Formalin Fixed Paraffin Embedded tissue samples, or FFPE tissue samples, are biopsied human tissue that are prepared for preservation and are exceptionally useful resources for studying, analyzing, and diagnosing various diseases, as well as aiding in the process of gene expression profiling. In order to convert tissue samples into FFPE tissue samples, a specific procedure must be followed. First, fresh tissue must be obtained. It is essential that the tissue be handled very carefully as it can easily be damaged after removal. Following the dissection, the specimen must be placed in a liquid fixing agent such as formalin (formaldehyde) which will help to harden and preserve the tissue in order to protect it from succeeding steps. The tissue must remain in the fixative long enough for it to penetrate through every part of the specimen; this usually takes around 6-24 hours depending on the size and type of tissue sample. Next, in order for the tissue to be properly infiltrated with melted paraffin wax, it must be dehydrated and cleared. This takes place by repeatedly immersing the tissue in ethanol of increasing levels of concentration ending in a 100% concentration of ethanol, whilst being careful, as the sample is still quite fragile. At this stage, almost all of the water has been removed, and a clearing agent must be used to ensure that all the ethanol is displaced. The clearing agent acts as an ethanol diffuser and also removes unnecessary fat from the tissue which would have otherwise made it difficult for the wax to penetrate. Xylene is a commonly used clearing agent and gives the tissue a transparent look. Despite its wide use, xylene is a toxic reagent and some laboratories prefer to use less toxic materials such as isopropanol, which in turn requires higher wax temperatures. At this point, the tissue can be infiltrated with paraffin wax that is around 60°C and then be left to cool so that it solidifies and can be easily cut into sections.
There are kits available that can help streamline this process, and make it easier to perform. FFPE tissues can be used to recover RNA, DNA, and proteins as well as discover signs of cancer or other disease. They can be stored for years, and are an essential part of how researchers and doctors leverage tissue samples for diagnosis and research.