Fundamentals of Advanced Omics Technologies
Transcripción
Fundamentals of Advanced Omics Technologies
Fundamentals of Advanced Omics Technologies: From Genes to Metabolites Comprehensive Analytical Chemistry Volume 63 ADVISORY BOARD Joseph A. Caruso University of Cincinnati, Cincinnati, OH, USA Hendrik Emons Joint Research Centre, Geel, Belgium Gary Hieftje Indiana University, Bloomington, IN, USA Kiyokatsu Jinno Toyohashi University of Technology, Toyohashi, Japan Uwe Karst University of Münster, Münster, Germany Gyrögy Marko-Varga AstraZeneca, Lund, Sweden Janusz Pawliszyn University of Waterloo, Waterloo, Ont., Canada Susan Richardson US Environmental Protection Agency, Athens, GA, USA Fundamentals of Advanced Omics Technologies: From Genes to Metabolites Comprehensive Analytical Chemistry Volume 63 Edited by Carolina Simó Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain Alejandro Cifuentes Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain Virginia Garcı́a-Cañas Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD PARIS • SAN DIEGO • SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Elsevier The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands Copyright © 2014 Elsevier B.V. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: [email protected]. Alternatively you can submit your request online by visiting the Elsevier web site at http://elsevier.com/locate/permissions, and selecting Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made British Library Cataloguing in Publication Data A catalog record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalogue record for this book is available from the Library of Congress ISBN: 978-0-444-62651-6 ISSN: 0166-526X For information on all Elsevier publications visit our website at store.elsevier.com Printed and bound in Poland 14 15 16 17 10 9 8 7 6 5 4 3 2 1 Contents Contributors to Volume 63 Series Editor’s Preface Preface 1. DNA Microarrays Technology: Overview and Current Status xiii xvii xix 1 Alex Sánchez-Pla 1. Introduction and Overview 1.1. A Brief History of Microarrays 2. Types of DNA Microarrays 2.1. Spotted or Printed Microarrays 2.2. In Situ Synthesized Microarrays 2.3. High-Density Bead Arrays 3. Applications of Microarrays 3.1. Microarrays for Gene Expression Analysis 3.2. SNP Arrays for Variation Analysis and Genotyping 3.3. CGH Arrays for Comparative Genomic Hybridization 3.4. ChIP-on-Chip Arrays for Transcription Factor Binding Analysis 3.5. Arrays for the Analysis of Alternative Splicing and Related Issues 4. Microarray Bioinformatics 4.1. The MIAME Standard 4.2. Microarray Databases 5. Discussion and Concluding Remarks References 2. Challenges and Future Trends in DNA Microarray Analysis 1 3 4 4 5 9 11 11 16 17 17 18 18 19 19 20 21 25 Abootaleb Sedighi and Paul C.H. Li 1. Introduction 2. Toward Microarray POC Devices 2.1. Microfluidic Microarrays 2.2. Label-Free Detection 2.3. Miniaturized Nanoarray Platforms 2.4. Integrated LOC Devices 3. Validity of Microarray Data 4. Clinical Adoption 25 27 28 33 35 36 37 39 v vi Contents 5. Future Trends of Microarray 6. Conclusion References 3. Next-Generation Sequencing: New Tools to Solve Old Challenges 41 43 44 47 I. Gobernado, A. Sanchez-Herranz and A. Jimenez-Escrig 1. Introduction 2. Basis for NGS 3. Sample Preparation for NGS 3.1. Clonal Amplification 3.2. Single-Molecule Sequencing 4. Sequencing Techniques 4.1. Sequencing-by-Synthesis 4.2. Sequencing-by-Ligation 4.3. Other Sequencing Technologies 5. NGS Data Analysis 6. Main Applications of NGS 6.1. Whole-Genome Sequencing 6.2. Targeted Region Resequencing 6.3. Metagenomics 6.4. RNA-Sequencing 6.5. Other NGS Applications 7. Integrating Omics Data References 4. Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications 47 50 51 51 52 54 54 59 59 63 63 63 66 68 69 70 72 73 81 Josep C. Jiménez-Chillarón, Rubén Dı́az and Marta Ramón-Krauel 1. Omics Meets Epigenetics 1.1. Omics 1.2. Epigenetics 1.3. Epigenomics: When -Omics Met Epigenetics 2. Methods in Epigenomics 2.1. DNA Methylation 2.2. Histone Modifications 2.3. Noncoding RNAs 3. Concluding Remarks References 5. An Overview of Quantitative Proteomic Approaches 81 81 82 86 87 87 96 99 106 106 111 Adam J. McShane, Vahid Farrokhi, Reza Nemati, Song Li and Xudong Yao 1. Introduction 2. Immuno-Based Detection Methods 111 112 Contents 2.1. Gel-Based Approaches 2.2. Non-Gel-Based Approaches 3. Mass Spectrometry-Based Detection Methods 3.1. Introduction 3.2. Mass Spectrometers 3.3. Derivatization-Free Techniques 3.4. Derivatization-Based Techniques 3.5. Activity-Based Probes 3.6. Sample Preparation 3.7. Liquid Chromatography 3.8. Software 3.9. Analyte Multiplexing and Sample Throughput 4. Conclusions Acknowledgments References 6. Emerging Nanotechniques in Proteomics vii 112 113 115 115 115 117 119 121 122 125 128 128 128 129 129 137 Noelia Dasilva, Maria Gonzalez-Gonzalez, Paula Diez, Ricardo Jara-Acevedo, Lucia Lourido, J.M. Sayagues, Alberto Orfao and Manuel Fuentes 1. Introduction 2. Overview of Protein Microarrays 2.1. Target Microarray 2.2. Reverse-Phase Protein Array (RPP) 2.3. In Situ Expressed Protein Array 3. Detection Platforms in Nanoproteomics 3.1. Label Detection Techniques 3.2. Label-Free Detection Methods 4. Biomarker Discovery by Nanoproteomics Approaches 4.1. AuNPs and QDs 4.2. Surface Plasmon Resonance 4.3. Microcantilevers and AFM 4.4. ESI-MS 4.5. CyTof Applications 5. Conclusions Acknowledgments References 137 138 139 139 140 140 141 141 146 148 148 150 150 152 154 154 155 7. Mass Spectrometry Imaging in Proteomics and Metabolomics 159 Benjamin Balluff, Ricardo J. Carreira and Liam A. McDonnell 1. The Need for Imaging-Based Proteomics and Metabolomics 2. Mass Spectrometry Imaging 2.1. Mass Spectrometry 159 161 161 viii Contents 2.2. Sample Preparation 2.3. Data Processing in MSI 2.4. Statistical Analysis of MSI Data 2.5. Strategies for the Identification of m/z Signals 3. Applications of MSI 3.1. Applications in Disease Pathology 3.2. Applications in Drug Imaging 4. Future Developments References 8. Advances in NMR-Based Metabolomics 168 170 172 175 178 178 179 180 181 187 G.A. Nagana Gowda and Daniel Raftery 1. Introduction 2. NMR Methods 2.1. One-Dimensional NMR Methods 2.2. Two-Dimensional NMR Methods 2.3. Isotope-Enhanced NMR Methods 3. Micro-Coil NMR 4. Fast NMR Methods 5. Hyperpolarization in NMR 6. Statistical and Data Analysis Methods 7. Spectral Assignment and Metabolite Quantitation Methods 7.1. Automation 7.2. Analysis of Heteronuclear 2D Spectra 8. STOCSY and RANSY Methods 9. Applications 10. Conclusions 11. Acknowledgment 12. Disclosure of Potential Conflict of Interest References 9. The Role of Mass Spectrometry in Nontargeted Metabolomics 187 188 189 190 191 193 195 195 196 198 199 199 200 201 204 205 205 205 213 Helen G. Gika, Ian D. Wilson and Georgios A. Theodoridis 1. 2. 3. 4. 5. Introduction Study Design Sample Preparation Analytical Strategies MS-Based Untargeted Metabolomics 5.1. LC Opportunities and Issues 5.2. GC Opportunities and Issues 5.3. MS Opportunities and Issues 6. Data Analysis 213 215 216 218 221 221 223 224 225 Contents 7. Identification of Biomarkers and Biochemical Pathway Visualization 8. Synopsis References 10. Direct Mass Spectrometry-Based Approaches in Metabolomics ix 227 230 231 235 Clara Ibáñez, Virginia Garcı́a-Cañas, Alberto Valdés and Carolina Simó 1. Introduction 2. Matrix-Assisted and Matrix-Free Laser Desorption/Ionization MS 3. Direct-Infusion MS 4. Ambient-Ionization MS 5. Imaging MS 6. Conclusions References 11. Functional Glycomics Analysis: Challenges and Methodologies 235 236 238 240 243 250 250 255 Nathan W. Stebbins and Ram Sasisekharan 1. Introduction 2. Structural Analysis of Glycans 2.1. General Consideration for Glycan Analysis 2.2. High-Performance Liquid Chromatography 2.3. Capillary Electrophoresis 2.4. MS for Glycomics 2.5. Lectins as Structural Probes 3. Functional Analysis of Glycans 3.1. Genetics Approach to Glycomics 3.2. Glycan Array and Synthesis Technologies 4. Integrating Structure and Function: A Case Study 5. Conclusions Acknowledgments References 12. Applications of Glycan Microarrays to Functional Glycomics 255 258 259 261 262 264 266 267 268 270 271 275 276 276 281 Ying Yu, Xuezheng Song, David F. Smith and Richard D. Cummings 1. Introduction 2. Generation of Glycan Microarrays 2.1. Glycan Sources 2.2. Glycan Immobilization 2.3. Shotgun Glycan Microarray (SGM) 281 283 283 285 288 x Contents 3. Examples of Reported Glycan Microarrays 4. Identification of Virus Receptors with Glycan Microarrays 4.1. Influenza Virus 4.2. Minute Virus of Mice 4.3. Rotavirus 5. Conclusions Acknowledgments References 290 294 294 297 298 299 300 300 13. High-Resolution Analytical Tools for Quantitative Peptidomics 305 Sayani Dasgupta and Lloyd D. Fricker 1. Introduction 2. Absolute Quantification 3. Relative Quantification 3.1. Label-Free Quantification 3.2. Metabolic Labeling 3.3. Chemical Labeling 3.4. Proteolytic Labeling 4. Concluding Remarks References 14. Analysis of Deep Sequencing Data: Insights and Challenges 305 306 307 308 311 312 319 320 320 325 Jacob W. Malcom and John H. Malone 1. Introduction 2. Fundamentals 2.1. Quality Control 2.2. Mapping 3. Applications 3.1. DNA Applications 3.2. RNA Applications 3.3. Relating Sequence and Expression Variation to Phenotypes 3.4. Application Pitfalls: Data Heterogeneity, Normalization, and False Discovery 4. The Computing Side of Deep Sequencing 4.1. Data Management and Computational Power 4.2. Visualization 4.3. Public Data 4.4. Communicating Analyses: Galaxy and Code Repositories 4.5. Resources 5. Summary and Future Directions Acknowledgments References 325 326 327 329 333 334 338 344 346 347 348 348 349 349 351 351 352 352 Contents 15. Gene Expression Analysis and Profiling of Microarrays Data and RNA-Sequencing Data xi 355 Javier De Las Rivas, Sara Aibar and Beatriz Roson 1. Human Genome and Transcriptome: From Gene Loci to Gene Products 1.1. Redefinition of Gene in the Context of Modern Transcriptomics 1.2. Types of Genes and RNA Complexity: Emerging Interest in ncRNAs 1.3. Protein-Coding Genes: cDNA Collections and ORFeomes 1.4. Biological Databases to Identify and Explore Expression of Protein-Coding Genes: Entrez Gene, ENSEMBL, GATExplorer, and ProteinAtlas 1.5. Gene Expression Regulation: Transcription Factors 2. Experimental Technologies for Genome-Wide Expression Analysis 2.1. Measuring Gene Expression: Real-Time qPCR 2.2. Microarrays 2.3. RNA Sequencing 2.4. Other High-Throughput Platforms to Investigate Regulation of Gene Expression 3. Bioinformatic Analysis of Gene Expression Data 3.1. Computational Methods to Achieve Gene Expression Profiling and Find Gene Signatures 3.2. Algorithms to Analyze Microarray Expression Data 3.3. Algorithms to Analyze RNA-Seq Data 3.4. Methods for Functional and Pathway Enrichment Analysis of Selected Gene Lists References 16. Bioinformatic Approaches to Increase Proteome Coverage 356 356 357 359 360 362 364 364 365 370 372 375 375 377 378 381 382 385 Francesco M. Mancuso, Salvatore Cappadona and Eduard Sabidó 1. Introduction 2. Increasing the Number of Fragmented Features 2.1. Protein-Level Separation 2.2. Peptide-Level Separation 2.3. MS-Level Separation 3. Reducing the Number of Unassigned Spectra 3.1. Reducing Rates of Unidentified Peptides 3.2. Increasing Rates of Identifiable Peptides 4. Summary Acknowledgments References 385 388 388 389 391 393 394 399 409 411 411 xii Contents 17. Transcriptome and Metabolome Data Integration—Technical Perquisites for Successful Data Fusion and Visualization 421 Michael Witting and Philippe Schmitt-Kopplin 1. Introduction 2. Extraction, Measurement, Raw Data Analysis, and Data Fusion 2.1. Transcriptomics 2.2. Metabolomics 2.3. Data Fusion Types 3. Visualization 3.1. Visualization on KEGG Pathways 3.2. Visualization on MetaCyc Pathways 3.3. Network Visualization and Analysis 4. MassTRIX Reloaded—Combined Analysis and Visualization of Metabolome and Trascriptome Data 4.1. Annotation of Mass Spectrometric Data 4.2. Analysis of Transcriptomic Data 4.3. Comparison Against Other Existing Resources 4.4. Future Directions for MassTRIX 5. Conclusions References 18. Computational Approaches for Visualization and Integration of Omics Data 421 424 424 427 430 433 433 435 435 436 436 437 437 439 440 441 443 Vasudha Sehgal, Tyler J. Moss and Prahlad T. Ram 1. Introduction 2. Data Overview 2.1. Data Types 2.2. Data Sources 3. Data Processing and Analyzing Tools 4. Network and Pathway Databases 4.1. Protein Interaction Databases 4.2. Pathway Commons 5. Visualization of Omics Data 5.1. Clustering and Heatmaps 5.2. Tools for Network Creation, Visualization, and Analysis 6. Conclusion References Index 443 444 444 445 448 448 449 449 450 450 451 453 453 455 Contributors to Volume 63 Sara Aibar, Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain Benjamin Balluff, Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands Salvatore Cappadona, Proteomics Unit, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Barcelona, Spain Ricardo J. Carreira, Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands Richard D. Cummings, Department of Biochemistry and the Glycomics Center, Emory University School of Medicine, Atlanta, Georgia, USA Sayani Dasgupta, Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA Noelia Dasilva, Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Javier De Las Rivas, Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain Rubén Dı́az, Hospital Sant Joan de Deu, Endocrinology, Fundacio per la Recerca Sant Joan de Deu, Barcelona, Spain Paula Diez, Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Vahid Farrokhi, Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA Lloyd D. Fricker, Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA Manuel Fuentes, Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Virginia Garcı́a-Cañas, Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain Helen G. Gika, Department of Chemical Engineering, Aristotle University Thessaloniki, Thessaloniki, Greece I. Gobernado, Servicio de Psiquiatrı́a, Hospital Ramón y Cajal, Madrid, Spain xiii xiv Contributors to Volume 63 Maria Gonzalez-Gonzalez, Centro de Investigación del Cáncer/IBMCC (USAL/ CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Clara Ibáñez, Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain Ricardo Jara-Acevedo, ImmunoStep, Edificio Centro de Investigación del Cáncer, Avda. Coimbra s/n, Campus Miguel de Unamuno, Salamanca, Spain A. Jimenez-Escrig, Servicio de Neurologı́a, Hospital Ramón y Cajal, Madrid, Spain Josep C. Jiménez-Chillarón, Hospital Sant Joan de Deu, Endocrinology, Fundacio per la Recerca Sant Joan de Deu, Barcelona, Spain Paul C.H. Li, Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada Song Li, Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA Lucia Lourido, Instituto de Investigación Biomedica da Coruña (INIBIC), Hospital Universitario A Coruña, A Coruña, Spain Jacob W. Malcom, Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA John H. Malone, Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA Francesco M. Mancuso, Proteomics Unit, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Barcelona, Spain Liam A. McDonnell, Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands Adam J. McShane, Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA Tyler J. Moss, Department of Systems Biology, UT MD Anderson Cancer Center, Houston, Texas, USA G.A. Nagana Gowda, Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, Washington, USA Reza Nemati, Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA Alberto Orfao, Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Daniel Raftery, Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Prahlad T. Ram, Department of Systems Biology, UT MD Anderson Cancer Center, Houston, Texas, USA Contributors to Volume 63 xv Marta Ramón-Krauel, Hospital Sant Joan de Deu, Endocrinology, Fundacio per la Recerca Sant Joan de Deu, Barcelona, Spain Beatriz Roson, Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain Eduard Sabidó, Proteomics Unit, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Barcelona, Spain A. Sanchez-Herranz, Servicio de Neurobiologı́a-Investigación, Unidad Central de Genómica Translacional, Hospital Ramón y Cajal, Madrid, Spain Alex Sánchez-Pla, Statistics Department, Facultat de Biologia, University of Barcelona, and Statistics and Bioinformatics Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain Ram Sasisekharan, Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA J.M. Sayagues, Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina Unidad de Proteomica & Servicio General de Citometrı́a, University of Salamanca, Salamanca, Spain Philippe Schmitt-Kopplin, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, and Chair of Analytical Food Chemistry, Technische Universität München, Freising-Weihenstephan, Germany Abootaleb Sedighi, Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada Vasudha Sehgal, Department of Systems Biology, UT MD Anderson Cancer Center, Houston, Texas, USA Carolina Simó, Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain David F. Smith, Department of Biochemistry and the Glycomics Center, Emory University School of Medicine, Atlanta, Georgia, USA Xuezheng Song, Department of Biochemistry and the Glycomics Center, Emory University School of Medicine, Atlanta, Georgia, USA Nathan W. Stebbins, Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Georgios A. Theodoridis, Department of Chemistry, Aristotle University Thessaloniki, Thessaloniki, Greece Alberto Valdés, Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC. Nicolás Cabrera 9, Madrid, Spain Ian D. Wilson, Department of Surgery and Cancer, Faculty of Medicine, Imperial College, South Kensington, London, United Kingdom xvi Contributors to Volume 63 Michael Witting, Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany Xudong Yao, Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA Ying Yu, Department of Biochemistry and the Glycomics Center, Emory University School of Medicine, Atlanta, Georgia, USA