Formalin‐fixed paraffin‐embedded tissue: The holy grail of clinical proteomics?

Abstract

Tissue is the most relevant biological material to gather insight in disease mechanisms by means of omics technologies. However, fresh frozen tissue, which is generally regarded as the best imaginable source for such studies, is often not available. In case it is available, the different ways of storage (e.g. -20°C, -80°C, liquid nitrogen, etc.) hamper the conduction of reproducible multicenter studies because of different protein degradation rates. Formalin-fixed paraffin-embedded (FFPE) tissue on the contrary is considered as a valuable alternative for fresh frozen tissue, because only a few standard operation procedures are applied worldwide for the preparation of these tissues and because they are all stored in the same way. However, a study on the impact of the different preparation protocols for FFPE tissue was still lacking. Therefore, Bronsert et al. in this issue [Bronsert, P., Weißer, J., Biniossek, M. L., Kuehs, M. et al., Proteomics Clin. Appl. 2014, 8 786-804] conducted such a study that provides proof that there is no significant effect between these sample preparations procedures, and thereby they further open the gate for FFPE tissues to enter the field of clinical proteomics.

Proteomic analysis of FFPE tissue: barriers to clinical impact

“…The remaining aspects of the workflow under the control of the researcher should be standardized to the extent possible. One impediment to achieving standardization is the small community of researchers with a long-standing interest in the elements of the FFPE workflow rather than just the proteomic outcome [19]. One way to overcome this obstacle is to establish a consortium of interested researchers organized under an umbrella organization such as the Biosciences Research Network of the National Cancer Institute (NCI).…”

Detecting Green Fluorescent Protein-tagged Cryptococcus neoformans by Immunofluorescence on Paraffin-embedded Brain Sections

“…7 Tissue fixation with formalin or paraformaldehyde is another way to retain excellent morphology and preservation for longer periods. 7,8 Moreover, antigen retrieval is essential for immunofluorescence of paraffin slices. 9 High temperatures, similar to those in microwave ovens or pressure cookers, is the most effective method for unmasking most antigens.…”

“…This is extremely helpful in understanding the pathogenic characteristics of C. neoformans such as its interaction with microvascular endothelial cells in the brain. However, it is difficult to maintain the integrity of fresh cryosections and tissue preservation for longer durations 7. Tissue fixation with formalin or paraformaldehyde is another way to retain excellent morphology and preservation for longer periods 7,8.…”

“…However, it is difficult to maintain the integrity of fresh cryosections and tissue preservation for longer durations 7. Tissue fixation with formalin or paraformaldehyde is another way to retain excellent morphology and preservation for longer periods 7,8. Moreover, antigen retrieval is essential for immunofluorescence of paraffin slices 9.…”