Journal
PROTEOMICS CLINICAL APPLICATIONS
Volume 2, Issue 10-11, Pages 1539-1547Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/prca.200800005
Keywords
Formalin fixed; Laser capture microdissection; Paraffin embedded tissue; Protein extraction; Reverse-phase protein array; Tissue lysate
Funding
- NIH, National Cancer Institute, Center for Cancer Research
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Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue offers significant diagnostic utility but is complicated due to the high level of covalently crosslinked proteins arising from formalin fixation. To address these challenges, we developed a reliable protein extraction method for FFPE tissue, based on heat-induced antigen retrieval within a pressure cooker. The protein extraction yield from archival FFPE tissue section is approximately 90% of that recovered from frozen tissue. This method demonstrates preservation of immunoreactivity and recovery of full-length proteins by Western blotting. Additionally, we developed a well-based RP protein array platform utilizing an electrochemfluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, remain stable over 1 month at room temperature. Theses data suggest that this new protein-profiling platform coupled with the protein extraction method can be used for molecular profiling analysis in FFPE tissue, and contribute to the validation and development of biomarkers in clinical studies.
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