Evaluation of the suitability of archival Bouin‐fixed paraffin‐embedded tissue specimens to proteomic investigation

Abstract

Bouin's solution has been used for over a century as a common fixative in several pathology laboratories worldwide. Therefore, a considerable number of Bouin-fixed paraffin-embedded (BFPE) tumor samples of various origin are available in hospital repositories as a powerful information mine for clinical investigations. To date, however, such archived tissues have not been subjected to a systematic study aimed to evaluate their potential use in proteomics. In this report, we investigated whether archival BFPE tissue specimens could be exploited for proteomic studies, upon application of protein extraction and proteomic analysis methods previously optimized for formalin-fixed samples. As a result, gastric BFPE protein extracts exhibited poor suitability for 2D-PAGE analysis, whereas over 300 unique proteins could be successfully detected when extracts were subjected to SDS-PAGE followed by LC-MS/MS (GeLC-MS/MS). Among these, several known markers for gastric cancer and normal gastric functionality were identified, indicative of biological and clinical significance of proteomic data mined from BFPE tissues. A quantitative and qualitative comparison of FFPE and BFPE tissue proteomes was also performed, and results are reported. In conclusion, we demonstrated that BFPE specimens can be analyzed by means of a proteomic approach such as GeLC-MS/MS. Although considerable molecular biases and technical constraints exist, BFPE tissue archives can be fruitfully exploited for gathering proteomic data from particularly precious samples.

Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues

“…For this purpose, in diagnostics, chemical fixatives are mainly used, and among them the most widely used is formalin, the aqueous solution of formaldehyde. However, Bouin’s fixative has been extensively used as an elective fixative for histological examination in some institutions worldwide [1]. Bouin’s fixative is a mixture of a saturated aqueous solution of picric acid, formalin, and acetic acid [2].…”

“…This fixation method has been used for specific purposes because it better preserves some morphological details, such as nuclear conformation [3]. In the past decades, several studies have already shown that Bouin’s-fixed samples are amenable for nucleic acid and protein analyses, but only to a certain point, as the fixative has resulted to be more detrimental compared to 10% buffered formalin mixture in the preservation of biomolecules [1,3,4]. Currently, no investigation has been carried out on the analysis performance with respect to miRNAs, despite the publication of two samples in a report [4].…”

Feasibility of MALDI-MSI-Based Proteomics Using Bouin-Fixed Pathology Samples: Untapping the Goldmine of Nephropathology Archives

“…Previous studies have attempted to investigate whether Bouinfixed specimens are suitable for proteomic analysis using traditional MS-based techniques (e.g., GeLC-MS/MS) and have suggested that BFPE tissue archives can be fruitfully exploited for gathering data from particularly precious cases, although molecular biases and technical constraints exist. 14 While studies have presented the application of MALDI-MSI on BFPE tissues (e.g., human testis) with promising results, none have preceded to assess the technical reliability of this method through the direct parallel analysis of coupled FFPE cases. 15 Thus, starting from our previous results on FFPE renal biopsies in the context of different kidney diseases, 7,10,16−18 here we sought to investigate whether BFPE samples are equally suitable for spatial proteomics analysis with MALDI-MSI in order to further enrich the capabilities of this tool and, subsequently, unlock a wide retrospective series of rare renal diseases that can be exploited to increase our knowledge in this field.…”

“…In renal pathology, tissue specimens have routinely been treated with Bouin for years, and pathology archives are enriched in BFPE tissue, representing a goldmine to be untapped for molecular and diagnostic research techniques. Previous studies have attempted to investigate whether Bouin-fixed specimens are suitable for proteomic analysis using traditional MS-based techniques (e.g., GeLC-MS/MS) and have suggested that BFPE tissue archives can be fruitfully exploited for gathering data from particularly precious cases, although molecular biases and technical constraints exist . While studies have presented the application of MALDI-MSI on BFPE tissues (e.g., human testis) with promising results, none have preceded to assess the technical reliability of this method through the direct parallel analysis of coupled FFPE cases .…”

Proteomic Characterization of Colorectal Cancer Cells versus Normal-Derived Colon Mucosa Cells: Approaching Identification of Novel Diagnostic Protein Biomarkers in Colorectal Cancer

“…A major advantage of the latter technique is that it can be performed on formalin-fixed paraffin-embedded (FFPE) CRC patient tissue [31]. FFPE in combination with 2D-PAGE is still insufficient [32]. The use of frozen tumor tissue is applicable with 2D-PAGE.…”