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Updated: May 15, 2026
Laser Capture Microdissection of Paraformaldehyde-Fixed Mouse Liver Tissue for RNA Analysis
Published on: April 17, 2026
Whole-genome DASL gene expression profiling of hepatocellular carcinoma sub-populations isolated by laser
Corina Gabriela Cotoi1, Shirin Elizabeth Khorsandi, I E Pleşea
1Institute of Liver Studies, King's College Hospital, London, UK. corina.cotoi@nhs.net
Abstract:
In the last ten years, a multitude of studies focusing on gene expression profiling have attempted to shed light on the molecular and genomic mechanisms leading to hepatocarcinogenesis. One of the downsides of the technology available until recently was that it was limited to RNA extracted from fresh/frozen tissue or cell cultures. Recent advances have made it possible to obtain good quality RNA from formalin-fixed paraffin-embedded (FFPE) tissue, allowing access to a virtually limitless archival resource to be available for retrospective and long-term prospective clinico-pathological studies. Laser-capture microdissection allows the isolation of specific cell populations or of specific microscopic areas of interest from tissue samples. This allows the selective evaluation of gene expression of targeted cell clusters, especially in a very heterogeneous environment as the malignant tissue. In our study, we demonstrated that by laser microdissecting the areas of interest from FFPE tissue we could obtain gene expression signals by running the purified RNA through the Whole Genome DASL assay. A large number of genes were expressed in both subpopulations of hepatocellular carcinoma (classical HCC and cholangiocellular differentiation) as well as in the cirrhotic and non-cirrhotic liver background.
Insights
Gene expression profiling of liver cancer (hepatocellular carcinoma) is now possible using archival formalin-fixed paraffin-embedded (FFPE) tissues. Laser-capture microdissection enables targeted gene analysis from these valuable FFPE samples.
Area of Science:
- Molecular Biology
- Genomics
- Hepatology
Background:
- Gene expression profiling is crucial for understanding hepatocarcinogenesis.
- Traditional methods required fresh/frozen tissue, limiting archival research.
- Formalin-fixed paraffin-embedded (FFPE) tissues offer a vast resource for retrospective studies.
Purpose of the Study:
- To evaluate the feasibility of gene expression analysis from FFPE tissues using laser-capture microdissection.
- To identify gene expression patterns in different liver tissue subtypes.
Main Methods:
- Utilized laser-capture microdissection to isolate specific cell populations from FFPE liver tissue.
- Extracted RNA from microdissected FFPE samples.
- Performed Whole Genome DASL assay for gene expression profiling.
Main Results:
- Successfully obtained gene expression signals from laser microdissected FFPE tissues.
- Identified a large number of expressed genes in hepatocellular carcinoma (HCC) subtypes and cirrhotic liver backgrounds.
- Demonstrated the utility of FFPE samples for comprehensive gene expression analysis.
Conclusions:
- Laser-capture microdissection combined with Whole Genome DASL assay is effective for gene expression profiling of FFPE tissues.
- This approach provides valuable insights into the molecular mechanisms of hepatocarcinogenesis.
- Enables large-scale retrospective studies using archival liver tissue.
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