Reliable Gene Expression Profiling from Small and Hematoxylin and Eosin-Stained Clinical Formalin-Fixed,...

Area of Science:

• Oncology
• Molecular Biology
• Biomarker Discovery

Background:

• Clinical biomarker studies face challenges with limited or poor-quality biological specimens.
• Formalin-fixed, paraffin-embedded (FFPE) tissue is a common archival source but often difficult to analyze.
• EdgeSeq offers a solution for transcriptomics analysis from small or challenging FFPE samples.

Purpose of the Study:

• To evaluate the EdgeSeq platform for analyzing gene expression profiles from stained FFPE tissue.
• To assess the impact of hematoxylin and eosin (H&E) and immunohistochemistry (IHC) staining on FFPE transcriptomics.
• To determine the feasibility of using EdgeSeq for small FFPE sample analysis.

Main Methods:

• EdgeSeq, a transcriptomics platform using quantitative nuclease protection assay and next-generation sequencing, was applied to unstained and stained FFPE slides (H&E and IHC) from lung cancer patients.
• Gene expression profiles were compared between stained and unstained slides.
• Analysis included assessing correlation coefficients and gene signature scores, as well as evaluating performance on small FFPE sample equivalents.

Main Results:

• Gene expression profiles from H&E-stained slides showed high correlation (0.86-0.97) with unstained slides, while IHC staining showed lower correlation (0.21-0.56).
• A 25-gene interferon-γ signature score correlated highly (0.92) with H&E-stained slides and showed significant correlation with immune scores.
• EdgeSeq demonstrated reliable performance on small FFPE sample equivalents (≥0.31 mm²), with alignment rates >69% and correlation coefficients ≥0.87.

Conclusions:

• EdgeSeq can successfully profile gene expression from small and H&E-stained FFPE tumor specimens.
• The platform enables biomarker data acquisition from limited tissue for oncology clinical trials.
• EdgeSeq facilitates research into the tumor microenvironment and immune cell interactions at the locoregional level.