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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Voutsadakis IA. Chromosome 20q11.21 Amplifications in Colorectal Cancer. Cancer Genomics Proteomics 2021; 18:487-496. [PMID: 33994370 DOI: 10.21873/cgp.20274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Colorectal cancer is the most common gastrointestinal carcinoma in western countries. Prognosis of metastatic colorectal cancer has improved in the last decades, but the disease continues to carry an adverse outcome in most cases. An improved understanding of molecular pathogenesis has provided incremental benefits in survival outcomes with the introduction of targeted therapies for specific sub-types and gives hope for further improvements. MATERIALS AND METHODS Publicly available data from genomic series of colorectal cancer published by the TCGA were analyzed with the aim of characterizing the sub-set of colorectal cancers carrying amplifications of chromosome 20q11.21, compared with cancers with no amplifications in this locus. Associations of 20q11.21-amplified cancers with other molecular lesions commonly observed in colorectal cancer were explored. mRNA expression of genes from the locus in amplified cases was analyzed. An exploratory survival analysis was also performed. RESULTS Amplifications of genes at chromosome arm 20q are observed in 7% to 9% of colorectal cancers, representing the most commonly amplified loci in this type of cancer. The 20q11.21 presents the highest amplification rate in the 20q arm. 20q11.21 amplified cancers display concomitant mutations in the KRAS pathway and SMAD4 less often than non-amplified cancers. Mutations in DNA repair genes are also less often encountered in 20q11.21 amplified colorectal cancers than non-amplified ones. CONCLUSION Amplification of genes at locus 20q11.21, representing the most frequently amplified locus in colorectal cancers, is associated with specific molecular characteristics and may have therapeutic implications.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, ON, Canada; .,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada
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Selas A, Martin-Encinas E, Fuertes M, Masdeu C, Rubiales G, Palacios F, Alonso C. A patent review of topoisomerase I inhibitors (2016-present). Expert Opin Ther Pat 2021; 31:473-508. [PMID: 33475439 DOI: 10.1080/13543776.2021.1879051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Topoisomerases are important targets for therapeutic improvement in the treatment of some diseases, including cancer. Inhibitors and poisons of topoisomerase I can limit the activity of this enzyme in its enzymatic cycle. This fact implies an anticancer effect of these drugs, since most cancer cells are characterized by both a higher activity of topoisomerase I and a higher replication rate compared to non-cancerous cells. Clinically approved inhibitors include camptothecin (CPT) and its derivatives. However, their limitations have encouraged different research groups to prepare new compounds, proof of which are the numerous research works and patents, some of them in the last five years. AREAS COVERED This review covers patent literature on topoisomerase I inhibitors and their application published between 2016-present. EXPERT OPINION The highest contribution toward patent development has been obtained from academics or small biotechnology companies. The most important fields of innovation include the preparation of prodrugs or inhibitors combined with other agents, as biocompatible polymers or antibodies. A promising development of topoisomerase I inhibitors is expected in the next years, directed to the treatment of diverse diseases, specifically toward different types of cancer and infectious diseases, among others.
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Affiliation(s)
- Asier Selas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Endika Martin-Encinas
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Maria Fuertes
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Carme Masdeu
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Francisco Palacios
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Concepción Alonso
- Departamento De Química Orgánica I, Facultad De Farmacia. Universidad Del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Vitoria-Gasteiz, Spain
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Gambaro K, Marques M, McNamara S, Couetoux du Tertre M, Diaz Z, Hoffert C, Srivastava A, Hébert S, Samson B, Lespérance B, Ko Y, Dalfen R, St‐Hilaire E, Sideris L, Couture F, Burkes R, Harb M, Camlioglu E, Gologan A, Pelsser V, Constantin A, Greenwood CM, Tejpar S, Kavan P, Kleinman CL, Batist G. Copy number and transcriptome alterations associated with metastatic lesion response to treatment in colorectal cancer. Clin Transl Med 2021; 11:e401. [PMID: 33931971 PMCID: PMC8087915 DOI: 10.1002/ctm2.401] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Therapeutic resistance is the main cause of death in metastatic colorectal cancer. To investigate genomic plasticity, most specifically of metastatic lesions, associated with response to first-line systemic therapy, we collected longitudinal liver metastatic samples and characterized the copy number aberration (CNA) landscape and its effect on the transcriptome. METHODS Liver metastatic biopsies were collected prior to treatment (pre, n = 97) and when clinical imaging demonstrated therapeutic resistance (post, n = 43). CNAs were inferred from whole exome sequencing and were correlated with both the status of the lesion and overall patient progression-free survival (PFS). We used RNA sequencing data from the same sample set to validate aberrations as well as independent datasets to prioritize candidate genes. RESULTS We identified a significantly increased frequency gain of a unique CN, in liver metastatic lesions after first-line treatment, on chr18p11.32 harboring 10 genes, including TYMS, which has not been reported in primary tumors (GISTIC method and test of equal proportions, FDR-adjusted p = 0.0023). CNA lesion profiles exhibiting different treatment responses were compared and we detected focal genomic divergences in post-treatment resistant lesions but not in responder lesions (two-tailed Fisher's Exact test, unadjusted p ≤ 0.005). The importance of examining metastatic lesions is highlighted by the fact that 15 out of 18 independently validated CNA regions found to be associated with PFS in this study were only identified in the metastatic lesions and not in the primary tumors. CONCLUSION This investigation of genomic-phenotype associations in a large colorectal cancer liver metastases cohort identified novel molecular features associated with treatment response, supporting the clinical importance of collecting metastatic samples in a defined clinical setting.
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Affiliation(s)
- Karen Gambaro
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Maud Marques
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Suzan McNamara
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
| | | | - Zuanel Diaz
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
| | - Cyrla Hoffert
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Archana Srivastava
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Steven Hébert
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Benoit Samson
- Charles LeMoyne Hospital3120 Taschereau Blvd.Greenfield ParkQuebecJ4V 2H1Canada
| | | | - Yoo‐Joung Ko
- Sunnybrook Health Science Centre2075 Bayview Ave.TorontoOntarioM4N 3M5Canada
| | - Richard Dalfen
- St. Mary's Hospital3830 LacombeMontrealQuebecH3T 1M5Canada
| | - Eve St‐Hilaire
- Georges Dumont Hospital220 Avenue UniversiteMonctonNew BrunswickE1C 2Z3Canada
| | - Lucas Sideris
- Hôpital Maisonneuve Rosemont5415 Assumption BlvdMontrealQuebecH1T 2M4Canada
| | - Felix Couture
- Hôtel‐Dieu de Quebec11 Cote du PalaisMontrealQuebecG1R 2J6Canada
| | - Ronald Burkes
- Mount Sinai Hospital600 University AvenueTorontoOntarioM5G 1X5Canada
| | - Mohammed Harb
- Moncton Hospital135 Macbeath AveMonctonNew BrunswickE1C 6Z8Canada
| | - Errol Camlioglu
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Adrian Gologan
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Vincent Pelsser
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - André Constantin
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Celia M.T. Greenwood
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Gerald Bronfman Department of OncologyMcGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Department of Epidemiology, Biostatistics and Occupational HealthMcGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Sabine Tejpar
- Digestive Oncology UnitKatholieke Universiteit LeuvenOude Markt 13Leuven3000Belgium
| | - Petr Kavan
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Claudia L. Kleinman
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Department of Human GeneticsLady Davis Research Institute, McGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Gerald Batist
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
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Yang H, Wei Q, Li D, Wang Z. Cancer classification based on chromatin accessibility profiles with deep adversarial learning model. PLoS Comput Biol 2020; 16:e1008405. [PMID: 33166290 PMCID: PMC7676699 DOI: 10.1371/journal.pcbi.1008405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/19/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
Given the complexity and diversity of the cancer genomics profiles, it is challenging to identify distinct clusters from different cancer types. Numerous analyses have been conducted for this propose. Still, the methods they used always do not directly support the high-dimensional omics data across the whole genome (Such as ATAC-seq profiles). In this study, based on the deep adversarial learning, we present an end-to-end approach ClusterATAC to leverage high-dimensional features and explore the classification results. On the ATAC-seq dataset and RNA-seq dataset, ClusterATAC has achieved excellent performance. Since ATAC-seq data plays a crucial role in the study of the effects of non-coding regions on the molecular classification of cancers, we explore the clustering solution obtained by ClusterATAC on the pan-cancer ATAC dataset. In this solution, more than 70% of the clustering are single-tumor-type-dominant, and the vast majority of the remaining clusters are associated with similar tumor types. We explore the representative non-coding loci and their linked genes of each cluster and verify some results by the literature search. These results suggest that a large number of non-coding loci affect the development and progression of cancer through its linked genes, which can potentially advance cancer diagnosis and therapy.
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Affiliation(s)
- Hai Yang
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai, PR China
| | - Qiang Wei
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dongdong Li
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai, PR China
| | - Zhe Wang
- Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai, PR China
- * E-mail:
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Oliveira DM, Santamaria G, Laudanna C, Migliozzi S, Zoppoli P, Quist M, Grasso C, Mignogna C, Elia L, Faniello MC, Marinaro C, Sacco R, Corcione F, Viglietto G, Malanga D, Rizzuto A. Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data. Oncotarget 2018; 9:20409-20425. [PMID: 29755661 PMCID: PMC5945505 DOI: 10.18632/oncotarget.24912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 02/28/2018] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined "common genes") and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined "site-associated genes"). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL1 was associated with good prognosis.
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Affiliation(s)
- Duarte Mendes Oliveira
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Gianluca Santamaria
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Carmelo Laudanna
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Simona Migliozzi
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Pietro Zoppoli
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Michael Quist
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catie Grasso
- University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Chiara Mignogna
- Dipartimento di Scienze della Salute, Università Magna Graecia, Catanzaro, Italy
| | - Laura Elia
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
| | | | - Cinzia Marinaro
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Rosario Sacco
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
| | | | - Giuseppe Viglietto
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Donatella Malanga
- Dipartimento di Medicina Sperimentale e Clinica, Università Magna Graecia, Catanzaro, Italy
| | - Antonia Rizzuto
- Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Graecia, Catanzaro, Italy
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Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer. Proteomes 2017; 5:proteomes5040028. [PMID: 29068423 PMCID: PMC5748563 DOI: 10.3390/proteomes5040028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein-protein interaction, and pharmacogenomics data, are indispensable to glean into the cancer genome and proteome and these approaches have generated multidimensional universal studies of genes and proteins (OMICS) data which has the potential to facilitate precision medicine. However, due to slow progress in computational technologies, the translation of big omics data into their clinical aspects have been slow. In this review, attempts have been made to describe the role of high-throughput genomic and proteomic technologies in identifying a panel of biomarkers which could be used for the early diagnosis and prognosis of cancer.
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Peters GJ, Smid K, Meijer E, van Groeningen CJ, Leon LG. Role of genomic factors beyond thymidylate synthase in the prediction of response to 5-fluorouracil. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:595-603. [PMID: 27906628 DOI: 10.1080/15257770.2016.1218020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
5-Fluorouracil (5FU) is still a major drug in combinations regimens for the treatment of colorectal cancer (CRC) both in the adjuvant and palliative setting. 5FU or its oral prodrug capecitabine is usually combined with irinotecan/oxaliplatin and the novel agents bevacizumab/cetuximab. Although this improved the outcome, the overall prognosis in patients with metastasized disease is still relatively poor. Although the target for 5FU, thymidylate synthase was shown to have a predictive value, this could only predict response in a subset of patients. Given the heterogeneous and complex nature of CRC, it is likely that other aberrations can affect therapeutic response. As an alternative, we investigated Copy number alterations using oligonucleotide-based high-throughput array-comparative-genomic-hybridization (aCGH) to obtain an unbiased screening of the whole genetic spectrum. Chromosomal aberrations have been identified in 85% of CRC patients and include genomic regions harboring copy number alterations in the DNA. These alterations may change the expression of many genes and might explain the differential response to therapy as shown in recent studies with several 5FU combinations. In order to clarify new predictive parameters for 5FU, we used aCGH in a historical cohort of patients, which received treatment with single agent 5FU, and an unsupervised clustering analysis showed a statistical (p < 0.05) difference between responding and nonresponding patients. We also find that several regions showed differences between responders/non-responders, such as losses in 12p12.3-12q15 and in 18p (where TS is located) in responding patients. Genome-wide analysis may provide an additional tool to discriminate between responders and nonresponders.
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Affiliation(s)
- Godefridus J Peters
- a Department of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands
| | - K Smid
- a Department of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands
| | - E Meijer
- a Department of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands
| | - C J van Groeningen
- a Department of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands.,b Amstelland Hospital , Amstelveen , The Netherlands
| | - L G Leon
- a Department of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands.,c Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa , Pisa , Italy
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Lorentzen A, Mitchelmore C. NDRG2 gene copy number is not altered in colorectal carcinoma. World J Clin Oncol 2017; 8:67-74. [PMID: 28246586 PMCID: PMC5309715 DOI: 10.5306/wjco.v8.i1.67] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/12/2016] [Accepted: 12/28/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate if the down-regulation of N-myc Downstream Regulated Gene 2 (NDRG2) expression in colorectal carcinoma (CRC) is due to loss of the NDRG2 allele(s).
METHODS The following were investigated in the human colorectal cancer cell lines DLD-1, LoVo and SW-480: NDRG2 mRNA expression levels using quantitative reverse transcription-polymerase chain reaction (qRT-PCR); interaction of the MYC gene-regulatory protein with the NDRG2 promoter using chromatin immunoprecipitation; and NDRG2 promoter methylation using bisulfite sequencing. Furthermore, we performed qPCR to analyse the copy numbers of NDRG2 and MYC genes in the above three cell lines, 8 normal colorectal tissue samples and 40 CRC tissue samples.
RESULTS As expected, NDRG2 mRNA levels were low in the three colorectal cancer cell lines, compared to normal colon. Endogenous MYC protein interacted with the NDRG2 core promoter in all three cell lines. In addition, the NDRG2 promoter was heavily methylated in these cell lines, suggesting an epigenetic regulatory mechanism. Unaltered gene copy numbers of NDRG2 were observed in the three cell lines. In the colorectal tissues, one normal and three CRC samples showed partial or complete loss of one NDRG2 allele. In contrast, the MYC gene was amplified in one cell line and in more than 40% of the CRC cases.
CONCLUSION Our study suggests that the reduction in NDRG2 expression observed in CRC is due to transcriptional repression by MYC and promoter methylation, and is not due to allelic loss.
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Alonso C, Fuertes M, González M, Rubiales G, Tesauro C, Knudsen BR, Palacios F. Synthesis and biological evaluation of indeno[1,5]naphthyridines as topoisomerase I (TopI) inhibitors with antiproliferative activity. Eur J Med Chem 2016; 115:179-90. [DOI: 10.1016/j.ejmech.2016.03.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 02/07/2023]
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12
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Xu L, Li X, Cai M, Chen J, Li X, Wu WKK, Kang W, Tong J, To KF, Guan XY, Sung JJY, Chan FKL, Yu J. Increased expression of Solute carrier family 12 member 5 via gene amplification contributes to tumour progression and metastasis and associates with poor survival in colorectal cancer. Gut 2016; 65:635-46. [PMID: 25947013 PMCID: PMC4819609 DOI: 10.1136/gutjnl-2014-308257] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 01/12/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Using whole genome sequencing, we identified gene amplification of solute carrier family 12 member 5 (SLC12A5) located at 20q13.12 in colorectal cancer (CRC). We analysed its amplification, overexpression, biological effects and prognostic significance in CRC. DESIGN SLC12A5 amplification status was evaluated by fluorescence in situ hybridisation (FISH). The effects of SLC12A5 re-expression or knockdown were determined in proliferation, apoptosis, invasion and metastasis assays. SLC12A5 target genes and related pathways were identified by reporter activity and cDNA microarray analyses. Clinical impact of SLC12A5 overexpression was assessed in 195 patients with CRC. RESULTS Amplification of SLC12A5 was verified in 78 out of 191 (40.8%) patients with primary CRC by FISH, which was positively correlated with its protein overexpression (p<0.001). Biofunctional investigation of SLC12A5 revealed that SLC12A5 significantly increased cell proliferation, G1-S cell cycle transition, invasion/migration abilities, but suppressed apoptosis in vitro and promoted xenograft tumour growth as well as lung metastasis in vivo. The antiapoptosis effect by SLC12A5 was mediated through inhibiting apoptosis-inducing factor and endonuclease G-dependent apoptotic signalling pathway; and the pro-metastasis role was by regulating key elements of the matrix architecture, including matrix metallopeptidase and fibronectin. After a median follow-up of 50.16 months, multivariate analysis revealed that patients with SLC12A5 protein overexpression had a significant decrease in overall survival. Kaplan-Meier survival curves showed that SLC12A5 overexpression was significantly associated with shortened survival in patients with CRC. CONCLUSIONS SLC12A5 plays a pivotal oncogenic role in colorectal carcinogenesis; its overexpression is an independent prognostic factor of patients with CRC.
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Affiliation(s)
- Lixia Xu
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong,Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxing Li
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Muyan Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jinna Chen
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xiangchun Li
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - William K K Wu
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Joanna Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, Hong Kong
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Francis K L Chan
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Jun Yu
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong
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Wang H, Liang L, Fang JY, Xu J. Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers. Oncogene 2015; 35:2011-9. [PMID: 26257062 DOI: 10.1038/onc.2015.304] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/07/2015] [Accepted: 07/12/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) results from the accumulation of genetic alterations, and somatic copy number alterations (CNAs) are crucial for the development of CRC. Genome-wide survey of CNAs provides opportunities for identifying cancer driver genes in an unbiased manner. The detection of aberrant CNAs may provide novel markers for the early diagnosis and personalized treatment of CRC. A major challenge in array-based profiling of CNAs is to distinguish the alterations that play causative roles from the random alterations that accumulate during colorectal carcinogenesis. In this view, we systematically discuss the frequent CNAs in CRC, focusing on functional genes that have potential diagnostic, prognostic and therapeutic significance.
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Affiliation(s)
- H Wang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - L Liang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J-Y Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - J Xu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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14
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Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJM, van de Wiel MA, Israeli D, van Essen HF, van Grieken NCT, Voorham QJM, Bosch LJW, Qu X, Kabbarah O, Verheul HMW, Nagtegaal ID, Punt CJA, Ylstra B, Meijer GA. Genomic landscape of metastatic colorectal cancer. Nat Commun 2014; 5:5457. [PMID: 25394515 PMCID: PMC4243240 DOI: 10.1038/ncomms6457] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022] Open
Abstract
Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumour biology. Here we describe the genomic landscape of tumour samples of a homogeneous well-annotated series of patients with metastatic CRC (mCRC) of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal subregions are associated with progression-free survival (PFS; uncorrected single-test P-values <0.005). These subregions are filtered for effect on messenger RNA expression, using an independent data set from The Cancer Genome Atlas which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1–q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of mCRC reveals a number of DNA copy number aberrations associated with response to drug therapy. Response to drug therapy in colorectal cancer (CRC) patients has been associated with tumour heterogeneity. Here the authors analyse DNA copy number aberrations in primary tumours from CRC patients and identify genetic variants that influence drug response.
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Affiliation(s)
- Josien C Haan
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien Tol
- Department of Medical Oncology, Radboud University Medical Centre, Route 452, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Leonie J M Mekenkamp
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Danielle Israeli
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Hendrik F van Essen
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Quirinus J M Voorham
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Linda J W Bosch
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Xueping Qu
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Omar Kabbarah
- Oncology Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080 USA
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Centre, Huispost 824, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, PO Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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Panczyk M. Pharmacogenetics research on chemotherapy resistance in colorectal cancer over the last 20 years. World J Gastroenterol 2014; 20:9775-827. [PMID: 25110414 PMCID: PMC4123365 DOI: 10.3748/wjg.v20.i29.9775] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/17/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023] Open
Abstract
During the past two decades the first sequencing of the human genome was performed showing its high degree of inter-individual differentiation, as a result of large international research projects (Human Genome Project, the 1000 Genomes Project International HapMap Project, and Programs for Genomic Applications NHLBI-PGA). This period was also a time of intensive development of molecular biology techniques and enormous knowledge growth in the biology of cancer. For clinical use in the treatment of patients with colorectal cancer (CRC), in addition to fluoropyrimidines, another two new cytostatic drugs were allowed: irinotecan and oxaliplatin. Intensive research into new treatment regimens and a new generation of drugs used in targeted therapy has also been conducted. The last 20 years was a time of numerous in vitro and in vivo studies on the molecular basis of drug resistance. One of the most important factors limiting the effectiveness of chemotherapy is the primary and secondary resistance of cancer cells. Understanding the genetic factors and mechanisms that contribute to the lack of or low sensitivity of tumour tissue to cytostatics is a key element in the currently developing trend of personalized medicine. Scientists hope to increase the percentage of positive treatment response in CRC patients due to practical applications of pharmacogenetics/pharmacogenomics. Over the past 20 years the clinical usability of different predictive markers has been tested among which only a few have been confirmed to have high application potential. This review is a synthetic presentation of drug resistance in the context of CRC patient chemotherapy. The multifactorial nature and volume of the issues involved do not allow the author to present a comprehensive study on this subject in one review.
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González-González M, Fontanillo C, Abad MM, Gutiérrez ML, Mota I, Bengoechea O, Santos-Briz Á, Blanco O, Fonseca E, Ciudad J, Fuentes M, De Las Rivas J, Alcazar JA, García J, Muñoz-Bellvis L, Orfao A, Sayagués JM. Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer. Cancer 2014; 120:1948-59. [DOI: 10.1002/cncr.28681] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/07/2014] [Accepted: 02/12/2014] [Indexed: 01/16/2023]
Affiliation(s)
- María González-González
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Celia Fontanillo
- Bioinformatics and Functional Genomics Unit; Institute of Molecular Biology and Cellular Oncology/Spanish National Research Council; University of Salamanca; Salamanca Spain
- Celgene Institute for Translational Research Europe (CITRE); Seville Spain
| | - María M. Abad
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - María L. Gutiérrez
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Ines Mota
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Oscar Bengoechea
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Ángel Santos-Briz
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Oscar Blanco
- Department of Pathology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Emilio Fonseca
- Service of Medical Oncology; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Juana Ciudad
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Manuel Fuentes
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Unit; Institute of Molecular Biology and Cellular Oncology/Spanish National Research Council; University of Salamanca; Salamanca Spain
| | - José A. Alcazar
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Jacinto García
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Luís Muñoz-Bellvis
- Department of General and Digestive Surgery; University Hospital of Salamanca-Salamanca Institute of Biomedical Research; Salamanca Spain
| | - Alberto Orfao
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
| | - José M. Sayagués
- General Cytometry Service-Nucleus; Department of Medicine and Cancer Research Center; Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research; University of Salamanca; Salamanca Spain
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17
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Orsetti B, Selves J, Bascoul-Mollevi C, Lasorsa L, Gordien K, Bibeau F, Massemin B, Paraf F, Soubeyran I, Hostein I, Dapremont V, Guimbaud R, Cazaux C, Longy M, Theillet C. Impact of chromosomal instability on colorectal cancer progression and outcome. BMC Cancer 2014; 14:121. [PMID: 24559140 PMCID: PMC4233623 DOI: 10.1186/1471-2407-14-121] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/07/2014] [Indexed: 01/16/2023] Open
Abstract
Background It remains presently unclear whether disease progression in colorectal carcinoma (CRC), from early, to invasive and metastatic forms, is associated to a gradual increase in genetic instability and to a scheme of sequentially occurring Copy Number Alterations (CNAs). Methods In this work we set to determine the existence of such links between CRC progression and genetic instability and searched for associations with patient outcome. To this aim we analyzed a set of 162 Chromosomal Instable (CIN) CRCs comprising 131 primary carcinomas evenly distributed through stage 1 to 4, 31 metastases and 14 adenomas by array-CGH. CNA profiles were established according to disease stage and compared. We, also, asked whether the level of genomic instability was correlated to disease outcome in stage 2 and 3 CRCs. Two metrics of chromosomal instability were used; (i) Global Genomic Index (GGI), corresponding to the fraction of the genome involved in CNA, (ii) number of breakpoints (nbBP). Results Stage 1, 2, 3 and 4 tumors did not differ significantly at the level of their CNA profiles precluding the conventional definition of a progression scheme based on increasing levels of genetic instability. Combining GGI and nbBP,we classified genomic profiles into 5 groups presenting distinct patterns of chromosomal instability and defined two risk classes of tumors, showing strong differences in outcome and hazard risk (RFS: p = 0.012, HR = 3; OS: p < 0.001, HR = 9.7). While tumors of the high risk group were characterized by frequent fractional CNAs, low risk tumors presented predominantly whole chromosomal arm CNAs. Searching for CNAs correlating with negative outcome we found that losses at 16p13.3 and 19q13.3 observed in 10% (7/72) of stage 2–3 tumors showed strong association with early relapse (p < 0.001) and death (p < 0.007, p < 0.016). Both events showed frequent co-occurrence (p < 1x10-8) and could, therefore, mark for stage 2–3 CRC susceptible to negative outcome. Conclusions Our data show that CRC disease progression from stage 1 to stage 4 is not paralleled by increased levels of genetic instability. However, they suggest that stage 2–3 CRC with elevated genetic instability and particularly profiles with fractional CNA represent a subset of aggressive tumors.
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Knudsen BR, Jepsen ML, Ho YP. Quantum dot-based nanosensors for diagnosis via enzyme activity measurement. Expert Rev Mol Diagn 2014; 13:367-75. [DOI: 10.1586/erm.13.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Stougaard M, Ho YP. DNA-based nanosensors for next-generation clinical diagnostics via detection of enzyme activity. Expert Rev Mol Diagn 2013; 14:1-3. [PMID: 24308335 DOI: 10.1586/14737159.2014.863151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specific and sensitive detection of DNA-modifying enzymes represents a cornerstone in modern medical diagnostics. Many of the currently prevalent methods are not preferred in the clinics because they rely heavily on pre-amplification or post-separation steps. This editorial highlights the potential of adopting DNA-based nanosensors for the assessment of the activities of DNA-modifying enzymes, with emphasis on the topoisomerase and tyrosyl-DNA phosphodiesterase families. By underlining the existing challenges, we expect that the DNA-nanosensors may soon be promoted to clinical diagnostics via enzyme detection.
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Affiliation(s)
- Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000 Aarhus C, Denmark +45 7846 3672
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20
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Eldai H, Periyasamy S, Al Qarni S, Al Rodayyan M, Muhammed Mustafa S, Deeb A, Al Sheikh E, Afzal Khan M, Johani M, Yousef Z, Aziz MA. Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner. PLoS One 2013; 8:e76251. [PMID: 24204606 PMCID: PMC3813709 DOI: 10.1371/journal.pone.0076251] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 08/22/2013] [Indexed: 12/13/2022] Open
Abstract
Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway and target prediction analysis of CNA affected genes and microRNAs, respectively indicates TGF-β signaling pathway to be involved in causing CRC. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.
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Affiliation(s)
- Hisham Eldai
- Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Sathish Periyasamy
- Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Saeed Al Qarni
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Maha Al Rodayyan
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Ahmad Deeb
- Research Office, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Ebthehal Al Sheikh
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | | | - Mishal Johani
- Endoscopy, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Zeyad Yousef
- Surgery, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammad Azhar Aziz
- Medical Biotechnology, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- * E-mail:
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Silvestri A, Pin E, Huijbers A, Pellicani R, Parasido EM, Pierobon M, Petricoin E, Liotta L, Belluco C. Individualized therapy for metastatic colorectal cancer. J Intern Med 2013; 274:1-24. [PMID: 23527888 DOI: 10.1111/joim.12070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Systemic therapeutic efficacy is central to determining the outcome of patients with metastatic colorectal cancer (CRC). In these patients, there is a critical need for predictive biomarkers to optimize efficacy whilst minimizing toxicity. The integration of a new generation of molecularly targeted drugs into the treatment of CRC, coupled with the development of sophisticated technologies for individual tumours as well as patient molecular profiling, underlines the potential for personalized medicine. In this review, we focus on the latest progress made within the genomic and proteomic fields, concerning predictive biomarkers for individualized therapy in metastatic CRC.
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Affiliation(s)
- A Silvestri
- Division of Experimental Oncology 2, CRO-IRCCS, National Cancer Institute, Aviano, Italy
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Marcussen LB, Jepsen ML, Kristoffersen EL, Franch O, Proszek J, Ho YP, Stougaard M, Knudsen BR. DNA-based sensor for real-time measurement of the enzymatic activity of human topoisomerase I. SENSORS 2013; 13:4017-28. [PMID: 23529147 PMCID: PMC3673067 DOI: 10.3390/s130404017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/16/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Abstract
Sensors capable of quantitative real-time measurements may present the easiest and most accurate way to study enzyme activities. Here we present a novel DNA-based sensor for specific and quantitative real-time measurement of the enzymatic activity of the essential human enzyme, topoisomerase I. The basic design of the sensor relies on two DNA strands that hybridize to form a hairpin structure with a fluorophore-quencher pair. The quencher moiety is released from the sensor upon reaction with human topoisomerase I thus enabling real-time optical measurement of enzymatic activity. The sensor is specific for topoisomerase I even in raw cell extracts and presents a simple mean of following enzyme kinetics using standard laboratory equipment such as a qPCR machine or fluorimeter. Human topoisomerase I is a well-known target for the clinically used anti-cancer drugs of the camptothecin family. The cytotoxic effect of camptothecins correlates directly with the intracellular topoisomerase I activity. We therefore envision that the presented sensor may find use for the prediction of cellular drug response. Moreover, inhibition of topoisomerase I by camptothecin is readily detectable using the presented DNA sensor, suggesting a potential application of the sensor for first line screening for potential topoisomerase I targeting anti-cancer drugs.
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Affiliation(s)
- Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
| | - Morten Leth Jepsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Emil Laust Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Joanna Proszek
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus C 8000, Denmark; E-Mail:
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (B.R.K.)
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark; E-Mails: (L.B.M.); (M.L.J.); (E.L.K.); (O.F.)
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (B.R.K.)
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23
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Yam YY, Hoh BP, Othman NH, Hassan S, Yahya MM, Zakaria Z, Ankathil R. Somatic copy-neutral loss of heterozygosity and copy number abnormalities in Malaysian sporadic colorectal carcinoma patients. GENETICS AND MOLECULAR RESEARCH 2013; 12:319-27. [PMID: 23420356 DOI: 10.4238/2013.february.7.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Colorectal cancer is one of the most common cancers in many countries, including Malaysia. The accumulation of genomic alterations is an important feature of colorectal carcinogenesis. A better understanding of the molecular events underlying the stages of colorectal carcinogenesis might be helpful in the detection and management of the disease. We used a commercially available single-nucleotide polymorphism genotyping array to detect both copy number abnormalities (CNAs) and copy-neutral loss of heterozygosity (LOH) in sporadic colorectal carcinomas. Matched tumor and normal tissues of 13 colorectal carcinomas (Dukes' stages A-D) were analyzed using a 250K single nucleotide polymorphism array. An additional assay was performed to determine the microsatellite instability status by using the National Cancer Institute-recommended BAT-26 panel. In general, copy number gain (92.3%) was most common, followed by copy number loss (53.8%) and copy-neutral LOH (46.2%). Frequent CNAs of gains and losses were observed on chromosomes 7p, 8, 13q, 17p, 18q, and 20q, and copy-neutral LOH was observed on chromosomes 2, 6, 12, 13q, 14q, 17, 20p, 19q, and 22q. Even though genomic alterations are associated with colorectal cancer progression, our results showed that DNA CNAs and copy-neutral LOH do not reflect disease progression in at least 50% tumors. Copy-neutral LOH was observed in both early and advanced tumors, which favors the involvement of these genomic alterations in the early stages of tumor development.
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Affiliation(s)
- Y Y Yam
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
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24
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Sawada T, Yamamoto E, Suzuki H, Nojima M, Maruyama R, Shioi Y, Akasaka R, Kamimae S, Harada T, Ashida M, Kai M, Adachi Y, Yamamoto H, Imai K, Toyota M, Itoh F, Sugai T. Association between genomic alterations and metastatic behavior of colorectal cancer identified by array-based comparative genomic hybridization. Genes Chromosomes Cancer 2012; 52:140-9. [PMID: 23073979 DOI: 10.1002/gcc.22013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/22/2012] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancers (CRCs) exhibit multiple genetic alterations, including allelic imbalances (copy number alterations, CNAs) at various chromosomal loci. In addition to genetic aberrations, DNA methylation also plays important roles in the development of CRC. To better understand the clinical relevance of these genetic and epigenetic abnormalities in CRC, we performed an integrative analysis of copy number changes on a genome-wide scale and assessed mutations of TP53, KRAS, BRAF, and PIK3CA and DNA methylation of six marker genes in single glands isolated from 39 primary tumors. Array-based comparative genomic hybridization (array-CGH) analysis revealed that genomic losses commonly occurred at 3q26.1, 4q13.2, 6q21.32, 7q34, 8p12-23.3, 15qcen and 18, while gains were commonly found at 1q21.3-23.1, 7p22.3-q34, 13q12.11-14.11, and 20. The total numbers and lengths of the CNAs were significantly associated with the aberrant DNA methylation and Dukes' stages. Moreover, hierarchical clustering analysis of the array-CGH data suggested that tumors could be categorized into four subgroups. Tumors with frequent DNA methylation were most strongly enriched in subgroups with infrequent CNAs. Importantly, Dukes' D tumors were enriched in the subgroup showing the greatest genomic losses, whereas Dukes' C tumors were enriched in the subgroup with the greatest genomic gains. Our data suggest an inverse relationship between chromosomal instability and aberrant methylation and a positive association between genomic losses and distant metastasis and between genomic gains and lymph node metastasis in CRC. Therefore, DNA copy number profiles may be predictive of the metastatic behavior of CRCs.
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Affiliation(s)
- Takeshi Sawada
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
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25
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Xie T, d’ Ario G, Lamb JR, Martin E, Wang K, Tejpar S, Delorenzi M, Bosman FT, Roth AD, Yan P, Bougel S, Di Narzo AF, Popovici V, Budinská E, Mao M, Weinrich SL, Rejto PA, Hodgson JG. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 2012; 7:e42001. [PMID: 22860045 PMCID: PMC3409212 DOI: 10.1371/journal.pone.0042001] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022] Open
Abstract
To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (58.6%), 4 q (26%) and 21 q (21.6%). MSS tumors have significantly more CNAs than microsatellite-instable (MSI) tumors: within the MSI tumors a novel deletion of the tumor suppressor WWOX at 16 q23.1 was identified (p<0.01). Focal aberrations identified by the GISTIC method confirmed amplifications of oncogenes including EGFR, ERBB2, CCND1, MET, and MYC, and deletions of tumor suppressors including TP53, APC, and SMAD4, and gene expression was highly concordant with copy number aberration for these genes. Novel amplicons included putative oncogenes such as WNK1 and HNF4A, which also showed high concordance between copy number and expression. Survival analysis associated a specific patient segment featured by chromosome 20 q gains to an improved overall survival, which might be due to higher expression of genes such as EEF1B2 and PTK6. The CNA clustering also grouped tumors characterized by a poor prognosis BRAF-mutant-like signature derived from mRNA data from this cohort. We further revealed non-random correlation between CNAs among unlinked loci, including positive correlation between 20 q gain and 8 q gain, and 20 q gain and chromosome 18 loss, consistent with co-selection of these CNAs. These results reinforce the non-random nature of somatic CNAs in stage-II/III CRC and highlight loci and genes that may play an important role in driving the development and outcome of this disease.
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Affiliation(s)
- Tao Xie
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail: (TX); (JGH)
| | | | - John R. Lamb
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Eric Martin
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Kai Wang
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Sabine Tejpar
- University Hospital Gasthuisberg, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Lausanne University Medical Center, Lausanne, Switzerland
| | - Fred T. Bosman
- Lausanne University Medical Center, Lausanne, Switzerland
| | | | - Pu Yan
- Lausanne University Medical Center, Lausanne, Switzerland
| | | | | | - Vlad Popovici
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eva Budinská
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mao Mao
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Scott L. Weinrich
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Paul A. Rejto
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - J. Graeme Hodgson
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail: (TX); (JGH)
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26
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Mekenkamp LJM, Tol J, Dijkstra JR, de Krijger I, Vink-Börger ME, van Vliet S, Teerenstra S, Kamping E, Verwiel E, Koopman M, Meijer GA, van Krieken JHJ, Kuiper R, Punt CJA, Nagtegaal ID. Beyond KRAS mutation status: influence of KRAS copy number status and microRNAs on clinical outcome to cetuximab in metastatic colorectal cancer patients. BMC Cancer 2012; 12:292. [PMID: 22804917 PMCID: PMC3508829 DOI: 10.1186/1471-2407-12-292] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 06/26/2012] [Indexed: 12/11/2022] Open
Abstract
Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth factor receptor (EGFR) antibodies in metastatic colorectal cancer (mCRC). Novel predictive markers are required to further improve the selection of patients for this treatment. We assessed the influence of modification of KRAS by gene copy number aberration (CNA) and microRNAs (miRNAs) in correlation to clinical outcome in mCRC patients treated with cetuximab in combination with chemotherapy and bevacizumab. Methods Formalin-fixed paraffin-embedded primary tumour tissue was used from 34 mCRC patients in a phase III trial, who were selected based upon their good (n = 17) or poor (n = 17) progression-free survival (PFS) upon treatment with cetuximab in combination with capecitabine, oxaliplatin, and bevacizumab. Gene copy number at the KRAS locus was assessed using high resolution genome-wide array CGH and the expression levels of 17 miRNAs targeting KRAS were determined by real-time PCR. Results Copy number loss of the KRAS locus was observed in the tumour of 5 patients who were all good responders including patients with a KRAS mutation. Copy number gains in two wild-type KRAS tumours were associated with a poor PFS. In KRAS mutated tumours increased miR-200b and decreased miR-143 expression were associated with a good PFS. In wild-type KRAS patients, miRNA expression did not correlate with PFS in a multivariate model. Conclusions Our results indicate that the assessment of KRAS CNA and miRNAs targeting KRAS might further optimize the selection of mCRC eligible for anti-EGFR therapy.
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Affiliation(s)
- Leonie J M Mekenkamp
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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27
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Chen Z, Liu Z, Deng X, Warden C, Li W, Garcia-Aguilar J. Chromosomal copy number alterations are associated with persistent lymph node metastasis after chemoradiation in locally advanced rectal cancer. Dis Colon Rectum 2012; 55:677-85. [PMID: 22595848 PMCID: PMC3356567 DOI: 10.1097/dcr.0b013e31824f873f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lymph node metastasis is an important indicator of oncologic outcome for patients with rectal cancer. Identifying predictive biomarkers of lymph node metastasis could therefore be clinically useful. OBJECTIVE The aim of this study was to assess whether chromosomal copy number alterations can assist in predicting persistent lymph node metastasis in patients with locally advanced rectal cancer treated with preoperative chemoradiation therapy. DESIGN This is a nonrandomized, prospective phase II study. SETTING This study took place in a multi-institutional setting. PATIENTS Ninety-five patients with stage II (cT3-4, cN0) or stage III (any cT, cN1-2) rectal cancer were included. INTERVENTION Patients were treated with preoperative chemoradiation therapy followed by total mesorectal excision. Pretreatment biopsy tumor DNA and surgical margin control DNA were extracted and analyzed by oligonucleotide array-based comparative genomic hybridization. Chromosomal copy number alterations were correlated with persistent lymph node metastasis. Finally, a model for predicting persistent lymph node metastasis was built. MAIN OUTCOME MEASURES The primary outcomes assessed were whether chromosomal copy number alterations are associated with persistent lymph node metastasis in patients with rectal cancer and the accuracy of oligonucleotide array-based comparative genomic hybridization for predicting lymph node metastasis. RESULTS Twenty-five of 95 (26%) patients had lymph node metastasis after chemoradiation. Losses of 28 chromosomal regions, most notably in chromosome 4, were significantly associated with lymph node metastasis. Our predictive model contained 65 probes and predicted persistent lymph node metastasis with 68% sensitivity, 93% specificity, and positive and negative predictive values of 77% and 89%. The use of this model accurately predicted lymph node status (positive or negative) after chemoradiation therapy in 82 of 95 patients (86%). LIMITATIONS The patient cohort was not completely homogeneous, which may have influenced their clinical outcome. In addition, although we performed rigorous, statistically sound internal validation, external validation will be important to further corroborate our findings. CONCLUSIONS Copy number alterations can help identify patients with rectal cancer who are at risk of lymph node metastasis after chemoradiation.
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Affiliation(s)
- Zhenbin Chen
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Zheng Liu
- Bioinformatics Core, Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Xutao Deng
- Bioinformatics Core, Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Charles Warden
- Bioinformatics Core, Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Wenyan Li
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, City of Hope, Duarte, CA 91010, USA,Corresponding Author: Julio Garcia-Aguilar, MD, PhD, Chair, Department of Surgery, City of Hope, 1500 E. Duarte Road, CA 91010. Tel: (626) 471-9309. Fax: (626) 301-8113.,
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28
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Pan S, Xia W, Ding Q, Shu Y, Xu T, Geng Y, Lu Y, Chen D, Xu J, Wang F, Zhao C, Huang P, Huang P, Shen H, Hu Z, Lu S. Can plasma DNA monitoring be employed in personalized chemotherapy for patients with advanced lung cancer? Biomed Pharmacother 2012; 66:131-7. [PMID: 22401927 DOI: 10.1016/j.biopha.2011.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 11/08/2011] [Indexed: 02/08/2023] Open
Abstract
Personalized chemotherapy is the ideal treatment usually chosen to help improve the survival chances of patients with advanced lung cancer. However, there is no short-term evaluation protocol for predicting the efficacy of the therapy. The aim of this study was to determine the value of using plasma DNA to monitor chemotherapeutic efficacy and to select most appropriate chemotherapeutic regimen for patients with advanced lung cancer. Eighty-eight lung cancer patients and 200 healthy controls were included in this study. Plasma DNA was extracted from plasma samples with internal controls by using the BILATEST DNA Kit. The quantity of plasma DNA was determined by using duplex real-time quantitative PCR. After first-line chemotherapy, plasma DNA levels of partial response patients were significantly different from those of stable disease patients or progressive disease patients, but with no statistical difference from healthy controls (P=0.014, P<0.001 and P=0.418, respectively). Survival analysis showed a statistically better survival time in patients who had lower levels of plasma DNA after the third cycle chemotherapy (P=0.031). In this study, the correlation of the kinetics of DNA concentrations with chemotherapeutic efficacy during the whole therapy was also observed. The quantification of plasma DNA is a sensitive indicator of chemotherapeutic efficacy in advanced lung cancer patients, and it can be useful in predicting response to therapy and guiding medication.
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Affiliation(s)
- Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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29
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Juul S, Ho YP, Koch J, Andersen FF, Stougaard M, Leong KW, Knudsen BR. Detection of single enzymatic events in rare or single cells using microfluidics. ACS NANO 2011; 5:8305-10. [PMID: 21936557 PMCID: PMC3823540 DOI: 10.1021/nn203012q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In the present study we demonstrate highly sensitive detection of rare, aberrant cells in a population of wild-type human cells by combining a rolling-circle-enhanced enzyme activity single-molecule detection assay with a custom-designed microfluidic device. Besides reliable detection of low concentrations of aberrant cells, the integrated system allowed multiplexed detection of individual enzymatic events at the single cell level. The single cell sensitivity of the presented setup relies on the combination of single-molecule rolling-circle-enhanced enzyme activity detection with the fast reaction kinetics provided by a picoliter droplet reaction volume and subsequent concentration of signals in a customized drop-trap device. This setup allows the fast reliable analyses of enzyme activities in a vast number of single cells, thereby offering a valuable tool for basic research as well as theranostics.
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Affiliation(s)
- Sissel Juul
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yi-Ping Ho
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Jørn Koch
- Department of Pathology and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Hospital, Denmark
| | - Felicie F. Andersen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Hospital, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Corresponding authorship shared between KWL and BRK. Contact information, KWL: ; BRK:
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
- Corresponding authorship shared between KWL and BRK. Contact information, KWL: ; BRK:
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30
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Lin CH, Lin JK, Chang SC, Chang YH, Chang HM, Liu JH, Li LH, Chen YT, Tsai SF, Chen WS. Molecular profile and copy number analysis of sporadic colorectal cancer in Taiwan. J Biomed Sci 2011; 18:36. [PMID: 21645411 PMCID: PMC3123622 DOI: 10.1186/1423-0127-18-36] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 06/07/2011] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) is a major health concern worldwide, and recently becomes the most common cancer in Asia. The case collection of this study is one of the largest sets of CRC in Asia, and serves as representative data for investigating genomic differences between ethnic populations. We took comprehensive and high-resolution approaches to compare the clinicopathologic and genomic profiles of microsatellite instability (MSI) vs. microsatellite stability (MSS) in Taiwanese sporadic CRCs. Methods 1,173 CRC tumors were collected from the Taiwan population, and sequencing-based microsatellite typing assay was used to determine MSI and MSS. Genome-wide SNP array was used to detect CN alterations in 16 MSI-H and 13 MSS CRCs and CN variations in 424 general controls. Gene expression array was used to evaluate the effects of CN alterations, and quantitative PCR methods were used to replicate the findings in independent clinical samples. Results These 1,173 CRC tumors can be classified into 75 high-frequency MSI (MSI-H) (6.4%), 96 low-frequency MSI (8.2%) and 1,002 MSS (85.4%). Of the 75 MSI-H tumors, 22 had a BRAF mutation and 51 showed MLH1 promoter hypermethylation. There were distinctive differences in the extent of CN alterations between CRC MSS and MSI-H subtypes (300 Mb vs. 42 Mb per genome, p-value < 0.001). Also, chr7, 8q, 13 and 20 gains, and 8p and 18 losses were frequently found in MSS but not in MSI-H. Nearly a quarter of CN alterations were smaller than 100 kb, which might have been missed in previous studies due to low-resolution technology. 514 expressed genes showed CN differences between subtypes, and 271 of them (52%) were differentially expressed. Conclusions Sporadic CRCs with MSI-H displayed distinguishable clinicopathologic features, which differ from those of MSS. Genomic profiling of the two types of sporadic CRCs revealed significant differences in the extent and distribution of CN alterations in the cancer genome. More than half of expressed genes showing CN differences can directly contribute to their expressional diversities, and the biological functions of the genes associated with CN changes in sporadic CRCs warrant further investigation to establish their possible clinical implications.
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Affiliation(s)
- Chien-Hsing Lin
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
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31
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Haan JC, Buffart TE, Eijk PP, van de Wiel MA, van Wieringen WN, Howdle PD, Mulder CJJ, van de Velde CJ, Quirke P, Nagtegaal ID, van Grieken NCT, Grabsch H, Meijer GA, Ylstra B. Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers. Ann Oncol 2011; 23:367-74. [PMID: 21586687 DOI: 10.1093/annonc/mdr122] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Small bowel adenocarcinoma (SBA) is a rare cancer and consequently, the options for clinical trials are limited. As they are treated according to either a colorectal or a gastric cancer regimen and the molecular biology of a tumor is a pivotal determinant for therapy response, chromosomal copy number aberrations were compared with the colorectal and gastric adenocarcinomas. MATERIALS AND METHODS A total of 85 microsatellite stable (MSS) adenocarcinomas from the stomach, colorectum and small bowel were selected from existing array comparative genomic hybridization (aCGH) datasets. We compared the aCGH profiles of the three tumor sites by supervised analysis and hierarchical clustering. RESULTS Hierarchical clustering revealed substantial overlap of 27 SBA copy number profiles with matched colorectal adenocarcinomas but less overlap with profiles of gastric adenocarcinomas. DNA copy number aberrations located at chromosomes 1p36.3-p34.3, 4p15.3-q35.2, 9p24.3-p11.1, 13q13.2-q31.3 and 17p13.3-p13.2 were the strongest features discriminating SBAs and colorectal adenocarcinomas from gastric adenocarcinomas. CONCLUSIONS We show that MSS SBAs are more similar to colorectal than to gastric cancer, based on the 27 genome-wide DNA copy number profiles that are currently available. These molecular similarities provide added support for treatment of MSS small bowel cancers according to colorectal cancer regimens.
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Affiliation(s)
- J C Haan
- Department of Pathology, VU University Medical Center, Amsterdam
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32
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Chen Z, Liu Z, Li W, Qu K, Deng X, Varma MG, Fichera A, Pigazzi A, Garcia-Aguilar J. Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer. Genes Chromosomes Cancer 2011; 50:689-99. [PMID: 21584903 DOI: 10.1002/gcc.20891] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/18/2011] [Indexed: 01/24/2023] Open
Abstract
Rectal cancer response to chemoradiation (CRT) varies from no response to a pathologic complete response (pCR). Identifying predictive biomarkers of response would therefore be useful. We assessed whether chromosomal copy number alterations (CNAs) can assist in predicting pCR. Pretreatment tumor biopsies and paired normal surgical tissues from the proximal resection margin were collected from 95 rectal cancer patients treated with preoperative CRT and total mesorectal excision in a prospective Phase II study. Tumor and control DNA were extracted, and oligonucleotide array-based comparative genomic hybridization (aCGH) was used to identify CNAs, which were correlated with pCR. Ingenuity pathway analysis (IPA) was then used to identify functionally relevant genes in aberrant regions. Finally, a predictive model for pCR was built using support vector machine (SVM), and leave-one-out cross validation assessed the accuracy of aCGH. Chromosomal regions most commonly affected by gains were 20q11.21-q13.33, 13q11.32-23, 7p22.3-p22.2, and 8q23.3-q24.3, and losses were present at 18q11.32-q23, 17p13.3-q11.1, 10q23.1, and 4q32.1-q32.3. The 25 (26%) patients who achieved a pCR had significantly fewer high copy gains overall than non-pCR patients (P = 0.01). Loss of chromosomal region 15q11.1-q26.3 was significantly associated with non-pCR (P < 0.00002; Q-bound < 0.0391), while loss of 12p13.31 was significantly associated with pCR (P < 0.0003; Q-bound < 0.097). IPA identified eight genes in the imbalanced chromosomal regions that associated with tumor response. SVM identified 58 probes that predict pCR with 76% sensitivity, 97% specificity, and positive and negative predictive values of 91% and 92%. Our data indicate that chromosomal CNAs can help identify rectal cancer patients more likely to develop a pCR to CRT.
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Affiliation(s)
- Zhenbin Chen
- Department of Surgery, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
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Andersen CL, Lamy P, Thorsen K, Kjeldsen E, Wikman F, Villesen P, Øster B, Laurberg S, Ørntoft TF. Frequent genomic loss at chr16p13.2 is associated with poor prognosis in colorectal cancer. Int J Cancer 2011; 129:1848-58. [DOI: 10.1002/ijc.25841] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/19/2010] [Indexed: 11/09/2022]
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Brosens RPM, Haan JC, Carvalho B, Rustenburg F, Grabsch H, Quirke P, Engel AF, Cuesta MA, Maughan N, Flens M, Meijer GA, Ylstra B. Candidate driver genes in focal chromosomal aberrations of stage II colon cancer. J Pathol 2010; 221:411-24. [PMID: 20593488 DOI: 10.1002/path.2724] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3 Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study was to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well-defined series of stage II colon cancers and assess their potential clinical relevance. High-resolution DNA copy number profiles were obtained from 38 formalin-fixed, paraffin-embedded colon cancer samples with matched normal mucosa as a reference using array comparative genomic hybridization. In total, 81 focal chromosomal aberrations were identified that harboured 177 genes. Statistical validation of focal aberrations and identification of candidate driver genes were performed by enrichment analysis and mapping copy number and mutation data of colorectal, breast, and pancreatic cancer and glioblastomas to loci of focal aberrations in stage II colon cancer. This analysis demonstrated a significant overlap with previously identified focal amplifications in colorectal cancer, but not with cancers from other sites. In contrast, focal deletions seemed less tumour type-specific since they also showed significant overlap with focal deletions of other sites. Focal deletions detected were significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The mRNA expression of these genes was significantly correlated with DNA copy number status, supporting the relevance of focal aberrations. Loss of 5q34 and gain of 13q22.1 were identified as independent prognostic factors of survival in this series of patients. In conclusion, focal chromosomal copy number aberrations in stage II colon cancer are enriched in cancer genes that contribute to and drive the process of colorectal cancer development. DNA copy number status of these genes correlates with mRNA expression and some are associated with clinical outcome.
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Affiliation(s)
- Rebecca P M Brosens
- Department of Surgery, VU University Medical Centre, Amsterdam, The Netherlands
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Scheinin I, Ferreira JA, Knuutila S, Meijer GA, van de Wiel MA, Ylstra B. CGHpower: exploring sample size calculations for chromosomal copy number experiments. BMC Bioinformatics 2010; 11:331. [PMID: 20565750 PMCID: PMC2911457 DOI: 10.1186/1471-2105-11-331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 06/17/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Several approaches for sample size determination have been developed for expression array studies, but so far none has been proposed for array comparative genomic hybridization (aCGH). RESULTS Here we explore power calculations for aCGH experiments comparing two groups. In a pilot experiment CGHpower estimates the biological diversity between groups and provides a statistical framework for estimating average power as a function of sample size. As the method requires pilot data, it can be used either in the planning stage of larger studies or in estimating the power achieved in past experiments. CONCLUSIONS The proposed method relies on certain assumptions. According to our evaluation with public and simulated data sets, they do not always hold true. Violation of the assumptions typically leads to unreliable sample size estimates. Despite its limitations, this method is, at least to our knowledge, the only one currently available for performing sample size calculations in the context of aCGH. Moreover, the implementation of the method provides diagnostic plots that allow critical assessment of the assumptions on which it is based and hence on the feasibility and reliability of the sample size calculations in each case.The CGHpower web application and the program outputs from evaluation data sets can be freely accessed at http://www.cangem.org/cghpower/
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Affiliation(s)
- Ilari Scheinin
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Temmink OH, Bijnsdorp IV, Prins HJ, Losekoot N, Adema AD, Smid K, Honeywell RJ, Ylstra B, Eijk PP, Fukushima M, Peters GJ. Trifluorothymidine resistance is associated with decreased thymidine kinase and equilibrative nucleoside transporter expression or increased secretory phospholipase A2. Mol Cancer Ther 2010; 9:1047-57. [PMID: 20371715 DOI: 10.1158/1535-7163.mct-09-0932] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Trifluorothymidine (TFT) is part of the novel oral formulation TAS-102, which is currently evaluated in phase II studies. Drug resistance is an important limitation of cancer therapy. The aim of the present study was to induce resistance to TFT in H630 colon cancer cells using two different schedules and to analyze the resistance mechanism. Cells were exposed either continuously or intermittently to TFT, resulting in H630-cTFT and H630-4TFT, respectively. Cells were analyzed for cross-resistance, cell cycle, protein expression, and activity of thymidine phosphorylase (TP), thymidine kinase (TK), thymidylate synthase (TS), equilibrative nucleoside transporter (hENT), gene expression (microarray), and genomic alterations. Both cell lines were cross-resistant to 2'-deoxy-5-fluorouridine (>170-fold). Exposure to IC(75)-TFT increased the S/G(2)-M phase of H630 cells, whereas in the resistant variants, no change was observed. The two main target enzymes TS and TP remained unchanged in both TFT-resistant variants. In H630-4TFT cells, TK protein expression and activity were decreased, resulting in less activated TFT and was most likely the mechanism of TFT resistance. In H630-cTFT cells, hENT mRNA expression was decreased 2- to 3-fold, resulting in a 5- to 10-fold decreased TFT-nucleotide accumulation. Surprisingly, microarray-mRNA analysis revealed a strong increase of secretory phospholipase-A2 (sPLA2; 47-fold), which was also found by reverse transcription-PCR (RT-PCR; 211-fold). sPLA2 inhibition reversed TFT resistance partially. H630-cTFT had many chromosomal aberrations, but the exact role of sPLA2 in TFT resistance remains unclear. Altogether, resistance induction to TFT can lead to different mechanisms of resistance, including decreased TK protein expression and enzyme activity, decreased hENT expression, as well as (phospho)lipid metabolism. Mol Cancer Ther; 9(4); 1047-57. (c)2010 AACR.
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Affiliation(s)
- Olaf H Temmink
- Department of Medical Oncology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands
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