Quantitative RNA assessment and long-term stability in the FFPE tumor samples using Digital Spatial Profiler

Area of Science:

• Biomolecular analysis
• Molecular pathology
• Cancer research

Background:

• Long-term storage of tissue slides can degrade RNA and protein biomarkers.
• Formalin-fixed and paraffin-embedded (FFPE) tissue sections are commonly used in diagnostics.
• Understanding RNA quality preservation during storage is crucial for accurate biomarker analysis.

Purpose of the Study:

• To evaluate the impact of long-term storage duration (0-36 weeks) and pre-storage treatment (non-paraffin vs. paraffin dipping) on RNA quality in FFPE tissue sections.
• To assess the performance of NanoString GeoMx Digital Spatial Profiling (DSP) for RNA analysis in FFPE samples under different storage conditions.

Main Methods:

• Human bladder cancer FFPE tissue sections were stored at 4°C for 0, 16, 24, and 36 weeks.
• Two treatment conditions were applied: non-paraffin dipping and paraffin dipping.
• RNA was profiled using NanoString GeoMx DSP to quantify RNA targets.

Main Results:

• Excellent consistency in quantitative DSP RNA counts was observed between treatment conditions (R > 0.97) and across storage time points (R > 0.96).
• No significant difference was found in the percentage of target genes with sufficient signal between treatment conditions at any time point.
• RNA signal remained robust and reproducible across all tested storage durations (up to 36 weeks) and treatment conditions.

Conclusions:

• The NanoString GeoMx DSP platform demonstrates robust and reproducible RNA profiling from FFPE tissue sections stored at 4°C for up to 36 weeks.
• Both non-paraffin and paraffin dipping methods yield comparable RNA results in terms of reproducibility and signal preservation.
• Paraffin dipping is recommended for optimizing sample storage and generating reproducible RNA results.