Matt van de Rijn, MDThe Life Raft Group GIST Collaborative Tissue Bank consists of a collection of tumor specimens from a large number of patients, stored at Stanford University. The advantages of having a tissue bank for a rare disease such as GIST are many. First, it provides a centralized location from which specimens can be sent for mutational analysis to Oregon Health & Science University, a very practical option for GIST patients. In addition, the collection of these samples can be used in a wide range of research studies— all with the goal of improving the survival of GIST patients in the future. One of the approaches we use at the tissue bank is to generate “tissue microarrays” from the samples, a procedure that will be explained in further detail below. At the moment, the tissue bank consists predominantly of so-called “paraffin blocks.”  These paraffin blocks are much easier to manage and store than frozen tissue specimens. Many of the technologies that researchers now use to study disease can be applied to material obtained from paraffin-embedded specimens. Thus, for practical reasons, the tissue bank has focused predominantly on paraffin block material.

What are paraffin blocks?

Whenever a patient undergoes surgery to remove a tumor, the material removed from the patient will be fixed in formalin, after which parts of the specimen will be submitted for microscopic analysis. Before the tissue can be analyzed by the pathologist, the fragments of tissue are impregnated with paraffin and a “paraffin block” is formed.

The fragments of tissue that are thus processed generally measure 1cm x 1cm x 0.3 cm. Very thin slices (0.5 micrometers) of these paraffin blocks will subsequently be examined under the microscope. The majority of the tissue actually remains in the paraffin block. The paraffin blocks are stored for many years in the archives of surgical pathology departments in the hospital where the tumor was removed.

When a tumor such as GIST is removed from a patient, the pathologist will submit one paraffin block per centimeter of tumor size. For example, if a patient has a tumor with a diameter of eight centimeters, eight separate blocks will be obtained and eight separate areas of the tumor will be examined under the microscope.

[blockquote quote=”…the collection of these samples can be used in a wide range of research studies— all with the goal of improving the survival of GIST patients in the future.”]

The reason for this is that tumors can vary in appearance from area to area and pathologists want to have a good overall sample size for each tumor The goal of The Life Raft Group is to obtain at least one paraffin block from each patient surgery to populate the tissue bank and ensure sufficient material is retained in the pathology archives of the hospitals where the surgery occurred. Therefore, samples will be available for researchers to perform studies that hopefully will benefit patients suffering from GIST.

Why concentrate paraffin blocks from multiple patients in a tissue bank?

The presence of a tissue bank has many advantages. Imagine, for example, a researcher who might have a hypothesis about why certain GIST tumors behave more aggressively than others. He or she will need an idea of how many samples might be available to study. In the absence of a centralized national tissue bank, the researcher will mostly look at the archives at his or her institute and perhaps the institutes of a few collaborators. This in itself is a very laborious process and often will take months to accomplish. Quite often, there are not enough specimens are available. The importance of a tissue bank for a disease that is rare, such as GIST, lies in the fact that a single phone call will suffice to ensure whether sufficient specimens are available and the project can progress, allowing the research process to move faster. Researchers often have a large number of hypotheses and information about the availability of specimens is extremely important.

In addition, the physical tissue bank containing the paraffin blocks is coupled with very high quality clinical information about patients from which these samples were obtained. This database, the “LRG Patient Registry,” has been organized through the efforts of the Life Raft Group and very quickly allows researchers to obtain (in a completely de-identified manner) the important features of the patient’s clinical history. The advantages of this are immense.

What is a tissue microarray (TMA)?

A tissue microarray is essentially a collection of very small fragments of tumor samples from multiple patients that are arranged in neat rows and columns in a paraffin block. Sections from this array contain a very small part of each tumor of all the patients represented and can be placed on a single glass slide. These slides can then be used for tests such as immunohistochemical staining, a technique in which the presence or absence of a particular protein can be demonstrated.

The advantage of having all tumors combined in a single array is that only one immunostaining experiment needs to be run. This saves an enormous amount of time and money and allows the researcher to test multiple hypotheses at a low cost.

The presence or absence of the proteins in question can then be correlated with the clinical data obtained from the LRG Patient Registry. In this way, one can very quickly determine whether a set of the proteins correlates with clinical outcome or can be used for diagnostic purposes. For example, we used a GIST TMA to quickly confirm that the novel diagnostic marker, DOG1 protein, was indeed present in the vast majority of GISTs.

It is important to realize that making a TMA does not destroy the original paraffin block in any way. Only a 0.6 mm tissue core is removed and the vast majority of the diagnostic tissue remains intact.

In summary, the tissue bank of GIST specimens, combined with the clinical data obtained by the Life Raft Group, forms an invaluable resource for researchers. TMAs offer an efficient and cost-effective way to study these specimens. In addition, TMAs provide a cost-efficient way to use the material for research. Since approximately 150 sections can be taken from each TMA block, and each original paraffin block has up to 50 tissue cores that can be used to generate new TMAs, there is a nearly unlimited quantity of specimens available. In my laboratory, we use these TMAs frequently to quickly assess the reliability of protein to serve as prognostic or diagnostic markers.