MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and...

Area of Science:

• Biomarker discovery
• Molecular diagnostics
• Cancer research

Background:

• Archival formalin-fixed paraffin-embedded (FFPE) tissues are valuable for microRNA (miRNA) biomarker identification.
• No standardized reference miRNAs exist for FFPE tissue normalization.
• This study addresses the need for stable reference miRNAs in FFPE samples from colorectal (CRC) and pancreatic (PC) cancer.

Purpose of the Study:

• Identify stable reference miRNAs for miRNA expression normalization in CRC and PC FFPE tissues.
• Quantify variability related to sample age and formalin fixation.
• Evaluate the impact of normalization strategies on data variability.

Main Methods:

• Utilized high-throughput miRNA profiling data from 203 CRC and 256 PC FFPE samples.
• Identified candidate reference miRNAs based on correlation with global mean expression.
• Analyzed miRNA stability, association with sample age, and fixation effects using regression and mixed-effects models.

Main Results:

• Identified miR-103a-3p as the most stable reference miRNA for both CRC and PC FFPE tissues.
• Determined optimal reference miRNA numbers: 4 for CRC, 10 for PC.
• Found formalin fixation decreased miRNA expression (30-65%), while sample age had a significant effect in PC but not CRC.

Conclusions:

• Established reliable reference miRNAs for miRNA expression studies in CRC and PC FFPE tissues.
• Formalin fixation substantially reduces miRNA expression.
• Sample age has a minimal clinical impact on miRNA expression in FFPE tissues.