Related Experiment Video
Updated: Apr 19, 2026
Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens
Published on: May 5, 2018
Analysis of microRNA from archived formalin-fixed paraffin-embedded specimens of amyotrophic lateral sclerosis
Koichi Wakabayashi1, Fumiaki Mori2, Akiyoshi Kakita3
1Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Japan. koichi@cc.hirosaki-u.ac.jp.
Background:
MicroRNAs (miRNAs) are noncoding small RNAs that regulate gene expression. This study investigated whether formalin-fixed paraffin-embedded (FFPE) specimens from postmortem cases of neurodegenerative disorders would be suitable for miRNA profiling.
Results:
Ten FFPE samples from 6 cases of amyotrophic lateral sclerosis (ALS) and 4 neurologically normal controls were selected for miRNA analysis on the basis of the following criteria for RNA quality: (i) a postmortem interval of less than 6 hours, (ii) a formalin fixation time of less than 4 weeks, (iii) an RNA yield per sample of more than 500 ng, and (iv) sufficient quality of the RNA agarose gel image. An overall RNA extraction success rate was 46.2%. For ALS, a total of 364 miRNAs were identified in the motor cortex, 91 being up-regulated and 233 down-regulated. Target genes were predicted using miRNA bioinformatics software, and the data applied to ontology analysis. This indicated that one of the miRNAs up-regulated in ALS (miR-338-3p) had already been identified in leukocytes, serum, cerebrospinal fluid and frozen spinal cord from ALS patients.
Conclusion:
Although analysis was possible for just under half of the specimens examined, we were able to show that informative miRNA data can be derived from archived FFPE samples from postmortem cases of neurodegenerative disorders.
Insights
Formalin-fixed paraffin-embedded (FFPE) samples from neurodegenerative disease cases can yield informative microRNA (miRNA) data. This study successfully profiled miRNAs in amyotrophic lateral sclerosis (ALS) FFPE tissues, identifying significant changes.
Area of Science:
- Molecular Biology
- Neuroscience
- Genetics
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression.
- Formalin-fixed paraffin-embedded (FFPE) tissues are common archival specimens.
- The suitability of FFPE for miRNA profiling in neurodegenerative disorders was unexplored.
Purpose of the Study:
- To assess the feasibility of miRNA profiling in postmortem FFPE specimens from neurodegenerative disease cases.
- To identify differentially expressed miRNAs in the motor cortex of amyotrophic lateral sclerosis (ALS) patients compared to controls.
Main Methods:
- Selected FFPE samples based on strict RNA quality criteria (short postmortem interval, fixation time, RNA yield).
- Performed miRNA profiling on extracted RNA using established techniques.
- Utilized bioinformatics and ontology analysis to predict miRNA targets and pathways.
Main Results:
- Achieved a 46.2% RNA extraction success rate from FFPE samples.
- Identified 364 miRNAs in ALS motor cortex, with 91 up-regulated and 233 down-regulated.
- Confirmed a previously identified ALS-associated miRNA (miR-338-3p) in FFPE samples.
Conclusions:
- Informative miRNA data can be obtained from archived FFPE samples of neurodegenerative disorders.
- Despite extraction challenges, FFPE tissues are a viable source for miRNA research.
- This validates FFPE as a valuable resource for retrospective miRNA studies in neurological diseases.
