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César López-Camarillo and Elena Aréchaga-Ocampo.Pdf ONCOGENOMICS AND CANCER PROTEOMICS – NOVEL APPROACHES IN BIOMARKERS DISCOVERY AND THERAPEUTIC TARGETS IN CANCER Edited by César López-Camarillo and Elena Aréchaga-Ocampo Oncogenomics and Cancer Proteomics – Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer http://dx.doi.org/10.5772/1745 Edited by César López-Camarillo and Elena Aréchaga-Ocampo Contributors Norfilza M. Mokhtar, Nor Azian Murad, Then Sue Mian, Rahman Jamal, Elena Aréchaga- Ocampo, Nicolas Villegas-Sepulveda, Eduardo Lopez-Urrutia, Mayra Ramos-Suzarte, César López-Camarillo, Carlos Perez-Plasencia, Claudia H. Gonzalez-de la Rosa, Cesar Cortes- Gonzalez, Luis A. Herrera, Laurence A. Marchat, Elisa Azuara-Liceaga, Carlos Pérez-Plasencia, Lizeth Fuentes-Mera, Miguel A. Fonseca-Sánchez, Ali Flores-Pérez, Pouya Jamshidi, Clark C. Chen, Lili Jiang, Xueshan Qiu, Daniela Ferreira, Filomena Adega, Raquel Chaves, Mª Dolores Pastor, Ana Nogal, Sonia Molina-Pinelo, Luis Paz-Ares, Amancio Carnero, Hiroko Kozuka-Hata, Yumi Goto, Masaaki Oyama, Olga Villamar-Cruz, Luis E. Arias-Romero Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2013 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Dimitri Jelovcan Typesetting InTech Prepress, Novi Sad Cover InTech Design Team First published March, 2013 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Oncogenomics and Cancer Proteomics – Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer, Edited by César López-Camarillo and Elena Aréchaga-Ocampo p. cm. ISBN 978-953-51-1041-5 Contents Preface IX Section 1 Genomic Expression Profiling in Cancer 1 Chapter 1 Genomic Expression Profiles: From Molecular Signatures to Clinical Oncology Translation 3 Norfilza M. Mokhtar, Nor Azian Murad, Then Sue Mian and Rahman Jamal Chapter 2 Biomarkers in Lung Cancer: Integration with Radiogenomics Data 49 Elena Aréchaga-Ocampo, Nicolas Villegas-Sepulveda, Eduardo Lopez-Urrutia, Mayra Ramos-Suzarte, Cesar Lopez-Camarillo, Carlos Perez-Plasencia, Claudia H. Gonzalez-de la Rosa, Cesar Cortes-Gonzalez and Luis A. Herrera Chapter 3 Functional Roles of microRNAs in Cancer: microRNomes and oncomiRs Connection 71 César López-Camarillo, Laurence A. Marchat, Elena Aréchaga-Ocampo, Elisa Azuara-Liceaga, Carlos Pérez-Plasencia, Lizeth Fuentes-Mera, Miguel A. Fonseca-Sánchez and Ali Flores-Pérez Chapter 4 Genetic Profiling: Searching for Novel Genetic Aberrations in Glioblastoma 91 Pouya Jamshidi and Clark C. Chen Chapter 5 MicroRNAs in Invasion and Metastasis in Lung Cancer 123 Lili Jiang and Xueshan Qiu Chapter 6 The Importance of Cancer Cell Lines as in vitro Models in Cancer Methylome Analysis and Anticancer Drugs Testing 139 Daniela Ferreira, Filomena Adega and Raquel Chaves VI Contents Section 2 Proteomic Expression Profiling in Cancer 167 Chapter 7 Oncoproteomic Approaches in Lung Cancer Research 169 Mª Dolores Pastor, Ana Nogal, Sonia Molina-Pinelo, Luis Paz-Ares and Amancio Carnero Chapter 8 Phosphoproteomics-Based Characterization of Cancer Cell Signaling Networks 185 Hiroko Kozuka-Hata, Yumi Goto and Masaaki Oyama Chapter 9 Phosphoproteomics for the Mapping of Altered Cell Signaling Networks in Breast Cancer 207 Olga Villamar-Cruz and Luis E. Arias-Romero Preface Today, cancer research is focused on determining how genome and proteome level information may be useful as tools in prevention, diagnosis, and prognosis. The development of “omics” technologies, such as proteomics and transcriptomics has opened new research areas for scientists working on cancer research. This book presents the latest advances in cancer genomics and proteomics focused on identification of tumoral biomarkers and potential therapeutic targets in the most common human neoplasias including glioblastoma, oral squamous cell carcinoma, and breast, lung, prostate, and colorectal cancers. In addition, critical reviews of the relevant roles of microRNAs, animal models and the application of gene regulatory networks to validate potential therapeutic targets in cancer are also included. Chapters in “Oncogenomics and Cancer Proteomics - Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer” present comprehensive and expert perspectives on the most common cancers from bench to bedside applications by an international team of experts in the field. This edited collection is subdivided into two sections titled: I) Genomic expression profiling in cancer, and II) Proteomic expression profiling in cancer. Proteomic technologies based on two-dimensional electrophoresis (2DPAGE and 2D-DIGE), or on isotope labeling methods followed by mass spectrometry (MS) analysis applied to the identification of differential protein expression in cancer are also discussed. This book will contribute greatly to the scientific and medical community by providing up-to-date discoveries of oncogenomics and their important roles in cancer translational research. It is intended for students, scientists, clinicians, oncologists and other health professionals working in the field of cancer research. Dr. César López-Camarillo Genomics Sciences Program, Autonomous University of Mexico City, Mexico Dr. Elena Aréchaga-Ocampo Cancer Biomedical Research Unit, National Institute of Cancerology, Mexico Section 1 Genomic Expression Profiling in Cancer Chapter 1 Genomic Expression Profiles: From Molecular Signatures to Clinical Oncology Translation Norfilza M. Mokhtar, Nor Azian Murad, Then Sue Mian and Rahman Jamal Additional information is available at the end of the chapter http://dx.doi.org/10.5772/53766 1. Introduction Study related to diseases such as cancer has changed tremendously for a decade. For many years, the study was restricted largely to a single gene or a few genes in cancer cells. The studies have uncovered the roles of individual genes in the uncontrolled behavior of cancer cells. Studying the functional roles of genes in cancer cells has deepened our understanding not only the cancer cells as well as normal cells. Since 2003 onwards, the trend of publications was focusing on the analysis of thousands of genes with related molecular pathways. Steps taken from this analysis is then translated to clinical practice for the biological markers for an early detection, monitoring, prognosis of the disease and response to therapy. The completion of the Human Genome Project in 2003 enabled a new era in biological sciences, in particular molecular medicine. The availability of the database of full sequences of approximately 3 billion base pairs and approximately 30,000 genes in human DNA will lead to a better understanding of physiological and pathophysiological changes in human body. Genome-wide expression technology allows the simultenous analysis of thousands of genes in a single experiment. The availability of the technology alters the way biological experiments can be designed. This has resulted of so called ‘discovery biology’. The large amount of data produced by microarray resulted to new and unexpected features of cellular functions. Since it was first introduced, microarrays are widely used for basic research, the development of prognostic tests, target discovery or toxicology researchs. The new form of cancer screening utilizes the molecular data generated from microarray studies. We will discuss the application of gene profiling data in the clinical screening of cancer. It is hopefully will give a broad picture the pipeline required to discover biomarkers of cancer. © 2013 Mokhtar et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Oncogenomics and Cancer Proteomics – 4 Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer The chapter is subdivided into a series of sections; each will discuss the scientific evidence on the molecular and cellular studies in selected cancers. We will try to critically assess the evidence upon which the theory on the cancer was built. The conversion of normal cells into cancer cells is a complex process and multistep processes. Scientists for many years tried to uncover the causes of cancer and emphasize certain oncogenes, or tumor suppressor genes or other groups of genes. Further information
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