Discovery of intestinal mRNA expression profiles correlated with mucosal healing of ustekinumab patients with Crohn’s disease: bioinformatics analysis and prospective cohort validation

Abstract

Abstract Background: Variations existed in responses to ustekinumab (UST) treatment in patients with Crohn's disease (CD), but the underlying cause remains unknown. Our objective was to investigate the involvement of immune cells and identify potential biomarkers that can predict the response to IL 12/23 inhibitors in patients with CD. Methods: GSE207022 dataset was analyzed, which consisted of 54 non-responders and 9 responders to UST in CD cohort. Differentially expressed genes (DEGs) were identified,followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. LASSO (Least absolute shrinkage and selection operator) regression was used to further screen the most powerful hub genes. ROC curve analysis was employed to evaluate the predictive performances of these genes. ssGSEA was used to estimate the proportion of immune cell types. These significantly altered genes were further subjected to clustering analysis into immune cell-related infiltration. To validate the reliability of the candidates, patients prescribed with UST as the first line biologics in a prospective cohort were included as an independent validation dataset. Results: A total of 99 DEGs were obtained from the integrated dataset. Analyses of GO and KEGG revealed a significant enrichment of immune response pathways in CD patients. Thirteen genes (SOCS3, CD55, KDM5D, IGFBP5, LCN2, SLC15A1, XPNPEP2, HLA-DQA2, HMGCS2, DDX3Y, ITGB2, CDKN2B and HLA-DQA1) which were primarily associated with the response versus non-response patients were identified and included to conduct the LASSO model. These genes accurately predicted treatment response with an area under the curve (AUC) of 0.938. Non-response individuals exhibited a relatively high Th1 cell polarization. Both LCN2 and KDM5D genes showed positive correlations with Th1 cells. Furthermore, we validated LCN2 and KDM5D genes as effective predictive markers using independent validation datasets and preliminary experimental verification. Conclusions: Th1 cell polarization was an important cause of non-response to UST therapy in CD patients. LCN2 and KDM5D could be used as predictive markers to identify non-response patients effectively. Trial registration: Trial registration number: NCT05542459; Date of registration: 2022-09-14; URL: https://www.clinicaltrials.gov.