1st Edition

Surrogate Tissue Analysis Genomic, Proteomic, and Metabolomic Approaches

Edited By Michael E. Burczynski, John C. Rockett Copyright 2006
    332 Pages 7 Color & 63 B/W Illustrations
    by CRC Press

    Despite rapidly expanding interest in potential applications of surrogate tissue analysis and intense competition to identify and validate biomarkers in appropriate surrogate tissues, very few peer reviewed publications describing the use of this approach have appeared in the scientific press. One of the first publications on this topic, Surrogate Tissue Analysis: Genomic, Proteomic, and Metabolomic Approaches describes initial applications and considerations for "omic" technologies in the field of surrogate tissue analysis.

    Highlighting important issues to consider when conducting profiling studies to identify novel biomarkers, the first section covers transcriptional approaches in surrogate tissues. It provides a review of important issues in peripheral blood profiling, summarizes results achieved when evaluations of various blood preparation platforms are used for the purpose of transcriptional profiling, and covers the relatively novel application of transcriptional profiling in neurological and oncological disease settings. The second section focuses on proteomic and protein-based methods for identifying markers in surrogate tissues, highlighting immunoassay and mass-spectrometry approaches for assessment of proteins in serum and other fluids, with a focus on the implications of protein-based biomarkers for detecting and monitoring early stages of cancer. The third section explores metabolomic approaches along with other novel molecular screens that can be applied in surrogate tissues to find biomarkers, and examines in detail the rapid development of metabolomics into a powerful technique for biomarker identification.

    The authors conclude with coverage of regulatory considerations, economic impact, and pan-omic strategies which will undoubtedly impact surrogate tissue analysis in the future. They explore current concepts in pan-omic approaches during drug development where a compendium of data generated by multiple profiling approaches are assessed and evaluated with its impact on the field of systems biology. The last chapter rounds out the coverage with a brief look ahead towards future analytical issues that will likely arise in the field of surrogate tissue analysis. The book is both an introduction to the various "omic" technologies in this young field and a fundamental reference for scientists interested in identifying biomarkers in surrogate tissues.

    INTRODUCTION TO SURROGATE TISSUE ANALYSIS
    Introduction to Surrogate Tissue Analysis, J.C. Rockett and M.E. Burczynski
    Introduction
    Areas That Could Benefit from Surrogate Tissue Analysis
    Challenges to the Use of Surrogate Tissues
    Summary
    References

    GENOMIC APPROACHES
    Impact of Sample Handling and Preparation on Gene Signatures as Exemplified for Transcriptome Analysis of Peripheral Blood, J.L. Schultze, S. Debey, R. Pillai, and T. Zander
    Introduction
    Application of Standards to Genomic Technologies
    Different Cell and RNA Preparation Methods from Whole Blood: An Introduction
    Comparison of Different Preparation Techniques of Whole Blood Samples
    Distinct Gene Expression Patterns in Peripheral Blood after Delayed Preparation
    Comparison of the QIAamp Method to PBMC
    Gene Expression Profiling of Whole Blood
    Requisites for Future Clinical Transcriptome Studies of Peripheral Blood
    Conclusions and Future Directions
    Acknowledgments
    References

    Blood Genomic Fingerprints of Brain Diseases, Y. Tang, D.L. Gilbert, T.A. Glauser, A.D. Hershey, A. Lu, R. Ran, H. Xu, and F.R. Sharp
    Introduction
    Methods
    Results
    Discussion
    Acknowledgments
    References

    Transcriptional Profiling of Peripheral Blood in Oncology, M.E. Burczynski
    Introduction
    Surrogate Tissue Profiling in Translational Medicine and Oncology Drug Development
    Class Discovery and Class Distinction in Surrogate Tissue Profiling Studies
    Relevance of Peripheral Blood in Assessment of Patients with Solid Tumors
    Pharmacogenomic Analysis of PBMCs in Renal Cell Carcinoma: A Case Study
    Other Surrogate Tissue Profiling Studies in Oncology
    Issues and Caveats with PBMC Profiling in Oncology Studies
    Summary
    Acknowledgments
    References

    Blood-Derived Transcriptomic Profiles as a Means to Monitor Levels of Toxicant Exposure and the Effects of Toxicants on Inaccessible Target Tissues, J.C. Rockett
    Introduction
    Blood Gene Expression as a Biomarker of Whole-Body Toxicant Exposure
    Blood as a Surrogate Tissue for Monitoring Gene Expression Changes in an Inaccessible Target Tissue
    Challenges to the Use of Blood as a Surrogate Tissue
    Summary
    References

    Spermatozoal RNAs as Surrogate Markers of Paternal Exposure, G.C. Ostermeier and S.A. Krawetz
    Introduction
    RNA in Sperm: Initial Observations
    Transcript Survey Techniques
    Defining the Normal Fertile Male
    Data Mining Sperm mRNAs
    Sperm as a Surrogate Tissue
    Application
    Acknowledgments
    References

    PROTEOMIC APPROACHES
    Proteomic Analysis of Surrogate Tissues: Mass Spectrometry-Based Profiling of the Circulatory Proteome for Cancer Detection and Stratification, E.F. Petricoin III, K.R. Calvo, J. Wulfkuhle, and L.A. Liotta
    Clinical Cancer Biomarkers: Is the Pipeline Dried Up?
    A Rich Potential Source of Candidate Biomarkers in the Low-Molecular-Weight Realm
    Points to Consider for Mass Spectrometry-Based Profiling Studies
    Biomarker Amplification via Carrier Protein Sequestration: Underpinnings of the Mass Spectral Information
    Concluding Remarks and a View to the Future
    Acknowledgments
    References

    Lymphocyte Integrins: Potential Surrogate Biomarkers for Evaluation of Endometrial Receptivity, K.V.R. Reddy, S.M. Gupta, and P.K. Meherji
    Introduction
    Endometrial Biomarkers in Implantation
    Integrins and Endometrial Function
    Embryonic Integrins and Implantation
    Integrins and Reproductive Dysfunction
    Integrins and Infertility
    Role of Peripheral Blood Lymphocytes in Endometrial Function
    Correlation between Endometrial Cell and Peripheral Lymphocyte Integrins
    Summary and Conclusions
    Acknowledgments
    References

    Nipple Aspirate Fluid to Diagnose Breast Cancer and Monitor Response to Treatment, E. Sauter
    Introduction
    Initial Studies of NAF Focus on Feasibility
    Studies Evaluating Cells in NAF
    Studies Evaluating Extracellular Fluid in NAF
    NAF as a Tool to Investigate the Presence of Mutagens in the Breast
    Effect of Botanicals on the Breast
    Assessing Response to Chemopreventive Agents
    Summary
    References

    METABOLOMICS AND OTHER APPROACHES
    Metabonomics: Metabolic Profiling and Pattern Recognition Analysis of Body Fluids and Tissues for Characterization of Drug Toxicity and Disease Diagnosis, J.L. Griffin and N.J. Waters
    Overview
    Introduction
    High-Throughput Metabolic Profiling in Drug Toxicology
    Mass Spectrometry, Metabonomics, and Toxicology
    Disease Diagnosis
    Correlation of Metabonomics with Other -omic Technologies
    Cryoprobe Technology
    High-Resolution Magic Angle Spinning 1 H NMR Spectroscopy
    Drug Development
    Metabonomics In Vivo
    Conclusions
    References

    Comprehensive Metabolomic Profiling of Serum and Cerebrospinal Fluid: Understanding Disease, Human Variability, and Toxicity, S. Ritchie
    Introduction
    Analytical Methodologies
    Searching for Biomarkers in a Sea of Human Variability
    Comprehensive Metabolomic Profile Analysis of Human Serum
    Comprehensive Metabolomic Profile Analysis of Human Cerebrospinal Fluid
    Application of Metabolomics to the Discovery of Toxicologic Markers
    Concluding Remarks
    References

    Lipidomic Analysis of Plasma and Tissues: Lipid-Derived Mediators of Inflammation and Markers of Disease, C.B. Clish and C.N. Serhan
    Introduction
    Membrane Architecture/Structure-Function
    Lipid Signals and Autocoids in Disease
    Comparative Mediator-Lipidomic Profiling of Engineered Experimental Animals
    Novel Extracellular Biosignals from Lipids: Pathways of Inflammation-Resolution
    Biomarker Lipidomics
    Summary
    Acknowledgments
    References

    Molecular Detection and Characterization of Circulating Tumor Cells and Micrometastases in Solid Tumors, R.A. Ghossein, H. Al-Ahmadie, and S. Bhattacharya
    Introduction
    PCR Technology
    Applications to Specific Tumor Types
    Future Trends
    References

    Methylation Profiling of Tumor Cells and Tumor DNA in Blood, Urine, and Body Fluids for Cancer Detection and Monitoring, I.H.N. Wong
    Introduction
    DNA Hypermethylation and Cancer Progression
    Concurrent Hypermethylation, Transcriptional Silencing, and Loss of Function
    Methylation Profiles in Circulating Tumor Cells Isolated from Blood of Patients with Cancer and Biological Implications
    Methylation Profiling of Circulating Tumor DNA in Plasma and Serum from Patients with Cancer
    Combinatorial Analyses of DNA Hypermethylation in Plasma/Serum and Conventional Protein Tumor Markers in Serum
    Molecular Monitoring of Human Cancers in Blood and Prognostic Implications
    Methylation Profiling of Tumor Cells and Tumor DNA in Urine from Patients with Cancer
    Methylation Profiling of Tumor Cells and Tumor DNA in Other Body Fluids from Patients with Cancer
    Qualitative and Quantitative Analyses of Aberrant Methylation Changes: Sensitivity and Specificity
    High-Throughput Methods for Methylation Profiling in Cancer Cells and the Selection of Target Genes as Epigenetic Markers in Blood and Body Fluids
    References

    FUTURE CONSIDERATIONS FOR SURROGATE TISSUE PROFILING
    Regulatory and Technical Challenges in Incorporating Surrogate Tissue Profiling Strategies into Clinical Development Programs, J.L. Oestreicher, M.J. Cahilly, D.P. Mounts, M.Z. Whitley, L.A. Speicher, W.L. Trepicchio, and M.E. Burczynski
    Introduction
    The Clinical Question of Interest
    Pharmacogenomic Study Logistics and Clinical Trial Design
    Transitioning the Clinical Pharmacogenomic Laboratory into a Regulatory Compliant Environment
    Assurance of Data Integrity Generated in Clinical Pharmacogenomic Studies: Establishing Validated Databases and Data Transfers
    Regulatory Considerations and Trial Design Issues during Pharmacogenomic Marker Development
    Summary
    References

    Considerations in the Economic Assessment of the Value of Molecular Profiling, S.C. Stallings, A.J. Sinskey, and S.N. Finkelstein
    Introduction
    Health Economics, Pharmacoeconomics, and Overcoming Inertia in the Adoption of Pharmacogenomic Strategies
    Economic Evaluations of Molecular Profiling in Clinical Practice
    Molecular Profiling in Drug Development
    Conclusion
    References

    The Impact and Challenges of Pan-Omic Approaches in Pharmaceutical Discovery and Development, W.D. Pennie, J.L. Colangelo, and M.P. Lawton
    Introduction
    The Genomics Sciences: Predictive and Investigative Opportunities
    Oncology and Drug-Induced Vasculitis: Examples of Progress and Practical Considerations in Applying Genomics Techniques
    Moving Forward
    References

    Current and Future Aspects of Surrogate Tissue Analysis, M.E. Burczynski
    Introduction
    Translational Medicine, Biomarkers, and Surrogate Tissues
    Variability, Reference Ranges, and Reference Standards in Surrogate Tissue Analysis
    Surrogate Tissue Profiling Will Ultimately Foster Basic Discoveries in Biological Research
    References

    Biography

    Michael E. Burczynski, John C. Rockett

    "In summary, the editors and their coauthors have done a very
    creditable job of expressing the breadth of the field of surrogate
    tissue analysis and provide many concrete examples of techniques
    for analysis. The treatment of this arising technology is
    at once learned and practical with examples of success and of
    the need for further research. The chapters at the end with perspective setting essays on economic and regulatory needs may
    help some not accustomed to these issues to understand the issues.
    However, the lesson to take away from this text is the great
    possibilities that exist to sharpen our view of biology and of
    medicine in particular. Future progress will involve refinement
    of the methods described here. There are methods that will not
    stand the test of time but taken as a whole, this book should
    be widely read. Every chapter has extensive bibliographic references
    and should serve as entrée into the literature even if the
    specific examples are of only passing interest. The editors and
    their coauthors are to be commended in providing a very thorough
    and interesting sampling of the methods being developed
    in the field."
    Sid Aaron, Sid Aaron Consultants, LLC, in the International Journal of Toxicology, May 2006