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Markowska M, Budzinska MA, Coenen-Stass A, Kang S, Kizling E, Kolmus K, Koras K, Staub E, Szczurek E. Synthetic lethality prediction in DNA damage repair, chromatin remodeling and the cell cycle using multi-omics data from cell lines and patients. Sci Rep 2023; 13:7049. [PMID: 37120674 PMCID: PMC10148866 DOI: 10.1038/s41598-023-34161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Discovering synthetic lethal (SL) gene partners of cancer genes is an important step in developing cancer therapies. However, identification of SL interactions is challenging, due to a large number of possible gene pairs, inherent noise and confounding factors in the observed signal. To discover robust SL interactions, we devised SLIDE-VIP, a novel framework combining eight statistical tests, including a new patient data-based test iSurvLRT. SLIDE-VIP leverages multi-omics data from four different sources: gene inactivation cell line screens, cancer patient data, drug screens and gene pathways. We applied SLIDE-VIP to discover SL interactions between genes involved in DNA damage repair, chromatin remodeling and cell cycle, and their potentially druggable partners. The top 883 ranking SL candidates had strong evidence in cell line and patient data, 250-fold reducing the initial space of 200K pairs. Drug screen and pathway tests provided additional corroboration and insights into these interactions. We rediscovered well-known SL pairs such as RB1 and E2F3 or PRKDC and ATM, and in addition, proposed strong novel SL candidates such as PTEN and PIK3CB. In summary, SLIDE-VIP opens the door to the discovery of SL interactions with clinical potential. All analysis and visualizations are available via the online SLIDE-VIP WebApp.
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Affiliation(s)
- Magda Markowska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki i Wigury 61, 02-091, Warsaw, Poland
| | - Magdalena A Budzinska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
- Ardigen S.A., Podole 76, 30-394, Cracow, Poland
| | - Anna Coenen-Stass
- Translational Medicine, Oncology Bioinformatics, Merck Healthcare KGaA, Frankfurt Strasse 250, 64293, Darmstadt, Germany
| | - Senbai Kang
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | - Ewa Kizling
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | | | - Krzysztof Koras
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | - Eike Staub
- Translational Medicine, Oncology Bioinformatics, Merck Healthcare KGaA, Frankfurt Strasse 250, 64293, Darmstadt, Germany
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland.
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Solanes-Casado S, Cebrián A, Rodríguez-Remírez M, Mahíllo I, García-García L, Río-Vilariño A, Baños N, de Cárcer G, Monfort-Vengut A, Castellano V, Fernández-Aceñero MJ, García-Foncillas J, Del Puerto-Nevado L. Overcoming PLK1 inhibitor resistance by targeting mevalonate pathway to impair AXL-TWIST axis in colorectal cancer. Biomed Pharmacother 2021; 144:112347. [PMID: 34700228 DOI: 10.1016/j.biopha.2021.112347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/06/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
New therapeutic targets are revolutionizing colorectal cancer clinical management, opening new horizons in metastatic patients' outcome. Polo Like Kinase1 (PLK1) inhibitors have high potential as antitumoral agents, however, the emergence of drug resistance is a major challenge for their use in clinical practice. Overcoming this challenge represents a hot topic in current drug discovery research. BI2536-resistant colorectal cancer cell lines HT29R, RKOR, SW837R and HCT116R, were generated in vitro and validated by IG50 assays and xenografts models by the T/C ratio. Exons 1 and 2 of PLK1 gene were sequenced by Sanger method. AXL pathway, Epithelial-to-Mesenchymal transition (EMT) and Multidrug Resistance (MDR1) were studied by qPCR and western blot in resistant cells. Simvastatin as a re-sensitizer drug was tested in vitro and the drug combination strategies were validated in vitro and in vivo. PLK1 gene mutation R136G was found for RKOR. AXL pathway trough TWIST1 transcription factor was identified as one of the mechanisms involved in HT29R, SW837R and HCT116R lines, inducing EMT and upregulation of MDR1. Simvastatin was able to impair the mechanisms activated by adaptive resistance and its combination with BI2536 re-sensitized resistant cells in vitro and in vivo. Targeting the mevalonate pathway contributes to re-sensitizing BI2536-resistant cells in vitro and in vivo, raising as a new strategy for the clinical management of PLK1 inhibitors.
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Affiliation(s)
- Sonia Solanes-Casado
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Arancha Cebrián
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain.
| | | | - Ignacio Mahíllo
- Department of Statistics, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Laura García-García
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Anxo Río-Vilariño
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Natalia Baños
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Guillermo de Cárcer
- Cell Cycle & Cancer Biomarkers Group, Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBm) CSIC-UAM, 28029 Madrid, Spain
| | - Ana Monfort-Vengut
- Cell Cycle & Cancer Biomarkers Group, Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBm) CSIC-UAM, 28029 Madrid, Spain
| | - Víctor Castellano
- Department of Pathology, Fundación Jiménez Díaz University Hospital (UAM), Madrid, Spain
| | - Maria Jesús Fernández-Aceñero
- Department of Pathology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Jesús García-Foncillas
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain.
| | - Laura Del Puerto-Nevado
- Translational Oncology Division, Oncohealth Institute, IIS - Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain.
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Yu J, Chang X. Topological Data Analysis: A New Method to Identify Genetic Alterations in Cancer. Asia Pac J Oncol Nurs 2021; 8:112-114. [PMID: 33688559 PMCID: PMC7934599 DOI: 10.4103/2347-5625.308301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/05/2022] Open
Abstract
Cancer is the largest health problem worldwide. A number of targeted therapies are currently employed for the treatment of different cancers. Determining the molecular mechanisms that are necessary for cancer development and progression is the most critical step in targeted therapies. Currently, many studies have identified a large number of frequently mutated cancer-associated genes using recurrence-based methods. However, only the cancer-associated mutations with a mutation frequency >15% can be identified by these methods. In other words, they cannot be used to identify driver genes that have low mutation frequency but play a major role in tumorigenesis and development. Thus, there is an urgent need for a method for identifying cancer-associated genes that are not based on recurrence. In a study, recently published in Nature Communications, research team led by Prof. Raúl Rabadán from the Columbia University successfully devised a novel topological data analysis approach to identify low-prevalence cancer-associated gene mutations using expression data from multiple cancers.
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Affiliation(s)
- Jie Yu
- Foreign Languages College, Tianjin Normal University, Tianjin, China
| | - Xinzhong Chang
- Department of Breast Surgery, Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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Rabadán R, Mohamedi Y, Rubin U, Chu T, Alghalith AN, Elliott O, Arnés L, Cal S, Obaya ÁJ, Levine AJ, Cámara PG. Identification of relevant genetic alterations in cancer using topological data analysis. Nat Commun 2020; 11:3808. [PMID: 32732999 PMCID: PMC7393176 DOI: 10.1038/s41467-020-17659-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
Large-scale cancer genomic studies enable the systematic identification of mutations that lead to the genesis and progression of tumors, uncovering the underlying molecular mechanisms and potential therapies. While some such mutations are recurrently found in many tumors, many others exist solely within a few samples, precluding detection by conventional recurrence-based statistical approaches. Integrated analysis of somatic mutations and RNA expression data across 12 tumor types reveals that mutations of cancer genes are usually accompanied by substantial changes in expression. We use topological data analysis to leverage this observation and uncover 38 elusive candidate cancer-associated genes, including inactivating mutations of the metalloproteinase ADAMTS12 in lung adenocarcinoma. We show that ADAMTS12-/- mice have a five-fold increase in the susceptibility to develop lung tumors, confirming the role of ADAMTS12 as a tumor suppressor gene. Our results demonstrate that data integration through topological techniques can increase our ability to identify previously unreported cancer-related alterations.
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Affiliation(s)
- Raúl Rabadán
- Departments of Systems Biology and Biomedical Informatics, Columbia University, 1130 St. Nicholas Ave., New York, NY, 10032, USA.
| | - Yamina Mohamedi
- Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Asturias, Spain
- IUOPA, Instituto Universitario de Oncologia, Oviedo, Asturias, Spain
| | - Udi Rubin
- Departments of Systems Biology and Biomedical Informatics, Columbia University, 1130 St. Nicholas Ave., New York, NY, 10032, USA
- Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Tim Chu
- Departments of Systems Biology and Biomedical Informatics, Columbia University, 1130 St. Nicholas Ave., New York, NY, 10032, USA
| | - Adam N Alghalith
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA, 19104, USA
| | - Oliver Elliott
- Departments of Systems Biology and Biomedical Informatics, Columbia University, 1130 St. Nicholas Ave., New York, NY, 10032, USA
| | - Luis Arnés
- Departments of Systems Biology and Biomedical Informatics, Columbia University, 1130 St. Nicholas Ave., New York, NY, 10032, USA
| | - Santiago Cal
- Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Asturias, Spain
- IUOPA, Instituto Universitario de Oncologia, Oviedo, Asturias, Spain
| | - Álvaro J Obaya
- IUOPA, Instituto Universitario de Oncologia, Oviedo, Asturias, Spain
- Departamento de Biologia Funcional, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Arnold J Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, 08540, USA.
| | - Pablo G Cámara
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA, 19104, USA.
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Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6763596. [PMID: 31008109 PMCID: PMC6441508 DOI: 10.1155/2019/6763596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023]
Abstract
The dysfunction of the DNA mismatch repair system results in microsatellite instability (MSI). MSI plays a central role in the development of multiple human cancers. In colon cancer, despite being associated with resistance to 5-fluorouracil treatment, MSI is a favourable prognostic marker. In gastric and endometrial cancers, its prognostic value is not so well established. Nevertheless, recognising the MSI tumours may be important for predicting the therapeutic effect of immune checkpoint inhibitors. Several gene expression signatures were trained on microarray data sets to understand the regulatory mechanisms underlying microsatellite instability in colorectal cancer. A wealth of expression data already exists in the form of microarray data sets. However, the RNA-seq has become a routine for transcriptome analysis. A new MSI gene expression signature presented here is the first to be valid across two different platforms, microarrays and RNA-seq. In the case of colon cancer, its estimated performance was (i) AUC = 0.94, 95% CI = (0.90 – 0.97) on RNA-seq and (ii) AUC = 0.95, 95% CI = (0.92 – 0.97) on microarray. The 25-gene expression signature was also validated in two independent microarray colon cancer data sets. Despite being derived from colorectal cancer, the signature maintained good performance on RNA-seq and microarray gastric cancer data sets (AUC = 0.90, 95% CI = (0.85 – 0.94) and AUC = 0.83, 95% CI = (0.69 – 0.97), respectively). Furthermore, this classifier retained high concordance even when classifying RNA-seq endometrial cancers (AUC = 0.71, 95% CI = (0.62 – 0.81). These results indicate that the new signature was able to remove the platform-specific differences while preserving the underlying biological differences between MSI/MSS phenotypes in colon cancer samples.
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Torshizi Esfahani A, Seyedna SY, Nazemalhosseini Mojarad E, Majd A, Asadzadeh Aghdaei H. MSI-L/EMAST is a predictive biomarker for metastasis in colorectal cancer patients. J Cell Physiol 2018; 234:13128-13136. [PMID: 30549036 DOI: 10.1002/jcp.27983] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) is a prognostic marker in colorectal cancer (CRC). The biological significance of MSI-low (MSI-L) phenotype and its differences with microsatellite stable (MSS) phenotype remains unclear. The aim of this study is indicating the role of mononucleotide repeat in identifying MSI-L and revealing the association of MSI-L with elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and oncologic outcome in CRC patients. METHODS MSI and EMAST status were analyzed using three quasimonomorphic panel (BAT-25, BAT-26, and NR-27) and five tetranucleotide repeats (D20S82, D20S85, D9S242, D8S321, and MYCL1), respectively, by capillary electrophoresis method without the need to fluorescent primers. The associations of MSI status with clinicopathological features, EMAST status, metastasis, and overall survival (OS) were investigated. RESULTS Among 159 CRC patient 22.0% were MSI-H, 40.3% were MSS, 37.7% were MSI-L, and 41.5% showed EMAST + phenotype. MSI-L were associated with advanced stages, EMAST+ tumors and worse OS ( p ≤ 0.001). Metastasis was relatively common in MSI-L/EMAST + CRCs and BAT-25 were the most unstable marker in these tumors. CONCLUSIONS MSI-L tumors have different clinicopathological features from MSS and MSI-H tumors. The MSI-L phenotype is a worse prognostic biomarker in CRC and when accompanied by EMAST could be a predictor for metastasis.
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Affiliation(s)
- Amir Torshizi Esfahani
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Seyed Yoosef Seyedna
- Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Department of Cancer, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Majd
- Department of Molecular Medicine, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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Chen L, Pan X, Hu X, Zhang YH, Wang S, Huang T, Cai YD. Gene expression differences among different MSI statuses in colorectal cancer. Int J Cancer 2018; 143:1731-1740. [PMID: 29696646 DOI: 10.1002/ijc.31554] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/30/2018] [Accepted: 04/18/2018] [Indexed: 12/28/2022]
Abstract
Colorectal cancer is the third most common cancer in males and second in females. This disease can be caused by genetic and acquired/environmental factors. Microsatellite instability (MSI) is one of the major mechanisms in colorectal cancer. This mechanism is a specific condition of genetic hyper mutability that results from incompetent DNA mismatch repair. MSI has been applied to classify different colorectal cancer subtypes. However, the effects of MSI status on gene expression are largely unknown. In our study, we integrated the gene expression profile and MSI status of all CRC samples from the TCGA database, and then categorized the CRC samples into three subgroups, namely, MSI-stable, MSI-low, and MSI-high, according to the MSI status. We applied a novel computational method based on machine learning and screened the genes specifically expressed for the different colorectal cancer subtypes. The results showed the distinct mechanisms of the different colorectal cancer subtypes with MSI status and provided the genes that may be the optimal standards to further classify the various molecular subtypes of colorectal cancer with distinct MSI status.
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Affiliation(s)
- Lei Chen
- College of Life Science, Shanghai University, Shanghai, 200444, People' Republic of China.,College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China
| | - Xiaoyong Pan
- Department of Medical Informatics, Erasmus MC, Rotterdam, Netherlands
| | - XiaoHua Hu
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - ShaoPeng Wang
- College of Life Science, Shanghai University, Shanghai, 200444, People' Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Yu-Dong Cai
- College of Life Science, Shanghai University, Shanghai, 200444, People' Republic of China
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Krizkova S, Kepinska M, Emri G, Eckschlager T, Stiborova M, Pokorna P, Heger Z, Adam V. An insight into the complex roles of metallothioneins in malignant diseases with emphasis on (sub)isoforms/isoforms and epigenetics phenomena. Pharmacol Ther 2017; 183:90-117. [PMID: 28987322 DOI: 10.1016/j.pharmthera.2017.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metallothioneins (MTs) belong to a group of small cysteine-rich proteins that are ubiquitous throughout all kingdoms. The main function of MTs is scavenging of free radicals and detoxification and homeostating of heavy metals. In humans, 16 genes localized on chromosome 16 have been identified to encode four MT isoforms labelled by numbers (MT-1-MT-4). MT-2, MT-3 and MT-4 proteins are encoded by a single gene. MT-1 comprises many (sub)isoforms. The known active MT-1 genes are MT-1A, -1B, -1E, -1F, -1G, -1H, -1M and -1X. The rest of the MT-1 genes (MT-1C, -1D, -1I, -1J and -1L) are pseudogenes. The expression and localization of individual MT (sub)isoforms and pseudogenes vary at intra-cellular level and in individual tissues. Changes in MT expression are associated with the process of carcinogenesis of various types of human malignancies, or with a more aggressive phenotype and therapeutic resistance. Hence, MT (sub)isoform profiling status could be utilized for diagnostics and therapy of tumour diseases. This review aims on a comprehensive summary of methods for analysis of MTs at (sub)isoforms levels, their expression in single tumour diseases and strategies how this knowledge can be utilized in anticancer therapy.
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Affiliation(s)
- Sona Krizkova
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Marta Kepinska
- Department of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, H-4032 Debrecen, Hungary
| | - Tomas Eckschlager
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Marie Stiborova
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-128 40 Prague 2, Czech Republic
| | - Petra Pokorna
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-128 40 Prague 2, Czech Republic; Department of Oncology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Zbynek Heger
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Vojtech Adam
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
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Kim EJ, Kwon KA, Lee YE, Kim JH, Kim SH, Kim JH. Korean Red Ginseng extract reduces hypoxia-induced epithelial-mesenchymal transition by repressing NF-κB and ERK1/2 pathways in colon cancer. J Ginseng Res 2017; 42:288-297. [PMID: 29983610 PMCID: PMC6026356 DOI: 10.1016/j.jgr.2017.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/02/2016] [Accepted: 03/22/2017] [Indexed: 12/23/2022] Open
Abstract
Background The incidence of colorectal cancer (CRC) is increasing, with metastasis of newly diagnosed CRC reported in a large proportion of patients. However, the effect of Korean Red Ginseng extracts (KRGE) on epithelial to mesenchymal transition (EMT) in CRC is unknown. Therefore, we examined the mechanisms by which KRGE regulates EMT of CRC in hypoxic conditions. Methods Human CRC cell lines HT29 and HCT116 were incubated under hypoxic (1% oxygen) and normoxic (21% oxygen) conditions. Western blot analysis and real-time PCR were used to evaluate the expression of EMT markers in the presence of KRGE. Furthermore, we performed scratched wound healing, transwell migration, and invasion assays to monitor whether KRGE affects migratory and invasive abilities of CRC cells under hypoxic conditions. Results KRGE-treated HT29 and HCT116 cells displayed attenuated vascular endothelial growth factor (VEGF) mRNA levels and hypoxia-inducible factor-1α (HIF-1α) protein expression under hypoxic conditions. KRGE repressed Snail, Slug, and Twist mRNA expression and integrin αVβ6 protein levels. Furthermore, hypoxia-repressed E-cadherin was restored in KRGE-treated cells; KRGE blocked the invasion and migration of colon cancer cells by repressing NF-κB and ERK1/2 pathways in hypoxia. Conclusions KRGE inhibits hypoxia-induced EMT by repressing NF-κB and ERK1/2 pathways in colon cancer cells.
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Affiliation(s)
- Eui Joo Kim
- Division of Gastroenterology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon, Republic of Korea
| | - Kwang An Kwon
- Division of Gastroenterology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon, Republic of Korea.,Gachon Medical Research Institute, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Young Eun Lee
- Division of Gastroenterology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon, Republic of Korea
| | - Ju Hyun Kim
- Division of Gastroenterology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon, Republic of Korea
| | - Se-Hee Kim
- Gachon Medical Research Institute, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Jung Ho Kim
- Division of Gastroenterology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon, Republic of Korea.,Gachon Medical Research Institute, Gachon University Gil Medical Center, Incheon, Republic of Korea
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10
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Investigation of Cross-Contamination and Misidentification of 278 Widely Used Tumor Cell Lines. PLoS One 2017; 12:e0170384. [PMID: 28107433 PMCID: PMC5249119 DOI: 10.1371/journal.pone.0170384] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/31/2016] [Indexed: 02/07/2023] Open
Abstract
In recent years, biological research involving human cell lines has been rapidly developing in China. However, some of the cell lines are not authenticated before use. Therefore, misidentified and/or cross-contaminated cell lines are unfortunately commonplace. In this study, we present a comprehensive investigation of cross-contamination and misidentification for a panel of 278 cell lines from 28 institutes in China by using short tandem repeat profiling method. By comparing the DNA profiles with the cell bank databases of ATCC and DSMZ, a total of 46.0% (128/278) cases with cross-contamination/misidentification were uncovered coming from 22 institutes. Notably, 73.2% (52 out of 71) of the cell lines established by the Chinese researchers were misidentified and accounted for 40.6% of total misidentification (52/128). Further, 67.3% (35/52) of the misidentified cell lines established in laboratories of China were HeLa cells or a possible hybrid of HeLa with another kind of cell line. Furthermore, the bile duct cancer cell line HCCC-9810 and degenerative lung cancer Calu-6 exhibited 88.9% match in the ATCC database (9-loci), indicating that they were from the same origin. However, when we used 21-loci to compare these two cell lines with the same algorithm, the percent match was only 48.2%, indicating that these two cell lines were different. The SNP profiles of HCCC-9810 and Calu-6 also revealed that they were different cell lines. 150 cell lines with unique profiles demonstrated a wide range of in vitro phenotypes. This panel of 150 genomically validated cancer cell lines represents a valuable resource for the cancer research community and will advance our understanding of the disease by providing a standard reference for cell lines that can be used for biological as well as preclinical studies.
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Kim CG, Ahn JB, Jung M, Beom SH, Kim C, Kim JH, Heo SJ, Park HS, Kim JH, Kim NK, Min BS, Kim H, Koom WS, Shin SJ. Effects of microsatellite instability on recurrence patterns and outcomes in colorectal cancers. Br J Cancer 2016; 115:25-33. [PMID: 27228287 PMCID: PMC4931375 DOI: 10.1038/bjc.2016.161] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 01/09/2023] Open
Abstract
Background: Among colorectal cancers (CRCs), high-frequency microsatellite instability (MSI-H) is associated with a better prognosis, compared with low-frequency MSI or microsatellite stability (MSI-L/MSS). However, it is unclear whether MSI affects the prognosis of recurrent CRCs. Methods: This study included 2940 patients with stage I–III CRC who underwent complete resection. The associations of MSI status with recurrence patterns, disease-free survival (DFS), overall survival from diagnosis to death (OS1), and overall survival from recurrence to death (OS2) were analysed. Results: A total of 261 patients (8.9%) had MSI-H CRC. Patients with MSI-H CRC had better DFS, compared to patients with MSI-L/MSS CRC (hazard ratio (HR): 0.619, P<0.001). High-frequency microsatellite instability CRC was associated with more frequent local recurrence (30.0% vs 12.0%, P=0.032) or peritoneal metastasis (40.0% vs 12.3%, P=0.003), and less frequent lung (10.0% vs 42.5%, P=0.004) or liver metastases (15.0% vs 44.7%, P=0.01). Recurrent MSI-H CRC was associated with worse OS1 (HR: 1.363, P=0.035) and OS2 (HR: 2.667, P<0.001). An analysis of patients with colon cancer yielded similar results. Conclusions: Recurrence patterns differed between MSI-H CRC and MSI-L/MSS CRC, and recurrent MSI-H CRCs had a worse prognosis.
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Affiliation(s)
- Chang Gon Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Joong Bae Ahn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Minkyu Jung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Seung Hoon Beom
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Chan Kim
- Division of Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, 59 Yatap-ro, Bundang-gu, Seongnam 463-712, South Korea
| | - Joo Hoon Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Su Jin Heo
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Hyung Soon Park
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Jee Hung Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Nam Kyu Kim
- Department of Surgery, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, Korea
| | - Byung Soh Min
- Department of Surgery, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Woong Sub Koom
- Department of Radiation Oncology, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Sang Joon Shin
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
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12
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Liu Q, Zhang B. Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability. J Proteome Res 2016; 15:766-76. [PMID: 26680540 PMCID: PMC4782175 DOI: 10.1021/acs.jproteome.5b00847] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 12/19/2022]
Abstract
Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers.
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Affiliation(s)
- Qi Liu
- Department
of Biomedical Informatics, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
- Center
for Quantitative Sciences, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
| | - Bing Zhang
- Department
of Biomedical Informatics, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
- Center
for Quantitative Sciences, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
- Department
of Cancer Biology, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
- Vanderbilt
Ingram Cancer Center, Vanderbilt University
School of Medicine, Nashville, Tennessee 37232, United States
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13
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Dziegiel P, Pula B, Kobierzycki C, Stasiolek M, Podhorska-Okolow M. The Role of Metallothioneins in Carcinogenesis. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2016. [DOI: 10.1007/978-3-319-27472-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Islam A, Gallaher DD. Wheat Type (Class) Influences Development and Regression of Colon Cancer Risk Markers in Rats. Nutr Cancer 2015; 67:1283-92. [PMID: 26473626 DOI: 10.1080/01635581.2015.1085585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We previously found red wheat more effective than white wheat in reducing colon cancer risk in rats when fed during initiation and postinitiation stages. Here we examine the effect of wheat on colon cancer risk in early and late postinitiation stages in carcinogen-treated rats. Four groups were fed a basal diet, 1 group a red wheat diet, and 1 group a white wheat diet. After 6 wk, 1 basal, the red and white groups were killed (early postinitiation stage). Of the remaining basal groups, 1 continued on the basal diet, 1 was switched to red and another to white wheat for 8 more wk (late postinitiation stage). Red and white wheat significantly reduced morphological [aberrant crypt foci (ACF)] and biochemical (β-catenin accumulated crypts) markers in both early and late postinitiation stages. Both wheat diets reduced dysplasia markers (sialomucin-expressing ACF and mucin depleted foci), compared to the basal diet, during the late postinitiation stage, but red wheat more so. Only red wheat significantly reduced the number of metallothionein-positive crypts, a stem cell mutation marker, in both stages. Overall, red wheat flour reduced risk markers more than white wheat flour, and this was more pronounced in the late post-initiation stage.
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Affiliation(s)
- Ajmila Islam
- a Department of Food Science and Nutrition , University of Minnesota , St. Paul , Minnesota , USA
| | - Daniel D Gallaher
- a Department of Food Science and Nutrition , University of Minnesota , St. Paul , Minnesota , USA
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15
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Kim JH, Hwang YJ, Han SH, Lee YE, Kim S, Kim YJ, Cho JH, Kwon KA, Kim JH, Kim SH. Dexamethasone inhibits hypoxia-induced epithelial-mesenchymal transition in colon cancer. World J Gastroenterol 2015; 21:9887-9899. [PMID: 26379394 PMCID: PMC4566382 DOI: 10.3748/wjg.v21.i34.9887] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/16/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To elucidate the effects of dexamethasone on hypoxia-induced epithelial-to-mesenchymal transition (EMT) in colon cancer.
METHODS: Human colon cancer HCT116 and HT29 cells were exposed to normoxic (21%) and hypoxic (1%) conditions. First, the effect of dexamethasone on cell viability was examined by MTT cell proliferation assay. In order to measure the expression levels of EMT markers (Snail, Slug, Twist, E-cadherin, and integrin αVβ6) and hypoxia-related genes [Hypoxia-inducible factor-1α (HIF-1α) and vascular endothelial growth factor (VEGF)] by dexamethasone, quantitative real-time polymerase chain reaction and western blot analysis were performed. Furthermore, the morphological changes of colon cancer cells and the expression pattern of E-cadherin by dexamethasone were detected through immunocytochemistry. Finally, the effects of dexamethasone on the invasiveness and migration of colon cancer cells were elucidated using matrigel invasion, migration, and wound healing migration assays.
RESULTS: Under hypoxia, dexamethasone treatment inhibited HIF-1α protein level and its downstream gene, VEGF mRNA level in the colon cancer cell lines, HCT116 and HT29. In addition, the presence of dexamethasone down-regulated the mRNA levels of hypoxia-induced Snail, Slug, and Twist, all transcriptional factors of EMT, as well as hypoxia-induced integrin αVβ6 protein level, a well-known EMT marker for colon cancer cells. Furthermore, reduced E-cadherin in hypoxic condition was found to be recoverable by treating with dexamethasone in both colon cancer cell lines. Similarly, under hypoxic conditions, dexamethasone restored the growth pattern and morphological phenotype reminiscent of colon cancer cells grown under normoxic conditions; dexamethasone blocked the migration and invasion of both colorectal cancer cell lines in hypoxia.
CONCLUSION: Our study suggested that dexamethasone has inhibitory effects on cell migration and invasion by suppressing EMT of colon cancer cell lines in hypoxic condition.
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16
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Slattery ML, Pellatt DF, Mullany LE, Wolff RK, Herrick JS. Gene expression in colon cancer: A focus on tumor site and molecular phenotype. Genes Chromosomes Cancer 2015; 54:527-41. [PMID: 26171582 DOI: 10.1002/gcc.22265] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 12/28/2022] Open
Abstract
Hundreds to thousands of genes are differentially expressed in tumors when compared to nontumor colonic tissue samples. We evaluated gene expression patterns to better understand differences in colon cancer by tumor site and tumor molecular phenotype. We analyzed RNA-seq data from tumor/normal paired samples from 175 colon cancer patients. We implemented a cross validation strategy with nonparametric tests to identify genes which displayed varying expression characteristics related to paired tumor/nontumor tissue across proximal and distal colon sites and by tumor molecular phenotypes, that is, TP53, KRAS, CpG Island Methylator Phenotype (CIMP), and microsatellite instability (MSI). We used Ingenuity Pathway Analysis (IPA) to determine networks associated with deregulated genes in our data. Genes showed significant differences in expression characteristics at the 0.01 level in both validation groups between tumor subsite (116 genes), CIMP high versus CIMP low (79 genes), MSI versus microsatellite stable (MSS) (49 genes), TP53-mutated versus not mutated (17genes), and KRAS-mutated versus not mutated (1 gene). Deregulated genes for CIMP high and MSI tumors were often down-regulated. In contrast to CIMP high and MSI tumors, genes that were deregulated in TP53 were likely to be up-regulated. ERK1, WNT, growth factors and inflammation-related factors were focal points of both CIMP and MSI IPA networks. The MUC family of genes was up-regulated MSI networks. Numerous genes showed differences in expression between proximal and distal tumors, nontumor proximal and distal tissue, and tumor molecular phenotype. Deregulated mucin genes appear to play an important role in MSI tumors.
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Affiliation(s)
- Martha L Slattery
- Department of Internal Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah, 84117
| | - Daniel F Pellatt
- Department of Internal Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah, 84117
| | - Lila E Mullany
- Department of Internal Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah, 84117
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah, 84117
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah, 84117
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17
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Abstract
White light endoscopy has proven to be a very powerful tool in oncology. There is still, however, a need for better endoscopic techniques to overcome the current limitations of white light optics. New technologies that allow higher sensitivity, improved microanatomy and molecular characterization have been available for in vitro microscopy and are now being translated into in vivo endoscopy. Endoscopic molecular imaging is still in its infancy but holds the promise for enhancing sensitivity for early lesions, thus allowing earlier diagnosis and enabling early image-guided endoscopic intervention. A key feature of endoscopic molecular imaging is its increased sensitivity and specificity, which will be illustrated in this article, as well as describing perspectives on its future use in oncologic surgery.
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Affiliation(s)
- Towhid Ali
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
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18
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Microsatellite instability status affects gene expression profiles in early onset colorectal cancer patients. J Surg Res 2013; 185:626-37. [PMID: 23992855 DOI: 10.1016/j.jss.2013.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/01/2013] [Accepted: 07/08/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND The association between microsatellite instability (MSI) status and gene expression profiles in the early onset sporadic colorectal cancer (CRC) has not been clearly established. The aim of this study was to identify the altered gene expression patterns depending on the MSI status of early onset CRC and determine specific biomarkers that could provide novel therapeutic molecular targets in the Turkish population. MATERIALS AND METHODS MSI markers (BAT25, BAT26, D2S123, D5S346, and D17S250) were investigated in tumors from 36 early onset sporadic CRC patients in whom gene expression profiles were analyzed previously. The relationship between the gene expression profiles depending on MSI status was evaluated. RESULTS A total of 15 tumors (16.66%) were identified as having MSI and 21 tumors (58.33%) were identified as having microsatellite stability (MSS). CK20 and MAP3K8 upregulation, observed in MSS tumors, was significantly associated with lymph node metastasis, recurrence, and/or distant metastasis and a short median survival (P < 0.05). REG1A upregulation is also correlated with recurrence and/or distant metastasis and a short median survival in patients with MSI tumors (P < 0.05). CONCLUSIONS High expression levels of CK20 and MAP3K8 in MSS tumors and REG1A in MSI tumors correlated with a poor prognosis in CRC patients. Further studies and validations are required; these genes may provide novel therapeutic molecular targets for the development of anticancer drugs related to MSI status for early onset CRC treatment.
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19
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Abstract
UNLABELLED Colorectal cancer was one of the first solid tumors to be classified on the basis of molecular profiling. Microsatellite instability has allowed researchers to distinguish a specific subtype of colorectal cancer that has a clearly identified molecular origin (mismatch repair deficiency), arises on a hereditary and sporadic basis, is linked to a clear clinicopathologic profile, and has prognostic implications. Inconclusive predictive data along with a paucity of targeted drug development have prevented this molecular classification system from being implemented in the clinical setting. New high-throughput genomic data have validated it, thus stressing the fact that it is ready to be applied clinically. SIGNIFICANCE Application of a molecular classification of colorectal cancer in the clinical arena is an unmet promise. Recent results of large-scale genomic analyses have provided confirmation and further insights into the molecular biology of already known colorectal cancer subgroups. The quintessential example is the microsatellite instability subgroup, which has been well characterized during the past 2 decades. Future drug development and clinical research initiatives in colorectal oncology should consider these and other known cancer subgroups and start targeting these selected patient populations.
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Affiliation(s)
- Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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20
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Bauer KM, Hummon AB. Effects of the miR-143/-145 microRNA cluster on the colon cancer proteome and transcriptome. J Proteome Res 2012; 11:4744-54. [PMID: 22897626 DOI: 10.1021/pr300600r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The miR-143/-145 cluster is greatly reduced in several cancers, including colon cancer. Both miR-143 and miR-145 have been shown to possess antitumorigenic activity with involvement in various cancer-related events such as proliferation, invasion, and migration. As the deregulation of the miR-143/-145 cluster is implicated in tumorigenesis, we combined SILAC and microarray analyses to systematically interrogate the impact of miR-143/-145 on the colon cancer proteome and transcriptome. Using SILAC, we identified over 2000 proteins after reintroduction of miR-143 and miR-145, in the colon cancer cell line SW480, individually, and then, in concert. Our goal was to determine whether these microRNAs function individually or synergistically. The resulting regulated gene products showed evidence of both mRNA destabilization and translational inhibition with a bias toward the former mechanism of regulation. Numerous candidate targets were identified whose expression is attributable to an individual microRNA or whose regulation was more apparent following reintroduction of the miR-143/-145 cluster. In addition, several shared targets of miR-143 and miR-145 were identified. Overall, our results indicate that the summed effects of individually introduced microRNAs produce distinct molecular changes from the consequences of the assembled cluster. We conclude that there is a need to investigate both the individual and combined functional implications of a microRNA cluster.
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Affiliation(s)
- Kerry M Bauer
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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21
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Mieczkowski J, Swiatek-Machado K, Kaminska B. Identification of pathway deregulation--gene expression based analysis of consistent signal transduction. PLoS One 2012; 7:e41541. [PMID: 22848524 PMCID: PMC3405133 DOI: 10.1371/journal.pone.0041541] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/22/2012] [Indexed: 01/20/2023] Open
Abstract
Signaling pathways belong to a complex system of communication that governs cellular processes. They represent signal transduction from an extracellular stimulus via a receptor to intracellular mediators, as well as intracellular interactions. Perturbations in signaling cascade often lead to detrimental changes in cell function and cause many diseases, including cancer. Identification of deregulated pathways may advance the understanding of complex diseases and lead to improvement of therapeutic strategies. We propose Analysis of Consistent Signal Transduction (ACST), a novel method for analysis of signaling pathways. Our method incorporates information regarding pathway topology, as well as data on the position of every gene in each pathway. To preserve gene-gene interactions we use a subject-sampling permutation model to assess the significance of pathway perturbations. We applied our approach to nine independent datasets of global gene expression profiling. The results of ACST, as well as three other methods used to analyze signaling pathways, are presented in the context of biological significance and repeatability among similar, yet independent, datasets. We demonstrate the usefulness of using information of pathway structure as well as genes’ functions in the analysis of signaling pathways. We also show that ACST leads to biologically meaningful results and high repeatability.
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Affiliation(s)
- Jakub Mieczkowski
- Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Pasteur 3, Warsaw, Poland.
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22
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Gene Signatures in Stage II Colon Cancer: A Clinical Review. CURRENT COLORECTAL CANCER REPORTS 2012; 8:225-231. [PMID: 23002390 DOI: 10.1007/s11888-012-0132-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Understanding the biology of cancer is the key to understanding its behavior. Stage II colon cancers represent a unique treatment challenge for medical oncologists because they contain a very heterogeneous group of tumors with a wide range of recurrence risks after resection. Defining these differences in biology can help to explain differences in behavior. To this end, gene signatures have been developed to define various prognostic groups beyond the clinicopathologic features alone. Adjuvant chemotherapy for stage II colon cancers as a group has not shown survival advantage in clinical trials. Future research to develop gene signatures to predict a group that will benefit from adjuvant chemotherapy will be helpful in the clinical decision-making process. The purpose of this review is to present the prognostic gene signatures currently available for use, those in development, and their utility in stratifying recurrence risk in stage II colon cancer patients.
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Yamamoto H, Adachi Y, Taniguchi H, Kunimoto H, Nosho K, Suzuki H, Shinomura Y. Interrelationship between microsatellite instability and microRNA in gastrointestinal cancer. World J Gastroenterol 2012; 18:2745-55. [PMID: 22719182 PMCID: PMC3374977 DOI: 10.3748/wjg.v18.i22.2745] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 03/02/2012] [Accepted: 03/09/2012] [Indexed: 02/06/2023] Open
Abstract
There is an increasing understanding of the roles that microsatellite instability (MSI) plays in Lynch syndrome (by mutations) and sporadic (by mainly epigenetic changes) gastrointestinal (GI) and other cancers. Deficient DNA mismatch repair (MMR) results in the strong mutator phenotype known as MSI, which is the hallmark of cancers arising within Lynch syndrome. MSI is characterized by length alterations within simple repeated sequences called microsatellites. Lynch syndrome occurs primarily because of germline mutations in one of the MMR genes, mainly MLH1 or MSH2, less frequently MSH6, and rarely PMS2. MSI is also observed in about 15% of sporadic colorectal, gastric, and endometrial cancers and in lower frequencies in a minority of other cancers where it is often associated with the hypermethylation of the MLH1 gene. miRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level and are critical in many biological processes and cellular pathways. There is accumulating evidence to support the notion that the interrelationship between MSI and miRNA plays a key role in the pathogenesis of GI cancer. As a possible new mechanism underlying MSI, overexpression of miR-155 has been shown to downregulate expression of MLH1, MSH2, and MSH6. Thus, a subset of MSI-positive (MSI+) cancers without known MMR defects may result from miR-155 overexpression. Target genes of frameshift mutation for MSI are involved in various cellular functions, such as DNA repair, cell signaling, and apoptosis. A novel class of target genes that included not only epigenetic modifier genes, such as HDAC2, but also miRNA processing machinery genes, including TARBP2 and XPO5, were found to be mutated in MSI+ GI cancers. Thus, a subset of MSI+ colorectal cancers (CRCs) has been proposed to exhibit a mutated miRNA machinery phenotype. Genetic, epigenetic, and transcriptomic differences exist between MSI+ and MSI− cancers. Molecular signatures of miRNA expression apparently have the potential to distinguish between MSI+ and MSI− CRCs. In this review, we summarize recent advances in the MSI pathogenesis of GI cancer, with the focus on its relationship with miRNA as well as on the potential to use MSI and related alterations as biomarkers and novel therapeutic targets.
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Morandi L, de Biase D, Visani M, Monzoni A, Tosi A, Brulatti M, Turchetti D, Baccarini P, Tallini G, Pession A. T([20]) repeat in the 3'-untranslated region of the MT1X gene: a marker with high sensitivity and specificity to detect microsatellite instability in colorectal cancer. Int J Colorectal Dis 2012; 27:647-56. [PMID: 22108904 DOI: 10.1007/s00384-011-1365-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2011] [Indexed: 02/08/2023]
Abstract
PURPOSE Stratifying patients defective in mismatch repair (dMMR) with high microsatellite instability (MSI-H) in colorectal cancer (CRC) is of increasing relevance and may provide a more tailored approach to CRC adjuvant therapy. Here, we describe the discovery of a new MSI marker for colorectal cancer located in the 3'-untranslated region (3'UTR, T20 mononucleotide repeat) of the metallothionein 1X gene (MT1XT20). METHODS We studied 340 consecutive CRCs using three multiplexed polymerase chain reactions amplifying BAT25, BAT26, TGFBR2, MybT22, BAT40, MT1XT20, NR21, NR24, CAT25, D2S123, D5S346, D17S250, D18S58, CSF1PO, D7S820, and D18S51. Fragments length was evaluated by automated capillary electrophoresis. RESULTS Based on the NCI/ICG-HNPCC criteria for MSI classification, 40 CRCs were found to be MSI-high (11.8%), 46 (13.5%) CRCs were MSI-low, and 254 CRCs (74.7%) were stable (MSS). MT1XT20 showed very high sensitivity (97.3%) comparable to BAT26 (97.5%) and CAT25 (97.1%) and the best specificity (100%) as well as MybT22 and CAT25. Indeed, MT1XT20 instability was detected in 36 out of 37 cases (97.3%) of MSI-high colorectal cancers, whereas no MT1XT20 alterations were observed in 254 MSS or in 46 MSI-low cases. On the contrary, BAT40 was found to be unstable in 8/46 MSI-low cases, BAT25 in 6/46, BAT26 4/46, NR21 1/46, and NR24 in 1/45. CONCLUSIONS Our results suggest that MT1XT20 represents a sensitive and specific marker for MSI testing and could be included in a complete set of MSI markers for the confident identification of familial or sporadic dMMR patients in CRCs.
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Affiliation(s)
- Luca Morandi
- Department of Haematology and Oncological Sciences L. and A. Seragnoli, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, via Altura 3, 40139 Bologna, Italy.
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25
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Yan DW, Fan JW, Yu ZH, Li MX, Wen YG, Li DW, Zhou CZ, Wang XL, Wang Q, Tang HM, Peng ZH. Downregulation of metallothionein 1F, a putative oncosuppressor, by loss of heterozygosity in colon cancer tissue. Biochim Biophys Acta Mol Basis Dis 2012; 1822:918-26. [PMID: 22426038 DOI: 10.1016/j.bbadis.2012.02.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 12/13/2022]
Abstract
PURPOSE Downregulation of metallothionein (MT) genes has been reported in several tumors with discrepant results. This study is to investigate molecular mechanism of MT gene regulation in colon cancer which is characterized by tumor suppressor gene alterations. EXPERIMENTAL DESIGN Integral analysis of microarray data with loss of heterozygosity (LOH) information was employed. Quantitative real-time PCR and immunohistochemistry were used to validate MT isoform expression in colon cancer tissues and cell lines. The effects of MT1F expression on RKO cell survival and tumorigenesis was analyzed. Bisulphite sequencing PCR (BSP) and methylation-specific PCR were employed to detect the methylation status of the MT1F gene in colon cancer tissues and cell lines. DNA sequencing was used to examine the LOH at the MT1F locus. RESULTS MT1F, MT1G, MT1X, and MT2A gene expression was significantly downregulated in colon cancer tissue (p<0.05). Exogenous MT1F expression increased RKO cell apoptosis and inhibited RKO cell migration, invasion and adhesion as well as in vivo tumorigenicity. Downregulation of MT1F gene in majority of human colon tumor tissues is mainly through mechanism by loss of heterozygosity (p=0.001) while CpG island methylation of MT1F gene promoter region was only observed in poorly differentiated, MSI-positive RKO and LoVo colon cancer cell lines. CONCLUSIONS MT1F is a putative tumor suppressor gene in colon carcinogenesis that is downregulated mainly by LOH in colon cancer tissue. Further studies are required to elucidate a possible role for MT1F downregulation in colon cancer initiation and/or progression.
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Affiliation(s)
- Dong-Wang Yan
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People's Hospital, 85 Wujin Road, People's Republic of China
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Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism. Cell Oncol (Dordr) 2012; 35:53-63. [PMID: 22278361 PMCID: PMC3308003 DOI: 10.1007/s13402-011-0065-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2011] [Indexed: 02/08/2023] Open
Abstract
Background Colorectal cancer develops in a multi-step manner from normal epithelium, through a pre-malignant lesion (so-called adenoma), into a malignant lesion (carcinoma), which invades surrounding tissues and eventually can spread systemically (metastasis). It is estimated that only about 5% of adenomas do progress to a carcinoma. Aim The present study aimed to unravel the biology of adenoma to carcinoma progression by mRNA expression profiling, and to identify candidate biomarkers for adenomas that are truly at high risk of progression. Methods Genome-wide mRNA expression profiles were obtained from a series of 37 colorectal adenomas and 31 colorectal carcinomas using oligonucleotide microarrays. Differentially expressed genes were validated in an independent colorectal gene expression data set. Gene Set Enrichment Analysis (GSEA) was used to identify altered expression of sets of genes associated with specific biological processes, in order to better understand the biology of colorectal adenoma to carcinoma progression. Results mRNA expression of 248 genes was significantly different, of which 96 were upregulated and 152 downregulated in carcinomas compared to adenomas. Classification of adenomas and carcinomas using the expression of these genes showed to be very accurate, also when tested in an independent expression data set. Gene-sets associated with ageing (which is related to senescence) and chromosomal instability were upregulated, and a gene-set associated with fatty acid metabolism was downregulated in carcinomas compared to adenomas. Moreover, gene-sets associated with chromosomal location revealed chromosome 4q22 loss and chromosome 20q gain of gene-set expression as being relevant in this progression. Concluding remark These data are consistent with the notion that adenomas and carcinomas are distinct biological entities. Disruption of specific biological processes like senescence (ageing), maintenance of chromosomal instability and altered metabolism, are key factors in the progression from adenoma to carcinoma. Electronic supplementary material The online version of this article (doi:10.1007/s13402-011-0065-1) contains supplementary material, which is available to authorized users.
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Benson AB, Hamilton SR. Path Toward Prognostication and Prediction: An Evolving Matrix. J Clin Oncol 2011; 29:4599-601. [DOI: 10.1200/jco.2011.37.8646] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Al B. Benson
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
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Andres SA, Wittliff JL. Relationships of ESR1 and XBP1 expression in human breast carcinoma and stromal cells isolated by laser capture microdissection compared to intact breast cancer tissue. Endocrine 2011; 40:212-21. [PMID: 21858728 DOI: 10.1007/s12020-011-9522-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
Abstract
Results from investigations of human genomics which utilize intact tissue biopsy specimens maybe compromised due to a host of uncontrolled variables including cellular heterogeneity of a sample collected under diverse conditions, then processed and stored using different protocols. To determine the cellular origin and assess relationships of mRNA expression of two genes reported to be co-expressed in human breast carcinoma (estrogen receptor-α, ESR1 and X-box binding protein 1, XBP1), gene expression analyses were performed with intact tissue sections and compared with those of laser capture microdissection (LCM)-procured carcinoma and stromal cells from serial sections of the same tissue. Frozen sections of human breast carcinomas were first evaluated for structural integrity and pathology after hematoxylin and eosin (H&E) staining. Total RNA preparations from intact tissue sections and LCM-procured carcinoma and stromal cells were reverse transcribed for measurements of ESR1 and XBP1 expression by quantitative PCR (qPCR). These results were compared with those obtained from microarray analyses of LCM-procured carcinoma cells. Levels of ESR1 and XBP1 were detected in the intact breast cancer tissue sections suggesting coordinate gene expression. Although coordinate expression of these genes was observed in the LCM-procured carcinoma cells, it was not discerned in LCM-procured stromal cells. The origin of coordinate expression of ESR1 and XBP1 observed in whole tissue sections of human breast cancer biopsies is due principally to their co-expression in carcinoma cells and not in the surrounding stromal cells as substantiated using LCM-procured cells. Collectively, a microgenomic process was established from human tissue preparation to RNA characterization and analysis to identify molecular signatures of specific cell types predicting clinical behavior.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/diagnosis
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Cell Separation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Histocytochemistry
- Humans
- Laser Capture Microdissection
- Molecular Diagnostic Techniques
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/metabolism
- RNA, Neoplasm/isolation & purification
- RNA, Neoplasm/metabolism
- Regulatory Factor X Transcription Factors
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction
- Stromal Cells/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- X-Box Binding Protein 1
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Affiliation(s)
- Sarah A Andres
- Hormone Receptor Laboratory, Department of Biochemistry & Molecular Biology, Brown Cancer Center and the Institute for Molecular Diversity & Drug Design, University of Louisville, Health Sciences Center A Bldg.-Room 604, Louisville, KY 40292, USA
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Coppola D, Nebozhyn M, Khalil F, Dai H, Yeatman T, Loboda A, Mulé JJ. Unique ectopic lymph node-like structures present in human primary colorectal carcinoma are identified by immune gene array profiling. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:37-45. [PMID: 21703392 DOI: 10.1016/j.ajpath.2011.03.007] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 02/21/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
We hypothesized that immune gene-related signatures would predict the presence of unique histological features of lymphoid cell infiltrates in colorectal carcinoma (CRC) that correlate with clinical parameters. Metagene analysis with gene chip technology was performed on 326 CRCs, which were then sorted by low versus high gene scores. Microscopically, CRCs with a high gene score revealed a marked host immune response organized, remarkably, as lymphoid follicles. Proliferation involved both B and T cells. In every case, the presence of CD79a(+) B-cell precursors was identified, suggesting that the lymphoid follicles represent newly formed, ectopic lymph node-like structures. CD21(+) dendritic cells were present within the follicular germinal centers, and CD3(+) T cells were localized mainly in the parafollicular cortex zone surrounding the B-cell area of the follicles. A strong correlation between a 12-chemokine gene subset of the molecular profile and the presence of ectopic lymph node-like structures was associated with better patient survival independent of tumor staging, site location, microsatellite instability or stability, and patient treatment. These findings suggest beneficial, intratumoral immune cell priming and raise the possibility of immunotherapy intervention decisions based on molecular signatures that can identify the presence of tumor-localized, ectopic lymph node-like structures.
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Affiliation(s)
- Domenico Coppola
- Anatomic Pathology Division, Moffitt Cancer Center, Tampa, FL 33612-9497, USA
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30
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Replication error deficient and proficient colorectal cancer gene expression differences caused by 3'UTR polyT sequence deletions. Proc Natl Acad Sci U S A 2010; 107:21058-63. [PMID: 21097699 DOI: 10.1073/pnas.1015604107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterized by inactivation of the DNA mismatch repair system. These cancers are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency, and have distinct pathologies. Regulatory sequences controlling all aspects of mRNA processing, especially including message stability, are found in the 3'UTR sequence of most genes. The relevant sequences are typically A/U-rich elements or U repeats. Microarray analysis of 14 RER+ (deficient) and 16 RER- (proficient) colorectal cancer cell lines confirms a striking difference in expression profiles. Analysis of the incidence of mononucleotide repeat sequences in the 3'UTRs, 5'UTRs, and coding sequences of those genes most differentially expressed in RER+ versus RER- cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3'UTR T repeats longer than 11 base pairs in the most differentially expressed genes. This enrichment was confirmed by analysis of two published consensus sets of RER differentially expressed probesets for a large number of primary colorectal cancers. Sequence analysis of the 3'UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. These data strongly imply that deregulation of mRNA stability through accumulation of mutations in repetitive regulatory 3'UTR sequences underlies the striking difference in expression profiles between RER+ and RER- colorectal cancers.
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Campbell PT, Jacobs ET, Ulrich CM, Figueiredo JC, Poynter JN, McLaughlin JR, Haile RW, Jacobs EJ, Newcomb PA, Potter JD, Le Marchand L, Green RC, Parfrey P, Younghusband HB, Cotterchio M, Gallinger S, Jenkins MA, Hopper JL, Baron JA, Thibodeau SN, Lindor NM, Limburg PJ, Martínez ME. Case-control study of overweight, obesity, and colorectal cancer risk, overall and by tumor microsatellite instability status. J Natl Cancer Inst 2010; 102:391-400. [PMID: 20208017 PMCID: PMC2841037 DOI: 10.1093/jnci/djq011] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 12/22/2009] [Accepted: 01/12/2010] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Being overweight or obese is an established risk factor for colorectal cancer, more so for men than for women. Approximately 10%-20% of colorectal tumors display microsatellite instability (MSI), defined as the expansion or contraction of small repeated sequences in the DNA of tumor tissue relative to nearby normal tissue. We evaluated associations between overweight or obesity and colorectal cancer risk, overall and by tumor MSI status. METHODS The study included 1794 case subjects with incident colorectal cancer who were identified through population-based cancer registries and 2684 of their unaffected sex-matched siblings as control subjects. Recent body mass index (BMI), BMI at age 20 years, and adult weight change were derived from self-reports of height and weight. Tumor MSI status, assessed at as many as 10 markers, was obtained for 69.7% of the case subjects and classified as microsatellite (MS)-stable (0% of markers unstable; n = 913), MSI-low (>0% but <30% of markers unstable; n = 149), or MSI-high (> or =30% of markers unstable; n = 188). Multivariable conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs). All statistical tests were two-sided. RESULTS Recent BMI, modeled in 5 kg/m(2) increments, was positively associated with risk of colorectal cancer for men and women combined (OR = 1.24; 95% CI = 1.15 to 1.34), for women only (OR = 1.20; 95% CI = 1.10 to 1.32), and for men only (OR = 1.30; 95% CI = 1.15 to 1.47). There was no interaction with sex (P = .22). Recent BMI, per 5 kg/m(2), was positively associated with the risk of MS-stable (OR = 1.38; 95% CI = 1.24 to 1.54) and MSI-low (OR = 1.33; 95% CI = 1.04 to 1.72) colorectal tumors, but not with the risk of MSI-high tumors (OR = 1.05; 95% CI = 0.84 to 1.31). CONCLUSION The increased risk of colorectal cancer associated with a high BMI might be largely restricted to tumors that display the more common MS-stable phenotype, suggesting further that colorectal cancer etiology differs by tumor MSI status.
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Affiliation(s)
- Peter T Campbell
- Epidemiology Research Program, American Cancer Society, National Home Office, 250 Williams St NW, Atlanta, GA 30303, USA.
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Abstract
Microsatellite instability (MSI) is the molecular fingerprint of a deficient mismatch repair system. Approximately 15% of colorectal cancers (CRC) display MSI owing either to epigenetic silencing of MLH1 or a germline mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2. Methods to detect MSI are well established and routinely incorporated into clinical practice. A clinical and molecular profile of MSI tumors has been described, leading to the concept of an MSI phenotype in CRC. Studies have confirmed that MSI tumors have a better prognosis than microsatellite stable CRC, but MSI cancers do not necessarily have the same response to the chemotherapeutic strategies used to treat microsatellite stable tumors. Specifically, stage II MSI tumors might not benefit from 5-fluorouracil-based adjuvant chemotherapy regimens. New data suggest possible advantages of irinotecan-based regimens, but these findings require further clarification. Characterization of the molecular basis of MSI in CRC is underway and initial results show that mutations in genes encoding kinases and candidate genes with microsatellite tracts are over-represented in MSI tumors. Transcriptome expression profiles of MSI tumors and systems biology approaches are providing the opportunity to develop targeted therapeutics for MSI CRC.
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Affiliation(s)
- Eduardo Vilar
- Department of Internal Medicine, University of Michigan Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Hong Y, Downey T, Eu KW, Koh PK, Cheah PY. A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics. Clin Exp Metastasis 2010; 27:83-90. [PMID: 20143136 DOI: 10.1007/s10585-010-9305-4] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 01/22/2010] [Indexed: 01/23/2023]
Abstract
Metastasis is the major cause of cancer mortality. We aimed to find a metastasis-prone signature for early stage mismatch-repair proficient sporadic colorectal cancer (CRC) patients for better prognosis and informed use of adjuvant chemotherapy. The genome-wide expression profiles of 82 age-, ethnicity- and tissue-matched patients and healthy controls were analyzed using the Affymetrix U133 Plus 2 array. Metastasis-negative patients have 5 years or more of follow-up. A 10 x 10 two-level nested cross-validation design was used with several families of classification models to identify the optimal predictor for metastasis. The best classification model yielded a 54 gene-set (74 probe sets) with an estimated prediction accuracy of 71%. The specificity, sensitivity, negative and positive predictive values of the signature are 0.88, 0.58, 0.84 and 0.65, respectively, indicating that the gene-set can improve prognosis for early stage sporadic CRC patients. These 54 genes, including node molecules YWHAB, MAP3K5, LMNA, APP, GNAQ, F3, NFATC2, and TGM2, integrate multiple bio-functions in various compartments into an intricate molecular network, suggesting that cell-wide perturbations are involved in metastasis transformation. Further, querying the ;Connectivity Map' with a subset (70%) of these genes shows that Gly-His-Lys and securinine could reverse the differential expressions of these genes significantly, suggesting that they have combinatorial therapeutic effect on the metastasis-prone patients. These two perturbagens promote wound-healing, extracellular matrix remodeling and macrophage activation thus highlighting the importance of these pathways in metastasis suppression for early-stage CRC.
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Affiliation(s)
- Yi Hong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, 169608, Singapore
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Abstract
Endoscopy has undergone explosive technological growth in recent years, and with the emergence of targeted imaging, its truly transformative power and impact on medicine lies just over the horizon. Today, our ability to see inside the digestive tract with medical endoscopy is headed toward exciting crossroads. The existing paradigm of making diagnostic decisions based on observing structural changes and identifying anatomic landmarks may soon be replaced by visualizing functional properties and imaging molecular expression. In this novel approach, the presence of intracellular and cell surface targets unique to disease are identified and used to predict the likelihood of mucosal transformation and response to therapy. This strategy could result in the development of new methods for early cancer detection, personalized therapy, and chemoprevention. This targeted approach will require further development of molecular probes and endoscopic instruments, and will need support from the US Food and Drug Administration for streamlined regulatory oversight. Overall, this molecular imaging modality promises to significantly broaden the capabilities of the gastroenterologist by providing a new approach to visualize the mucosa of the digestive tract in a manner that has never been seen before.
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Affiliation(s)
- Meng Li
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Michigan, Ann Arbor, MI USA, 48109
| | - Thomas D Wang
- Division of Gastroenterology and Hepatology, Department of Medicine, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI USA, 48109
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35
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Poynter JN, Siegmund KD, Weisenberger DJ, Long TI, Thibodeau SN, Lindor N, Young J, Jenkins MA, Hopper JL, Baron JA, Buchanan D, Casey G, Levine AJ, Le Marchand L, Gallinger S, Bapat B, Potter JD, Newcomb PA, Haile RW, Laird PW. Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening. Cancer Epidemiol Biomarkers Prev 2009; 17:3208-15. [PMID: 18990764 DOI: 10.1158/1055-9965.epi-08-0512] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Microsatellite instability (MSI) occurs in 10% to 20% of colorectal cancers (CRC) and has been attributed to both MLH1 promoter hypermethylation and germline mutation in the mismatch repair (MMR) genes. We present results from a large population- and clinic-based study of MLH1 methylation, immunohistochemistry, and MMR germline mutations that enabled us to (a) estimate the prevalence of MMR germline mutations and MLH1 methylation among MSI-H cases and help us understand if all MSI-H CRC is explained by these mechanisms and (b) estimate the associations between MLH1 methylation and sex, age, and tumor location within the colon. MLH1 methylation was measured in 1,061 population-based and 172 clinic-based cases of CRC. Overall, we observed MLH1 methylation in 60% of population-based MSI-H cases and in 13% of clinic-based MSI-H cases. Within the population-based cases with MMR mutation screening and conclusive immunohistochemistry results, we identified a molecular event in MMR in 91% of MSI-H cases: 54% had MLH1 methylation, 14% had a germline mutation in a MMR gene, and 23% had immunohistochemistry evidence for loss of a MMR protein. We observed a striking age difference, with the prevalence of a MMR germline mutation more than 4-fold lower and the prevalence of MLH1 methylation more than 4-fold higher in cases diagnosed after the age of 50 years than in cases diagnosed before that age. We also determined that female sex is an independent predictor of MLH1 methylation within the MSI-H subgroup. These results reinforce the importance of distinguishing between the underlying causes of MSI in studies of etiology and prognosis.
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Affiliation(s)
- Jenny N Poynter
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033-9176, USA
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Hu D, Su X, Sun R, Yang G, Wang H, Ren J, Sun L, Wu X, Hu X, Yu Y, Wang L. Human microsatellite DNA mimicking oligodeoxynucleotides down-regulate TLR9-dependent and -independent activation of human immune cells. Mol Immunol 2009; 46:1387-96. [PMID: 19201477 DOI: 10.1016/j.molimm.2008.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 12/04/2008] [Indexed: 02/06/2023]
Abstract
To develop novel immunoregulatory oligodeoxynucleotides (ODNs), we have designed a series of ODNs based on the sequences in human microsatellite (MS) DNA. The ODNs, designated as human MS DNA mimicking ODNs (MS ODNs), have been studied for their inhibitory effects on human immune cells activated by TLR9-dependent and -independent stimulations. We find for the first time that MS08, a MS ODN composed entirely of TC dinucleotide (TC) repeats, inhibits CpG ODN (TLR9 ligand)-induced human PBMCs proliferation, CD80 and CD86 expression and production of interferon. In addition, MS08 also inhibits the proliferation of human PBMCs stimulated by PHA, PMA and alloantigens in a TLR9-independent manner. The inhibition correlates with competition of binding and uptake between MS08 and CpG ODN in human PBMCs. Structurally, TC, CT or CCT are revealed as essential suppressive motifs required for the inhibition. These findings suggest that TC repeat containing MS ODN could be of therapeutic use in pathologic situations due to excessive activation of immune cells.
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Affiliation(s)
- Dali Hu
- Department of Immunology, Norman Bethune College of Medical Sciences, Jilin University, Changchun 130021, China
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Sun BK, Tsao H. Small RNAs in development and disease. J Am Acad Dermatol 2009; 59:725-37; quiz 738-40. [PMID: 19119093 DOI: 10.1016/j.jaad.2008.08.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 04/13/2008] [Accepted: 08/13/2008] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are classes of regulatory small RNA molecules, ranging from 18 to 24 nucleotides in length, whose roles in development and disease are becoming increasingly recognized. They function by altering the stability or translational efficiency of messenger RNAs (mRNAs) with which they share sequence complementarity, and are predicted to affect up to one-third of all human genes. Computer algorithms and microarray data estimate the presence of nearly 1000 human miRNAs, and direct examination of candidate miRNAs has validated their involvement in various cancers, disorders of neuronal development, cardiac hypertrophy, and skin diseases such as psoriasis. This article reviews the history of miRNA and siRNA discovery, key aspects of their biogenesis and mechanism of action, and known connections to human health, with an emphasis on their roles in skin development and disease.
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Affiliation(s)
- Bryan K Sun
- Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
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Andersen CL, Christensen LL, Thorsen K, Schepeler T, Sørensen FB, Verspaget HW, Simon R, Kruhøffer M, Aaltonen LA, Laurberg S, Ørntoft TF. Dysregulation of the transcription factors SOX4, CBFB and SMARCC1 correlates with outcome of colorectal cancer. Br J Cancer 2009; 100:511-23. [PMID: 19156145 PMCID: PMC2658541 DOI: 10.1038/sj.bjc.6604884] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to identify deregulated transcription factors (TFs) in colorectal cancer (CRC) and to evaluate their relation with the recurrence of stage II CRC and overall survival. Microarray-based transcript profiles of 20 normal mucosas and 424 CRC samples were used to identify 51 TFs displaying differential transcript levels between normal mucosa and CRC. For a subset of these we provide in vitro evidence that deregulation of the Wnt signalling pathway can lead to the alterations observed in tissues. Furthermore, in two independent cohorts of microsatellite-stable stage II cancers we found that high SOX4 transcript levels correlated with recurrence (HR 2.7; 95% CI, 1.2–6.0; P=0.01). Analyses of ∼1000 stage I–III adenocarcinomas, by immunohistochemistry, revealed that patients with tumours displaying high levels of CBFB and SMARCC1 proteins had a significantly better overall survival rate (P=0.0001 and P=0.0275, respectively) than patients with low levels. Multivariate analyses revealed that a high CBFB protein level was an independent predictor of survival. In conclusion, several of the identified TFs seem to be involved in the progression of CRC.
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Affiliation(s)
- C L Andersen
- Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus N DK8200, Denmark
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Jorissen RN, Lipton L, Gibbs P, Chapman M, Desai J, Jones IT, Yeatman TJ, East P, Tomlinson IPM, Verspaget HW, Aaltonen LA, Kruhøffer M, Orntoft TF, Andersen CL, Sieber OM. DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2009; 14:8061-9. [PMID: 19088021 DOI: 10.1158/1078-0432.ccr-08-1431] [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 About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes and downstream effects of differential gene expression. EXPERIMENTAL DESIGN DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy-number data. RESULTS MSI-associated gene expression changes in colorectal cancers were found to be highly consistent across multiple studies of primary tumors and cancer cell lines from patients of different ethnicities (P < 0.001). Clustering based on consistent changes separated additional test cases by MSI status, and classification of individual samples predicted MSI status with a sensitivity of 96% and specificity of 85%. Genes associated with immune response were up-regulated in MSI cancers, whereas genes associated with cell-cell adhesion, ion binding, and regulation of metabolism were down-regulated. Differential gene expression was shown to reflect systematic differences in DNA copy-number aberrations between MSI and MSS tumors (P < 0.001). CONCLUSIONS Our results show cross-study consistency of MSI-associated gene expression changes in colorectal cancers. DNA copy-number alterations partly cause the differences in gene expression between MSI and MSS cancers.
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Affiliation(s)
- Robert N Jorissen
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Parkville, Victoria, Australia
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D'Errico M, de Rinaldis E, Blasi MF, Viti V, Falchetti M, Calcagnile A, Sera F, Saieva C, Ottini L, Palli D, Palombo F, Giuliani A, Dogliotti E. Genome-wide expression profile of sporadic gastric cancers with microsatellite instability. Eur J Cancer 2008; 45:461-9. [PMID: 19081245 DOI: 10.1016/j.ejca.2008.10.032] [Citation(s) in RCA: 250] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 10/17/2008] [Indexed: 12/18/2022]
Abstract
Gastric cancers with mismatch repair (MMR) inactivation are characterised by microsatellite instability (MSI). In this study, the transcriptional profile of 38 gastric cancers with and without MSI was analysed. Unsupervised analysis showed that the immune and apoptotic gene networks efficiently discriminated these two cancer types. Hierarchical clustering analysis revealed numerous gene expression changes associated with the MSI phenotype. Amongst these, the p53-responsive genes maspin and 14-3-3 sigma were significantly more expressed in tumours with than without MSI. A tight immunosurveillance coupled with a functional p53 gene response is consistent with the better prognosis of MSI cancers. Frequent silencing of MLH1 and downregulation of MMR target genes, such as MRE11 and MBD4, characterised MSI tumours. The downregulation of SMUG1 was also a typical feature of these tumours. The DNA repair gene expression profile of gastric cancer with MSI is of relevance for therapy response.
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Affiliation(s)
- Mariarosaria D'Errico
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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Kim JC, Kim SY, Roh SA, Cho DH, Kim DD, Kim JH, Kim YS. Gene expression profiling: Canonical molecular changes and clinicopathological features in sporadic colorectal cancers. World J Gastroenterol 2008; 14:6662-72. [PMID: 19034969 PMCID: PMC2773308 DOI: 10.3748/wjg.14.6662] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate alternative or subordinate pathways involved in colorectal tumorigenesis and tumor growth, possibly determining at-risk populations and predicting responses to treatment.
METHODS: Using microarray gene-expression analysis, we analyzed patterns of gene expression relative to canonical molecular changes and clinicopathological features in 84 sporadic colorectal cancer patients, standardized by tumor location. Subsets of differentially expressed genes were confirmed by real-time reverse-transcript polymerase chain reaction (RT-PCR).
RESULTS: The largest number of genes identified as being differentially expressed was by tumor location, and the next largest number by lymphovascular or neural invasion of tumor cells and by mismatch repair (MMR) defects. Amongst biological processes, the immune response was significantly implicated in entire molecular changes observed during colorectal tumorigenesis (P < 0.001). Amongst 47 differentially expressed genes, seven (PISD, NIBP, BAI2, STOML1, MRPL21, MRPL16, and MKKS) were newly found to correlate with tumorigenesis and tumor growth. Most location-associated molecular changes had distinct effects on gene expression, but the effects of the latter were sometimes contradictory.
CONCLUSION: We show that several differentially expressed genes were associated with canonical molecular changes in sporadic colorectal cancers, possibly constituting alternative or subordinate pathways of tumorigenesis. As tumor location was the dominant factor influencing differential gene expression, location-specific analysis may identify location-associated pathways and enhance the accuracy of class prediction.
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Imai K, Yamamoto H. Carcinogenesis and microsatellite instability: the interrelationship between genetics and epigenetics. Carcinogenesis 2008; 29:673-80. [PMID: 17942460 DOI: 10.1093/carcin/bgm228] [Citation(s) in RCA: 307] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA mismatch repair (MMR) deficiency results in a strong mutator phenotype and high-frequency microsatellite instability (MSI-H), which are the hallmarks of tumors arising within Lynch syndrome. MSI-H is characterized by length alterations within simple repeated sequences, microsatellites. Lynch syndrome is primarily due to germline mutations in one of the DNA MMR genes; mainly hMLH1 or hMSH2 and less frequently hMSH6 and rarely hPMS2. Germline hemiallelic methylation of MLH1, termed epimutation, has been reported to be a new cause of Lynch syndrome. MSI-H is also observed in approximately 15% of colorectal, gastric and endometrial cancers and in lower frequencies in a minority of other tumors, where it is associated with the hypermethylation of the promoter region of hMLH1. MSI-H underlies a distinctive tumorigenic pathway because cancers with MSI-H exhibit many differences in genotype and phenotype relative to cancers without MSI-H, irrespective of their hereditary or sporadic origins. Genetic, epigenetic and transcriptomic differences exist between cancers with and those without the MSI-H. The BRAF V600E mutation is associated with sporadic MSI-H colorectal cancers (CRCs) harboring hMLH1 methylation but not Lynch syndrome-related CRCs. The differences in genotype and phenotype between cancers with and those without MSI-H are likely to be causally linked to their differences in biological and clinical features. Therefore, the diagnosis of MSI-H in cancers is thus considered to be of increasing relevance, because MSI-H is a useful screening marker for identifying patients with Lynch syndrome, a better prognostic factor and could affect the efficacy of chemotherapy. This review addresses recent advances in the field of microsatellite instability research.
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Affiliation(s)
- Kohzoh Imai
- Sapporo Medical University, South 1, West 17, Chuo-ku, Sapporo 060-8556, Japan.
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43
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Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow JE, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman TJ, Coffey RJ, Aronow BJ. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol 2008; 8:R131. [PMID: 17615082 PMCID: PMC2323222 DOI: 10.1186/gb-2007-8-7-r131] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 02/12/2007] [Accepted: 07/05/2007] [Indexed: 12/27/2022] Open
Abstract
Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5. Background The expression of carcino-embryonic antigen by colorectal cancer is an example of oncogenic activation of embryonic gene expression. Hypothesizing that oncogenesis-recapitulating-ontogenesis may represent a broad programmatic commitment, we compared gene expression patterns of human colorectal cancers (CRCs) and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. Results We report here that 39 colon tumors from four independent mouse models and 100 human CRCs encompassing all clinical stages shared a striking recapitulation of embryonic colon gene expression. Compared to normal adult colon, all mouse and human tumors over-expressed a large cluster of genes highly enriched for functional association to the control of cell cycle progression, proliferation, and migration, including those encoding MYC, AKT2, PLK1 and SPARC. Mouse tumors positive for nuclear β-catenin shifted the shared embryonic pattern to that of early development. Human and mouse tumors differed from normal embryonic colon by their loss of expression modules enriched for tumor suppressors (EDNRB, HSPE, KIT and LSP1). Human CRC adenocarcinomas lost an additional suppressor module (IGFBP4, MAP4K1, PDGFRA, STAB1 and WNT4). Many human tumor samples also gained expression of a coordinately regulated module associated with advanced malignancy (ABCC1, FOXO3A, LIF, PIK3R1, PRNP, TNC, TIMP3 and VEGF). Conclusion Cross-species, developmental, and multi-model gene expression patterning comparisons provide an integrated and versatile framework for definition of transcriptional programs associated with oncogenesis. This approach also provides a general method for identifying pattern-specific biomarkers and therapeutic targets. This delineation and categorization of developmental and non-developmental activator and suppressor gene modules can thus facilitate the formulation of sophisticated hypotheses to evaluate potential synergistic effects of targeting within- and between-modules for next-generation combinatorial therapeutics and improved mouse models.
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Affiliation(s)
- Sergio Kaiser
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Young-Kyu Park
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - Ming Yu
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Walter J Jessen
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Johannes Freudenberg
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaodi Chen
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin Haigis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Anil G Jegga
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sue Kong
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bhuvaneswari Sakthivel
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Huan Xu
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Timothy Reichling
- Division of Human Cancer Genetics, The Ohio State University College of Medicine, Columbus, Ohio 43210-2207, USA
| | - Mohammad Azhar
- Institute for Collaborative BioResearch, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Gregory P Boivin
- University of Cincinnati, Department of Pathology and Laboratory Medicine, Cincinnati, OH 45267, USA
| | - Reade B Roberts
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anika C Bissahoyo
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Fausto Gonzales
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Greg C Bloom
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Steven Eschrich
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Scott L Carter
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeremy E Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John Kleimeyer
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael Kleimeyer
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Vivek Ramaswamy
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Stephen H Settle
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Braden Boone
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Shawn Levy
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Jonathan M Graff
- University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Thomas Doetschman
- Institute for Collaborative BioResearch, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Joanna Groden
- Division of Human Cancer Genetics, The Ohio State University College of Medicine, Columbus, Ohio 43210-2207, USA
| | - William F Dove
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - David W Threadgill
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy J Yeatman
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert J Coffey
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Bruce J Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Abstract
Colorectal carcinoma continues to be a leading cause of cancer morbidity and mortality despite widespread adoption of screening methods. Targeted detection and therapy using recent advances in our knowledge of in vivo cancer biomarkers promise to significantly improve methods for early detection, risk stratification, and therapeutic intervention. The behavior of molecular targets in transformed tissues is being comprehensively assessed using new techniques of gene expression profiling and high throughput analyses. The identification of promising targets is stimulating the development of novel molecular probes, including significant progress in the field of activatable and peptide probes. These probes are being evaluated in small animal models of colorectal neoplasia and recently in the clinic. Furthermore, innovations in optical imaging instrumentation are resulting in the scaling down of size for endoscope compatibility. Advances in target identification, probe development, and novel instruments are progressing rapidly, and the integration of these technologies has a promising future in molecular medicine.
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Affiliation(s)
- Pei-Lin Hsiung
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA USA, 94305
| | - Thomas Wang
- Division of Gastroenterology and Hepatology, University of Michigan School of Medicine, Ann Arbor, MI USA, 48109
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Abstract
The identification, purification and characterization of cancer stem cells (CSCs) holds tremendous promise for improving the treatment of cancer. Mounting evidence is demonstrating that only certain tumour cells (i.e. the CSCs) can give rise to tumours when injected and that these purified cell populations generate heterogeneous tumours. While the cell of origin is still not determined definitively, specific molecular markers for populations containing these CSCs have been found for leukaemia, brain cancer and breast cancer, among others. Systems approaches, particularly molecular profiling, have proven to be of great utility for cancer diagnosis and characterization. These approaches also hold significant promise for identifying distinctive properties of the CSCs, and progress is already being made.
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Abstract
In recent decades there have been significant advances in our understanding of the genes that underlie hereditary susceptibility to colorectal cancer (CRC). In 2007 it is well established that mutations in DNA repair genes (MLH1, MSH2, MSH6, MYH) and Wnt pathway signal transduction inhibitors (APC) underlie a significant percentage of hereditary CRC susceptibility. However, it also is clear that the known CRC susceptibility genes do not explain fully the inherited risk seen even in families meeting the revised Bethesda guidelines. Furthermore, the optimal medical management of these syndromes is still being defined. What underlies CRC susceptibility in these highly unusual families that do not have identifiable mutations in the known genes, often referred to as syndrome X? This review addresses this important question that is relevant to our current understanding of the management of individuals with hereditary predisposition to CRC.
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Affiliation(s)
- Steven M Lipkin
- Cancer Genetics Clinic, Chao Family NCI Designated Comprehensive Cancer Center, University of California, Irvine, CA 92697-4038, USA.
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47
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Schmitt M, Mengele K, Schueren E, Sweep FCGJ, Foekens JA, Brünner N, Laabs J, Malik A, Harbeck N. European Organisation for Research and Treatment of Cancer (EORTC) Pathobiology Group standard operating procedure for the preparation of human tumour tissue extracts suited for the quantitative analysis of tissue-associated biomarkers. Eur J Cancer 2007; 43:835-44. [PMID: 17321128 DOI: 10.1016/j.ejca.2007.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 01/04/2007] [Indexed: 11/20/2022]
Abstract
With the new concept of 'individualized treatment and targeted therapies', tumour tissue-associated biomarkers have been given a new role in selection of cancer patients for treatment and in cancer patient management. Tumour biomarkers can give support to cancer patient stratification and risk assessment, treatment response identification, or to identifying those patients who are expected to respond to certain anticancer drugs. As the field of tumour-associated biomarkers has expanded rapidly over the last years, it has become increasingly apparent that a strong need exists to establish guidelines on how to easily disintegrate the tumour tissue for assessment of the presence of tumour tissue-associated biomarkers. Several mechanical tissue (cell) disruption techniques exist, ranging from bead mill homogenisation and freeze-fracturing through to blade or pestle-type homogenisation, to grinding and ultrasonics. Still, only a few directives have been given on how fresh-frozen tumour tissues should be processed for the extraction and determination of tumour biomarkers. The PathoBiology Group of the European Organisation for Research and Treatment of Cancer therefore has devised a standard operating procedure for the standardised preparation of human tumour tissue extracts which is designed for the quantitative analysis of tumour tissue-associated biomarkers. The easy to follow technical steps involved require 50-300 mg of deep-frozen cancer tissue placed into small size (1.2 ml) cryogenic tubes. These are placed into the shaking flask of a Mikro-Dismembrator S machine (bead mill) to pulverise the tumour tissue in the capped tubes in the deep-frozen state by use of a stainless steel ball, all within 30 s of exposure. RNA is isolated from the pulverised tissue following standard procedures. Proteins are extracted from the still frozen pulverised tissue by addition of Tris-buffered saline to obtain the cytosol fraction of the tumour or by the Tris buffer supplemented with the non-ionic detergent Triton X-100, and, after high-speed centrifugation, are found in the tissue supernatant. The resulting tissue cell debris sediment is a rich source of genomic DNA.
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Affiliation(s)
- Manfred Schmitt
- Clinical Research Unit, Department of Obstetrics and Gynecology, Technical University of Munich, Germany.
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48
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Xu Q, Chen W. Developing effective tumor vaccines: basis, challenges and perspectives. FRONTIERS OF MEDICINE IN CHINA 2007; 1:11-19. [PMID: 24557610 DOI: 10.1007/s11684-007-0003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Accepted: 10/20/2006] [Indexed: 06/03/2023]
Abstract
A remarkable advance in tumor immunology during the last decade is the elucidation of the antigenic basis of tumor recognition and destruction. A variety of tumor antigens have been identified using several strategies including conventional experiments and newly developed bioinformatics. Among these antigens, cancer/testis antigen (CT antigen) is considered to be the most promising target for immunotherapy by vaccination. Successful immunotherapy of tumors requires understanding of the natural relationship between the immune system and tumor in the status of differentiation, invasion and maturation. Continued progress in development of effective cancer vaccines depends on the identification of appropriate target antigens, the establishment of optimal immunization strategies without harmful autoimmune responses and the ability of manipulating tumor microenvironment to circumvent immune suppression and to augment the anti-tumor immune response.
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Affiliation(s)
- Qingwen Xu
- Department of Immunology, Peking University Health Science Center, Beijing, 100083, China
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49
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Trautmann K, Terdiman JP, French AJ, Roydasgupta R, Sein N, Kakar S, Fridlyand J, Snijders AM, Albertson DG, Thibodeau SN, Waldman FM. Chromosomal instability in microsatellite-unstable and stable colon cancer. Clin Cancer Res 2007; 12:6379-85. [PMID: 17085649 DOI: 10.1158/1078-0432.ccr-06-1248] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
PURPOSE The genomic instability in colon cancer can be divided into at least two major types, microsatellite instability (MSI) or chromosomal instability (CIN). Although initially felt to be mutually exclusive, recent evidence suggests that there may be overlap between the two. The aim of this study was to identify chromosomal alterations at high resolution in sporadic colon cancers with high-level microsatellite instability (MSI-H) and to compare them to those present in a set of matched microsatellite stable (MSS) tumors. EXPERIMENTAL DESIGN Array-based comparative genomic hybridization was used to analyze a set of 23 sporadic MSI-H and 23 MSS colon cancers matched for location, gender, stage, and age. The arrays consisted of 2,464 bacterial artificial chromosome clones. RESULTS MSI and MSS colon cancers differed significantly with respect to frequency and type of chromosomal alterations. The median fraction of genome altered was lower among MSI-H tumors than MSS tumors (2.8% versus 30.7%, P=0.00006). However, the MSI-H tumors displayed a range of genomic alterations, from the absence of detectable alterations to extensive alterations. Frequent alterations in MSI-H tumors included gains of chromosomes 8, 12, and 13, and loss of 15q14. In contrast, the most frequent alterations in MSS tumors were gains of 7, 13, 8q, and 20, and losses of 8p, 17p, and 18. A small, previously uncharacterized, genomic deletion on 16p13.2, found in 35% of MSI-H and 21% of MSS tumors, was confirmed by fluorescence in situ hybridization. CONCLUSION MSI and CIN are not mutually exclusive forms of genomic instability in sporadic colon cancer, with MSI tumors also showing varying degrees of CIN.
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Affiliation(s)
- Karolin Trautmann
- Comprehensive Cancer Center, Department of Medicine, University of California San Francisco, San Francisco, California 94143-0808, USA
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50
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Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Res 2006; 35:e8. [PMID: 17158151 PMCID: PMC1802630 DOI: 10.1093/nar/gkl871] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able to show that there are two types of positional artifacts in microarray data introducing spurious correlations between genes. First, we find that genes that are close on the microarray chips tend to have higher correlations between their expression profiles. We call this the ‘chip artifact’. Our calculations suggest that the carry-over during the printing process is one of the major sources of this type of artifact, which is later confirmed by our experiments. Based on our experiments, the measured intensity of a microarray spot contains 0.1% (for fully-hybridized spots) to 93% (for un-hybridized ones) of noise resulting from this artifact. Secondly, we, for the first time, show that genes that are close on the microtiter plates in microarray experiments also tend to have higher correlations. We call this the ‘plate artifact’. Both types of artifacts exist with different severity in all cDNA microarray experiments that we analyzed. Therefore, we develop an automated web tool—COP (COrrelations by Positional artifacts) to detect these artifacts in microarray experiments. COP has been integrated with the microarray data normalization tool, ExpressYourself, which is available at . Together, the two can eliminate most of the common noises in microarray data.
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Affiliation(s)
- Haiyuan Yu
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Katherine Nguyen
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Tom Royce
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Jiang Qian
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Kenneth Nelson
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Michael Snyder
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale UniversityCT 06520, USA
- Department of Computer Science266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
- To whom correspondence should be addressed. Tel: + 203 4325405; Fax: + 413 4102140;
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