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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
Published on: September 2, 2013
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Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease
Kensuke Kojima1, Craig April2, Claudia Canasto-Chibuque1
1Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Plos One
|February 6, 2014
Summary
Archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissues can provide transcriptome profiles for retrospective analysis, though RNA quality is lower than freshly cut (FC) FFPE tissues. These AS-FFPE tissues are valuable for biomarker development when other options are unavailable.
Area of Science:
- Biomedical Science
- Molecular Biology
- Oncology Research
Background:
- Archived tissues are crucial for biomarker development but often have degraded RNA.
- Sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissues are common but may yield poor RNA quality due to air exposure.
- Freshly cut (FC) FFPE tissues offer better RNA quality for retrospective studies.
Purpose of the Study:
- To evaluate if archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissues yield comparable transcriptome profiles to freshly cut (FC) FFPE tissues.
- To determine the feasibility of using AS-FFPE tissues for retrospective class prediction analysis.
- To assess the utility of AS-FFPE tissues for biomarker development in hepatocellular carcinoma (HCC) and liver cirrhosis.
Main Methods:
- Genome-wide transcriptome profiling of 83 HCC and 47 liver cirrhosis AS-FFPE samples using DASL and nCounter assays.
- Comparison of transcriptome profiles from AS-FFPE tissues with previously generated FC-FFPE profiles from the same tissue blocks.
- Gene signature-based prediction of HCC subclasses and prognosis using both AS-FFPE and FC-FFPE data.
Main Results:
- RNA quality and assay reproducibility in AS-FFPE samples were comparable to intermediate-to-poor quality FC-FFPE samples.
- Analyzable transcriptome profiles were obtained in 77% of both HCC and cirrhosis AS-FFPE samples.
- Retrospective class predictions were successfully reproduced in a high percentage of AS-FFPE samples (97% for HCC, 85% for cirrhosis) compared to FC-FFPE profiles.
Conclusions:
- AS-FFPE tissues yield lower quality RNA and transcriptome profiles than FC-FFPE tissues.
- Retrospective transcriptome-based class prediction is feasible in a significant proportion of AS-FFPE samples.
- AS-FFPE tissues serve as a valuable resource for retrospective analysis when they are the only available material.
