Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.

Area of Science:

• Molecular Biology
• Histopathology
• Biotechnology

Background:

• Formalin-fixed, paraffin-embedded (FFPE) tissues are standard for clinical diagnostics but yield compromised nucleic acid (NA) quality.
• Existing NA isolation protocols for aged FFPE tissues require improvement for reliable molecular analysis.

Purpose of the Study:

• To compare the efficiency of various NA extraction methods for FFPE tissues of varying age and origin.
• To identify optimal protocols for maximizing NA yield and purity for downstream applications.

Main Methods:

• Evaluated multiple NA extraction methods on FFPE tissues of diverse age and origin.
• Assessed NA purity and amplicon length using phenol-chloroform isoamyl alcohol (PCI) and a commercial Qiagen protocol.
• Developed and tested a rapid 1-hour tissue lysis procedure for DNA extraction.
• Analyzed DNA quality using single and multiplex PCR, and RNA integrity using RNA integrity numbers (RIN).

Main Results:

• PCI and Qiagen protocols provided the highest NA purity.
• PCI protocol successfully amplified the longest DNA fragments from FFPE samples dating back to the 1970s.
• The 1-hour lysis protocol was time- and cost-effective, yielding slightly shorter amplicons but enabling successful amplification of single-copy genes.
• Isolated RNA, though degraded, had RIN values above the acceptable threshold of 1.4.

Conclusions:

• Optimized NA extraction methods, including PCI and Qiagen protocols, can yield high-quality nucleic acids from aged FFPE tissues.
• A rapid 1-hour lysis procedure is a viable, efficient alternative for DNA extraction from FFPE samples for routine molecular analyses.
• Nucleic acids from FFPE tissues over 40 years old can be successfully utilized for molecular analyses, depending on the specific application.