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Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
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Zhang L, Luo M, Yang H, Zhu S, Cheng X, Qing C. Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients. J Ovarian Res 2019; 12:19. [PMID: 30786925 PMCID: PMC6381667 DOI: 10.1186/s13048-019-0494-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/07/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is one of the most malignant gynecological tumors, associated with excess death rate (50-60%) in ovarian cancer patients. Particularly, among newly occurred ovarian cancer patients, 70% of clinical cases are diagnosed at the advanced stage, which definitely delay the timely treatment and lead to high mortality rate within 5 years post diagnosis. Therefore, identification of sensitive gene markers, as well as development of reliable genetic diagnosis, are important for the early detection and precise therapy for OC patients. This study aims to identify novel genetic mutations and develop a feasible clinical approach for early OC diagnosis. METHODS The OC tissue-derived DNA sample was acquired from 31 OC patients, and the somatic gene mutations will be identified after comparison with normal samples, using Genome-wide analysis and next-generation sequencing. RESULTS A total of 463 somatic mutations, which were considered as potential pathogenic sites, were assigned to 473 genes. Among them, 15 genes (TP53, TTN, MUC16, OR4N2, BRCA1, CAD, CCDC129, INSR, NAV3, NELL2, NRAS, OBSCN, PGLYRP4, RBM15B and TRPC7) were mutated on at least two sites. These genes were mapped to RNA sequencing (RNAseq) data, and a total of 117 genes had an absolute fold- change ≥ 2 and p ≤ 0.01. Five genes were mutated in at least two OC patients. Gene ontology (GO) classification indicated that a majority of genes participated in biological processes. Kyoto Enrichment of Genes and Genomes (KEGG) enrichment pathway analysis revealed that the genes were mainly involved in the regulation of metabolic signaling pathways. CONCLUSIONS Taken together, this study identified several novel genetic alterations pathway for early clinical diagnosis and provided abundant information for understanding molecular mechanisms of the OC occurrence and development.
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Affiliation(s)
- Lei Zhang
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China.,Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, 519 Kunzhou Road, Xishan District, Kunming, Yunnan, 650118, People's Republic of China
| | - Min Luo
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Hongying Yang
- Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, 519 Kunzhou Road, Xishan District, Kunming, Yunnan, 650118, People's Republic of China
| | - Shaoyan Zhu
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Xianliang Cheng
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China
| | - Chen Qing
- School of Pharmaceutical Sciences & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Cheng Gong District, Kunming, Yunnan, 650500, People's Republic of China.
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Functional characterisation of a novel ovarian cancer cell line, NUOC-1. Oncotarget 2018; 8:26832-26844. [PMID: 28460465 PMCID: PMC5432300 DOI: 10.18632/oncotarget.15821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/20/2017] [Indexed: 12/04/2022] Open
Abstract
Background Cell lines provide a powerful model to study cancer and here we describe a new spontaneously immortalised epithelial ovarian cancer cell line (NUOC-1) derived from the ascites collected at a time of primary debulking surgery for a mixed endometrioid / clear cell / High Grade Serous (HGS) histology. Results This spontaneously immortalised cell line was found to maintain morphology and epithelial markers throughout long-term culture. NUOC-1 cells grow as an adherent monolayer with a doubling time of 58 hours. The cells are TP53 wildtype, positive for PTEN, HER2 and HER3 expression but negative for oestrogen, progesterone and androgen receptor expression. NUOC-1 cells are competent in homologous recombination and non-homologous end joining, but base excision repair defective. Karyotype analysis demonstrated a complex tetraploid karyotype. SNP array analysis of parent and derived subpopulations (NUOC-1-A1 and NUOC-1-A2) cells demonstrated heterogeneous cell populations with numerous copy number alterations and a pro-amplification phenotype. The characteristics of this new cell line lends it to be an excellent model for investigation of a number of the identified targets. Materials and Methods The cell line has been characterised for growth, drug sensitivity, expression of common ovarian markers and mutations, clonogenic potential and ability to form xenografts in SCID mice. Copy number changes and clonal evolution were assessed by SNP arrays.
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Gambaro K, Quinn MCJ, Cáceres-Gorriti KY, Shapiro RS, Provencher D, Rahimi K, Mes-Masson AM, Tonin PN. Low levels of IGFBP7 expression in high-grade serous ovarian carcinoma is associated with patient outcome. BMC Cancer 2015; 15:135. [PMID: 25886299 PMCID: PMC4381406 DOI: 10.1186/s12885-015-1138-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insulin-like growth factor binding protein 7 (IGFBP7) has been suggested to act as a tumour suppressor gene in various human cancers, yet its role in epithelial ovarian cancer (EOC) has not yet been investigated. We previously observed that IGFBP7 was one of several genes found significantly upregulated in an EOC cell line model rendered non-tumourigenic as consequence of genetic manipulation. The aim of the present study was to investigate the role of IGFBP7 in high-grade serous ovarian carcinomas (HGSC), the most common type of EOC. METHODS We analysed IGFBP7 gene expression in 11 normal ovarian surface epithelial cells (NOSE), 79 high-grade serous ovarian carcinomas (HGSC), and seven EOC cell lines using a custom gene expression array platform. IGFBP7 mRNA expression profiles were also extracted from publicly available databases. Protein expression was assessed by immunohistochemistry of 175 HGSC and 10 normal fallopian tube samples using tissue microarray and related to disease outcome. We used EOC cells to investigate possible mechanisms of gene inactivation and describe various in vitro growth effects of exposing EOC cell lines to human recombinant IGFBP7 protein and conditioned media. RESULTS All HGSCs exhibited IGFBP7 expression levels that were significantly (p = 0.001) lower than the mean of the expression value of NOSE samples and that of a whole ovary sample. IGFBP7 gene and protein expression were lower in tumourigenic EOC cell lines relative to a non-tumourigenic EOC cell line. None of the EOC cell lines harboured a somatic mutation in IGFBP7, although loss of heterozygosity (LOH) of the IGFBP7 locus and epigenetic methylation silencing of the IGFBP7 promoter was observed in two of the cell lines exhibiting loss of gene/protein expression. In vitro functional assays revealed an alteration of the EOC cell migration capacity. Protein expression analysis of HGSC samples revealed that the large majority of tumour cores (72.6%) showed low or absence of IGFBP7 staining and revealed a significant correlation between IGFBP7 protein expression and a prolonged overall survival (p = 0.044). CONCLUSION The low levels of IGFPB7 in HGSC relative to normal tissues, and association with survival are consistent with a purported role in tumour suppressor pathways.
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Affiliation(s)
- Karen Gambaro
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Michael C J Quinn
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Katia Y Cáceres-Gorriti
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Rebecca S Shapiro
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada.
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada. .,Department of Obstetric-Gynecology, Université de Montréal, Montreal, H2L 4M1, Canada.
| | - Kurosh Rahimi
- Department of Pathology, Université de Montréal, Montreal, H3C 3J7, Canada.
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada. .,Department of Medicine, Université de Montréal, Montreal, H3C 3J7, Canada.
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, H4A 3J1, Canada. .,Department of Medicine, McGill University, Montreal, H3G 1A4, Canada. .,Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Site Glen Pavillion Block E, Cancer Research Program E026217 (cubicle E), Montreal, Quebec, H4A 3J1, Canada.
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Kamieniak MM, Rico D, Milne RL, Muñoz-Repeto I, Ibáñez K, Grillo MA, Domingo S, Borrego S, Cazorla A, García-Bueno JM, Hernando S, García-Donas J, Hernández-Agudo E, Y Cajal TR, Robles-Díaz L, Márquez-Rodas I, Cusidó M, Sáez R, Lacambra-Calvet C, Osorio A, Urioste M, Cigudosa JC, Paz-Ares L, Palacios J, Benítez J, García MJ. Deletion at 6q24.2-26 predicts longer survival of high-grade serous epithelial ovarian cancer patients. Mol Oncol 2014; 9:422-36. [PMID: 25454820 PMCID: PMC5528660 DOI: 10.1016/j.molonc.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/12/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022] Open
Abstract
Standard treatments for advanced high-grade serous ovarian carcinomas (HGSOCs) show significant side-effects and provide only short-term survival benefits due to disease recurrence. Thus, identification of novel prognostic and predictive biomarkers is urgently needed. We have used 42 paraffin-embedded HGSOCs, to evaluate the utility of DNA copy number alterations, as potential predictors of clinical outcome. Copy number-based unsupervised clustering stratified HGSOCs into two clusters of different immunohistopathological features and survival outcome (HR = 0.15, 95%CI = 0.03-0.81; Padj = 0.03). We found that loss at 6q24.2-26 was significantly associated with the cluster of longer survival independently from other confounding factors (HR = 0.06, 95%CI = 0.01-0.43, Padj = 0.005). The prognostic value of this deletion was validated in two independent series, one consisting of 36 HGSOCs analyzed by fluorescent in situ hybridization (P = 0.04) and another comprised of 411 HGSOCs from the Cancer Genome Atlas study (TCGA) (HR = 0.67, 95%CI = 0.48-0.93, Padj = 0.019). In addition, we confirmed the association of low expression of the genes from the region with longer survival in 799 HGSOCs (HR = 0.74, 95%CI = 0.61-0.90, log-rank P = 0.002) and 675 high-FIGO stage HGSOCs (HR = 0.76, 95%CI = 0.61-0.96, log-rank P = 0.02) available from the online tool KM-plotter. Finally, by integrating copy number, RNAseq and survival data of 296 HGSOCs from TCGA we propose a few candidate genes that can potentially explain the association. Altogether our findings indicate that the 6q24.2-26 deletion is an independent marker of favorable outcome in HGSOCs with potential clinical value as it can be analyzed by FISH on tumor sections and guide the selection of patients towards more conservative therapeutic strategies in order to reduce side-effects and improve quality of life.
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Affiliation(s)
- Marta M Kamieniak
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel Rico
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne 3004, Australia; Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street Carlton, Melbourne 3010, Victoria, Australia
| | - Ivan Muñoz-Repeto
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Kristina Ibáñez
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Miguel A Grillo
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Samuel Domingo
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Salud Borrego
- Departments of Genetics, Reproduction, and Fetal Medicine, IBIS, University Hospital Virgen del Rocio/CSIC/University of Seville, Avda. Manuel Siurot, s/n., 41013 Sevilla, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Alicia Cazorla
- Pathology Department, Fundación Jiménez Díaz, Avda. Reyes Católicos, 2, 28040 Madrid, Spain
| | - José M García-Bueno
- Oncology Department, Hospital General de Albacete, Calle Hermanos Falco, 37, 02006 Albacete, Spain
| | - Susana Hernando
- Oncology Department, Fundación Hospital Alcorcón, Calle Valdelaguna, 1, 28922 Alcorcón, Spain
| | - Jesús García-Donas
- Medical Oncology Service, Oncologic Center Clara Campal, Calle Oña, 10, 28050 Madrid, Spain
| | - Elena Hernández-Agudo
- Breast Cancer Clinical Research Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Teresa Ramón Y Cajal
- Medical Oncology Service, Hospital Sant Pau, Carrer de Sant Quintí, 89, 08026 Barcelona, Spain
| | - Luis Robles-Díaz
- Familial Cancer Unit and Medical Oncology Department, Hospital 12 de Octubre, Avda de Córdoba, s/n, 28041 Madrid, Spain
| | - Ivan Márquez-Rodas
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, Calle Doctor Esquerdo, 46, 28007 Madrid, Spain
| | - Maite Cusidó
- Obstetrics and Gynecology Department, Institut Universitari Dexeus, Carrer de Sabino Arana, 5, 08028 Barcelona, Spain
| | - Raquel Sáez
- Laboratory of Genetics, Hospital Donostia, Calle Doctor Begiristain, 117, 20080 San Sebastián, Spain
| | - Carmen Lacambra-Calvet
- Department of Internal Medicine, Hospital Severo Ochoa, Avd. de Orellana, s/n., 28911 Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Juan C Cigudosa
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Luis Paz-Ares
- Medical Oncology Department, University Hospital Virgen del Rocio, Avda. Manuel Siurot s/n., 41013 Sevilla, Spain
| | - José Palacios
- Pathology Department, Hospital Universitario Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, 28034 Madrid, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - María J García
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain.
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Genomic aberrations of BRCA1-mutated fallopian tube carcinomas. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1871-6. [PMID: 24726640 DOI: 10.1016/j.ajpath.2014.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/20/2014] [Accepted: 02/20/2014] [Indexed: 01/30/2023]
Abstract
Intraepithelial carcinomas of the fallopian tube are putative precursors to high-grade serous carcinomas of the ovary and peritoneum. Molecular characterization of these early precursors is limited but could be the key to identifying tumor biomarkers for early detection. This study presents a genome-wide copy number analysis of occult fallopian tube carcinomas identified through risk-reducing prophylactic oophorectomy from three women with germline BRCA1 mutations, demonstrating that extensive genomic aberrations are already established at this early stage. We found no indication of a difference in the level of genomic aberration observed in fallopian tube carcinomas compared with high-grade serous ovarian carcinomas. These findings suggest that spread to the peritoneal cavity may require no or very little further tumor evolution, which raises the question of what is the real window of opportunity to detect high-grade serous peritoneal carcinoma arising from the fallopian tube before it spreads. Nonetheless, the similarity of the genomic aberrations to those observed in high-grade serous ovarian carcinomas suggests that genetic biomarkers identified in late-stage disease may be relevant for early detection.
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Smebye ML, Sveen A, Haugom L, Davidson B, Tropé CG, Lothe RA, Heim S, Skotheim RI, Micci F. Chromosome 19 rearrangements in ovarian carcinomas: zinc finger genes are particularly targeted. Genes Chromosomes Cancer 2014; 53:558-67. [PMID: 24634323 DOI: 10.1002/gcc.22166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/04/2013] [Indexed: 01/21/2023] Open
Abstract
Chromosome 19 is frequently rearranged in ovarian carcinomas, but the pathogenetic consequences of this are not clearly understood. We performed microarray gene expression analysis on 12 ovarian carcinomas that carry a rearranged chromosome 19 in their karyotype. These aberrant chromosomes have previously been microdissected and analyzed by array-based CGH. In the current study, we wanted to explore whether the genomic alterations thus detected correlated with changes in gene expression. The microarray gene expression analysis gave information on 407 genes mapping in gained genomic regions on chromosome 19, of which 92 showed association between DNA gain and upregulated expression. Of the genes showing this association, 39 (42%) showed gain in at least two samples. The majority of these 39 genes of interest (n = 24, 62%) encode zinc finger proteins, which otherwise make up only 15% of the approximately 1,400 genes on chromosome 19. The strongest association was found for ZNF223 which was upregulated in samples with genomic gain compared with samples without gain. We suggest that DNA copy number changes brought about by rearrangements of chromosome 19 contribute to ovarian carcinogenesis by leading to upregulation of ZNF223 and other zinc finger genes. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Marianne L Smebye
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
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The pathogenesis of atypical proliferative Brenner tumor: an immunohistochemical and molecular genetic analysis. Mod Pathol 2014; 27:231-7. [PMID: 23887305 PMCID: PMC4612641 DOI: 10.1038/modpathol.2013.142] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 12/24/2022]
Abstract
Brenner tumors are ovarian tumors, usually benign, containing epithelium that resembles transitional epithelium. As with other epithelial tumors there exist frankly malignant tumors and tumors that display greater proliferation than the benign Brenner tumors but lack destructive infiltrative growth, and these have been designated 'atypical proliferative' (borderline) Brenner tumors. There have been no well-documented cases of atypical proliferative Brenner tumors that have exhibited malignant behavior. Based on shared morphologic features it is generally believed that atypical proliferative Brenner tumors develop from benign Brenner tumors. The aim of the present study was to confirm this impression by investigating the immunohistochemical and molecular genetic features of benign and atypical proliferative Brenner tumors. Immunohistochemical staining for p16, fluorescence in-situ hybridization (FISH) for CDKN2A (p16-encoding gene) and mutational analysis of the genes commonly mutated in ovarian tumors were performed. p16 immunostaining was positive in the epithelial component of 12 (92%) of 13 benign Brenner tumors, but completely negative in all 7 atypical proliferative Brenner tumors. FISH identified homozygous deletion of CDKN2A in the epithelial component of all atypical proliferative Brenner tumors, but CDKN2A was retained in all benign Brenner tumors. Two PIK3CA somatic mutations were detected in the stromal component in 1 (5%) of 20 Brenner tumors and 3 somatic mutations (1 in KRAS and 2 in PIK3CA) were identified in the atypical epithelial component of 2 (29%) of 7 atypical proliferative Brenner tumors. In summary, our findings suggest that loss of CDKN2A and, to a lesser extent, KRAS and PIK3CA somatic mutations have a role in the progression of a benign to an atypical proliferative Brenner tumor.
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9
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Ross JS, Ali SM, Wang K, Palmer G, Yelensky R, Lipson D, Miller VA, Zajchowski D, Shawver LK, Stephens PJ. Comprehensive genomic profiling of epithelial ovarian cancer by next generation sequencing-based diagnostic assay reveals new routes to targeted therapies. Gynecol Oncol 2013; 130:554-9. [PMID: 23791828 DOI: 10.1016/j.ygyno.2013.06.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/12/2013] [Accepted: 06/12/2013] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Targeted next generation sequencing (NGS) was evaluated for its ability to identify unanticipated targetable genomic alterations (GA) for patients with relapsed ovarian epithelial carcinoma (OC). METHODS DNA sequencing was performed for 3320 exons of 182 cancer-related genes and 37 introns of 14 genes frequently rearranged in cancer on indexed, adaptor ligated, hybridization-captured libraries using DNA isolated from FFPE sections from 48 histologically verified relapsed OC specimens. The original primary tumor was sequenced in 26 (54%) of the cases and recurrent/metastatic tumor site biopsies were sequenced in 22 (46%) of the cases. Actionability was defined as: GA that predict sensitivity or resistance to approved or standard therapies or are inclusion or exclusion criteria for specific experimental therapies in NCI registered clinical trials. RESULTS There were 38 (80%) serous, 5 (10%) endometrioid, 3 (6%) clear cell, 1 mucinous (2%) and 1 (2%) undifferentiated carcinomas. 141 GA were identified with an average of 2.9 GA (range 0-8) per tumor, of which 67 were actionable for an average of 1.4 actionable GA per patient (range 0-5). 33/48 (69%) of OC patient samples harbored at least one actionable GA. Most common GA were TP53 (79%); MYC (25%); BRCA1/2 (23%); KRAS (16.6%) and NF1 (14.5%). One tumor featured an ERBB2 point mutation. One of 3 (33%) of clear cell tumors featured cMET amplification validated by both FISH and IHC. CONCLUSIONS NGS assessment of therapy resistant OC identifies an unexpectedly high frequency of GA that could influence targeted therapy selection for the disease.
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Affiliation(s)
- J S Ross
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY 12208, USA.
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10
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Oros KK, Arcand SL, Bayani J, Squire JA, Mes-Masson AM, Tonin PN, Greenwood CM. Analysis of genomic abnormalities in tumors: a review of available methods for Illumina two-color SNP genotyping and evaluation of performance. Cancer Genet 2013; 206:103-15. [DOI: 10.1016/j.cancergen.2013.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 10/26/2022]
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11
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Davis SJ, Sheppard KE, Pearson RB, Campbell IG, Gorringe KL, Simpson KJ. Functional analysis of genes in regions commonly amplified in high-grade serous and endometrioid ovarian cancer. Clin Cancer Res 2013; 19:1411-21. [PMID: 23362323 DOI: 10.1158/1078-0432.ccr-12-3433] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE Ovarian cancer has the highest mortality rate of all the gynecologic malignancies and is responsible for approximately 140,000 deaths annually worldwide. Copy number amplification is frequently associated with the activation of oncogenic drivers in this tumor type, but their cytogenetic complexity and heterogeneity has made it difficult to determine which gene(s) within an amplicon represent(s) the genuine oncogenic driver. We sought to identify amplicon targets by conducting a comprehensive functional analysis of genes located in the regions of amplification in high-grade serous and endometrioid ovarian tumors. EXPERIMENTAL DESIGN High-throughput siRNA screening technology was used to systematically assess all genes within regions commonly amplified in high-grade serous and endometrioid cancer. We describe the results from a boutique siRNA screen of 272 genes in a panel of 18 ovarian cell lines. Hits identified by the functional viability screen were further interrogated in primary tumor cohorts to determine the clinical outcomes associated with amplification and gene overexpression. RESULTS We identified a number of genes as critical for cellular viability when amplified, including URI1, PAK4, GAB2, and DYRK1B. Integration of primary tumor gene expression and outcome data provided further evidence for the therapeutic use of such genes, particularly URI1 and GAB2, which were significantly associated with survival in 2 independent tumor cohorts. CONCLUSION By taking this integrative approach to target discovery, we have streamlined the translation of high-resolution genomic data into preclinical in vitro studies, resulting in the identification of a number of genes that may be specifically targeted for the treatment of advanced ovarian tumors.
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Affiliation(s)
- Sally J Davis
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
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12
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Baumbusch LO, Helland Å, Wang Y, Liestøl K, Schaner ME, Holm R, Etemadmoghadam D, Alsop K, Brown P, Mitchell G, Fereday S, DeFazio A, Bowtell DDL, Kristensen GB, Lingjærde OC, Børresen-Dale AL. High levels of genomic aberrations in serous ovarian cancers are associated with better survival. PLoS One 2013; 8:e54356. [PMID: 23372714 PMCID: PMC3553118 DOI: 10.1371/journal.pone.0054356] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/11/2012] [Indexed: 01/31/2023] Open
Abstract
Genomic instability and copy number alterations in cancer are generally associated with poor prognosis; however, recent studies have suggested that extreme levels of genomic aberrations may be beneficial for the survival outcome for patients with specific tumour types. We investigated the extent of genomic instability in predominantly high-grade serous ovarian cancers (SOC) using two independent datasets, generated in Norway (n = 74) and Australia (n = 70), respectively. Genomic instability was quantified by the Total Aberration Index (TAI), a measure of the abundance and genomic size of copy number changes in a tumour. In the Norwegian cohort, patients with TAI above the median revealed significantly prolonged overall survival (p<0.001) and progression-free survival (p<0.05). In the Australian cohort, patients with above median TAI showed prolonged overall survival (p<0.05) and moderately, but not significantly, prolonged progression-free survival. Results were confirmed by univariate and multivariate Cox regression analyses with TAI as a continuous variable. Our results provide further evidence supporting an association between high level of genomic instability and prolonged survival of high-grade SOC patients, possibly as disturbed genome integrity may lead to increased sensitivity to chemotherapeutic agents.
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Affiliation(s)
- Lars O Baumbusch
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.
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13
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Gambaro K, Quinn MCJ, Wojnarowicz PM, Arcand SL, de Ladurantaye M, Barrès V, Ripeau JS, Killary AM, Davis EC, Lavoie J, Provencher DM, Mes-Masson AM, Chevrette M, Tonin PN. VGLL3 expression is associated with a tumor suppressor phenotype in epithelial ovarian cancer. Mol Oncol 2013; 7:513-30. [PMID: 23415753 DOI: 10.1016/j.molonc.2012.12.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 12/11/2022] Open
Abstract
Previous studies have implicated vestigial like 3 (VGLL3), a chromosome 3p12.3 gene that encodes a putative transcription co-factor, as a candidate tumor suppressor gene (TSG) in high-grade serous ovarian carcinomas (HGSC), the most common type of epithelial ovarian cancer. A complementation analysis based on microcell-mediated chromosome transfer (MMCT) using a centric fragment of chromosome 3 (der3p12-q12.1) into the OV-90 ovarian cancer cell line haploinsufficient for 3p and lacking VGLL3 expression was performed to assess the effect on tumorigenic potential and growth characteristics. Genetic characterization of the derived MMCT hybrids revealed that only the hybrid that contained an intact VGLL3 locus exhibited alterations of tumorigenic potential in a nude mouse xenograft model and various in vitro growth characteristics. Only stable OV-90 transfectant clones expressing low levels of VGLL3 were derived. These clones exhibited an altered cytoplasmic morphology characterized by numerous single membrane bound multivesicular-bodies (MVB) that were not attributed to autophagy. Overexpression of VGLL3 in OV-90 was achieved using a lentivirus-based tetracycline inducible gene expression system, which also resulted in MVB formation in the infected cell population. Though there was no significant differences in various in vitro and in vivo growth characteristics in a comparison of VGLL3-expressing clones with empty vector transfectant controls, loss of VGLL3 expression was observed in tumors derived from mouse xenograft models. VGLL3 gene and protein expression was significantly reduced in HGSC samples (>98%, p < 0.05) relative to either normal ovarian surface epithelial cells or epithelial cells of the fallopian tube, possible tissues of origin of HGSC. Also, there appeared to be to be more cases with higher staining levels in stromal tissue component from HGSC cases that had a prolonged disease-free survival. The results taken together suggest that VGLL3 is involved in tumor suppressor pathways, a feature that is characterized by the absence of VGLL3 expression in HGSC samples.
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Affiliation(s)
- Karen Gambaro
- Department of Human Genetics, McGill University, Montreal General Hospital, 1650 Cedar Avenue, Montreal H3G 1A4, Quebec, Canada
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14
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Abstract
Ovarian cancer (OC) is a relatively frequent malignant disease with a lifetime risk approaching to approximately 1 in 70. As many as 15-25 % OC arise due to known heterozygous germ-line mutations in DNA repair genes, such as BRCA1, BRCA2, RAD51C, NBN (NBS1), BRIP, and PALB2. Sporadic ovarian cancers often phenocopy the features of BRCA1-related hereditary disease (so-called BRCAness), i.e., show biallelic somatic inactivation of the BRCA1 gene. Tumor-specific BRCA1 deficiency renders selective sensitivity of transformed cells to platinating compounds and several other anticancer drugs, which explains high response rates of OC to systemic therapies. High-throughput molecular profiling of OC is instrumental for further progress in identification of novel OC diagnostic markers as well as for the development of new OC-specific treatments. However, interpretation of the huge bulk of incoming data may present a challenge. There is a critical need in the development of bioinformatic tools capable to integrate the multiplicity of available data sets into biologically and medically meaningful pieces of knowledge.
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Affiliation(s)
- Evgeny N Imyanitov
- Laboratory of Molecular Oncology, NN Petrov Institute of Oncology, St-Petersburg, Russia
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15
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Bayani J, Kuzmanov U, Saraon P, Fung WA, Soosaipillai A, Squire JA, Diamandis EP. Copy number and expression alterations of miRNAs in the ovarian cancer cell line OVCAR-3: impact on kallikrein 6 protein expression. Clin Chem 2012; 59:296-305. [PMID: 23136250 DOI: 10.1373/clinchem.2012.193060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Kallikrein-related peptidase 6 (KLK6), a member of the serine protease family of kallikrein (KLK) genes, is dysregulated in ovarian carcinomas (OCa) and its overexpression is associated with poor prognosis. Regulation of its expression is poorly understood and is likely to be influenced by multiple mechanisms. The KLK locus is subject to copy number changes and heterogeneity in serous OCas. These copy number imbalances generally correlate with KLK6 protein expression; however, this is not always the case. In this study we explored the role of miRNAs in the posttranscriptional control of KLK6 expression and the contributions of copy numbers, not only of the KLK locus, but also of the miRNAs predicted to regulate it. METHODS AND RESULTS By miRNA profiling of the KLK6-overexpressing OCa cell line, OVCAR-3, we identified overexpressed and underexpressed miRNAs. Publically available miRNA databases identified the human miRNA lethal 7 (hsa-let-7) family members as putative regulating miRNAs, from which hsa-let-7a was chosen for functional analysis. The transient transfection of hsa-let-7a to OVCAR-3 resulted in a decrease of KLK6 secreted protein. Moreover, such transfection was also able to weakly affect the expression of another member of the KLK gene family, KLK10 (kallikrein-related peptidase 10). Cytogenomic analysis, including array comparative genomic hybridization, fluorescence in situ hybridization, and spectral karyotyping revealed the overall net copy number losses of hsa-let-7a and other miRNAs predicted to target KLK6. CONCLUSIONS The hsa-let-7 family member hsa-let-7a is a modulator of KLK6 protein expression that is independent of the KLK6 copy number status.
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Affiliation(s)
- Jane Bayani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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16
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Hunter SM, Gorringe KL, Christie M, Rowley SM, Bowtell DD, Campbell IG. Pre-Invasive Ovarian Mucinous Tumors Are Characterized by CDKN2A and RAS Pathway Aberrations. Clin Cancer Res 2012; 18:5267-77. [DOI: 10.1158/1078-0432.ccr-12-1103] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Fathabadi EG, Shelling AN, Al-Kassas R. Nanocarrier systems for delivery of siRNA to ovarian cancer tissues. Expert Opin Drug Deliv 2012; 9:743-54. [DOI: 10.1517/17425247.2012.683173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Kinross KM, Montgomery KG, Kleinschmidt M, Waring P, Ivetac I, Tikoo A, Saad M, Hare L, Roh V, Mantamadiotis T, Sheppard KE, Ryland GL, Campbell IG, Gorringe KL, Christensen JG, Cullinane C, Hicks RJ, Pearson RB, Johnstone RW, McArthur GA, Phillips WA. An activating Pik3ca mutation coupled with Pten loss is sufficient to initiate ovarian tumorigenesis in mice. J Clin Invest 2012; 122:553-7. [PMID: 22214849 DOI: 10.1172/jci59309] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/16/2011] [Indexed: 01/03/2023] Open
Abstract
Mutations in the gene encoding the p110α subunit of PI3K (PIK3CA) that result in enhanced PI3K activity are frequently observed in human cancers. To better understand the role of mutant PIK3CA in the initiation or progression of tumorigenesis, we generated mice in which a PIK3CA mutation commonly detected in human cancers (the H1047R mutation) could be conditionally knocked into the endogenous Pik3ca locus. Activation of this mutation in the mouse ovary revealed that alone, Pik3caH1047R induced premalignant hyperplasia of the ovarian surface epithelium but no tumors. Concomitantly, we analyzed several human ovarian cancers and found PIK3CA mutations coexistent with KRAS and/or PTEN mutations, raising the possibility that a secondary defect in a co-regulator of PI3K activity may be required for mutant PIK3CA to promote transformation. Consistent with this notion, we found that Pik3caH1047R mutation plus Pten deletion in the mouse ovary led to the development of ovarian serous adenocarcinomas and granulosa cell tumors. Both mutational events were required for early, robust Akt activation. Pharmacological inhibition of PI3K/mTOR in these mice delayed tumor growth and prolonged survival. These results demonstrate that the Pik3caH1047R mutation with loss of Pten is enough to promote ovarian cell transformation and that we have developed a model system for studying possible therapies.
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Affiliation(s)
- Kathryn M Kinross
- Cancer Research Division, Peter MacCallum Cancer Centre (Peter Mac), East Melbourne, Victoria, Australia
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19
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Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnol 2011; 30:61-8. [DOI: 10.1038/nbt.2053] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/28/2011] [Indexed: 01/14/2023]
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20
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Birch AH, Arcand SL, Oros KK, Rahimi K, Watters AK, Provencher D, Greenwood CM, Mes-Masson AM, Tonin PN. Chromosome 3 anomalies investigated by genome wide SNP analysis of benign, low malignant potential and low grade ovarian serous tumours. PLoS One 2011; 6:e28250. [PMID: 22163003 PMCID: PMC3232202 DOI: 10.1371/journal.pone.0028250] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 11/04/2011] [Indexed: 02/01/2023] Open
Abstract
Ovarian carcinomas exhibit extensive heterogeneity, and their etiology remains unknown. Histological and genetic evidence has led to the proposal that low grade ovarian serous carcinomas (LGOSC) have a different etiology than high grade carcinomas (HGOSC), arising from serous tumours of low malignant potential (LMP). Common regions of chromosome (chr) 3 loss have been observed in all types of serous ovarian tumours, including benign, suggesting that these regions contain genes important in the development of all ovarian serous carcinomas. A high-density genome-wide genotyping bead array technology, which assayed >600,000 markers, was applied to a panel of serous benign and LMP tumours and a small set of LGOSC, to characterize somatic events associated with the most indolent forms of ovarian disease. The genomic patterns inferred were related to TP53, KRAS and BRAF mutations. An increasing frequency of genomic anomalies was observed with pathology of disease: 3/22 (13.6%) benign cases, 40/53 (75.5%) LMP cases and 10/11 (90.9%) LGOSC cases. Low frequencies of chr3 anomalies occurred in all tumour types. Runs of homozygosity were most commonly observed on chr3, with the 3p12-p11 candidate tumour suppressor region the most frequently homozygous region in the genome. An LMP harboured a homozygous deletion on chr6 which created a GOPC-ROS1 fusion gene, previously reported as oncogenic in other cancer types. Somatic TP53, KRAS and BRAF mutations were not observed in benign tumours. KRAS-mutation positive LMP cases displayed significantly more chromosomal aberrations than BRAF-mutation positive or KRAS and BRAF mutation negative cases. Gain of 12p, which harbours the KRAS gene, was particularly evident. A pathology review reclassified all TP53-mutation positive LGOSC cases, some of which acquired a HGOSC status. Taken together, our results support the view that LGOSC could arise from serous benign and LMP tumours, but does not exclude the possibility that HGOSC may derive from LMP tumours.
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Affiliation(s)
- Ashley H. Birch
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Suzanna L. Arcand
- The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Kathleen K. Oros
- Division of Clinical Epidemiology and Segal Cancer Centre, Lady Davis Research Institute, Jewish General Hospital, Montreal, Canada
| | - Kurosh Rahimi
- Department of Pathology, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Canada
| | - A. Kevin Watters
- Department of Pathology, McGill University and McGill University Health Centre (MUHC), Montréal, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Institut du cancer de Montréal, Montreal, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada
| | - Celia M. Greenwood
- Division of Clinical Epidemiology and Segal Cancer Centre, Lady Davis Research Institute, Jewish General Hospital, Montreal, Canada
- Department of Oncology, McGill University, Montreal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Institut du cancer de Montréal, Montreal, Canada
- Department of Medicine, Université de Montréal, Montreal, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, Canada
- The Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Medicine, McGill University, Montreal, Canada
- * E-mail:
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21
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Mullany LK, Fan HY, Liu Z, White LD, Marshall A, Gunaratne P, Anderson ML, Creighton CJ, Xin L, Deavers M, Wong KK, Richards JS. Molecular and functional characteristics of ovarian surface epithelial cells transformed by KrasG12D and loss of Pten in a mouse model in vivo. Oncogene 2011; 30:3522-36. [PMID: 21423204 PMCID: PMC3139785 DOI: 10.1038/onc.2011.70] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 12/16/2010] [Accepted: 01/03/2011] [Indexed: 12/16/2022]
Abstract
Ovarian cancer is a complex and deadly disease that remains difficult to detect at an early curable stage. Furthermore, although some oncogenic (Kras, Pten/PI3K and Trp53) pathways that are frequently mutated, deleted or amplified in ovarian cancer are known, how these pathways initiate and drive specific morphological phenotypes and tumor outcomes remain unclear. We recently generated Pten(fl/fl); Kras(G12D); Amhr2-Cre mice to disrupt the Pten gene and express a stable mutant form of Kras(G12D) in ovarian surface epithelial (OSE) cells. On the basis of histopathologic criteria, the mutant mice developed low-grade ovarian serous papillary adenocarcinomas at an early age and with 100% penetrance. This highly reproducible phenotype provides the first mouse model in which to study this ovarian cancer subtype. OSE cells isolated from ovaries of mutant mice at 5 and 10 weeks of age exhibit temporal changes in the expression of specific Mullerian epithelial marker genes, grow in soft agar and develop ectopic invasive tumors in recipient mice, indicating that the cells are transformed. Gene profiling identified specific mRNAs and microRNAs differentially expressed in purified OSE cells derived from tumors of the mutant mice compared with wild-type OSE cells. Mapping of transcripts or genes between the mouse OSE mutant data sets, the Kras signature from human cancer cell lines and the human ovarian tumor array data sets, documented significant overlap, indicating that KRAS is a key driver of OSE transformation in this context. Two key hallmarks of the mutant OSE cells in these mice are the elevated expression of the tumor-suppressor Trp53 (p53) and its microRNA target, miR-34a-c. We propose that elevated TRP53 and miR-34a-c may exert negatively regulatory effects that reduce the proliferative potential of OSE cells leading to the low-grade serous adenocarcinoma phenotype.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Carcinoma, Ovarian Epithelial
- Cell Line, Transformed
- Cell Transformation, Neoplastic/genetics
- Cells, Cultured
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/metabolism
- Cystadenocarcinoma, Serous/pathology
- Disease Models, Animal
- Epithelial Cells/metabolism
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Mice
- Mice, Knockout
- MicroRNAs/genetics
- Neoplasm Transplantation
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/metabolism
- Neoplasms, Glandular and Epithelial/pathology
- Oligonucleotide Array Sequence Analysis
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovary/cytology
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/metabolism
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- L K Mullany
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Stuckey A, Fischer A, Miller DH, Hillenmeyer S, Kim KK, Ritz A, Singh RK, Raphael BJ, Brard L, Brodsky AS. Integrated genomics of ovarian xenograft tumor progression and chemotherapy response. BMC Cancer 2011; 11:308. [PMID: 21781307 PMCID: PMC3155912 DOI: 10.1186/1471-2407-11-308] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 07/22/2011] [Indexed: 11/10/2022] Open
Abstract
Background Ovarian cancer is the most deadly gynecological cancer with a very poor prognosis. Xenograft mouse models have proven to be one very useful tool in testing candidate therapeutic agents and gene function in vivo. In this study we identify genes and gene networks important for the efficacy of a pre-clinical anti-tumor therapeutic, MT19c. Methods In order to understand how ovarian xenograft tumors may be growing and responding to anti-tumor therapeutics, we used genome-wide mRNA expression and DNA copy number measurements to identify key genes and pathways that may be critical for SKOV-3 xenograft tumor progression. We compared SKOV-3 xenografts treated with the ergocalciferol derived, MT19c, to untreated tumors collected at multiple time points. Cell viability assays were used to test the function of the PPARγ agonist, Rosiglitazone, on SKOV-3 cell growth. Results These data indicate that a number of known survival and growth pathways including Notch signaling and general apoptosis factors are differentially expressed in treated vs. untreated xenografts. As tumors grow, cell cycle and DNA replication genes show increased expression, consistent with faster growth. The steroid nuclear receptor, PPARγ, was significantly up-regulated in MT19c treated xenografts. Surprisingly, stimulation of PPARγ with Rosiglitazone reduced the efficacy of MT19c and cisplatin suggesting that PPARγ is regulating a survival pathway in SKOV-3 cells. To identify which genes may be important for tumor growth and treatment response, we observed that MT19c down-regulates some high copy number genes and stimulates expression of some low copy number genes suggesting that these genes are particularly important for SKOV-3 xenograft growth and survival. Conclusions We have characterized the time dependent responses of ovarian xenograft tumors to the vitamin D analog, MT19c. Our results suggest that PPARγ promotes survival for some ovarian tumor cells. We propose that a combination of regulated expression and copy number can identify genes that are likely important for chemotherapy response. Our findings suggest a new approach to identify candidate genes that are critical for anti-tumor therapy.
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Affiliation(s)
- Ashley Stuckey
- Molecular Therapeutics Laboratory, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants7 Hospital, Alpert Medical School of Brown University, Providence, RI 02905, USA
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Anglesio MS, George J, Kulbe H, Friedlander M, Rischin D, Lemech C, Power J, Coward J, Cowin PA, House CM, Chakravarty P, Gorringe KL, Campbell IG, Australian Ovarian Cancer Study Group, Okamoto A, Birrer MJ, Huntsman DG, de Fazio A, Kalloger SE, Balkwill F, Gilks CB, Bowtell DD. IL6-STAT3-HIF signaling and therapeutic response to the angiogenesis inhibitor sunitinib in ovarian clear cell cancer. Clin Cancer Res 2011; 17:2538-48. [PMID: 21343371 DOI: 10.1158/1078-0432.ccr-10-3314] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Collaborators] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE Ovarian clear cell adenocarcinoma (OCCA) is an uncommon histotype that is generally refractory to platinum-based chemotherapy. We analyze here the most comprehensive gene expression and copy number data sets, to date, to identify potential therapeutic targets of OCCA. EXPERIMENTAL DESIGN Gene expression and DNA copy number were carried out using primary human OCCA tumor samples, and findings were confirmed by immunohistochemistry on tissue microarrays. Circulating interleukin (IL) 6 levels were measured in serum from patients with OCCA or high-grade serous cancers and related to progression-free and overall survival. Two patients were treated with sunitinib, and their therapeutic responses were measured clinically and by positron emission tomography. RESULTS We find specific overexpression of the IL6-STAT3-HIF (interleukin 6-signal transducer and activator of transcription 3-hypoxia induced factor) pathway in OCCA tumors compared with high-grade serous cancers. Expression of PTHLH and high levels of circulating IL6 in OCCA patients may explain the frequent occurrence of hypercalcemia of malignancy and thromboembolic events in OCCA. We describe amplification of several receptor tyrosine kinases, most notably MET, suggesting other potential therapeutic targets. We report sustained clinical and functional imaging responses in two OCCA patients with chemotherapy-resistant disease who were treated with sunitinib, thus showing significant parallels with renal clear cell cancer. CONCLUSIONS Our findings highlight important therapeutic targets in OCCA, suggest that more extensive clinical trials with sunitinib in OCCA are warranted, and provide significant impetus to the growing realization that OCCA is molecularly and clinically distinct to other forms of ovarian cancer.
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Collaborators
D Bowtell, A Green, P Webb, A deFazio, D Gertig,
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Bayani J, Marrano P, Graham C, Zheng Y, Li L, Katsaros D, Lassus H, Butzow R, Squire JA, Diamandis EP. Genomic instability and copy-number heterogeneity of chromosome 19q, including the kallikrein locus, in ovarian carcinomas. Mol Oncol 2011; 5:48-60. [PMID: 20800559 PMCID: PMC3110681 DOI: 10.1016/j.molonc.2010.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 08/03/2010] [Accepted: 08/04/2010] [Indexed: 12/28/2022] Open
Abstract
Many tissue kallikrein (KLK) genes and proteins are candidate diagnostic, prognostic and predictive biomarkers for ovarian cancer (OCa). We previously demonstrated that the KLK locus (19q13.3/4) is subject to copy-number gains and structural rearrangements in a pilot study of cell lines and ovarian cancer primary tissues, shown to overexpress KLK gene family members. To determine the overall frequency of genomic instability and copy-number changes, a retrospective study was conducted using formalin-fixed paraffin embedded (FFPE) tissues. Eighty-one chemotherapy naïve serous OCas were examined using 3-colour fluorescence in situ hybridization (FISH) to identify structural and numerical changes on 19q, including the KLK locus; in addition to immunohistochemistry (IHC) for KLK6, which has been shown to be overexpressed in OCa. The KLK locus was subject to copy-number changes in ∼83% of cases: net gain in 51%, net loss in 30% and amplified in 2%; and found to be chromosomally unstable (p < 0.001). All cases showed a wide range of immuoreactivity for KLK6 by IHC. Although no strong correlation could be found with copy-number, the latter was contributing factor to the observed KLK6 protein overexpression. Moreover, univariate and multivariate analyses showed an association between the net loss of the KLK locus and longer disease-free survival. Interestingly, FISH analyses indicated that chromosome 19q was subjected to structural rearrangement in 62% of cases and was significantly correlated to tumor grade (p < 0.001). We conclude that numerical and structural aberrations of chromosome 19q, affect genes including the KLK gene members, may contribute to ovarian carcinoma progression and aggressiveness.
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Affiliation(s)
- Jane Bayani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, 6th Floor, Room 6-201, Box 32, 60 Murray Street, Toronto, Ontario M5T 3L9, Canada
| | - Paula Marrano
- Department of Laboratory Medicine and Pathobiology, Hospital for Sick Children, 555 University Ave., 3rd Floor, Toronto, Ontario M5G 1X8, Canada
| | - Cassandra Graham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Hospital for Sick Children, 555 University Ave., 3rd Floor, Toronto, Ontario M5G 1X8, Canada
| | - Yingye Zheng
- Department of Biostatistics & Bioinfomatics, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, PO Box 19024, Seattle, WA 98109 1024, USA
| | - Lin Li
- Department of Biostatistics & Bioinfomatics, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, PO Box 19024, Seattle, WA 98109 1024, USA
| | - Dionyssios Katsaros
- Department of Obstetrics and Gynecology, University of Turin, via Ventimiglia 3, 10126 Torino, Italy
| | - Heini Lassus
- Department of Pathology, University of Helsinki, Research Laboratory, Haartmaninkatu 8 FIN-00029 HUS Helsinki, Finland
| | - Ralf Butzow
- Department of Pathology, University of Helsinki, Research Laboratory, Haartmaninkatu 8 FIN-00029 HUS Helsinki, Finland
| | - Jeremy A. Squire
- Department of Laboratory Medicine and Pathobiology, Queen's University, Kingston General Hospital, Translational Laboratory Research, NCIC Clinical Trials Group, Room 201e, 88 Stuart St Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, 6th Floor, Room 6-201, Box 32, 60 Murray Street, Toronto, Ontario M5T 3L9, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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Abstract
Germline mutation in either BRCA1 or BRCA2 is associated with an increased risk of ovarian cancer, particularly the most common invasive histotype - serous carcinoma. In addition, serous ovarian cancers have an unusually high frequency of other molecular events involving BRCA pathway dysfunction. Recent findings show a high frequency of TP53 mutation, chromosomal instability, distinct molecular subtypes and DNA copy number-driven changes in gene expression. These findings suggest a model in which homologous recombination repair deficiency initiates a cascade of molecular events that sculpt the evolution of high-grade serous ovarian cancer and dictate its response to therapy.
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Affiliation(s)
- David D L Bowtell
- Peter MacCallum Cancer Centre, Department of Biochemistry, University of Melbourne, Melbourne 3002, Australia.
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Cowin PA, Anglesio M, Etemadmoghadam D, Bowtell DDL. Profiling the cancer genome. Annu Rev Genomics Hum Genet 2010; 11:133-59. [PMID: 20590430 DOI: 10.1146/annurev-genom-082509-141536] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer profiling studies have had a profound impact on our understanding of the biology of cancers in a number of ways, including providing insights into the biological heterogeneity of specific cancer types, identification of novel oncogenes and tumor suppressors, and defining pathways that interact to drive the growth of individual cancers. Several large-scale genomic studies are underway that aim to catalog all biologically significant mutational events in each cancer type, and these findings will allow researchers to understand how mutational networks function within individual tumors. The identification of molecular predictive and prognostic tools to facilitate treatment decisions is an important step for individualized patient therapy and, ultimately, in improving patient outcomes. Whereas there are still significant challenges to implementing genomic testing and targeted therapy into routine clinical practice, rapid technological advancements provide hope for overcoming these obstacles.
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Affiliation(s)
- Prue A Cowin
- Peter MacCallum Cancer Center, East Melbourne, Australia 3002.
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Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. PLoS One 2010; 5:e9983. [PMID: 20386695 PMCID: PMC2851616 DOI: 10.1371/journal.pone.0009983] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 03/07/2010] [Indexed: 01/02/2023] Open
Abstract
Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (>40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r≥0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2.
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28
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Dhiman N, Smith DI, Poland GA. Next-generation sequencing: a transformative tool for vaccinology. Expert Rev Vaccines 2009; 8:963-7. [PMID: 19627178 PMCID: PMC2843135 DOI: 10.1586/erv.09.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neelam Dhiman
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA and Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, MN 55905, USA, Tel.: +1 507 266 3065, Fax: +1 507 266 4716,
| | - David I Smith
- Laboratory of Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA, Tel.: +1 507 266 0309, Fax: +1 507 266 4716,
| | - Gregory A Poland
- Director, Mayo Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, USA, Tel.: +1 507 284 4968, Fax: +1 507 266 4716, and Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, MN 55905, USA
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29
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Large-scale genomic analysis of ovarian carcinomas. Mol Oncol 2008; 3:157-64. [PMID: 19383377 DOI: 10.1016/j.molonc.2008.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 12/08/2008] [Accepted: 12/11/2008] [Indexed: 01/31/2023] Open
Abstract
Epithelial ovarian cancers are typified by frequent genomic aberrations that have been difficult to unravel. Recently, high-resolution array technologies have provided the first glimpse of the remarkable complexity of these aberrations with some ovarian cancers containing hundreds of copy number breakpoints, micro-deletions and amplifications. Many of these alterations contain cancer-related genes suggesting that the majority is disease-associated and not just the product of random genomic instability. Future developments such as next-generation sequencing and integrated analysis of data from multiple array platforms on large numbers of samples are poised to revolutionize our understanding of this complex disease.
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