—  SHORT COURSE #47  —

Molecular Analysis of Tissues Using Gene Expression Arrays and Tissue Microarrays

Section I: Principles and Applications of Gene Expression Arrays

Edward Gabrielson
The Johns Hopkins University School of Medicine
Baltimore, MD

Section II: The Principles, Uses and Construction of Tissue Microarrays in Pathology Research

Angelo M. De Marzo and Helen Fedor
The Johns Hopkins University School of Medicine
Baltimore, MD

Ramaswamy Anbazhagan is acknowledged for his contributions
to this USCAP course in the year 2001 and to this handout




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Section 1 - Principles and Applications of Gene Expression Arrays

Powerpoint Presentation

Introduction
High throughput gene array technologies offer new opportunities to find new markers for disease states and recognize patterns of gene expression that may fingerprint distinct classes of disease. High-throughput tissue microarrays offer an effective mechanism to test and validate candidate markers (or proposed classes of disease). These two approaches are often used in combination to accelerate discovery and validation in molecular pathology.

This short course will provide a broad overview of different gene array technology platforms and the application of these technologies to the analysis of tissue samples. The depth of discussion is limited by time constraints, but the course should provide a general background on this technology and help pathologists who are contemplating use arrays in future work. With reference to gene expression arrays, the course will cover three general topics: 1) array technology (manufacturing processes, hybridization methods, and data acquisition), 2) data management and analysis, and 3) specimen requirements.



Section 2 - The Principles, Uses and Construction of Tissue Microarrays
in Pathology Research

Powerpoint Presentation

Introduction
Genomic approaches such as RNA profiling are providing a new powerful means to discover disease-related genes. One of the most challenging aspects presented by high throughput gene expression approaches is that they usually generate a large battery of potential targets. Determination of which genes are truly important for classification in terms of diagnosis, prognosis, and therapy represents a bottleneck. How does one begin to validate and prioritize potential targets? Often the first step in attempts to discover the disease relevance of a given gene is the elucidation of the precise cells that express it in normal and diseased human tissues. This is even more powerful if it can be done simultaneously with an assessment of clinical significance. A major limitation, however, is that in situ based molecular analysis is cumbersome and often limited by the availability of suitable reagents such as high quality antibodies or a robust system for in situ hybridization. In addition, adequate validation of biomarker expression often requires large patient cohorts with long-term clinical follow-up. Finally, interpretation of expression results requires a pathologist. While many of these limitations have yet to be solved, Tissue Microarrays (TMAs) are emerging as a breakthrough in our ability to rapidly analyze the expression of existing and new biomarkers using archival pathology specimens.

Multi-tissue blocks were first introduced by Battifora et al. in the so-called "sausage" or Multi-Tissue Tumor Block (MTTB) where up to 100 separate tissues were processed together into a single paraffin block1. Recently, Kononen et al. introduced a new method of combining multiple tissues into a single paraffin block that uses a novel sampling approach, with regular size and shaped tissues. This allows for many more specimens that are precisely arrayed to be inserted into the blocks.