Protein extraction method improvement for FFPE kidney tissue samples

The vast majority of tissue biopsies from patients in hospital environments are included in paraffin (FFPE- formalin-fixed and paraffin-embedded) for long-term storage. This fixation process produces a modification in the proteins called "crosslinks", which improves protein stability, necessary for their conservation. Currently, these samples are mainly used in clinical practice for performing immunohistochemical techniques, since these modifications do not suppose a drawback for this technique; however, crosslinks makes the protein extraction process a challenging one. Accordingly, these modifications make the development of a good protein extraction protocol necessary. Due to the specific characteristics of each tissue, the same extraction buffers or deparaffinization protocols are not equally effective in all cases. Therefore, it is necessary to obtain a specific protocol for each tissue. This work aims to establish a deparaffinization and protein extraction protocol from paraffin-embedded kidney samples, which finally allows us to obtain high quantity and quality protein, suitable for the application of proteomic techniques. To achieve this; we have designed different protocols using a range of buffers with diverse compositions and characteristics. Our results showed that xylene can eliminate the formalin fixation from the kidney tissue. Moreover, strong detergents (SDS-sodium dodecil sulfate- or analogues) and reducing agents (e.g. DTT- Dithiothreitol-) in the extraction buffer appear to be more important to obtain a good protein extraction yields and a good number of proteins identifications by LC-MSMS.