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DIGE Saturation Labeling for Scarce Amounts of Protein from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue
1Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland. paul.dowling@nuim.ie.
Insights
Difference gel electrophoresis (DIGE) enables global protein detection in formalin-fixed paraffin-embedded (FFPE) tissues. This proteomics platform is valuable for discovering cancer biomarkers from scarce clinical samples.
Area of Science:
- Proteomics
- Biomarker Discovery
- Cancer Research
Background:
- Formalin-fixed paraffin-embedded (FFPE) tissues are a stable, accessible resource for retrospective clinical studies.
- FFPE tissues are standard in pathology, offering a vast archive for research.
- Limited viable protein yield from FFPE tissues presents a challenge for traditional proteomics.
Purpose of the Study:
- To describe the utility of difference gel electrophoresis (DIGE) for proteomics analysis of FFPE tissues.
- To highlight DIGE's application in biomarker discovery for cancer development and progression.
- To demonstrate DIGE's effectiveness with limited protein amounts from FFPE samples.
Main Methods:
- Utilizing difference gel electrophoresis (DIGE) as a proteomics platform.
- Applying DIGE for global protein detection in FFPE tissues.
- Adapting DIGE technology for labeling low-level proteins from FFPE samples.
Main Results:
- DIGE facilitates the global detection of expressed proteins in FFPE tissues.
- The technology is effective for biomarker discovery and identification in cancer.
- DIGE successfully analyzes proteins from scarce FFPE tissue samples.
Conclusions:
- DIGE is a valuable proteomics tool for analyzing FFPE tissues.
- This method aids in identifying protein biomarkers relevant to cancer.
- DIGE overcomes limitations of low protein yield in FFPE samples for biomarker research.
Abstract:
In this chapter, we describe the utility of difference gel electrophoresis (DIGE) as a proteomics platform for the global detection of expressed proteins in formalin-fixed paraffin-embedded (FFPE) tissues and its use for biomarker discovery/identification of proteins that may contribute to cancer development and progression. Formalin fixation and paraffin embedding of tissue is the standard processing methodology practiced in pathology laboratories worldwide, resulting in a highly stable form of tissue that is easily stored due to its inherent stability at room temperature. Consequently, FFPE tissues represent an attractive reservoir of clinical material for conducting retrospective protein biomarker analysis. A limitation for proteomics research in this type of clinical sample is the amount of viable protein that can be obtained from fixed tissues. Tissue biopsies are precious samples that can generally be acquired in very small amounts due to the invasive nature of the sample collection, mainly during surgery or biopsy. Subsequently, the amount of extracted protein can be, in many cases, very limited. The saturation DIGE technology has emerged as a useful method for protein analysis where only scarce amounts of protein are available. This approach can be adapted successfully to label low-level protein isolated from FFPE tissue.
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