Biomarker Edited by Tapan Kumar Khan doc

BIOMARKER Edited by Tapan Kumar Khan Biomarker Edited by Tapan Kumar Khan Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 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. As for readers, this license allows users to download, copy and build upon published chapters 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. 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 Bojan Rafaj Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published April, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Biomarker, Edited by Tapan Kumar Khan p. cm. ISBN 978-953-51-0577-0 Contents Preface IX Chapter 1 MicroRNAs are Novel Biomarkers for Detection of Colorectal Cancer 1 Muhammad Imran Aslam, Maleene Patel, Baljit Singh, John Stuart Jameson and James Howard Pringle Chapter 2 Epigenetics in Cancer: The Myelodysplastic Syndrome as a Model to Study Epigenetic Alterations as Diagnostic and Prognostic Biomarkers 19 Teresa de Souza Fernandez, André Mencalha and Cecília de Souza Fernandez Chapter 3 Biomarkers in Gastrointestinal Cancer: Focus on Colon, Pancreatic and Gastric Cancer 49 Vanessa Deschoolmeester, Filip Lardon, Patrick Pauwels and Marc Peeters Chapter 4 Inorganic Signatures of Physiology: The X-Ray Fluorescence Microscopy Revolution 77 Lydia Finney Chapter 5 Urinary Water-Soluble Vitamins as Nutritional Biomarker to Estimate Their Intakes 87 Tsutomu Fukuwatari and Katsumi Shibata Chapter 6 Potential Muscle Biomarkers of Chronic Myalgia in Humans – A Systematic Review of Microdialysis Studies 103 Björn Gerdle and Britt Larsson Chapter 7 Genotoxicity Biomarkers: Application in Histopathology Laboratories 133 Carina Ladeira, Susana Viegas, Elisabete Carolino, Manuel Carmo Gomes and Miguel Brito VI Contents Chapter 8 Biomarkers and Therapeutic Drug Monitoring in Psychiatry 155 R. Lozano, R. Marin, A. Pascual, MJ. Santacruz, A. Lozano and F. Sebastian Chapter 9 A Comparison of Biomarker and Fingerprint-Based Classifiers of Disease 179 Brian T. Luke and Jack R. Collins Chapter 10 8-Nitroguanine, a Potential Biomarker to Evaluate the Risk of Inflammation-Related Carcinogenesis 201 Ning Ma, Mariko Murata, Shiho Ohnishi, Raynoo Thanan, Yusuke Hiraku and Shosuke Kawanishi Chapter 11 Profiling of Endogenous Peptides by Multidimensional Liquid Chromatography 225 Egle Machtejeviene and Egidijus Machtejevas Chapter 12 Salivary Hormones, Immunes and Other Secretory Substances as Possible Stress Biomarker 247 Shusaku Nomura Chapter 13 Novel Tissue Types for the Development of Genomic Biomarkers 271 Zinaida Sergueeva, Heather Collins, Sally Dow, Mollie McWhorter and Mark L. Parrish Chapter 14 Computer Simulation Model System for Interpretation and Validation of Algorithms for Monitoring of Cancer Patients by Use of Serial Serum Concentrations of Biomarkers in the Follow-Up After Surgical Procedures and Other Treatments – A Computer Simulation Model System Based on the Breast Cancer Biomarker TPA 295 Flemming Lund, György Sölétormos, Merete Frejstrup Pedersen and Per Hyltoft Petersen Chapter 15 Using miRNA as Biomarkers to Evaluate the Alcohol-Induced Oxidative Stress 319 Yueming Tang, Christopher B. Forsyth and Ali Keshavarzian Chapter 16 The Discovery of Cancer Tissue Specific Proteins in Serum: Case Studies on Prostate Cancer 333 Spiros D. Garbis and Paul A. Townsend Chapter 17 Serum Peptidomics 261 Kaihua Wei, Qingwei Ma, Yunbo Sun, Xiaoming Zhou, Weirong Guo and Jian Yuan Preface The impact of biomarkers in present day health care system, health management and healthy life is enormous. Clinicians need them for diagnosis, prognosis, effect of therapeutic intervention, and most importantly, for early detection of a disease. Pharmaceutical industries need them for new drug discovery and drug efficiency test. Regulatory authorities need them for testing toxicity and environmental impact. Epidemiologists need them for population screening and risk factor determination. In post genomic era biomarkers would have a huge impact in personalized medicine and personalized health management. This scope of this book is not limited to just a few of the most important aspects of biomarkers but covers wide variety of subjects, from biomarkers cancer to neurodegenerative diseases. Chapters cover variety of aspects, from modern cell based technologies to molecular imaging; from drug discovery to critical care prognosis. A great amount of information is also devoted to bioinformatics and statistics. There is an enormous potential for commercial value of biomarkers. The global diagnostic market accounts for only 1-2% of government healthcare expense, however, it influences on 60-70% decisions in healthcare. My sincere thanks go to all the contributors of this book who took the extra effort beyond their busy schedules. Last, but not least I would like to express my gratitude to the publishing group for their tireless support. Tapan Kumar Khan, PhD Blanchette Rockefeller Neurosciences Institute, West Virginia University, USA [...]... the nucleus PrimiRNA transcript is further processed by the nuclear ribo-nuclease enzyme ‘Drosha’ thereby resulting in a hairpin intermediate of about 70–100 nucleotides, called pre-miRNA The pre-miRNA is then transported out of the nucleus by a transporting protein exportin-5 4 Biomarker In the cytoplasm, the pre-miRNA is once again processed by another ribonuclease enzyme ‘Dicer’ into a mature double-stranded... exosomes involves removal of cells and debris with either a filtration process or by a series of centrifugations (differential centrifugation), followed by a final high speed centrifugation (ultracentrifugation) to pellet the exosomes Exosomes have a specific density and can be purified by floatation in a sucrose density gradient or by sucrosedeuterium oxide (D2O) cushions Another purification method is based... 2003.25; 425(6956):415-9 16 Biomarker Lee DY, Deng Z, Wang CH, Yang BB MicroRNA-378 promotes cell survival, tumor growth, and angiogenesis by targeting SuFu and Fus-1 expression Proc Natl Acad Sci U S A 2007.18; 104(51):20350-5 Link A, Balaguer F, Shen Y, Nagasaka T, Lozano JJ, Boland CR, Goel A Fecal MicroRNAs as novel biomarkers for colon cancer screening Cancer Epidemiol Biomarkers Prev 2010;19(7):1766-74... CpG islands) at promoter regions (Robertson et al., 1999; Tabby & Issa, 2010; Worn & Gulberg, 2002) DNA methylation is frequently associated to transcriptional gene repression It has been suggested that repression occurs by physically interfering in transcriptional factors binding at gene promoter regions, modified by 5’-methylcitosine or by recruiting methylated-DNA binding domain (MBD) proteins that... diagnostic biomarkers The discovery of tumour specific microRNAs (miRNAs) has opened a new era of biomarker research that holds great potential for future cancer detection strategies 4 What are MicroRNAs MicroRNAs are single-stranded, evolutionarily conserved, small (17–25 ribonucleotides) noncoding (Lee, et al, 1993) RNA molecules MiRNAs function as negative regulators of 3 MicroRNAs are Novel Biomarkers... (MDS), some research groups have been showed the importance to study epigenetic alterations as new diagnostic, prognostic and risk stratification biomarkers The 20 Biomarker MDS comprises a heterogeneous group of clonal bone marrow disorders characterized by varying degrees of pancytopenia, morphological and functional abnormalities of hematopoietic cells and increased risk of transformation into acute... of new diagnostic and prognostic epigenetic biomarkers 2 The role of epigenetics in cancer Epigenetics alterations have been growing as a promisor tool to understand cancer development, for better clinical therapy management, to identify new cancer biomarkers, which can help in monitoring disease evolution It is known that epigenetics corresponds basically by two majority modifications: DNA methylation... modification of the cytosine ring 5’ position of a CpG dinucleotide, whereby a methyl group is deposited on carbon 5 of that ring using Sadenosyl methionine as a methyl donor This transfer of methyl group is a replicationdependent reaction catalyzed by DNA methyltrasferases (DNMTs) (Figure 1) Humans DNA methyltransferases are represented basically by three proteins: DNMT1, DNMT3A and DNMT3B In general, DNMT1 are... 2005.16;293(7):799-809 14 Biomarker Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing Nature 2005;436(7051):740-4 Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ.Real-time quantification of microRNAs by stem-loop... focus of miRNA studies towards the isolation of tissue specific circulating exosomes and their encompassed miRNAs Exosomes are membrane bound small vesicles (20 to 100 nm in diameter) of endocytic origin and are released by a variety of cells in both healthy and disease conditions (Théry, et al, 2002 & Keller, et al, 2006) Exosomes correspond to the internal vesicles of multivesicular bodies (MVBs) and . BIOMARKER Edited by Tapan Kumar Khan Biomarker Edited by Tapan Kumar Khan Published by InTech Janeza Trdine 9, 51000 Rijeka,. orders@intechopen.com Biomarker, Edited by Tapan Kumar Khan p. cm. ISBN 978-953-51-0577-0 Contents Preface IX Chapter 1 MicroRNAs are Novel Biomarkers for Detection. group for their tireless support. Tapan Kumar Khan, PhD Blanchette Rockefeller Neurosciences Institute, West Virginia University, USA 1 MicroRNAs are Novel Biomarkers for Detection of Colorectal