1st Edition

Surrogate Tissue Analysis
Genomic, Proteomic, and Metabolomic Approaches




ISBN 9780849328404
Published November 10, 2005 by CRC Press
332 Pages 7 Color & 63 B/W Illustrations

USD $200.00

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Book Description

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.

Table of Contents

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

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Reviews

"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