Evaluation of the suitability of archival Bouin-fixed paraffin-embedded tissue specimens to proteomic investigation.
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.
Proteomics Laboratory, Porto Conte Ricerche Srl, Tramariglio, Alghero, Italy.
Alessandro
A
Tanca
Maria Filippa
MF
Addis
Maria Paola
MP
Simula
Daniela
D
Pagnozzi
Grazia
G
Biosa
Salvatore
S
Pisanu
Marica
M
Garziera
Renato
R
Cannizzaro
Vincenzo
V
Canzonieri
Valli
V
De Re
Sergio
S
Uzzau
D019342:Acetic Acid / Q000737:chemistry*; D014408:Biomarkers, Tumor / Q000032:analysis / Q000737:chemistry; D002853:Chromatography, Liquid / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D016612:Paraffin Embedding / Q000379:methods*; D010851:Picrates / Q000737:chemistry*; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D013270:Stomach / Q000737:chemistry; D013274:Stomach Neoplasms / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods
D014408:Biomarkers, Tumor; D010851:Picrates; D011506:Proteins; D020543:Proteome; D005557:Formaldehyde; C026239:Bouin's solution; D019342:Acetic Acid