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Cell Type-specific Gene Expression Profiling in the Mouse Liver
Published on: September 17, 2019
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval
Sayaka Sobue1, Keita Sakata2, Yuki Sekijima3
1Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan.
Experimental and Molecular Pathology
|May 18, 2016
Summary
Postmortem tissue RNA remains viable for gene expression analysis up to 18 hours after death. Despite maintained RNA quality, some gene expression changes observed via microarray analysis were not validated, indicating potential postmortem modifications.
Area of Science:
- Molecular Biology
- Genomics
- Pathology
Background:
- Establishing autopsy tissue banks is crucial for disease research.
- Understanding postmortem RNA stability is vital for accurate gene expression profiling.
Purpose of the Study:
- To determine the duration of RNA availability for microarray analysis in postmortem tissues.
- To characterize gene expression profiles of up- and down-regulated genes during the postmortem interval.
Main Methods:
- RNA extraction from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) mouse brains and livers at different postmortem intervals (0h, 3h, 18h).
- Microarray analysis to identify differentially expressed genes (>1.3-fold or <0.77-fold).
- Hierarchical cluster analysis and DAVID gene ontology analysis for gene classification.
Main Results:
- RNA quality was maintained in brain and liver tissues up to 18 hours postmortem.
- Cytoskeleton-related genes were enriched among up-regulated genes.
- Serine protease inhibitors were enriched among down-regulated genes.
- High RNA integrity number (RIN) did not guarantee validation of up-regulated genes by quantitative PCR, suggesting potential fragmentation or modification.
Conclusions:
- Gene expression profiles reflecting disease pathology can be analyzed from postmortem tissues under typical autopsy conditions.
- Awareness of postmortem gene expression fluctuations is essential for accurate interpretation of results.
- Further investigation is needed to understand the mechanisms behind unvalidated gene expression changes.
