravo
- Molecular Medicine Laboratory, Faculty of Medicine and Surgery, University of Salerno, Baronissi, Italy
| | - Alessandro Weisz
- Molecular Medicine Laboratory, Faculty of Medicine and Surgery, University of Salerno, Baronissi, Italy
| | - Pietro Zoppoli
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
- Department of Biological and Environmental Studies, University of Sannio, Benevento, Italy
| | - Michele Ceccarelli
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
- Department of Biological and Environmental Studies, University of Sannio, Benevento, Italy
| | - Gerardo Botti
- Fondazione “G Pascale”, National Cancer Institute, Naples, Italy
| | - Donatella Malanga
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
- Department of Experimental and Clinical Medicine, University Magna Graecia Catanzaro, Italy
| | - Giuseppe Viglietto
- Biogem scarl, Institute for Genetic Research “Gaetano Salvatore”, Ariano Irpino (Avellino), Italy
- Department of Experimental and Clinical Medicine, University Magna Graecia Catanzaro, Italy
- * E-mail:
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Han C, Ma J, Zhao J, Zhou Y, Jing W, Zou H. EGFR mutations, gene amplification, and protein expression and KRAS mutations in primary and metastatic tumors of nonsmall cell lung cancers and their clinical implications: a meta-analysis. Cancer Invest 2012; 29:626-34. [PMID: 22011285 DOI: 10.3109/07357907.2011.621914] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A meta-analysis was performed to determine EGFR mutations, gene amplification, and protein expression and KRAS mutations in primary and metastatic nonsmall cell lung cancer (NSCLC). We found that KRAS gene mutation frequencies were higher in primary than in metastatic tumors. There was no significant difference in EGFR mutation frequency between the primary and metastatic tumors. These results suggest that KRAS mutations in primary NSCLC foci may be a more accurate biomarker than in metastases to reflect KRAS mutation status. Combined detection of EGFR and KRAS mutations in primary NSCLC foci appears to be an optimal approach for first-line EGFR-TKI therapy.
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Affiliation(s)
- Chengbo Han
- Department of Oncology, Shengjing Hospital of China Medical University, China
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Baladandayuthapani V, Ji Y, Talluri R, Nieto-Barajas LE, Morris JS. Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data. J Am Stat Assoc 2012; 105:1358-1375. [PMID: 21512611 DOI: 10.1198/jasa.2010.ap09250] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Array-based comparative genomic hybridization (aCGH) is a high-resolution high-throughput technique for studying the genetic basis of cancer. The resulting data consists of log fluorescence ratios as a function of the genomic DNA location and provides a cytogenetic representation of the relative DNA copy number variation. Analysis of such data typically involves estimation of the underlying copy number state at each location and segmenting regions of DNA with similar copy number states. Most current methods proceed by modeling a single sample/array at a time, and thus fail to borrow strength across multiple samples to infer shared regions of copy number aberrations. We propose a hierarchical Bayesian random segmentation approach for modeling aCGH data that utilizes information across arrays from a common population to yield segments of shared copy number changes. These changes characterize the underlying population and allow us to compare different population aCGH profiles to assess which regions of the genome have differential alterations. Our method, referred to as BDSAcgh (Bayesian Detection of Shared Aberrations in aCGH), is based on a unified Bayesian hierarchical model that allows us to obtain probabilities of alteration states as well as probabilities of differential alteration that correspond to local false discovery rates. We evaluate the operating characteristics of our method via simulations and an application using a lung cancer aCGH data set.
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Abstract
Lung cancer is a heterogeneous disease clinically, biologically, histologically, and molecularly. Understanding the molecular causes of this heterogeneity, which might reflect changes occurring in different classes of epithelial cells or different molecular changes occurring in the same target lung epithelial cells, is the focus of current research. Identifying the genes and pathways involved, determining how they relate to the biological behavior of lung cancer, and their utility as diagnostic and therapeutic targets are important basic and translational research issues. This article reviews current information on the key molecular steps in lung cancer pathogenesis, their timing, and clinical implications.
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Affiliation(s)
- Jill E Larsen
- Hamon Center for Therapeutic Oncology Research, Simmons Cancer Center, 6000 Harry Hines Boulevard, University of Texas Southwestern Medical Center, Dallas, TX 75390-8593, USA
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Martinez VD, Vucic EA, Adonis M, Gil L, Lam WL. Arsenic biotransformation as a cancer promoting factor by inducing DNA damage and disruption of repair mechanisms. Mol Biol Int 2011. [PMID: 22091411 DOI: 10.4061/2011/718974]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chronic exposure to arsenic in drinking water poses a major global health concern. Populations exposed to high concentrations of arsenic-contaminated drinking water suffer serious health consequences, including alarming cancer incidence and death rates. Arsenic is biotransformed through sequential addition of methyl groups, acquired from s-adenosylmethionine (SAM). Metabolism of arsenic generates a variety of genotoxic and cytotoxic species, damaging DNA directly and indirectly, through the generation of reactive oxidative species and induction of DNA adducts, strand breaks and cross links, and inhibition of the DNA repair process itself. Since SAM is the methyl group donor used by DNA methyltransferases to maintain normal epigenetic patterns in all human cells, arsenic is also postulated to affect maintenance of normal DNA methylation patterns, chromatin structure, and genomic stability. The biological processes underlying the cancer promoting factors of arsenic metabolism, related to DNA damage and repair, will be discussed here.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
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Larsen JE, Cascone T, Gerber DE, Heymach JV, Minna JD. Targeted therapies for lung cancer: clinical experience and novel agents. Cancer J 2011; 17:512-27. [PMID: 22157296 PMCID: PMC3381956 DOI: 10.1097/ppo.0b013e31823e701a] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although lung cancer remains the leading cancer killer in the United States, recently a number of developments indicate future clinical benefit. These include evidence that computed tomography-based screening decreases lung cancer mortality, the use of stereotactic radiation for early-stage tumors, the development of molecular methods to predict chemotherapy sensitivity, and genome-wide expression and mutation analysis data that have uncovered oncogene "addictions" as important therapeutic targets. Perhaps the most significant advance in the treatment of this challenging disease is the introduction of molecularly targeted therapies, a term that currently includes monoclonal antibodies and small-molecule tyrosine kinase inhibitors. The development of effective targeted therapeutics requires knowledge of the genes and pathways involved and how they relate to the biologic behavior of lung cancer. Drugs targeting the epidermal growth factor receptor, anaplastic lymphoma kinase, and vascular endothelial growth factor are now U.S. Food and Drug Administration approved for the treatment of advanced non-small cell lung cancer. These agents are generally better tolerated than conventional chemotherapy and show dramatic efficacy when their use is coupled with a clear understanding of clinical data, mechanism, patient selection, drug interactions, and toxicities. Integrating genome-wide tumor analysis with drug- and targeted agent-responsive phenotypes will provide a wealth of new possibilities for lung cancer-targeted therapeutics. Ongoing research efforts in these areas as well as a discussion of emerging targeted agents being evaluated in clinical trials are the subjects of this review.
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Affiliation(s)
- Jill E. Larsen
- Hamon Center for Therapeutic Oncology Research, Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas
| | - Tina Cascone
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - David E. Gerber
- Department of Internal Medicine, Division of Hematology-Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - John V. Heymach
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas
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EGFR and KRAS mutations and altered c-Met gene copy numbers in primary non-small cell lung cancer and associated stage N2 lymph node-metastasis. Cancer Lett 2011; 314:63-72. [PMID: 21982684 DOI: 10.1016/j.canlet.2011.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/10/2011] [Accepted: 09/13/2011] [Indexed: 11/21/2022]
Abstract
This study aimed to detect mutations in EGFR and KRAS and alterations of c-Met gene copy number (GCN) changes in primary and lymph node-metastatic NSCLCs. The data showed the concordant rate of EGFR genotype in primary and stage N2 lymph node-metastatic tumors was 95.45%. c-Met GCN in stage N2 lymph nodes was significantly higher than that of the primary tumors (P=0.038). The results suggest both primary and lymph-node metastases have relatively consistent EGFR mutations and EGFR mutations are not relevant to changes in c-Met GCN. c-Met GCN was increased significantly in EGFR TKI-naive patients with lymph node-metastatic tumors.
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Thu KL, Pikor LA, Chari R, Wilson IM, Macaulay CE, English JC, Tsao MS, Gazdar AF, Lam S, Lam WL, Lockwood WW. Genetic disruption of KEAP1/CUL3 E3 ubiquitin ligase complex components is a key mechanism of NF-kappaB pathway activation in lung cancer. J Thorac Oncol 2011; 6:1521-9. [PMID: 21795997 PMCID: PMC3164321 DOI: 10.1097/jto.0b013e3182289479] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta (IKBKB) (IKK-β/IKK-2), which activates NF-κB, is a substrate of the KEAP1-CUL3-RBX1 E3-ubiquitin ligase complex, implicating this complex in NF-κB pathway regulation. We investigated complex component gene disruption as a novel genetic mechanism of NF-κB activation in non-small cell lung cancer. METHODS A total of 644 tumor- and 90 cell-line genomes were analyzed for gene dosage status of the individual complex components and IKBKB. Gene expression of these genes and NF-κB target genes were analyzed in 48 tumors. IKBKB protein levels were assessed in tumors with and without complex or IKBKB genetic disruption. Complex component knockdown was performed to assess effects of the E3-ligase complex on IKBKB and NF-κB levels, and phenotypic importance of IKBKB expression was measured by pharmacological inhibition. RESULTS We observed strikingly frequent genetic disruption (42%) and aberrant expression (63%) of the E3-ligase complex and IKBKB in the samples examined. Although both adenocarcinomas and squamous cell carcinomas showed complex disruption, the patterns of gene disruption differed. IKBKB levels were elevated with complex disruption, knockdown of complex components increased activated forms of IKBKB and NF-κB proteins, and IKBKB inhibition detriments cell viability, highlighting the biological significance of complex disruption. NF-κB target genes were overexpressed in samples with complex disruption, further demonstrating the effect of complex disruption on NF-κB activity. CONCLUSIONS Gene dosage alteration is a prominent mechanism that disrupts each component of the KEAP1-CUL3-RBX1 complex and its NF-κB stimulating substrate, IKBKB. Herein, we show that, multiple component disruption of this complex represents a novel mechanism of NF-κB activation in non-small cell lung cancer.
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Affiliation(s)
- Kelsie L Thu
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada.
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Martinez VD, Vucic EA, Adonis M, Gil L, Lam WL. Arsenic biotransformation as a cancer promoting factor by inducing DNA damage and disruption of repair mechanisms. Mol Biol Int 2011; 2011:718974. [PMID: 22091411 PMCID: PMC3200225 DOI: 10.4061/2011/718974] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/06/2011] [Indexed: 11/20/2022] Open
Abstract
Chronic exposure to arsenic in drinking water poses a major global health concern. Populations exposed to high concentrations of arsenic-contaminated drinking water suffer serious health consequences, including alarming cancer incidence and death rates. Arsenic is biotransformed through sequential addition of methyl groups, acquired from s-adenosylmethionine (SAM). Metabolism of arsenic generates a variety of genotoxic and cytotoxic species, damaging DNA directly and indirectly, through the generation of reactive oxidative species and induction of DNA adducts, strand breaks and cross links, and inhibition of the DNA repair process itself. Since SAM is the methyl group donor used by DNA methyltransferases to maintain normal epigenetic patterns in all human cells, arsenic is also postulated to affect maintenance of normal DNA methylation patterns, chromatin structure, and genomic stability. The biological processes underlying the cancer promoting factors of arsenic metabolism, related to DNA damage and repair, will be discussed here.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
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Koç E, Caner V, Büyükpınarbaşılı N, Tepeli E, Türk NS, Ozan Çetin G, Bağcı G. The determination of relationship between "excision repair cross-complementing group 1" (ERCC1) gene T19007C and C8092A single nucleotide polymorphisms and clinicopathological parameters in non-small cell lung cancer. Mol Biol Rep 2011; 39:375-80. [PMID: 21553053 DOI: 10.1007/s11033-011-0748-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 04/27/2011] [Indexed: 12/11/2022]
Abstract
DNA repair plays a key role in prevention of carcinogenesis and one of the most important DNA repair mechanisms is nucleotide excision repair (NER) pathway. This pathway includes a number of genes such as excision repair cross-complementing group 1 (ERCC1) gene which are responsible for the 5' incision of damaged DNA. A reduced DNA repair capacity associated with ERCC1 mRNA level has been observed in lung carcinogenesis. Two single nucleotide polymorphisms (SNPs) in ERCC1 gene, T19007C (rs11615) and C8092A (rs3212986), reportedly predict to affect the mRNA of ERCC1 in non-small cell lung cancer (NSCLC). To examine the role of two common SNPs in ERCC1 gene further, we conducted this study where 80 cases histopatologically diagnosed as NSCLC were genotyped. Genomic DNA was extracted from formalin-fixed, paraffin embedded tissues and two SNPs were analyzed using real-time PCR. The distributions of TT, TC, and CC genotypes of the T19007C SNP were 40, 44 and 16%, respectively. Significantly increased frequency of the patients carrying at least one 19007C allele was observed in early stage compared to advanced stage (P=0.002). And also, the frequency of TC and CC genotypes significantly increased in younger patients compared to older patients (P=0.035). Regarding C8092A SNP, the distribution of CC, CA, and AA genotypes was 38, 51 and 11%, respectively. There was no significant difference in the genotype distribution between C8092A SNP and clinicopathological parameters. This study indicated that harboring at least one 19007C allele may have protective effect in NSCLC.
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Affiliation(s)
- Esin Koç
- Department of Medical Biology, Pamukkale University, School of Medicine, Morfoloji Binasi Kat: 3, 20070, Kinikli, Denizli, Turkey.
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Broët P, Dalmasso C, Tan EH, Alifano M, Zhang S, Wu J, Lee MH, Régnard JF, Lim D, Koong HN, Agasthian T, Miller LD, Lim E, Camilleri-Broët S, Tan P. Genomic profiles specific to patient ethnicity in lung adenocarcinoma. Clin Cancer Res 2011; 17:3542-50. [PMID: 21521776 DOI: 10.1158/1078-0432.ccr-10-2185] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE East-Asian (EA) patients with non-small-cell lung cancer (NSCLC) are associated with a high proportion of nonsmoking women, epidermal growth factor receptor (EGFR)-activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We sought to identify novel molecular differences between NSCLCs from EA and Western European (WE) patients. EXPERIMENTAL DESIGN A total of 226 lung adenocarcinoma samples from EA (n = 90) and WE (n = 136) patients were analyzed for copy number aberrations (CNA) by using a common high-resolution SNP (single nucleotide polymorphism) microarray platform. Univariate and multivariate analyses were carried out to identify CNAs specifically related to smoking history, EGFR mutation status, and ethnicity. RESULTS The overall genomic profiles of adenocarcinomas from EA and WE patients were highly similar. Univariate analyses revealed several CNAs significantly associated with ethnicity, EGFR mutation, and smoking, but not to gender, and KRAS or p53 mutations. A multivariate model identified four ethnic-specific recurrent CNAs-significantly higher rates of copy number gain were observed on 16p13.13 and 16p13.11 in EA tumors, whereas higher rates of genomic loss on 19p13.3 and 19p13.11 were observed in tumors from WE patients. We identified several potential driver genes in these regions, showing a positive correlation between cis-localized copy number changes and transcriptomic changes. CONCLUSION 16p copy number gains (EA) and 19p losses (WE) are ethnic-specific chromosomal aberrations in lung adenocarcinoma. Patient ethnicity should be considered when evaluating future NSCLC therapies targeting genes located on these areas.
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Newnham GM, Conron M, McLachlan S, Dobrovic A, Do H, Li J, Opeskin K, Thompson N, Wright GM, Thomas DM. Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer. BMC Cancer 2011; 11:93. [PMID: 21385341 PMCID: PMC3058106 DOI: 10.1186/1471-2407-11-93] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 03/07/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The aim of this study was to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies. METHODS Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest. RESULTS Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; KRAS mutation; TP53 mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in TP53 in adenocarcinoma. A prognostic signature for disease recurrence, reflecting KRAS pathway activation, was validated in an independent test set. CONCLUSIONS These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease.
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Affiliation(s)
- Genni M Newnham
- Department of Oncology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Matthew Conron
- Department of Respiratory Medicine, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - SueAnne McLachlan
- Department of Oncology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Alexander Dobrovic
- Department of Pathology, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
- Department of Pathology, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Hongdo Do
- Department of Pathology, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
- Department of Pathology, The University of Melbourne, (Tin Alley), Melbourne, (3010), Australia
| | - Jason Li
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
| | - Kenneth Opeskin
- Department of Anatomical Pathology, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - Natalie Thompson
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
| | - Gavin M Wright
- Department of Thoracic Surgery, St Vincent's Hospital, (Victoria Pde), Melbourne, (3065), Australia
| | - David M Thomas
- Centre for Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, (St Andrews Place), East Melbourne, (3002), Australia
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Yang IA, Relan V, Wright CM, Davidson MR, Sriram KB, Savarimuthu Francis SM, Clarke BE, Duhig EE, Bowman RV, Fong KM. Common pathogenic mechanisms and pathways in the development of COPD and lung cancer. Expert Opin Ther Targets 2011; 15:439-56. [PMID: 21284573 DOI: 10.1517/14728222.2011.555400] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Lung cancer and COPD commonly coexist in smokers, and the presence of COPD increases the risk of developing lung cancer. In addition to smoking cessation and preventing smoking initiation, understanding the shared mechanisms of these smoking-related lung diseases is critical, in order to develop new methods of prevention, diagnosis and treatment of lung cancer and COPD. AREAS COVERED This review discusses the common mechanisms for susceptibility to lung cancer and COPD, which in addition to cigarette smoke, may involve inflammation, epithelial-mesenchymal transition, abnormal repair, oxidative stress, and cell proliferation. Furthermore, we discuss the underlying genomic and epigenomic changes (single nucleotide polymorphisms (SNPs), copy number variation, promoter hypermethylation and microRNAs) that are likely to alter biological pathways, leading to susceptibility to lung cancer and COPD (e.g., altered nicotine receptor biology). EXPERT OPINION Strategies to study genomics, epigenomics and gene-environment interaction will yield greater insight into the shared pathogenesis of lung cancer and COPD, leading to new diagnostic and therapeutic modalities.
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Affiliation(s)
- Ian A Yang
- The Prince Charles Hospital, Department of Thoracic Medicine, Thoracic Research Laboratory, Brisbane, Australia.
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Han C, Zou H, Ma J, Zhou Y, Zhao J. [Comparison of EGFR and KRAS status between primary non-small cell lung cancer and corresponding metastases: a systematic review and meta-analysis]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2010; 13:882-91. [PMID: 20840818 PMCID: PMC6000337 DOI: 10.3779/j.issn.1009-3419.2010.09.09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Epidermal growth factor receptor (EGFR) and KRAS status were particularly critical for the choice of first-line targeted therapy of non-small cell lung cancer (NSCLC), while the primary tumor and metastases might be different in the EGFR and KRAS gene status. The aim of this pooled analysis is to compare EGFR and KRAS status in matching primary NSCLC and metastases and further to guide clinical practice. METHODS Systematic computerized searches of the Pubmed and Medline databases (up to May 10, 2010) meeting specified search criteria were performed, followed by a further screening according to inclusive and exclusive criteria. RESULTS Fourteen articles were selected into the final meta-analysis with paired primary and metastatic cases of 598. Expression level of EGFR protein and mutation frequency of KRAS gene in primary tumors were higher than that in metastases, relative risk (RR)=1.13 (95%CI: 0.98-1.31, P=0.09) and RR=1.39 (95%CI: 0.95-2.03, P=0.09), respectively. EGFR gene copy number in metastases was higher than that in primary tumor, RR=0.74 (95%CI: 0.53-1.02, P=0.06). There was no statistically significant difference of EGFR mutation frequency in primary tumors and metastases (P=0.31). The discordant rate in primary and metastases was 17.09% for EGFR mutation, 27.07% for EGFR amplification, 27.84% for EGFR protein expression and 25.91% for KRAS mutation. CONCLUSIONS The systematic analysis showed that the EGFR mutation status in primary lung cancer and corresponding metastases was more stable than KRAS gene. KRAS mutation in primary lung cancerous foci seems to better reflect systemically cancerous genetic characteristics of KRAS gene. Determination of KRAS gene status based merely on metastatic foci might lead to more resistant selections of EGFR tyrosine kinase inhibitor (TKI) therapy. Combined detection of EGFR and KRAS mutation from primary NSCLC foci might serve as a better predictive biomarker for anti-EGFR targeted therapy.
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Affiliation(s)
- Chengbo Han
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110022, China.
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Job B, Bernheim A, Beau-Faller M, Camilleri-Broët S, Girard P, Hofman P, Mazières J, Toujani S, Lacroix L, Laffaire J, Dessen P, Fouret P. Genomic aberrations in lung adenocarcinoma in never smokers. PLoS One 2010; 5:e15145. [PMID: 21151896 PMCID: PMC2997777 DOI: 10.1371/journal.pone.0015145] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 10/26/2010] [Indexed: 12/17/2022] Open
Abstract
Background Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide. Methods and Findings We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity. Conclusions The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers.
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Affiliation(s)
- Bastien Job
- Plate-forme de Biologie intégrée, Institut de recherche intégrée en Cancérologie à Villejuif, Villejuif, France
| | - Alain Bernheim
- INSERM Génétique des tumeurs U985, INSERM, Villejuif, France
| | - Michèle Beau-Faller
- Laboratoire de Biochimie et de Biologie Moléculaire (Hôpital de Hautepierre), CHU Strasbourg, Strasbourg, France
| | - Sophie Camilleri-Broët
- INSERM JE2492, INSERM, Kremlin-Bicêtre, France
- Université Paris-Sud, Kremlin-Bicêtre, France
| | - Philippe Girard
- Département Thoracique, Institut Mutualiste Montsouris, Paris, France
| | - Paul Hofman
- Laboratoire de Pathologie Clinique et Expérimentale (Hôpital Pasteur), CHU Nice, Nice, France
| | - Julien Mazières
- Unité de Cancérologie Cervico Thoracique (Hôpital Larrey), CHU Toulouse, Toulouse, France
| | - Saloua Toujani
- INSERM Génétique des tumeurs U985, INSERM, Villejuif, France
| | - Ludovic Lacroix
- Laboratoire de Recherche Translationnelle, Institut de cancérologie Gustave-Roussy, Villejuif, France
| | | | - Philippe Dessen
- INSERM Génétique des tumeurs U985, INSERM, Villejuif, France
- Université Paris-Sud, Kremlin-Bicêtre, France
| | - Pierre Fouret
- INSERM Génétique des tumeurs U985, INSERM, Villejuif, France
- Université Pierre et Marie Curie, Paris, France
- * E-mail:
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Lin YX, Baladandayuthapani V, Bonato V, Do KA. Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method. Cancer Inform 2010; 9:229-49. [PMID: 21082039 PMCID: PMC2978932 DOI: 10.4137/cin.s5614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
MOTIVATION Existing methods for estimating copy number variations in array comparative genomic hybridization (aCGH) data are limited to estimations of the gain/loss of chromosome regions for single sample analysis. We propose the linear-median method for estimating shared copy numbers in DNA sequences across multiple samples, demonstrate its operating characteristics through simulations and applications to real cancer data, and compare it to two existing methods. RESULTS Our proposed linear-median method has the power to estimate common changes that appear at isolated single probe positions or very short regions. Such changes are hard to detect by current methods. This new method shows a higher rate of true positives and a lower rate of false positives. The linear-median method is non-parametric and hence is more robust in estimating copy number. Additionally the linear-median method is easily computable for practical aCGH data sets compared to other copy number estimation methods.
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Affiliation(s)
- Y-X Lin
- Centre for Statistical and Survey Methodology, School of Mathematics and Applied Statistics, University of Wollongong NSW 2522, Australia
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Abstract
Background: Lung squamous cell carcinomas (SqCCs) occur at higher rates following arsenic exposure. Somatic DNA copy-number alterations (CNAs) are understood to be critical drivers in several tumour types. We have assembled a rare panel of lung tumours from a population with chronic arsenic exposure, including SqCC tumours from patients with no smoking history. Methods: Fifty-two lung SqCCs were analysed by whole-genome tiling-set array comparative genomic hybridisation. Twenty-two were derived from arsenic-exposed patients from Northern Chile (10 never smokers and 12 smokers). Thirty additional cases were obtained for comparison from North American smokers without arsenic exposure. Twenty-two blood samples from healthy individuals from Northern Chile were examined to identify germline DNA copy-number variations (CNVs) that could be excluded from analysis. Results: We identified multiple CNAs associated with arsenic exposure. These alterations were not attributable to either smoking status or CNVs. DNA losses at chromosomes 1q21.1, 7p22.3, 9q12, and 19q13.31 represented the most recurrent events. An arsenic-associated gain at 19q13.33 contains genes previously identified as oncogene candidates. Conclusions: Our results provide a comprehensive approach to molecular characteristics of the arsenic-exposed lung cancer genome and the non-smoking lung SqCC genome. The distinct and recurrent arsenic-related alterations suggest that this group of tumours may be considered as a separate disease subclass.
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Gazdar AF, Girard L, Lockwood WW, Lam WL, Minna JD. Lung cancer cell lines as tools for biomedical discovery and research. J Natl Cancer Inst 2010; 102:1310-21. [PMID: 20679594 DOI: 10.1093/jnci/djq279] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Lung cancer cell lines have made a substantial contribution to lung cancer translational research and biomedical discovery. A systematic approach to initiating and characterizing cell lines from small cell and non-small cell lung carcinomas has led to the current collection of more than 200 lung cancer cell lines, a number that exceeds those for other common epithelial cancers combined. The ready availability and widespread dissemination of the lines to investigators worldwide have resulted in more than 9000 citations, including multiple examples of important biomedical discoveries. The high (but not perfect) genomic similarities between lung cancer cell lines and the lung tumor type from which they were derived provide evidence of the relevance of their use. However, major problems including misidentification or cell line contamination remain. Ongoing studies and new approaches are expected to reveal the full potential of the lung cancer cell line panel.
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Affiliation(s)
- Adi F Gazdar
- University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390-8593, USA.
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Kohno T, Otsuka A, Girard L, Sato M, Iwakawa R, Ogiwara H, Sanchez-Cespedes M, Minna JD, Yokota J. A catalog of genes homozygously deleted in human lung cancer and the candidacy of PTPRD as a tumor suppressor gene. Genes Chromosomes Cancer 2010; 49:342-52. [PMID: 20073072 DOI: 10.1002/gcc.20746] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A total of 176 genes homozygously deleted in human lung cancer were identified by DNA array-based whole genome scanning of 52 lung cancer cell lines and subsequent genomic PCR in 74 cell lines, including the 52 cell lines scanned. One or more exons of these genes were homozygously deleted in one (1%) to 20 (27%) cell lines. These genes included known tumor suppressor genes, e.g., CDKN2A/p16, RB1, and SMAD4, and candidate tumor suppressor genes whose hemizygous or homozygous deletions were reported in several types of human cancers, such as FHIT, KEAP1, and LRP1B/LRP-DIP. CDKN2A/p16 and p14ARF located in 9p21 were most frequently deleted (20/74, 27%). The PTPRD gene was most frequently deleted (8/74, 11%) among genes mapping to regions other than 9p21. Somatic mutations, including a nonsense mutation, of the PTPRD gene were detected in 8/74 (11%) of cell lines and 4/95 (4%) of surgical specimens of lung cancer. Reduced PTPRD expression was observed in the majority (>80%) of cell lines and surgical specimens of lung cancer. Therefore, PTPRD is a candidate tumor suppressor gene in lung cancer. Microarray-based expression profiling of 19 lung cancer cell lines also indicated that some of the 176 genes, such as KANK and ADAMTS1, are preferentially inactivated by epigenetic alterations. Genetic/epigenetic as well as functional studies of these 176 genes will increase our understanding of molecular mechanisms behind lung carcinogenesis.
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Affiliation(s)
- Takashi Kohno
- Biology Division, National Cancer Center Research Institute, Tokyo, Japan
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48
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Bae JS, Choi JS, Baik SH, Park WC, Song BJ, Kim JS, Lim Y, Jung SS. Genomic alterations of primary tumor and blood in invasive ductal carcinoma of breast. World J Surg Oncol 2010; 8:32. [PMID: 20409316 PMCID: PMC2865462 DOI: 10.1186/1477-7819-8-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic alterations are important events in the origin and progression of various cancers, with DNA copy number changes associated with progression and treatment response in cancer. Array CGH is potentially useful in the identification of genomic alterations from primary tumor and blood in breast cancer patients. The aim of our study was to compare differences of DNA copy number changes in blood and tumor tissue in breast cancer. METHODS DNA copy number changes in blood were compared to those in tumor tissue using array-comparative genomic hybridization in samples obtained from 30 breast cancer patients. The relative degree of chromosomal changes was analyzed using log2 ratios and data was validated by real-time polymerase chain reaction. RESULTS Forty-six regions of gains present in more than 30% of the tissues and 70 regions of gains present in more than 30% of blood were identified. The most frequently gained region was chromosome 8q24. In total, agreement of DNA copy numbers between primary tumor and blood was minimal (Kappa = 0.138, p < 0.001). CONCLUSION Although there was only a slight agreement of DNA copy number alterations between the primary tumor and the blood samples, the blood cell copy number variation may have some clinical significance as compared to the primary tumor in IDC breast cancer patients.
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Affiliation(s)
- Ja Seong Bae
- Department of Surgery, The Catholic University, Seoul, Korea
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49
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Varella-Garcia M, Schulte AP, Wolf HJ, Feser WJ, Zeng C, Braudrick S, Yin X, Hirsch FR, Kennedy TC, Keith RL, Barón AE, Belinsky SA, Miller YE, Byers T, Franklin WA. The detection of chromosomal aneusomy by fluorescence in situ hybridization in sputum predicts lung cancer incidence. Cancer Prev Res (Phila) 2010; 3:447-53. [PMID: 20332298 DOI: 10.1158/1940-6207.capr-09-0165] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lung cancer usually is disseminated (advanced) and has a poor prognosis at diagnosis. Current and former smokers are at a high risk for lung cancer and are candidates for prevention and early detection strategies. Sputum is a potential source of biomarkers that might determine either lung cancer risk or the presence of early lung cancer, but no current sputum test is sufficiently sensitive and specific for effective screening. We used fluorescence in situ hybridization (FISH) to measure chromosomal aneusomy (CA) in sputum samples collected prospectively from 100 incident lung cancer cases and 96 controls (matched on age, gender, and date of collection) nested within an ongoing high-risk cohort. The CA-FISH assay was aimed at four DNA targets: epidermal growth factor receptor, MYC, 5p15, and CEP 6. The sensitivity of a positive CA-FISH assay (abnormal for two or more of the four markers) for lung cancer was substantially higher for samples collected within 18 months (76% sensitivity) than for samples collected more than 18 months (31%) before lung cancer diagnosis. Sensitivity was higher for squamous cell cancers (94%) than for other histologic types (69%). CA-FISH specificity based on samples collected within 18 months before diagnosis was 88%. The adjusted odds ratio (OR) of lung cancer for specimens collected within 18 months before a cancer diagnosis was higher for the CA-FISH assay [OR, 29.9; 95% confidence interval (95% CI), 9.5-94.1] than for previously studied ORs of cytologic atypia (OR, 1.8; 95% CI, 1.3-2.6) and gene promoter methylation (OR, 6.5; 95% CI, 1.2-35.5). Whether CA-FISH is an indicator of extreme risk for incident lung cancer or detects exfoliated cancer cells is unknown. The apparent promise of CA-FISH in sputum for assessing lung cancer risk and/or for lung cancer early detection now needs to be validated in a clinical screening trial.
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Jung SH, Yim SH, Hu HJ, Jung CK, Lee SH, Kim DH, Chung YJ. Copy number alterations and expression profiles of candidate genes in a pulmonary inflammatory myofibroblastic tumor. Lung Cancer 2010; 70:152-7. [PMID: 20185201 DOI: 10.1016/j.lungcan.2010.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 01/08/2010] [Accepted: 01/29/2010] [Indexed: 10/19/2022]
Abstract
Inflammatory myofibroblastic tumor (IMT) is a soft tissue neoplasm composed of myofibroblastic spindle cells accompanied by the inflammatory infiltrate. In addition to its phenotypic ambiguity, pathogenic mechanisms of the IMT also remain elusive. Although several chromosomal aberrations have been identified by karyotyping, detailed characteristics and extent of copy number alterations in IMT are unknown. Copy number alterations of an IMT case were examined using 30K whole-genome oligoarray-comparative genomic hybridization. RNA expression of putative cancer-related genes located in the chromosomal altered regions was assessed by qRT-PCR. We identified seven copy number gained regions, seven lost regions, nine amplifications and six homozygous deletions, which covers 2.5% of total genome. In homozygously deleted regions, RNA levels of putative tumor suppressors, SEMA3B, SEMA3F and SULT2A1, were significantly repressed being consistent with copy number status. In high-level amplification regions, RNA expression of four potential cancer-related genes was examined; GSTT1, ESR1, EVI1 and MITF. Among them, GSTT1 and ESR1 were significantly up-regulated, but EVI1 and MITF showed insignificant elevation of RNA expression. To our knowledge, this is the first genome-wide analysis of copy number alterations in IMT. Most of the putative cancer-related genes identified in this study are supposedly novel in IMT. Taken together, our results will help to elucidate the pathogenic mechanisms of IMT.
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Affiliation(s)
- Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701, Republic of Korea
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