Paraffin-Embedded Tissue as a Novel Matrix in Metabolomics Study: Optimization of Metabolite Extraction Method

Tissue is considered as a highly informative matrix in omics studies. Most commonly used tissues in metabolomics are fresh-frozen specimens. However, an alternative metabolomics matrix, up to now most often applies in immunohistochemistry or histopathology, is formalin-fixed, paraffin-embedded tissue (FFPE). The main advantages of FFPE tissues over fresh-frozen ones are the possibility to be stored at ambient temperature which is a cost-effective method and, consequently, their higher availability in biobanks. The main aim of the study was to develop and optimize the preparation protocol for FFPE samples in metabolomics, using cancer tissue and corresponding control tissue sections. Several conditions were evaluated: type and volume of deparaffinization solvent, number of purification cycles, solvent used in purification step, extraction solvent, and thickness of FFPE samples. Samples were analyzed by gas chromatography coupled with mass spectrometry (GC–MS). As a result, a sample preparation protocol of FFPE tissues for metabolomics was developed. Moreover, applicability of the proposed method was tested with the use of FFPE tissues obtained from prostate cancer patient and non-cancer controls.