The collection of tissue is a fundamental procedure for research and clinical biology. Before collection it is important to consider which method will be used to preserve the tissue and prepare it for histology or molecular analysis. There are two options to choose from when collecting and preserving tissue: frozen or formalin-fixed paraffin-embedded (ffpe). Each has its strengths and weaknesses, but these are only apparent when the intended use of the tissue is considered.
There are two ways to freeze tissue: One method is used to prepare it for histology and the other is to prepare it for molecular analysis.
1. When preparing tissue for histology, it is common to place it directly into a cold sucrose solution for a few hours to overnight prior to flash freezing in dry-ice-cooled isopentane. The sucrose solution helps to dehydrate the tissue and prevent freezing artifact from water expanding during the rapid freezing transition. If the collection, dehydration, and freezing steps are performed correctly, the frozen tissue will have excellently preserved morphology and will be more sensitive to immunological staining. Sometimes, when necessary, the frozen tissue can be used for delicate immunohistochemistry without the standard brief fixation in formalin. The fixation step is only skipped when the antigen will be hidden by the crosslinking induced by formalin.
2. A second way to freeze tissue is reserved for tissue intended for molecular analysis only. This tissue must be placed directly into a phenol solution and flash frozen within minutes of dissection or biopsy. The samples will then be stable at -80°C for many months to years if necessary. The samples can then be used directly for DNA/RNA extraction and molecular analysis by qPCR or next generation sequencing.
FFPE tissue is collected and extensively fixed in formalin prior to being embedded in paraffin. The major benefit to this method is that the tissue is no longer heat sensitive and can be stored and worked with at room temperature, which saves valuable freezer space. Another benefit is that the morphology of the samples is usually better preserved as ffpe tissue doesn’t have as great of a potential to smear or tear as easily during sectioning. There also isn’t any threat of freezing artifact. Unfortunately, the ffpe process creates extensive crosslinking throughout the tissue, which can mask sensitive antigens from being detected with standard immunohistochemistry, and can interfere with native molecular signatures. DNA can be extracted from ffpe tissue, but the quality is lower than that collected from frozen samples.
A combination of methods is often the best strategy for obtaining the greatest variety of information from a tissue sample. Either way, it is always good to weigh the pros and cons of each method and take plenty of time to plan ahead of time so that on collection day the samples can be processed properly.