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Updated: May 26, 2026
Comprehensive Autopsy Program for Individuals with Multiple Sclerosis
Published on: July 19, 2019
Prospects of transcript profiling for mRNAs and MicroRNAs using formalin-fixed and paraffin-embedded dissected
Sylvia Eisele1, Markus Krumbholz, Marie-Therese Fischer
1Institute of Clinical Neuroimmunology, University Hospital Großhadern, Ludwig-Maximilians-University, Munich, Germany.
Abstract:
The elaboration of novel pathogenic aspects of multiple sclerosis (MS) requires the analysis of well-defined stages of lesion development. However, specimens of certain stages and lesion types are either present in small brain biopsies, insufficient in size for further molecular studies or available as formalin-fixed and paraffin-embedded (FFPE) material only. Therefore, application of current molecular biology techniques to FFPE tissue is warranted. We compared FFPE and frozen tissue by using quantitative polymerase chain reaction and report: (1) FFPE material is highly heterogeneous regarding the utility for transcript profiling of mRNAs; well-preserved FFPE samples had about a 100-fold reduced sensitivity compared with frozen tissue, but gave similar results for genes of sufficient abundance; (2) FFPE samples not suitable for mRNA analysis are still highly valuable for miRNA quantification; (3) the length of tissue fixation greatly affects utility for mRNA but not for miRNA analysis; (4) FFPE samples can be processed via a hot water bath for dissection of defined lesion areas; and (5) in situ hybridization for proteolipid protein (PLP) helps to identify samples not suitable for mRNA amplification. In summary, we present a detailed protocol how to use autoptic FFPE tissue for transcript profiling in dissected tissue areas.
Insights
Formalin-fixed and paraffin-embedded (FFPE) tissue offers valuable insights into multiple sclerosis (MS) pathology. While mRNA analysis is less sensitive in FFPE samples, miRNA quantification remains highly effective, enabling detailed transcript profiling in dissected lesion areas.
Area of Science:
- Neuroscience
- Molecular Biology
- Pathology
Background:
- Understanding multiple sclerosis (MS) requires analyzing distinct lesion development stages.
- Limited availability of fresh tissue necessitates molecular analysis of formalin-fixed and paraffin-embedded (FFPE) samples.
Purpose of the Study:
- To evaluate the utility of FFPE tissue for molecular analyses, specifically transcript profiling in multiple sclerosis (MS).
- To compare the efficacy of FFPE versus frozen tissue for mRNA and miRNA quantification.
Main Methods:
- Quantitative polymerase chain reaction (qPCR) was employed to compare FFPE and frozen tissues.
- In situ hybridization for proteolipid protein (PLP) was used to assess sample suitability.
- Hot water bath processing was utilized for dissecting specific lesion areas from FFPE samples.
Main Results:
- FFPE tissue exhibits heterogeneity for mRNA transcript profiling, with reduced sensitivity but comparable results for abundant genes compared to frozen tissue.
- FFPE samples unsuitable for mRNA analysis are valuable for miRNA quantification.
- Tissue fixation duration impacts mRNA utility but not miRNA analysis.
Conclusions:
- FFPE tissue can be effectively utilized for transcript profiling in dissected multiple sclerosis (MS) lesion areas.
- A detailed protocol is presented for processing autoptic FFPE tissue for molecular studies.
- FFPE tissue remains a valuable resource for studying MS pathogenesis when appropriate methods are applied.
