Surrogate Tissue Analysis: Genomic, Proteomic, and Metabolomic Approaches, 1st Edition (Hardback) book cover

Surrogate Tissue Analysis

Genomic, Proteomic, and Metabolomic Approaches, 1st Edition

Edited by Michael E. Burczynski, John C. Rockett

CRC Press

332 pages | 7 Color Illus. | 63 B/W Illus.

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Hardback: 9780849328404
pub: 2005-11-10
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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.

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

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

Subject Categories

BISAC Subject Codes/Headings:
MED009000
MEDICAL / Biotechnology
MED071000
MEDICAL / Pharmacology
MED096000
MEDICAL / Toxicology