GeoMx and RNAscope: A Comparative Assessment of Their Utility for Spatial mRNA Expression Profiling in Formalin-Fixed...

Area of Science:

• Biomedical research
• Molecular pathology
• Cancer genomics

Background:

• Accurate mRNA expression analysis in formalin-fixed tissues is crucial for biomarker discovery and understanding the tumor microenvironment.
• High-plex spatial transcriptomics (NanoString GeoMx) and in situ hybridization (RNAscope) are key technologies for this analysis.

Purpose of the Study:

• To compare quantitative mRNA expression estimates between NanoString GeoMx Digital Spatial Profiler and RNAscope in mammary cancer tissues.
• To evaluate the correlation and performance characteristics of both platforms for biomarker assessment.

Main Methods:

• Serial tissue sections from mammary cancer TMAs were analyzed using GeoMx Cancer Transcriptomics Atlas (CTA) and RNAscope probes for GATA3, SOX10, and PD-L1.
• Expression was quantified as counts/cell (GeoMx) and average dots/cell (RNAscope).
• Positivity thresholds were established for each method.

Main Results:

• A high correlation was observed for GATA3 (R=0.87) and SOX10 (R=0.77) expression between GeoMx and RNAscope.
• RNAscope demonstrated higher sensitivity and a broader dynamic range compared to GeoMx.
• PD-L1 analysis was limited due to localized high expression.

Conclusions:

• NanoString GeoMx CTA and RNAscope exhibit strong quantitative correlation for mRNA expression analysis in breast cancer.
• GeoMx is suitable for highly multiplexed gene expression profiling, whereas RNAscope excels in sensitivity and single-cell resolution.
• Method selection should align with specific research objectives in spatial transcriptomics.