[Proteomics and glycomics in pathology : Potential of autopsy and FFPE tissue for diagnostics and research]

The repertoire of disease-associated, formalin-fixed, paraffin-embedded (FFPE) samples collected and archived over decades is vast. When combined with frequently available and detailed clinical information on patients, disease progression, and outcomes, these samples represent a unique resource for investigating disease mechanisms at the molecular level. However, due to the specific sample preparation process, which involves chemical modifications of the tissue, the direct use of FFPE material in many analytical procedures has been limited.This review article reports on advances in analytical methods from the fields of proteomics and glycomics for the use of FFPE samples. A particular focus is placed on the analytical approach we developed for glycan headgroups of glycosphingolipids. Glycosphingolipids are components of the outer plasma membrane whose sugar chains extend into the extracellular space and are highly diverse and complexly regulated. Their glycosylation reflects the cellular state and mirrors pathological changes.The analytical characterization of glycosphingolipid glycans is challenging and has not yet been part of routine diagnostics. In this article, we describe a sample preparation strategy for FFPE tissue that preserves the characteristic glycosphingolipid repertoire and enables analysis by capillary gel electrophoresis coupled to laser-induced fluorescence detection (CGE-LIF). Using this approach, we identified a novel glycosphingolipid-based biomarker for bladder cancer in patient urine, which is also enriched in corresponding tumor FFPE samples.The goal of this article is to demonstrate the potential of FFPE and autopsy samples for systematic molecular analyses. This methodological combination opens access to extensive FFPE archives and enables the study of glycosphingolipid glycosylation in various tissues and diseases, facilitating the identification of new biomarkers and providing deeper insights into disease mechanisms.