Circulating microRNAs as biomarkers of disease activity and treatment response in Crohn’s disease patients receiving infliximab or vedolizumab: a longitudinal cohort study

Background: Crohn's disease (CD) is a chronic transmural inflammatory disorder with heterogeneous response to biologic therapies. Faecal calprotectin and C-reactive protein, the dominant non-invasive biomarkers in current practice, have well-recognized limitations in predicting treatment outcomes, distinguishing inflammatory from fibrostenotic disease behaviour and capturing transmural disease biology. Circulating microRNAs (miRNAs) have emerged as candidate biomarkers owing to their stability in blood and biological relevance to immune and barrier function, yet longitudinal data linking serum miRNA levels to biologic induction outcomes remain scarce. Aims: To evaluate whether serum miRNAs track disease activity and predict clinical, biochemical, and endoscopic outcomes during biologic induction in CD, and to determine whether they provide information complementary to established non-invasive biomarkers. Materials and Methods: A prospective single-centre cohort study enrolled 39 adults with active CD initiating infliximab (n = 20) or vedolizumab (n = 19) and 10 healthy controls. Serum was collected at the first and fourth infusions. Six pre-specified target miRNAs were quantified by reverse transcription quantitative PCR (RT-qPCR) and normalized to the geometric mean of miR-93-5p and miR-425-5p. Harvey–Bradshaw Index (HBI), C-reactive protein (CRP) and faecal calprotectin (FC) were recorded at baseline, post-induction, and 12 months; Simple Endoscopic Score for CD (SES-CD) was assessed at baseline and 12 months where clinically indicated. Four pre-specified analysis families were tested with Benjamini–Hochberg false discovery rate (FDR) correction for multiple testing; statistical significance is reported as q-values (FDR-adjusted p-values). Sensitivity analyses included severity adjustment, leave-one-out stability, and single-reference normalisation. Results: Serum miR-21-5p and miR-146b-5p were significantly reduced in CD patients versus healthy controls (q < 0.05). Post-induction miR-424-5p correlated with concurrent faecal calprotectin (Spearman ρ = +0.52, q = 0.004) and CRP (ρ = +0.44, q = 0.030), with associations robust to severity adjustment, leave-one-out removal, and single-reference normalisation. Baseline miR-146b-5p and miR-106a-5p inversely predicted post-induction CRP independently of baseline disease severity. An exploratory post-hoc analysis identified an association between treatment-induced miR-106a-5p upregulation and the Montreal B3 (penetrating) phenotype (permutation p = 0.019). Conclusions: Serum miRNAs exhibited both concurrent biomarker potential (post induction miR 424 5p) and predictive capacity (baseline miR 146b 5p and miR-106a-5p), providing information complementary to faecal calprotectin. The observed relationship between miR 106a 5p dynamics during biologic induction and penetrating disease behaviour suggests a mechanistic link between miRNA response and disease phenotype that warrants prospective evaluation. These findings identify candidate miRNA biomarkers that should be validated in independent, multicentre cohorts before clinical application.