TNF-α Quantification in Formalin-Fixed Paraffin-Embedded Tissues as a Predictive Biomarker in Ulcerative Colitis

Objectives: Anti-TNF-α therapies have transformed the management of Inflammatory Bowel Disease (IBD), yet a substantial proportion of patients fail to respond, highlighting the urgent need for predictive biomarkers. Mucosal TNF-α mRNA quantification in fresh biopsies has shown promise but showed several problems for routine clinical use. This study aimed to validate a clinically feasible method for TNF-α quantification in formalin-fixed paraffin-embedded (FFPE) tissues and to assess its correlation with established measures of disease activity. Methods: FFPE and matched fresh-frozen biopsies from 54 ulcerative colitis patients were analyzed. Total RNA was extracted from FFPE sections, and TNF-α RNA was quantified by RT-qPCR and compared with fresh tissue expression levels. Molecular data were correlated with clinical (pMayo), endoscopic (Mayo Endoscopic Score, MES), and histological (Geboes) indices. Results: TNF-α expression in FFPE samples strongly correlated with fresh tissue levels (r = 0.83, p < 0.0001). High TNF-α expression in FFPE tissue was significantly associated with active endoscopic mucosal disease (MES ≥ 1; OR 28, 95% CI 3.31–237; p < 0.0001) and with histological inflammation (Geboes ≥ 3.1; OR 0.12, 95% CI 0.02–0.59; p = 0.009). Fresh tissue TNF-α levels showed similar associations. Clinical parameters such as age, sex, and pMayo score did not significantly correlate with mucosal TNF-α expression. RT-qPCR quantification of TNF-α in FFPE tissue is a reliable, cost-effective surrogate for fresh biopsy analysis and correlates strongly with endoscopic and histological disease activity. Conclusions: This method offers a practical approach for integrating molecular biomarkers into routine pathology workflows, supporting the implementation of personalized treatment strategies in IBD.