miRNA profiling identifies biomarkers and regulatory networks involving TGF-β/T-cell pathways in food protein–induced enterocolitis syndrome

BACKGROUND: Acute food protein-induced enterocolitis syndrome (FPIES) is a potentially life-threatening, non-IgE-mediated food allergy that primarily affects young children. Currently, diagnosis relies on clinical presentation and oral food challenges, which carry inherent risks. Consequently, FPIES is often misdiagnosed, leading to unnecessary interventions and delayed management. Despite its clinical relevance, the molecular mechanisms underlying FPIES remain poorly understood. OBJECTIVE: We investigated the role of microRNAs (miRNAs) in FPIES and assessed their diagnostic potential. METHODS: We analyzed miRNA expression profiles in peripheral blood from 29 children with oral food challenge-confirmed moderate to severe FPIES reactions, collected on the challenge day at baseline (TP1), reaction onset (TP2), and 4 hours after reaction onset (TP3). Using a hybrid ensemble feature selection approach, we compared these profiles to those of 26 children with acute gastroenteritis and sepsis to identify FPIES-specific miRNA signatures. RESULTS: Longitudinal analysis revealed an early heterogeneous miRNA response that evolved into a more consistent profile in TP3, suggesting a dynamic and evolving regulatory response. Eleven miRNAs emerged as key regulators, highlighting pathways partially shared with other allergic and inflammatory conditions. In silico pathway analysis identified TGF-β signaling and T-cell differentiation as candidate pathways potentially involved in FPIES. Importantly, we discovered and validated 26 miRNAs signatures that accurately distinguish FPIES from sepsis and acute gastroenteritis, including a minimal 2-miRNA diagnostic signature (area under the curve = 0.98). miRNA-29a correlated with severe FPIES reactions, suggesting involvement in severity mechanisms. CONCLUSION: Our study reveals novel miRNA-mediated mechanisms in FPIES and identifies candidate biomarkers with diagnostic utility, paving the way for new molecular tools and therapeutic strategies.