Exploratory transcriptomic analysis suggests candidate genes associated with loss of response to ustekinumab in Crohn’s disease

Background Despite the favorable safety and efficacy of ustekinumab in clinical practice for Crohn’s disease, a subset of Crohn’s disease patients still experience loss of response to this treatment. This study was thus conducted to investigate the differential gene expression underlying ustekinumab loss of response in Crohn’s disease patients. Methods This prospective study, grouped by response to ustekinumab, collected peripheral blood mononuclear cells from refractory moderate-to-severe adult Crohn’s disease patients (8 vs. 9) who were admitted to the Second Affiliated Hospital of Guangzhou Medical University and received initial ustekinumab treatment between January 2024 and June 2025 for RNA sequencing. For exploratory pathway analysis, differentially expressed genes identified by DESeq2 using exploratory thresholds (|FC| > 1.5, P < 0.05) were subjected to GO and KEGG enrichment, WGCNA, and PPI network analyses. Additionally, another 16 patients were included for the preliminary validation of candidate genes by qPCR. Furthermore, we conducted a clinical influence factor analysis on 81 patients who had already received medication. Results RNA sequencing identified 510 differentially expressed genes between ustekinumab responders and non-responders. Trait association analysis showed that the cyan module was the module most strongly associated with both ustekinumab non-response and stricturing behavior, consistent with the independent influence of stricturing behavior identified in the retrospective clinical study. This module was enriched in platelet activation, neutrophil extracellular trap formation, and focal adhesion (KEGG), as well as coagulation and platelet aggregation (GO). Among the 10 candidate genes selected for validation, FFAR2, ITGA2B, SOCS3, and KCNJ15 exhibited statistically significant differential expression. Conclusion Our findings suggest that loss of response may be potentially associated with pro-inflammatory pathways independent of the drug’s action pathways, as well as a “pro-fibrotic immune microenvironment” linked to intestinal strictures. Additionally, preliminary validation indicated that FFAR2, ITGA2B, SOCS3, and KCNJ15 may provide new perspectives for candidate differentially expressed genes associated with ustekinumab loss of response.