1
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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2
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Chen D, Cao Y, Tang H, Zang L, Yao N, Zhu Y, Jiang Y, Zhai S, Liu Y, Shi M, Zhao S, Wang W, Wen C, Peng C, Chen H, Deng X, Jiang L, Shen B. Comprehensive machine learning-generated classifier identifies pro-metastatic characteristics and predicts individual treatment in pancreatic cancer: A multicenter cohort study based on super-enhancer profiling. Theranostics 2023; 13:3290-3309. [PMID: 37351165 PMCID: PMC10283048 DOI: 10.7150/thno.84978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/13/2023] [Indexed: 06/24/2023] Open
Abstract
Rationale: Accumulating evidence illustrated that the reprogramming of the super-enhancers (SEs) landscape could promote the acquisition of metastatic features in pancreatic cancer (PC). Given the anatomy-based TNM staging is limited by the heterogeneous clinical outcomes in treatment, it is of great clinical significance to tailor individual stratification and to develop alternative therapeutic strategies for metastatic PC patients based on SEs. Methods: In our study, ChIP-Seq analysis for H3K27ac was performed in primary pancreatic tumors (PTs) and hepatic metastases (HMs). Bootstrapping and univariate Cox analysis were implemented to screen prognostic HM-acquired, SE-associated genes (HM-SE genes). Then, based on 1705 PC patients from 14 multicenter cohorts, 188 machine-learning (ML) algorithm integrations were utilized to develop a comprehensive super-enhancer-related metastatic (SEMet) classifier. Results: We established a novel SEMet classifier based on 38 prognostic HM-SE genes. Compared to other clinical traits and 33 published signatures, the SEMet classifier possessed robust and powerful performance in predicting prognosis. In addition, patients in the SEMetlow subgroup owned dismal survival rates, more frequent genomic alterations, and more activated cancer immunity cycle as well as better benefits in immunotherapy. Remarkably, there existed a tight correlation between the SEMetlow subgroup and metastatic phenotypes of PC. Among 18 SEMet genes, we demonstrated that E2F7 may promote PC metastasis through the upregulation of TGM2 and DKK1. Finally, after in silico screening of potential compounds targeted SEMet classifier, results revealed that flumethasone could enhance the sensitivity of metastatic PC to routine gemcitabine chemotherapy. Conclusion: Overall, our study provided new insights into personalized treatment approaches in the clinical management of metastatic PC patients.
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Affiliation(s)
- Dongjie Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yizhi Cao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Haoyu Tang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Longjun Zang
- Department of General Surgery, Taiyuan Central Hospital, Shanxi, P.R. China
| | - Na Yao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Youwei Zhu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yongsheng Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shuyu Zhai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yihao Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Weishen Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Chenlei Wen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Chenghong Peng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
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3
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Ding SM, Lu AL, Xu BQ, Shi SH, Edoo MIA, Zheng SS, Li QY. Accuracy of brush cytology in biliopancreatic strictures: a single-center cohort study. J Int Med Res 2021; 49:300060520987771. [PMID: 33557655 PMCID: PMC7876769 DOI: 10.1177/0300060520987771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Objective False positive and negative results are associated with biliary tract cell
brushing cytology during endoscopic retrograde cholangiopancreatography
(ERCP). The causes are uncertain. The purpose of this study was to evaluate
the accuracy of diagnoses made via cell brushing in our center, and to
explore the factors influencing diagnosis. Methods The clinical data of patients who underwent cell brushing at our center from
January 2016 to August 2019 were retrospectively analyzed. These included
age, gender, stricture location, thickness of the bile duct wall in the
narrow segment, maximum diameter of the biliary duct above the stricture,
number of cell brush smears, carbohydrate antigen 19-9, and carcinoembryonic
antigen. Positive brush cytology results were compared with results of
surgical histology or tumor biopsy as well as with the patient’s clinical
course. Results Of the 48 patients who underwent cell brushing cytology, 27 (56.3%) had
positive results. The sensitivity and specificity of biliary duct cell
brushing was 79.4%, and 85.7%, respectively. None of the above-mentioned
factors were associated with positive cytology brushing results. Conclusions Cell brushing cytology remains a reliable method for diagnosis of
pancreaticobiliary malignancies.
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Affiliation(s)
- Song-Ming Ding
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, Zhejiang, P.R. China
| | - Ai-Li Lu
- Division of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Bing-Qian Xu
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, Zhejiang, P.R. China
| | - Shao-Hua Shi
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, Zhejiang, P.R. China
| | - Muhammad Ibrahim Alhadi Edoo
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health; Key Laboratory of Organ Transplantation, Zhejiang Province; Hangzhou, Zhejiang, P.R. China.,Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Shu-Sen Zheng
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, Zhejiang, P.R. China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health; Key Laboratory of Organ Transplantation, Zhejiang Province; Hangzhou, Zhejiang, P.R. China.,Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Qi-Yong Li
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University, Shulan International Medical College, Hangzhou, Zhejiang, P.R. China
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Hata T, Suenaga M, Marchionni L, Macgregor-Das A, Yu J, Shindo K, Tamura K, Hruban RH, Goggins M. Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1723-1733. [PMID: 29684357 PMCID: PMC6024190 DOI: 10.1016/j.ajpath.2018.03.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/23/2018] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
To obtain a better understanding of the genetic alterations of high-grade pancreatic intraepithelial neoplasia (HG-PanIN), we performed whole-genome copy number analysis by using single nucleotide polymorphism microarrays and targeted next-generation sequencing of 11 microdissected HG-PanIN and two low-grade PanIN lesions associated with HG-PanIN. HG-PanIN mutation profiles were compared with those of their associated invasive pancreatic ductal adenocarcinoma. All PanIN lesions harbored somatic KRAS mutations. The most common copy number losses in the HG-PanIN were at the CDKN2A (9p21), TP53 (17p13), and SMAD4 (18q21) loci. Chromosomal losses in HG-PanIN were also found at 6p25-p24, 6q11-q27, 12q24, and 17q23-q24. Biallelic inactivation of CDKN2A and TP53 was detected in five of eight and in three of eight evaluable PanIN lesions, respectively. None of the HG-PanIN lesions had SMAD4 mutations or homozygous deletion. Copy number gains were noted at the MYC (8q24) and CCNE1 (19q12) loci and at 1q25-q31. Four HG-PanINs and one low-grade PanIN harbored chromothripsis-like regions. Five of seven pancreatic ductal adenocarcinomas evaluated had additional mutations that were not found in their associated HG-PanIN. HG-PanIN harbors widespread copy number alterations and commonly shows evidence of biallelic inactivation of CDKN2A and TP53 but not SMAD4. Chromothripsis events contribute to the copy number alterations of HG-PanIN.
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Affiliation(s)
- Tatsuo Hata
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Masaya Suenaga
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Luigi Marchionni
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anne Macgregor-Das
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jun Yu
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Koji Shindo
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Koji Tamura
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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5
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Rausch V, Krieg A, Camps J, Behrens B, Beier M, Wangsa D, Heselmeyer-Haddad K, Baldus SE, Knoefel WT, Ried T, Stoecklein NH. Array comparative genomic hybridization of 18 pancreatic ductal adenocarcinomas and their autologous metastases. BMC Res Notes 2017; 10:560. [PMID: 29110683 PMCID: PMC5674747 DOI: 10.1186/s13104-017-2886-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 10/31/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Mortality rates of pancreatic cancer remain high, which is mainly due to advanced disease and metastasis. We hypothesized that genomic copy number alterations are enriched in metastatic cells compared to autologous primary tumors, which may inform on cancer-related pathways possibly serving as potential targets for specific therapies. We investigated 18 pancreatic ductal adenocarcinomas, including 39 lymph node and 5 distant metastases after surgical resection. Analysis was performed with array-based comparative genomic hybridization (aCGH). RESULTS Metastases acquire a higher frequency of copy number alterations with the highest in distant metastasis (median = 42, lymph node metastases: median = 23, primary tumors: median = 17). In lymph node metastases, gains were prevalent on chromosome bands 8q11.23-q24.3, 12q14.1, 17p12.1, 21q22.12, and losses on 3p21.31, 4p14, 8p23.3-p11.21,17p12-11.2. Genes on amplified regions are involved in cancer-related pathways such as WNT-signaling, also involved in metastasis. CONCLUSIONS Pancreatic cancers show a high degree of intratumor heterogeneity, which could lead to resistance of chemotherapy and worse outcome. ACGH analysis reveals regions preferentially gained or lost in synchronous metastases encoding for genes involved in cancer-related pathways, which could lead to novel therapeutic opportunities.
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Affiliation(s)
- Valentin Rausch
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Andreas Krieg
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Jordi Camps
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Present Address: Gastrointestinal and Pancreatic Oncology Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Bianca Behrens
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Manfred Beier
- Institute of Human Genetics and Anthropology, Heinrich-Heine-University and University Hospital, Duesseldorf, Germany
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Stephan E. Baldus
- Department of Pathology, Heinrich-Heine-University and University Hospital, Duesseldorf, Germany
| | - Wolfram T. Knoefel
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Thomas Ried
- Section of Cancer Genomics, Genetics Branch, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Center for Cancer Research, Bethesda, MD USA
| | - Nikolas H. Stoecklein
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
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6
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Fessart D, Domblides C, Avril T, Eriksson LA, Begueret H, Pineau R, Malrieux C, Dugot-Senant N, Lucchesi C, Chevet E, Delom F. Secretion of protein disulphide isomerase AGR2 confers tumorigenic properties. eLife 2016; 5. [PMID: 27240165 PMCID: PMC4940162 DOI: 10.7554/elife.13887] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/28/2016] [Indexed: 12/31/2022] Open
Abstract
The extracellular matrix (ECM) plays an instrumental role in determining the spatial orientation of epithelial polarity and the formation of lumens in glandular tissues during morphogenesis. Here, we show that the Endoplasmic Reticulum (ER)-resident protein anterior gradient-2 (AGR2), a soluble protein-disulfide isomerase involved in ER protein folding and quality control, is secreted and interacts with the ECM. Extracellular AGR2 (eAGR2) is a microenvironmental regulator of epithelial tissue architecture, which plays a role in the preneoplastic phenotype and contributes to epithelial tumorigenicity. Indeed, eAGR2, is secreted as a functionally active protein independently of its thioredoxin-like domain (CXXS) and of its ER-retention domain (KTEL), and is sufficient, by itself, to promote the acquisition of invasive and metastatic features. Therefore, we conclude that eAGR2 plays an extracellular role independent of its ER function and we elucidate this gain-of-function as a novel and unexpected critical ECM microenvironmental pro-oncogenic regulator of epithelial morphogenesis and tumorigenesis. DOI:http://dx.doi.org/10.7554/eLife.13887.001 Cancer cells multiply abnormally fast and therefore produce protein molecules faster than normal cells. To avoid becoming stressed by this overproduction, cancer cells make use of proteins that fold the new proteins inside the cell. One of these protein folders is called anterior gradient-2 (or AGR2 for short) and is produced at high levels in so-called epithelial cancers, such as breast and lung cancer. Previous research has shown that AGR2 inside cancer cells can help them grow and survive and AGR2 can also be found outside cells, such as in the blood or the urine of cancer patients. Therefore some researchers have suggested that measuring the levels of AGR2 in bodily fluids may be a useful marker for detecting cancers. Fessart et al. hypothesized that – apart from becoming a promising diagnostic tool – the AGR2 protein itself, specifically when found outside cells, might make cancer cells more aggressive. Fessart et al. used a range of techniques to test this hypothesis. For example, healthy lung cells and lung cancer cells were grown into miniature replicas of lung organs in the laboratory, and in a key experiment, AGR2 was added to the lung organoids grown from the healthy cells. The addition of AGR2 protein was enough to change the non-tumor organoids into tumor organoids and boosted their growth about ten-fold. Further experiments then revealed that AGR2 also makes cells more invasive and capable of moving, both important features of aggressive cancer cells. Overall, Fessart et al. have proven that AGR2 is a signalling molecule found outside cancer cells that makes them more aggressive. In future, more research addressing how AGR2 achieves this may lead to new therapeutic strategies against some forms of cancer. DOI:http://dx.doi.org/10.7554/eLife.13887.002
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Affiliation(s)
- Delphine Fessart
- Oncogenesis, Stress and Signaling Laboratory, ERL440 Inserm, Université de Rennes 1, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.,INSERM U1218, Actions for onCogenesis understanding and Target Identification in ONcology (ACTION), Bordeaux, France.,Bergonié Cancer Institute, Bordeaux, France
| | | | - Tony Avril
- Oncogenesis, Stress and Signaling Laboratory, ERL440 Inserm, Université de Rennes 1, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | | | - Raphael Pineau
- Animalerie mutualisée, Université de Bordeaux, Bordeaux, France
| | - Camille Malrieux
- INSERM U1218, Actions for onCogenesis understanding and Target Identification in ONcology (ACTION), Bordeaux, France.,Bergonié Cancer Institute, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | | | - Carlo Lucchesi
- Bergonié Cancer Institute, Bordeaux, France.,Site de Recherche Intégrée sur le Cancer, Bordeaux Recherche Intégrée en Oncologie, Bordeaux, France
| | - Eric Chevet
- Oncogenesis, Stress and Signaling Laboratory, ERL440 Inserm, Université de Rennes 1, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Frederic Delom
- INSERM U1218, Actions for onCogenesis understanding and Target Identification in ONcology (ACTION), Bordeaux, France.,Bergonié Cancer Institute, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
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7
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Afify A, Huang EC, Jeong M, Urayama S. Immunoisolation of pancreatic epithelial cells from endoscopic ultrasound-guided fine needle aspirates with magnetic beads for downstream molecular application. Diagn Cytopathol 2015; 44:32-8. [DOI: 10.1002/dc.23383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/24/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Alaa Afify
- Division of Cytopathology, Department of Pathology and Laboratory Medicine; University of California, Davis; Sacramento California 95817
| | - Eric C. Huang
- Division of Cytopathology, Department of Pathology and Laboratory Medicine; University of California, Davis; Sacramento California 95817
| | - Matthew Jeong
- Division of Gastroenterology and Hepatology, Department of Internal Medicine; University of California; Davis California
| | - Shiro Urayama
- Division of Gastroenterology and Hepatology, Department of Internal Medicine; University of California; Davis California
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8
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Liang JW, Shi ZZ, Shen TY, Che X, Wang Z, Shi SS, Xu X, Cai Y, Zhao P, Wang CF, Zhou ZX, Wang MR. Identification of genomic alterations in pancreatic cancer using array-based comparative genomic hybridization. PLoS One 2014; 9:e114616. [PMID: 25502777 PMCID: PMC4263743 DOI: 10.1371/journal.pone.0114616] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/12/2014] [Indexed: 12/13/2022] Open
Abstract
Background Genomic aberration is a common feature of human cancers and also is one of the basic mechanisms that lead to overexpression of oncogenes and underexpression of tumor suppressor genes. Our study aims to identify frequent genomic changes in pancreatic cancer. Materials and Methods We used array comparative genomic hybridization (array CGH) to identify recurrent genomic alterations and validated the protein expression of selected genes by immunohistochemistry. Results Sixteen gains and thirty-two losses occurred in more than 30% and 60% of the tumors, respectively. High-level amplifications at 7q21.3–q22.1 and 19q13.2 and homozygous deletions at 1p33–p32.3, 1p22.1, 1q22, 3q27.2, 6p22.3, 6p21.31, 12q13.2, 17p13.2, 17q21.31 and 22q13.1 were identified. Especially, amplification of AKT2 was detected in two carcinomas and homozygous deletion of CDKN2C in other two cases. In 15 independent validation samples, we found that AKT2 (19q13.2) and MCM7 (7q22.1) were amplified in 6 and 9 cases, and CAMTA2 (17p13.2) and PFN1 (17p13.2) were homozygously deleted in 3 and 1 cases. AKT2 and MCM7 were overexpressed, and CAMTA2 and PFN1 were underexpressed in pancreatic cancer tissues than in morphologically normal operative margin tissues. Both GISTIC and Genomic Workbench software identified 22q13.1 containing APOBEC3A and APOBEC3B as the only homozygous deletion region. And the expression levels of APOBEC3A and APOBEC3B were significantly lower in tumor tissues than in morphologically normal operative margin tissues. Further validation showed that overexpression of PSCA was significantly associated with lymph node metastasis, and overexpression of HMGA2 was significantly associated with invasive depth of pancreatic cancer. Conclusion These recurrent genomic changes may be useful for revealing the mechanism of pancreatic carcinogenesis and providing candidate biomarkers.
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Affiliation(s)
- Jian-Wei Liang
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhi-Zhou Shi
- Faculty of Medicine, Kunming University of Science and Technology, Kunming, China
- * E-mail: (MRW); (ZZS)
| | - Tian-Yun Shen
- Faculty of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xu Che
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zheng Wang
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Su-Sheng Shi
- Department of Pathology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xin Xu
- State Key Laboratory of Molecular Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yan Cai
- State Key Laboratory of Molecular Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ping Zhao
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Cheng-Feng Wang
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhi-Xiang Zhou
- Department of Abdominal Surgical Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, Cancer Hospital and Institute, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- * E-mail: (MRW); (ZZS)
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9
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Molecular characterization of patient-derived human pancreatic tumor xenograft models for preclinical and translational development of cancer therapeutics. Neoplasia 2014; 15:1138-50. [PMID: 24204193 DOI: 10.1593/neo.13922] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 12/16/2022] Open
Abstract
Preclinical evaluation of novel cancer agents requires models that accurately reflect the biology and molecular characteristics of human tumors. Molecular profiles of eight pancreatic ductal adenocarcinoma patient tumors were compared to corresponding passages of xenografts obtained by grafting tumor fragments into immunocompromised mice. Molecular characterization was performed by copy number analysis, gene expression and microRNA microarrays, mutation analysis, short tandem repeat (STR) profiling, and immunohistochemistry. Xenografts were found to be highly representative of their respective tumors, with a high degree of genetic stability observed by STR profiling and mutation analysis. Copy number variation (CNV) profiles of early and late xenograft passages were similar, with recurrent losses on chromosomes 1p, 3p, 4q, 6, 8p, 9, 10, 11q, 12p, 15q, 17, 18, 20p, and 21 and gains on 1q, 5p, 8q, 11q, 12q, 13q, 19q, and 20q. Pearson correlations of gene expression profiles of tumors and xenograft passages were above 0.88 for all models. Gene expression patterns between early and late passage xenografts were highly stable for each individual model. Changes observed in xenograft passages largely corresponded to human stromal compartment genes and inflammatory processes. While some differences exist between the primary tumors and corresponding xenografts, the molecular profiles remain stable after extensive passaging. Evidence for stability in molecular characteristics after several rounds of passaging lends confidence to clinical relevance and allows for expansion of models to generate the requisite number of animals required for cohorts used in drug screening and development studies.
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10
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Gutiérrez ML, Muñoz-Bellvis L, Sarasquete ME, Hernández-Mejía DG, Abad MDM, Bengoechea O, Corchete L, González-González M, García-García J, Gonzalez M, Mota I, Orfao A, Sayagues JM. Altered interphase fluorescence in situ hybridization profiles of chromosomes 4, 8q24, and 9q34 in pancreatic ductal adenocarcinoma are associated with a poorer patient outcome. J Mol Diagn 2014; 16:648-59. [PMID: 25157969 DOI: 10.1016/j.jmoldx.2014.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/21/2014] [Accepted: 06/24/2014] [Indexed: 02/09/2023] Open
Abstract
Most patients with pancreatic ductal adenocarcinoma (PDAC) die within 6 months of diagnosis. However, 20% to 25% patients undergoing total tumor resection remain alive and disease-free 5 years after diagnostic surgery. Few studies on tumor markers have predicted patient prognosis and/or survival. We evaluated the effect of tumor cytogenetic copy number changes detected by interphase fluorescence in situ hybridization on overall survival (OS) of 55 PDAC patients. The prognostic value of copy number changes showing an effect on OS was validated in an external cohort of 44 surgically resected PDAC patients by comparative genomic hybridization arrays, and the genes coded in altered chromosomes with prognostic value were identified by high-density single-nucleotide polymorphism arrays in 20 cases. Copy number changes of chromosomes 4 and 9q34 with gains of 8q24 were independently associated with shorter OS. On the basis of these three chromosomal alterations, a score is proposed that identifies patients with significantly different (P < 0.001) 5-year OS rates: 60% ± 20%, 16% ± 8%, and 0% ± 0%, respectively. Our results show an association between tumor cytogenetics and OS of PDAC patients and provide the basis for further prognostic stratification of patients undergoing complete tumor resection. Further studies to identify specific genes coded in these chromosomes and their functional consequences are necessary to understand the clinical effect of these changes.
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Affiliation(s)
- María L Gutiérrez
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
| | - Luis Muñoz-Bellvis
- Department of General and Digestive Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - María E Sarasquete
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Salamanca, Spain
| | - David G Hernández-Mejía
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
| | - María del Mar Abad
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Oscar Bengoechea
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Luis Corchete
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Salamanca, Spain
| | - María González-González
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
| | - Jacinto García-García
- Department of General and Digestive Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Marcos Gonzalez
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Salamanca, Spain
| | - Ines Mota
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.
| | - José M Sayagues
- Cytometry General Service-NUCLEUS, Department of Medicine and Cancer Center Research and Institute of Molecular Biology and Cellular Oncology, Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
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11
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Metastasis-associated in colon cancer 1 is a novel survival-related biomarker for human patients with renal pelvis carcinoma. PLoS One 2014; 9:e100161. [PMID: 24949951 PMCID: PMC4064998 DOI: 10.1371/journal.pone.0100161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/22/2014] [Indexed: 12/23/2022] Open
Abstract
Metastasis-associated in colon cancer 1 (MACC1) has recently been identified as a novel independent prognostic indicator for metastasis occurrence, overall survival and cancer-free survival for patients with colon cancer and other solid tumors. In this study, we investigated the role of MACC1 in the development and progression of renal pelvis carcinoma, a form of upper tract urothelial carcinomas. MACC1 protein has been found in the cytoplasm as well as in the nucleus of the transitional epithelial cells of the normal renal pelvis in immunohistochemical (IHC) assays. Quantitative IHC examinations revealed that MACC1 abnormal abundance in cancerous tissues might represent a biological indicator clinically suggestive of tumor malignancy in the renal pelvis. Furthermore, investigation of the association of MACC1 protein levels with clinicopathological parameters in this study has suggested a correlation of MACC1 expression with tumor-node-metastasis stage and histopathological grade of patients with renal pelvis carcinoma, with elevated MACC1 protein levels frequently associated with higher aggressiveness of the disease. Moreover, both disease-free survival and overall survival for the patients in the high MACC1 expression group were significantly lower than those in the low expression group. Multivariate analysis with a Cox proportional-hazards model suggested that MACC1 is indeed an independent prognostic indicator of overall survival and cancer-free survival for patients with renal pelvis carcinoma. Thus, MACC1 may represent a promising prognostic biomarker candidate, as well as a potential therapeutic target for this disease.
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12
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Hagemann C, Fuchs S, Monoranu CM, Herrmann P, Smith J, Hohmann T, Grabiec U, Kessler AF, Dehghani F, Löhr M, Ernestus RI, Vince GH, Stein U. Impact of MACC1 on human malignant glioma progression and patients' unfavorable prognosis. Neuro Oncol 2013; 15:1696-709. [PMID: 24220141 DOI: 10.1093/neuonc/not136] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Metastasis-associated in colon cancer 1 (MACC1) has been established as an independent prognostic indicator of metastasis formation and metastasis-free survival for patients with colon cancer and other solid tumors. However, no data are available concerning MACC1 expression in human astrocytic tumors. Glioblastoma multiforme (GBM) is the most prevalent primary brain tumor of adulthood, and due to its invasive and rapid growth, patients have unfavorable prognoses. Although these tumors rarely metastasize, their invasive and migratory behavior is similar to those of metastatic cells of tumors of different origin. Thus, we hypothesized that MACC1 may be involved in progression of human gliomas. METHODS We performed real-time measurements of proliferation and migration in MACC1-transfected GBM cell lines (U138, U251) and evaluated tumor formation in organotypic hippocampal slice cultures of mice. Semiquantitative and quantitative real-time reverse transcription PCR analyses were performed for MACC1 and for its transcriptional target c-Met in human astrocytoma of World Health Organization grade II (low-grade astrocytoma) and GBM biopsies. Data were validated by MACC1 immunohistochemistry in independent matched samples of low-grade astrocytoma and GBM. RESULTS MACC1 increases the proliferative, migratory, and tumor-formation abilities of GBM cells. The c-Met inhibitor crizotinib reduced MACC1-induced migration and tumor formation in organotypic hippocampal slice cultures of mice. Analyzing patients' biopsies, MACC1 expression increased concomitantly with increasing World Health Organization grade. Moreover, MACC1 expression levels allowed discrimination of dormant and recurrent low-grade astrocytomas and of primary and secondary GBM. Strong MACC1 expression correlated with reduced patient survival. CONCLUSIONS MACC1 may represent a promising biomarker for prognostication and a new target for treatment of human gliomas.
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Affiliation(s)
- Carsten Hagemann
- Corresponding Author: Ulrike Stein, PhD, Experimental and Clinical Research Center, Charité University Medicine Berlin and the Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
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13
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Gress TM, Kestler HA, Lausser L, Fiedler L, Sipos B, Michalski CW, Werner J, Giese N, Scarpa A, Buchholz M. Differentiation of multiple types of pancreatico-biliary tumors by molecular analysis of clinical specimens. J Mol Med (Berl) 2011; 90:457-64. [PMID: 22119958 DOI: 10.1007/s00109-011-0832-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/11/2011] [Accepted: 10/28/2011] [Indexed: 12/30/2022]
Abstract
Timely and accurate diagnosis of pancreatic ductal adenocarcinoma (PDAC) is critical in order to provide adequate treatment to patients. However, the clinical signs and symptoms of PDAC are shared by several types of malignant or benign tumors which may be difficult to differentiate from PDAC with conventional diagnostic procedures. Among others, these include ampullary cancers, solid pseudopapillary tumors, and adenocarcinomas of the distant bile duct, as well as inflammatory masses developing in chronic pancreatitis. Here, we report an approach to accurately differentiate between these different types of pancreatic masses based on molecular analysis of biopsy material. A total of 156 bulk tissue and fine needle aspiration biopsy samples were analyzed using a dedicated diagnostic cDNA array and a composite classification algorithm developed based on linear support vector machines. All five histological subtypes of pancreatic masses were clearly separable with 100% accuracy when using all 156 individual samples for classification. Generalized performance of the classification system was tested by 10 × 10-fold cross validation (100 test runs). Correct classification into the five diagnostic groups was demonstrated for 81.5% of 1,560 test set predictions. Performance increased to 85.3% accuracy when PDAC and distant bile duct carcinomas were combined in a single diagnostic class. Importantly, overall sensitivity of detection of malignant disease was 92.2%. The molecular diagnostic approach presented here is suitable to significantly aid in the differential diagnosis of undetermined pancreatic masses. To our knowledge, this is the first study reporting accurate differentiation between several types of pancreatico-biliary tumors in a single molecular analytical procedure.
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Affiliation(s)
- Thomas M Gress
- Division of Gastroenterology, University Hospital, Philipps-Universitaet Marburg, Marburg, Germany.
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14
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Luebke AM, Baudis M, Matthaei H, Vashist YK, Verde PE, Hosch SB, Erbersdobler A, Klein CA, Izbicki JR, Knoefel WT, Stoecklein NH. Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma. Pancreatology 2011; 12:16-22. [PMID: 22487468 DOI: 10.1016/j.pan.2011.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we tested the prognostic impact of genomic alterations in operable localized pancreatic ductal adenocarcinoma (PDAC). Fifty-two formalin-fixed and paraffin-embedded primary PDAC were laser micro-dissected and were investigated by comparative genomic hybridization after whole genome amplification using an adapter-linker PCR. Chromosomal gains and losses were correlated to clinico-pathological parameters and clinical follow-up data. The most frequent aberration was loss on chromosome 17p (65%) while the most frequent gains were detected at 2q (41%) and 8q (41%), respectively. The concomitant occurrence of losses at 9p and 17p was found to be statistically significant. Higher rates of chromosomal losses were associated with a more advanced primary tumor stage and losses at 9p and 18q were significantly associated with presence of lymphatic metastasis (chi-square: p = 0.03, p = 0.05, respectively). Deletions on chromosome 4 were of prognostic significance for overall survival and tumor recurrence (Cox-multivariate analysis: p = 0.026 and p = 0.021, respectively). In conclusion our data suggest the common alterations at chromosome 8q, 9p, 17p and 18q as well as the prognostic relevant deletions on chromosome 4q as relevant for PDAC progression. Our comprehensive data from 52 PDAC should provide a basis for future studies with a higher resolution to discover the relevant genes located within the chromosomal aberrations identified.
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MESH Headings
- Adenocarcinoma/genetics
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Chromosome Aberrations
- Chromosome Deletion
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 8
- Chromosomes, Human, Pair 9
- Comparative Genomic Hybridization
- Female
- Humans
- Male
- Middle Aged
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Prognosis
- Survival Analysis
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Affiliation(s)
- A M Luebke
- Klinik und Poliklinik für Allgemein-, Visceral- und Thoraxchirurgie, Universitätsklinikum Hamburg-Eppendorf, Germany
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15
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Funel N, Giovannetti E, Pollina LE, del Chiaro M, Mosca F, Boggi U, Campani D. Critical role of laser microdissection for genetic, epigenetic and proteomic analyses in pancreatic cancer. Expert Rev Mol Diagn 2011; 11:695-701. [PMID: 21902531 DOI: 10.1586/erm.11.62] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease, and molecular studies to unravel novel biomarkers and therapeutic targets are warranted. However, PDAC is characterized by different precursor lesions, as well as by an intense desmoplastic reaction, with islet of neoplastic cells often representing a minor population. Moreover, normal ductal cells, which are considered to be the normal counterpart of pancreatic adenocarcinoma cells, comprise approximately 5% of the total population of cells making up this organ. For all these reasons, molecular techniques to identify critical mutations, as well as the pattern of altered mRNA/microRNA/protein expression should be performed on selected pancreatic cell subpopulations. Therefore, the use of the newest laser microdissection techniques is critical for the analysis of PDAC biological characteristics. This article highlights the most recent and clinically relevant aspects of genetic, epigenetic and proteomic analyses of PDAC from the perspective of the application of laser microdissection.
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Affiliation(s)
- Niccola Funel
- Department of Surgery, Unit of Experimental Surgical Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy.
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16
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Gutiérrez ML, Muñoz-Bellvis L, Abad MDM, Bengoechea O, González-González M, Orfao A, Sayagués JM. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology. PLoS One 2011; 6:e22315. [PMID: 21811587 PMCID: PMC3141022 DOI: 10.1371/journal.pone.0022315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/19/2011] [Indexed: 11/28/2022] Open
Abstract
The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterogenity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.
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Affiliation(s)
- María Laura Gutiérrez
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Luís Muñoz-Bellvis
- Unidad de Cirugía Hepatobiliopancreática y Trasplante de Páncreas, Departamento de Cirugía, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María del Mar Abad
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Oscar Bengoechea
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María González-González
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - José María Sayagués
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
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Birnbaum DJ, Adélaïde J, Mamessier E, Finetti P, Lagarde A, Monges G, Viret F, Gonçalvès A, Turrini O, Delpero JR, Iovanna J, Giovannini M, Birnbaum D, Chaffanet M. Genome profiling of pancreatic adenocarcinoma. Genes Chromosomes Cancer 2011; 50:456-65. [PMID: 21412932 DOI: 10.1002/gcc.20870] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/15/2011] [Indexed: 02/06/2023] Open
Abstract
Pancreatic adenocarcinoma is one of the most aggressive human cancers. It displays many different chromosomal abnormalities and mutations. By using 244 K high-resolution array-comparative genomic hybridization (aCGH) we studied the genome alterations of 39 fine-needle aspirations from pancreatic adenocarcinoma and eight human adenocarcinoma pancreatic cell lines. Using both visual inspection and GISTIC analysis, recurrent losses were observed on 1p, 3p, 4p, 6, 8p, 9, 10, 11q, 15q, 17, 18, 19p, 20p, 21, and 22 and comprised several known or suspected tumor suppressor genes such as ARHGEF10, ARID1A, CDKN2A/B, FHIT, PTEN, RB1, RUNX1-3, SMAD4, STK11/LKB1, TP53, and TUSC3. Heterozygous deletion of the 1p35-p36 chromosomal region was identified in one-third of the tumors and three of the cell lines. This region, commonly deleted in human cancers, contains several tumor suppressor genes including ARID1A and RUNX3. We identified frequent genetic gains on chromosome arms 1q, 3q, 5p, 6p, 7q, 8q, 12q, 15q, 18q, 19q, and 20q. Amplifications were observed in 16 tumors. AKT2, CCND3, CDK4, FOXA2, GATA6, MDM2, MYC, and SMURF1 genes were gained or amplified. The most obvious amplification was located at 18q11.2 and targeted the GATA6 gene, which plays a predominant role in the initial specification of the pancreas and in pancreatic cell type differentiation. In conclusion, we have identified novel biomarkers and potential therapeutic targets in pancreatic adenocarcinoma.
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Affiliation(s)
- David J Birnbaum
- Centre de Recherche en Cancérologie de Marseille, Laboratoire d'Oncologie Moléculaire, UMR891 Inserm, Institut Paoli-Calmettes, Marseille, France
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18
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Tan X, Zhou L, Wang W, Wang B, Egami H, Baba H, Dai X. Genomic analysis of invasion-metastasis-related factors in pancreatic cancer cells. Exp Ther Med 2010; 1:211-216. [PMID: 23136617 DOI: 10.3892/etm_00000034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/19/2009] [Indexed: 12/21/2022] Open
Abstract
Pancreatic cancer is known to be an extremely lethal neoplasm, one of the reasons being that pancreatic cancer itself has an extremely high potential of invasion-metastasis. In our previous study, two pancreatic cancer cell lines with a different potential for invasion-metastasis, PC-1 with a low potential and PC-1.0 with a high potential of invasion-metastasis after intrapancreatic transplantation, were established in a Syrian golden hamster. To determine the invasion-metastasis-related factors, a cDNA microarray that represented a set of 27,000 genes was hybridized with a labeled cDNA probe and screened for molecular profiling analysis. Furthermore, Gene Ontology and Pathway differential expression of candidate genes was further validated using RT-PCR. One hundred and forty-one differentially expressed genes (>3.0-fold change) were identified in the present study, including 46 up-regulated genes (e.g., nup107, tjp-2 and MMP-13) and 95 down-regulated genes (e.g., Spc21, plau and CD44) in the PC-1.0 cells. Our present results suggest that a highly organized and structured process of tumor invasion-metastasis exists in the pancreas. Analysis of gene expression profiles by cDNA microarray provides useful information for clarifying the mechanism underlying this invasion and metastasis. Furthermore, the identification of invasion-metastasis-specific genes may allow us to develop new therapeutic and diagnostic targets for the invasion-metastasis of pancreatic cancer.
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Affiliation(s)
- Xiaodong Tan
- Department of Hepato-pancreato-biliary Tumor Surgery, China Medical University Shengjing Hospital, Shenyang, P.R. China
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19
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Buchholz M, Gress TM. Molecular changes in pancreatic cancer. Expert Rev Anticancer Ther 2009; 9:1487-97. [PMID: 19828010 DOI: 10.1586/era.09.107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
As with many human malignancies, pancreatic cancer is a complex genetic disorder. Several thousand disease-associated alterations on the DNA, mRNA, miRNA and protein levels have been reported to date. Some of these alterations, including a number of gatekeeper mutations, which are of pre-eminent importance for the onset and progression of the disease, have been extensively studied in primary tissues, in vitro experiments and transgenic mouse models. For the vast majority of alterations, however, data about the functional significance are lacking. The situation is complicated by the fact that no certainty exists concerning the identity of the cells that originally undergo malignant transformation nor about the precise nature and fate of premalignant lesions that are observed in pancreatic tissues.
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Affiliation(s)
- Malte Buchholz
- Klinik f. Innere Medizin, SP Gastroenterologie, Universitätsklinikum Marburg, Baldingerstrasse 35043 Marburg, Germany.
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Warner SL, Stephens BJ, Nwokenkwo S, Hostetter G, Sugeng A, Hidalgo M, Trent JM, Han H, Von Hoff DD. Validation of TPX2 as a potential therapeutic target in pancreatic cancer cells. Clin Cancer Res 2009; 15:6519-28. [PMID: 19861455 DOI: 10.1158/1078-0432.ccr-09-0077] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The targeting protein for Xklp2 (TPX2) has recently gained attention as a putative oncogene possibly amplified in several human malignancies, including pancreatic adenocarcinoma. In this work, we sought to evaluate the copy number and expression of TPX2 in pancreatic cancer cell lines and tumor tissues and to further explore the potential of TPX2 as a therapeutic target. EXPERIMENTAL DESIGN The DNA copy number and expression of the TPX2 gene were surveyed in pancreatic cancer cell lines and tumor tissues and compared with those of immortalized normal pancreatic ductal cells and normal pancreatic tissues. The cellular effects of TPX2 knockdown using small interfering RNA oligonucleotides in pancreatic cancer cells, such as growth in tissue culture, in soft agar, and in nude mice; apoptosis; and sensitivity to paclitaxel, were also investigated using various assays. RESULTS Low-copy-number TPX2 amplification was found in pancreatic cancer cell lines and low-passage pancreatic cancer tumor xenografts. TPX2 expression was upregulated in pancreatic cancer cell lines at both the mRNA and protein levels relative to the immortalized pancreatic ductal epithelial cell line HPDE6. Immunohistochemical staining of a tissue microarray showed that TPX2 expression was higher in pancreatic tumors compared with their normal counterparts. Treatment with TPX2 targeting small interfering RNAs effectively reduced pancreatic cancer cell growth in tissue culture, induced apoptosis, and inhibited growth in soft agar and in nude mice. Knockdown of TPX2 also sensitized pancreatic cancer cells to paclitaxel treatment. CONCLUSIONS Our results suggest that TPX2 might be an attractive target for pancreatic cancer therapy.
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Affiliation(s)
- Steven L Warner
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
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Legoffic A, Calvo E, Cano C, Folch-Puy E, Barthet M, Delpero JR, Ferrés-Masó M, Dagorn JC, Closa D, Iovanna J. The reg4 gene, amplified in the early stages of pancreatic cancer development, is a promising therapeutic target. PLoS One 2009; 4:e7495. [PMID: 19834624 PMCID: PMC2760775 DOI: 10.1371/journal.pone.0007495] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 09/28/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The aim of our work was to identify the genes specifically altered in pancreatic adenocarcinoma and especially those that are altered early in cancer development. METHODOLOGY/PRINCIPAL FINDINGS Gene copy number was systematically assessed with an ultra-high resolution CGH oligonucleotide microarray in DNA from samples of pancreatic cancer. Several new cancer-associated variations were observed. In this work we focused on one of them, involving the reg4 gene. Gene copy number gain of the reg4 gene was confirmed by qPCR in 14 cancer samples. It was also found with increased copy number in most PanIN3 samples. The relationship betweena gain in reg4 gene copy number and cancer development was investigated on the human pancreatic cancer cell line Mia-PaCa2 xenografted under the skin of nude mice. When cells were transfected with a vector allowing reg4 expression, they generated tumors almost twice larger in size. In addition, these tumors were more resistant to gemcitabine treatment than control tumors. Interestingly, weekly intraperitoneal administration of a monoclonal antibody to reg4 halved the size of tumors generated by Mia-PaCa2 cells, suggesting that the antibody interfered with a paracrine/autocrine mechanism involving reg4 and stimulating cancer progression. The addition of gemcitabine resulted in further reduction, tumors becoming 5 times smaller than control. Exposure to reg4 antibody resulted in a significant decrease in intra-tumor levels of pAkt, Bcl-xL, Bcl-2, survivin and cyclin D1. CONCLUSIONS/SIGNIFICANCE It was concluded that adjuvant therapies targeting reg4 could improve the standard treatment of pancreatic cancer with gemcitabine.
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Affiliation(s)
- Aude Legoffic
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille France
| | - Ezequiel Calvo
- Molecular Endocrinology and Oncology Research Center, CHUL Research Center, Québec, Canada
| | - Carla Cano
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille France
| | - Emma Folch-Puy
- Experimental Pathology Department, IIBB-CSIC-IDIBAPS, CIBERehd, Barcelona, Spain
| | - Marc Barthet
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille France
| | - Jean Robert Delpero
- Département de Chirurgie Oncologique, Institut Paoli-Calmettes, Marseille, France
| | - Montse Ferrés-Masó
- Experimental Pathology Department, IIBB-CSIC-IDIBAPS, CIBERehd, Barcelona, Spain
| | - Jean Charles Dagorn
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille France
| | - Daniel Closa
- Experimental Pathology Department, IIBB-CSIC-IDIBAPS, CIBERehd, Barcelona, Spain
| | - Juan Iovanna
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille France
- * E-mail:
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MACC1 - more than metastasis? Facts and predictions about a novel gene. J Mol Med (Berl) 2009; 88:11-8. [PMID: 19787327 DOI: 10.1007/s00109-009-0537-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 08/30/2009] [Accepted: 09/04/2009] [Indexed: 01/05/2023]
Abstract
We recently identified the metastasis-associated in colon cancer 1 (MACC1) gene by a genome-wide search for differentially expressed genes in human colon cancer tissues, metastases, and normal tissues. Based on MACC1 expression in primary colon cancers, which did not present with metastases, our negative and positive prediction for metachronous metastasis was correct in 80% and 74% of cases, respectively. The 5-year-survival was 80% for MACC1 low expressors, but 15% for individuals who showed high MACC1 expression in their primary tumors. MACC1 induces migration, invasion and proliferation in cell culture, and liver and lung metastases in xenograft models. Here, we describe features of MACC1 beyond its utility as an indicator of metastasis. We elucidate its genomic localization and organization, its predicted splice variants, and single nucleotide polymorphisms. We discuss the MACC1 protein domain structure, posttranslational modifications, its conservation through evolution, and some family ties to SH3BP4. Furthermore, we summarize the predicted expressions of MACC1 in normal and malignant human tissues. We also evaluate the MACC1 levels in the context of one of its transcriptional targets, the receptor tyrosine kinase Met that activates the hepatocyte growth factor/Met signaling pathway, leading to enhanced cell motility, invasion, and metastasis.
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Hildenbrand R, Niedergethmann M, Marx A, Belharazem D, Allgayer H, Schleger C, Ströbel P. Amplification of the urokinase-type plasminogen activator receptor (uPAR) gene in ductal pancreatic carcinomas identifies a clinically high-risk group. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 174:2246-53. [PMID: 19435784 DOI: 10.2353/ajpath.2009.080785] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The serine protease urokinase-type plasminogen activator (uPA) and its receptor (uPAR) are known to be involved in the invasion and metastasis of many solid tumors. In this study, we analyzed the role of the uPAR/uPA system in both the development and progression of pancreatic cancer in invasive ductal adenocarcinomas of the pancreas (PDA) and their premalignant precursors (PanIN lesions) in 50 patients with long-term clinical follow-up. We found overexpression of the uPAR in 48 of 50 invasive carcinomas as well as in a large proportion of high-grade PanIN lesions by immunohistochemistry and in situ hybridization. Fluorescence in situ hybridization analysis showed both high- and low-level amplification of the uPAR gene in approximately 50% of cases with strictly identical patterns between invasive cancers and their accompanying precursor lesions. These results suggest that PDA may develop from PanIN lesions along an alternative rather than a sequential molecular pathway. The detection of the gene amplification of uPAR was a highly significant, adverse prognostic parameter (P < 0.001) because it likely renders the tumors more sensitive to uPA and its proproliferative and anti-apoptotic signals. We conclude that the activation of the uPAR/uPA system is an early event in the development of PDA and that uPAR gene amplifications identify a subgroup of particularly aggressive tumors, making the uPAR/uPA system a critical and highly promising target for therapeutic interventions.
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Affiliation(s)
- Ralf Hildenbrand
- Institut für Pathologie, Heilsbachstrasse 15, 53123 Bonn, Germany.
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Zhu Z, Gao W, Qian Z, Miao Y. Genetic variation of miRNA sequence in pancreatic cancer. Acta Biochim Biophys Sin (Shanghai) 2009; 41:407-13. [PMID: 19430705 DOI: 10.1093/abbs/gmp023] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of 20-22 nucleotides (nts) and constitute a novel class of gene regulators that negatively regulate gene expression at the post-transcriptional level. The expression of miRNA is deregulated in many types of cancers. Alterations in miRNA expression may be an important contributor to the development of pancreatic carcinoma. We hypothesized that genetic variations in miRNA genes were associated with pancreatic carcinoma and analyzed genomic sequences coding for the precursors of eight miRNA genes in both pancreatic carcinoma tissues and cancer cell lines. Four novel mutations in primary miRNA transcripts were identified. TaqMan miRNA assays showed that miR-21 was significantly overexpressed in 20 pancreatic carcinomas and 6 cancer cell lines compared with paired benign tissues and normal pancreas. Two mutations of miR-21 did not notably alter the activity of the promoter of the miRNA gene. Although most of these mutations seem to have no effect on miRNA processing, an A-G mutation at 29-nt downstream of pre-miR-21 led to a conformational change of the secondary structure close to the stem reaching into the pre-miR-21 and a relative reduction of the mature miR-21 expression in vivo. These results suggested that miRNA might play an important role in pancreatic tumorigenesis, but the molecular mechanism underlying the particular sequence variations in miRNA that can cause aberrant expression remains to be determined.
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Affiliation(s)
- Zheng Zhu
- Department of General Surgery, The First Clinic Medical College of Nanjing Medical University, Nanjing, China
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Legoffic A, Calvo EL, Barthet M, Delpero JR, Dagorn JC, Iovanna JL. Identification of genomic alterations associated with the aggressiveness of pancreatic cancer using an ultra-high-resolution CGH array. Pancreatology 2009; 9:267-72. [PMID: 19407481 DOI: 10.1159/000212092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 07/03/2008] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genomic alterations present in pancreatic adenocarcinoma have been described only partially. In addition, the relations between these alterations and the aggressiveness of the phenotype remain unknown. METHODS Genomic DNA and total RNA from 5 pancreatic cell lines, of which 2 have an aggressive phenotype and are gemcitabine-resistant (Mia-Paca2 and Panc-1), and 3 less aggressive and gemcitabine-sensitive (Capan-1, Capan-2 and BxPC3), have been purified. DNA abnormalities have been analyzed using an ultra-high-resolution CGH array and mRNA expression was studied with an Affymetrix GeneChip expression array. RESULTS We identified 573 amplified and 30 deleted genes common to all 5 cell lines. Some of them have already been described, whereas other genes, implicated in signal transduction, apoptosis, cell cycle or cell migration, are described for the first time as being related to this cancer. Comparison of genomic abnormalities between the 2 most aggressive and the 3 less aggressive cell lines led to the identification of 368 genes specifically amplified in the aggressive cell lines. However, no specific gene deletion seems to be associated with the aggressive phenotype. CONCLUSION Using a high-resolution approach, we could precisely describe the genomic alterations associated with pancreatic adenocarcinoma and determine those associated with an aggressive phenotype.
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Affiliation(s)
- Aude Legoffic
- INSERM U.624, Stress Cellulaire, Parc Scientifique et Technologique de Luminy, Marseille, France
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Ranganathan P, Harsha HC, Pandey A. Molecular alterations in exocrine neoplasms of the pancreas. Arch Pathol Lab Med 2009; 133:405-12. [PMID: 19260746 DOI: 10.5858/133.3.405] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2008] [Indexed: 11/06/2022]
Abstract
CONTEXT Pancreatic cancer is one of the leading causes of cancer-related deaths. Most cases are diagnosed at an advanced stage when the disease is beyond surgical intervention. Molecular studies during the past decade have contributed greatly to our understanding of this disease. Various germ-line and somatic mutations associated with pancreatic cancers have been characterized, along with abnormal variations in the gene expression patterns. A thorough characterization of molecular alterations such as genetic and epigenetic changes, alterations in the expression of genes and changes in proteins, and posttranslational modifications in pancreatic cancer could lead to a better understanding of its pathogenesis. OBJECTIVE To provide an overview of the various molecular alterations in pancreatic cancer and the methodologies used to catalog such alterations. DATA SOURCES Published studies about various molecular alterations at the genomic, epigenetic, transcriptomic, and proteomic levels in pancreatic cancer. CONCLUSIONS The available data from pancreatic cancer suggests that there are a large number of molecular alterations at genomic, epigenetic, transcriptomic, and proteomic levels. It is now possible to initiate a systems approach to studying pancreatic cancer especially in light of newer initiatives to dissect the pancreatic cancer genome.
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Harada T, Chelala C, Crnogorac-Jurcevic T, Lemoine NR. Genome-wide analysis of pancreatic cancer using microarray-based techniques. Pancreatology 2008; 9:13-24. [PMID: 19077451 DOI: 10.1159/000178871] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND/AIMS Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes. METHODS We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (6 cell lines and 23 microdissected tissue specimens) using 1-Mb-spaced CGH arrays. The transcript levels of all genes within the identified regions of genetic alterations were then screened using our Pancreatic Expression Database. RESULTS In addition to 238 high-level amplifications and 35 homozygous deletions, we identified 315 minimal common regions of 'non-random' genetic alterations (115 gains and 200 losses) which were consistently observed across our tumour samples. The small size of these aberrations (median size of 880 kb) contributed to the reduced number of candidate genes included (on average 12 Ensembl-annotated genes). The database has further specified the genes whose expression levels are consistent with their copy number status. Such genes were UQCRB, SQLE, DDEF1, SLA, ERICH1 and DLC1, indicating that these may be potential target candidates within regions of aberrations. CONCLUSION This study has revealed multiple novel regions that may indicate the locations of oncogenes or tumour suppressor genes in PDAC. Using the database, we provide a list of novel target genes whose altered DNA copy numbers could lead to significant changes in transcript levels in PDAC.
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Affiliation(s)
- Tomohiko Harada
- Centre for Molecular Oncology, Cancer Research UK, Institute of Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
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Buchholz M, Kestler H, Gress TM. Differential diagnosis of pancreatic tumors by molecular analysis of clinical specimens. Pancreatology 2008; 8:551-7. [PMID: 18818507 DOI: 10.1159/000159213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To describe the capabilities and limitations of the current state of the art in pancreatic cancer diagnostics and to discuss recent progress in the development of novel, highly accurate molecular diagnostic approaches. RESULTS Molecular analyses currently under evaluation as novel diagnostic tests include detection of point mutations, genomic imbalances, aberrant methylation patterns and gene expression changes on the mRNA and protein levels in pancreatic juice, fine needle aspiration biopsies and brush cytologies. CONCLUSIONS In exploratory studies, several candidate molecular markers show great potential to serve as general indicators of malignancy, but need to be validated in large, controlled, prospective studies. Multiplexing of diagnostic tests, e.g. in the form of specialized DNA microarrays, may provide more differentiated diagnoses such as the distinction of various tumor types or prognostic information for individual patients. The MolDiag-Paca consortium is strongly engaged in advancing these developments on a European level.
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Affiliation(s)
- Malte Buchholz
- Division of Gastroenterology, University Hospital, Philipps-Universität Marburg, Marburg, Germany
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Puces à ADN (CGH-array) : application pour le diagnostic de déséquilibres cytogénétiques cryptiques. ACTA ACUST UNITED AC 2008; 56:368-74. [DOI: 10.1016/j.patbio.2008.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/16/2008] [Indexed: 01/05/2023]
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Yuan M, Tomlinson V, Lara R, Holliday D, Chelala C, Harada T, Gangeswaran R, Manson-Bishop C, Smith P, Danovi SA, Pardo O, Crook T, Mein CA, Lemoine NR, Jones LJ, Basu S. Yes-associated protein (YAP) functions as a tumor suppressor in breast. Cell Death Differ 2008; 15:1752-9. [PMID: 18617895 DOI: 10.1038/cdd.2008.108] [Citation(s) in RCA: 250] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Yes-associated protein (YAP) has been shown to positively regulate p53 family members and to be negatively regulated by the AKT proto-oncogene product in promoting apoptosis. On the basis of this function and its location at 11q22.2, a site of frequent loss of heterozygosity (LOH) in breast cancer, we investigated whether YAP is a tumor suppressor in breast. Examination of tumors by immunohistochemistry demonstrated significant loss of YAP protein. LOH analysis revealed that protein loss correlates with specific deletion of the YAP gene locus. Functionally, short hairpin RNA knockdown of YAP in breast cell lines suppressed anoikis, increased migration and invasiveness, inhibited the response to taxol and enhanced tumor growth in nude mice. This is the first report indicating YAP as a tumor suppressor, revealing its decreased expression in breast cancer as well as demonstrating the functional implications of YAP loss in several aspects of cancer signaling.
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Affiliation(s)
- M Yuan
- Cell Survival Signalling Laboratory, Centre for Molecular Oncology, Institute of Cancer, Charterhouse Square, London, UK
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Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays. Oncogene 2007; 27:1951-60. [PMID: 17952125 DOI: 10.1038/sj.onc.1210832] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To identify genomic abnormalities characteristic of pancreatic ductal adenocarcinoma (PDAC) in vivo, a panel of 27 microdissected PDAC specimens were analysed using high-density microarrays representing approximately 116 000 single nucleotide polymorphism (SNP) loci. We detected frequent gains of 1q, 2, 3, 5, 7p, 8q, 11, 14q and 17q (> or =78% of cases), and losses of 1p, 3p, 6, 9p, 13q, 14q, 17p and 18q (> or =44%). Although the results were comparable with those from array CGH, regions of those genetic changes were defined more accurately by SNP arrays. Integrating the Ensembl public data, we have generated 'gene' copy number indices that facilitate the search for novel candidates involved in pancreatic carcinogenesis. Copy numbers in a subset of the genes were validated using quantitative real-time PCR. The SKAP2/SCAP2 gene (7p15.2), which belongs to the src family kinases, was most frequently (63%) amplified in our sample set and its recurrent overexpression (67%) was confirmed by reverse transcription-PCR. Furthermore, fluorescence in situ hybridization and in situ RNA hybridization analyses for this gene have demonstrated a significant correlation between DNA copy number and mRNA expression level in an independent sample set (P<0.001). These findings indicate that the dysregulation of SKAP2/SCAP2, which is mostly caused by its increased gene copy number, is likely to be associated with the development of PDAC.
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Aspinall-O'Dea M, Costello E. The pancreatic cancer proteome - recent advances and future promise. Proteomics Clin Appl 2007; 1:1066-79. [DOI: 10.1002/prca.200700144] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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