Surrogate Tissue Analysis describes initial applications and considerations for "omic" technologies in the field of surrogate tissue analysis.

Features:

• Discusses the range of disease states and surrogate tissue profiling applications from cancer to reproduction to inflammation
• Covers the transcriptional profiling of peripheral blood in detail with specific chapters focused on analytical considerations and additional chapters dealing with specific disease indications
• Explores the nature of surrogate tissue profiles of toxic exposure in preclinical studies where transcriptional effects in both target and surrogate tissues can be compared
• Focuses on expression profiling in non-blood based tissues, such as semen or nipple aspirate fluid, which can be utilized as surrogate tissues of exposure or disease progress
• Provides an excellent overview of lipidomics and how it can be used in surrogate tissues to provide an understanding of dynamic inflammatory responses in hosts
• Examines the burgeoning need for well-characterized and reproducible surrogate tissue analysis approaches
• Addresses recent FDA guidelines on the use of genomic and proteomic data in new drug applications

Contents

Introduction to Surrogate Tissue Analysis

• Areas That Could Benefit from Surrogate Tissue Analysis
• Challenges to the Use of Surrogate Tissues

Impact of Sample Handling and Preparation on Gene Signatures as Exemplified for Transcriptome Analysis of Peripheral Blood

• 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

Blood Genomic Fingerprints of Brain Diseases

• Methods
• Results

Transcriptional Profiling of Peripheral Blood in Oncology

• 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

Blood-Derived Transcriptomic Profiles as a Means to Monitor Levels of Toxicant Exposure and the Effects of Toxicants on Inaccessible Target Tissues

• 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

Spermatozoal RNAs as Surrogate Markers of Paternal Exposure

• RNA in Sperm: Initial Observations
• Transcript Survey Techniques
• Defining the Normal Fertile Male
• Data Mining Sperm mRNAs
• Sperm as a Surrogate Tissue

Proteomic Analysis of Surrogate Tissues: Mass Spectrometry-Based Profiling of the Circulatory Proteome for Cancer Detection and Stratification

• 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

Lymphocyte Integrins: Potential Surrogate Biomarkers for Evaluation of Endometrial Receptivity

• 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

Nipple Aspirate Fluid to Diagnose Breast Cancer and Monitor Response to Treatment, E. Sauter

• 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

Metabonomics: Metabolic Profiling and Pattern Recognition Analysis of Body Fluids and Tissues for Characterization of Drug Toxicity and Disease Diagnosis

• 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

Comprehensive Metabolomic Profiling of Serum and Cerebrospinal Fluid: Understanding Disease, Human Variability, and Toxicity

• 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

Lipidomic Analysis of Plasma and Tissues: Lipid-Derived Mediators of Inflammation and Markers of Disease

• 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

Molecular Detection and Characterization of Circulating Tumor Cells and Micrometastases in Solid Tumors

• PCR Technology
• Applications to Specific Tumor Types

Methylation Profiling of Tumor Cells and Tumor DNA in Blood, Urine, and Body Fluids for Cancer Detection and Monitoring

• 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

Regulatory and Technical Challenges in Incorporating Surrogate Tissue Profiling Strategies into Clinical Development Programs

• 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

Considerations in the Economic Assessment of the Value of Molecular Profiling

• 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

The Impact and Challenges of Pan-Omic Approaches in Pharmaceutical Discovery and Development

• The Genomics Sciences: Predictive and Investigative Opportunities Oncology and Drug-Induced Vasculitis: Examples of Progress and Practical Considerations in Applying Genomics Techniques

Current and Future Aspects of Surrogate Tissue Analysis

• 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

Index

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