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TNF-α Quantification in Formalin-Fixed Paraffin-Embedded Tissues as a Predictive Biomarker in Ulcerative Colitis.
Anna Viola1, Walter Giuseppe Giordano2, Rasmus Goll3
1Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy.
Diagnostics (Basel, Switzerland)
|December 11, 2025
Summary
Quantifying tumor necrosis factor-alpha (TNF-α) mRNA in formalin-fixed paraffin-embedded (FFPE) tissues is a reliable method for predicting Inflammatory Bowel Disease (IBD) activity. This cost-effective approach correlates with endoscopic and histological disease markers.
Area of Science:
- Gastroenterology and Hepatology
- Molecular Pathology
- Biomarker Discovery
Background:
- Anti-tumor necrosis factor-alpha (TNF-α) therapies are crucial for Inflammatory Bowel Disease (IBD) management.
- A significant portion of IBD patients do not respond to anti-TNF-α therapy, necessitating predictive biomarkers.
- Previous methods for quantifying mucosal TNF-α mRNA in fresh biopsies present challenges for routine clinical application.
Purpose of the Study:
- To validate a clinically feasible method for TNF-α quantification in formalin-fixed paraffin-embedded (FFPE) tissues.
- To assess the correlation between FFPE-derived TNF-α levels and established measures of IBD disease activity.
- To evaluate the utility of FFPE TNF-α quantification as a surrogate for fresh tissue analysis in IBD.
Main Methods:
- Analysis of matched FFPE and fresh-frozen biopsies from 54 ulcerative colitis patients.
- RNA extraction from FFPE sections and quantification of TNF-α mRNA using RT-qPCR.
- Correlation of molecular data with clinical (pMayo), endoscopic (Mayo Endoscopic Score, MES), and histological (Geboes) indices.
Main Results:
- Strong correlation between TNF-α expression in FFPE samples and fresh tissue levels (r = 0.83, p < 0.0001).
- High FFPE TNF-α expression significantly associated with active endoscopic disease (MES ≥ 1; OR 28) and histological inflammation (Geboes ≥ 3.1; OR 0.12).
- RT-qPCR quantification of TNF-α in FFPE tissue demonstrated reliability, cost-effectiveness, and strong correlation with disease activity indices.
Conclusions:
- FFPE TNF-α quantification is a valid and practical method for assessing IBD activity.
- This approach offers a cost-effective surrogate for fresh tissue analysis, integrating molecular biomarkers into routine pathology.
- The validated method supports personalized treatment strategies for IBD patients by providing reliable disease activity insights.
