Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919), страница 2
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van Eyk, Michael J. DunnCopyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 3-527-30596-3XContents3Heart Failure: A Genomics Approach3.13.23.33.43.53.6Choong Chin LiewOverview of Heart Failure 45Pathophysiology of Heart Failure 46Genomic Approach to Heart Failure 50Conclusion 57Acknowledgements 58References 584Principles of cDNA Microarrays as Applied in Heart Failure Research4.14.24.34.44.54.64.74.84.94.104.114.124.134.144.154.164.17Sara Arab, Mansoor Husain, and Peter LiuThe Clinical Problem 61The Need for a New Paradigm 61The Potential Role of the Microarray 62Strengths of Microarray Technology 63Caveats of Using the Microarray Technology 64Experimental Design 65Tissue Preparation and Preservation 66RNA Isolation 67RNA Amplification 67Probe Labeling 68Data Analysis and Bioinformatics 69Application: New Classification of Disease 72Application: Pathogenesis of Disease 75Application: Early Disease Markers and Prognosis 75Application: Therapeutic Insights 78Acknowledgements 78References 795Gene Profiling in the Heart by Subtractive Hybridization5.15.1.15.1.25.1.35.25.2.15.2.25.35.45.4.15.4.25.4.35.55.65.7Christophe DepreStrategies and Limitations of Genome Profiling 83The Biological Problem 83The Model 84The Technological Approach 85Analyzing Gene Expression by Subtractive Hybridization 85Methodology 86Advantages and Disadvantages 89Genomics of Myocardial Ischemia 90Subtractive Hybridization of Myocardial Ischemia 91Myocardial Stunning 91Genomic Profile of Myocardial Stunning 91Chasing Novel Genes 93Summary 94Acknowledgements 95References 95458161Contents6DNA Microarray Gene Profiling:A Tool for the Elucidation of Cardioprotective Genes 996.6.56.6.66.76.8Elizabeth Murphy, Cynthia A.
Afshari, John G. Petranka,and Charles SteenbergenIntroduction 99Candidates for Cardioprotective Genes and Possible Mechanism(s)of Protection 99Candidate Genes Involved in Cardioprotection 99Potential Mechanisms of Cardioprotection 102Is There a Common Set of Cardioprotective Genes? 102Effects of Long-term Activation and Dosageof Cardioprotective Genes 103Approaches to Identify Genes Involved in Cardioprotection 103Preconditioning 104Transgenic Models of Protection 104Cardioprotection in Females 105Human Studies 105Practical Considerations in Microarray Technology 106Sample Selection 106Variability in Hybridization 107Cross-hybridization of Sequences 107Importance of Replicate Hybridizations and Validationof Significantly Changed Genes 107Changes in Gene Expression versus Protein or Activity 108Bioinformatics or How to Tell the Forest from the Trees 108Summary 109References 1097Pitfalls Associated with cDNA Microarrays – A Cautionary Tale7.17.27.37.47.57.67.77.87.9Alfred C.
Aplin and Charles E. MurryIntroduction 113Phase 1: The Original Experimental Design 114Phase 2: Validation and Troubleshooting 116Phase 3: “Postmortem” Analysis at ResGen 118Phase 4: Future Directioins 120Caveat Emptor: Suggestions for New Array Users 120Final Thoughts 123Acknowledgements 124References 1246.16.26.2.16.2.26.36.46.56.5.16.5.26.5.36.5.46.66.6.16.6.26.6.36.6.488.18.2113Application of Biologic Skepticism to Analysisof Expression Phenotypes 127Lawrence Adams, Roger E.
Bumgarner, and Stephen Mark SchwartzWhat is an Array? 127Applications of Array Analysis 128XIXIIContents8.2.18.2.28.2.38.2.48.2.58.2.68.2.78.2.88.38.48.58.6Catalogs by Function 128Functional Genomics 130Phenotypic Definitions 131Methodological Biases in Array Interpretation 131Usefulness of Clustered Genes 132False Associations 133Hypotheses Based on Expression Phenotypes 133Multiple Venn Diagrams: Decreasing the Size of the CatalogAnalysis of Measurement Errors 135Standards and Statistical Validation 137Summary 137References 1389Genes Involved in Atherosclerosis and Plaque Formation9.19.29.39.49.59.6Tiina T.
Tuomisto and Seppo Ylä-HerttualaIntroduction 141Genes Influencing Atherogenesis 142DNA Arrays: The Principle 143DNA Arrays in the Research of Atherosclerosis 145Acknowledgements 149References 149Section 2Proteomics10Gene Expression Profiling in Pulmonaryand Systemic Vascular Cells Exposed to Biomechanical Stimuli10.110.210.310.3.110.3.210.3.310.3.410.410.51111.111.211.311.4134141153155Shwu-Fan Ma, Shui Qing Ye, and Joe G.
N. GarciaIntroduction 155Principles of Array, SAGE and Mini SAGE Technologies 156Analysis of Gene Expression Profiling in Vascular Cells 157Endothelial Cells 159Smooth Muscle Cells 165Fibroblasts 167Monocytes/Macrophages 167Future Perspectives 168References 169Proteomics, a Step Beyond Genomics:Applications to Cardiovascular DiseaseEmma McGregor and Michael J. DunnIntroduction 173Protein Solubilization 174Protein Separation 174Protein Detection/Visualisation 179173Contents11.811.9Protein Identification 183Bioinformatics 185Cardiovascular Proteomics 186Heart 2DE Protein Databases 187Dilated Cardiomyopathy 187Animal Models of Heart Disease 188Proteomic Characterization of Cardiac Antigens in Heart Diseaseand Transplantation 189Summary 189References 19012Mass Spectrometry – A Powerful Analytical Tool12.112.212.312.3.112.3.212.3.312.3.412.4Helen L. Byers and Malcolm A. WardIonisation Processes 195Mass Analysers 196Strategies for Protein and Characterisation 199Protein Identification by MALDI-TOF 199Protein Identification by Tandem MX/MS 201Database Searching 204Post Translational Modifications 205References 20811.511.611.711.7.111.7.211.7.311.7.413195Differential Expression Proteomic Analysis Using IsotopeCoded Affinity Tags 21313.513.613.713.8Michael E.
Wright and Ruedi AebersoldIntroduction 213Traditional Methodologies for Measuring Protein Abundance 214Isotopic Methodologies to Quantitative Proteomics 218Isotope-Coded Affinity Tags (ICATTM)for Quantitative Proteome Analysis 221Biological Applications of the ICAT Method 223Conclusions and Future Directions 227Acknowledgements 230References 23014Protein Chip Technology in Proteomics Analysis14.114.214.314.414.4.114.4.214.4.2.114.4.2.2Rosalind E. Jenkins and Stephen R. PenningtonIntroduction 235Two-dimensional Gel Electrophoresis 236Alternative Approaches to Protein Separation 237Protein Arrays 238Protein Recognition Molecules 239Immobilisation of PRMs 241Arraying of Proteinaceous PRMs 241Arraying of Nucleic Acid PRMs 24313.113.213.313.4235XIIIXIVContents14.4.2.314.514.614.7Arraying of Synthetic PRMs 243Detection Methods 244Conclusions 245References 24615Recent Applications of Functional Proteomics:Investigations in Smooth Muscle Cell Physiology25515.115.1.115.1.215.1.315.215.2.115.2.215.2.315.315.415.515.6Justin A.
MacDonald and Timothy A. J. HaysteadIntroduction to Functional Proteomics 255Expression Proteomics (Catalogue) 256Functional Proteomics (Applied) 256Structural Proteomics 257Proteomic Tools for Smooth Muscle Physiologists 257Protein Separation: The 2DE Technology 257Mass Spectrometers 259Protein Identification by Database Searching 260Defining Signal Transduction Modules in Smooth Muscle 262Proteome Mining of the Smooth Muscle Cell 269Acknowledgements 274References 27416Identification of Targets of Phosphorylation in Heart Mitochondria16.116.216.2.116.2.216.2.316.2.416.2.516.316.3.116.3.216.3.316.3.416.3.516.3.616.3.716.3.816.4Roberta A. Gottlieb and Huaping HeExperimental Approach and Pitfalls 279Perspective and Comments 286Analysis of Post-translational Modifications 286Detection of Phosphoproteins by Comparisonof Two Conditions Can Be a Tool to Select Proteinsof Potential Interest for Proteomic Analysis 286Selection of an Organelle Simplifies the Analysis 287Further Simplification of the Mixture of Proteinsto be Analyzed is Desirable 287Selection of a Protein Separation Strategy is Essential 287Specific Methods Employed 288Isolated Perfused Heart 288Isolation of Cytosol and Mitochondria 288In Vitro Phosphorylation Reactions 289Submitochondrial Fractionation 289Preparation of Samples for 2D PAGE and MS 290In-gel Digest of p46 290MALDI Analysis 290Peptide Sequencing by MS/MS Analysis 290References 291279Contents1717.117.1.117.1.217.217.2.117.2.217.317.417.51818.118.218.2.118.2.218.2.318.2.418.2.518.2.618.318.3.118.3.218.418.518.61919.119.219.2.119.2.219.2.3Proteomic Characterization of Protein Kinase C Signaling Tasksin the Heart 293Thomas M.
Vondriska, Ph. D., Jun Zhang M. S., and Peipei Ping, Ph. D.Protein Kinase C Signaling Complexes 293Metabolism-targeted Proteomics 294Transcription-targeted Proteomics 295Subproteomic Analysis of PKCe Signaling 296Introduction 296Functional Proteomic Platform 297Metabolic and Transcription/Translation Functionsof the PKCe Complex 301Conclusion 303References 303Identification of Secreted Oxidative Stress-induced Factors (SOXF)and Associated Proteins: Proteomics in Vascular Biology 307Zheng-Gen Jin, Duan-Fang Liao, Chen Yan, and Bradford C. BerkIntroduction 307Identification of SOXF by Tandem MS 308Secreted Factors Are Involved in Regulationof ERK1/2 Activation by Oxidative Stress 308A Trypsin-sensitive Secreted Oxidative Stress-induced Factor (SOXF)is Released in Response to LY83583 308Purification of SOXF and Identification of SOXF Candidate Proteinsby Mass Spectrometry 309LY83583 Stimulates Release of HSP90-a Specifically from VSMC 310Human Recombinant HSP90-aand Cyclophilin A (CyPA) Activate ERK1/2 311Human Recombinant Cyclophilin a Stimulates VSMC Growthand Protects VSMC against Apoptosis 311Identification of SOXF-associated Proteins by MALDI-TOF MS 312Identification of SOXF-associated Proteins by MALDI-TOF MS 312Confirmation of 43-kD CyPA-binding Protein as a a-Actin 312Conclusions 313Acknowledgements 314References 314Myofilament Proteomics: Understanding Contractile Dysfunctionin Cardiorespiratory Disease 317J.
A. Simpson, S. Iscoe, and J. E. Van EykRegulation of Muscle Contraction 318Disease States and the Myofilament Proteins 320Myofilament Protein Mutations Cause Disease 321Myofilament Protein Isoform Alterations in Disease 321Myofilament Protein Post-translational Modifications in Disease 322XVXVIContents19.419.519.6Proteomic Analysis of the Myofilament Proteins 322Creating a Myofilament Proteome 323Protein Separation – 2-DE 327Detection, Quantification and Identification 330Alternative Methods of Protein Separation 332The Next Step – Clinical Applications of Proteomics:The Development of Biomarkers 333Conclusion 333Acknowledgements 334References 334Section 3Future Perspectives20Genomics Perspective for Drug Discovery20.120.220.320.3.120.3.220.3.320.3.420.3.520.420.5A.
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