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Validation of a robust proteomic analysis carried out on formalin‐fixed paraffin‐embedded tissues of the pancreas obtained from mouse and human
Author(s) -
Kojima Kyoko,
Bowersock Gregory J.,
Kojima Chinatsu,
Klug Christopher A.,
Grizzle William E.,
Mobley James A.
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100663
Subject(s) - pancreatic cancer , proteomics , biology , computational biology , pancreas , biomarker discovery , pathology , microbiology and biotechnology , bioinformatics , cancer , medicine , gene , biochemistry , genetics
A number of reports have recently emerged with focus on extraction of proteins from formalin‐fixed paraffin‐embedded ( FFPE ) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice ( n = 8) were analyzed using 1 D ‐nano LC ‐ MS ( MS ) 2 following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens ( n = 11) as compared to uninvolved tissues ( n = 8), where 47 potential pancreatic ductal adenocarcinoma markers were identified as significantly increased, of which 28 were previously reported. Further, these proteins share strongly overlapping pathway associations to pancreatic cancer that include estrogen receptor α. Together, these data support the validation of an approach for the proteomic analysis of FFPE tissues that is straightforward and highly robust, which can also be effectively applied toward translational studies of disease.