Protein extraction enables comparison of histological samples on the protein level. Two breast cancer biopsy samples, both scored 2+ for the receptor tyrosine kinase HER2 by immunohistochemistry, were processed using the Qproteome FFPE Tissue Kit and analyzed by protein lysate array and western blotting. In sample B, HER2 gene amplification was confirmed by FISH (data not shown). The housekeeping gene β-actin was analyzed as a control. Data kindly provided by Karl-Friedrich Becker and Christina Schott, Technical University of Munich, Germany.
Protein yields from FFPE tissues using the Qproteome kit are comparable to those from frozen material. Protein yields from frozen and FFPE tissues were compared by processing material in parallel, separation by SDS-PAGE, and western blotting. Controls were lysates from SW480 colorectal adenocarcinoma cells (colon), Huh7 human hepatoma cells (liver), SH-SY5Y neuroblastoma cells (rat brain).
Identification of a biomarker specific to certain types of lymphoma. The transcription factor E2A was detected after western blotting of proteins extracted from FFPE lymphoma preparations. E2A was detected in the B-cell lymphoma samples, but was absent in the T-cell lymphoma preparations. The housekeeping gene β-actin was analyzed as a control. (Data kindly provided by Susan Eckerle, Institute for Pathology, University Clinic, Frankfurt, Germany.)
The Qproteome Kit provides standardized and reproducible extraction from FFPE sections. Six FFPE colon tissue samples were processed in parallel. Equal volumes of extracted protein were separated by SDS-PAGE. Proteins were detected using β-actin and Erk2 antibodies after western blotting.
Proteins are efficiently extracted from FFPE tissue. Samples were obtained from formalin-fixed paraffin-embedded liver preparations using a 1 mm diameter punch, and proteins extracted using the Qproteome FFPE Tissue Kit. Four samples of each size were processed. Protein concentration in the final supernatant was determined using a BCA assay. Data kindly provided by Prof. Dr. Anja Bosserhoff, Institute of Pathology/Molecular Pathology, University of Regensburg, Germany.