P0162 Distinct mucin RNA isoform expression in the blood of Inflammatory Bowel Disease patients with variable degree of inflammation
Authors: Arras W , Jauregui-Amezaga A , Oosterlinck B , Macken E , Somers M , De Man J , De Winter B , Smet A ,   Laboratory of experimental medicine and pediatrics
Published: January 2025

Abstract

Background
Mucosal healing is considered as a key therapeutic endpoint in inflammatory bowel diseases (IBD) and comprises endoscopic improvement of inflammation without taking barrier healing into account. Mucins are critical components of the intestinal mucosal barrier function that give rise to structurally diverse isoforms. In a recent study, we demonstrated that intestinal region-specific mucin RNA isoform expression captured the heterogeneity of the IBD patient population and showed great potential to indicate barrier function enhancing IBD management [1]. Given that epithelial cells can enter the bloodstream because of epithelial barrier injury upon inflammation, we further investigated whether intestinal-type mucin RNA isoforms have the potential as non-invasive biomarkers for IBD disease monitoring.

Methods
Using bulk RNA sequencing data (Illumina) mapped to our recently designed mucin RNA isoform landscape [1], we assessed mucin RNA isoform expression in the blood from 45 IBD patients (22 UC, 23 CD) and 19 controls and correlated the data to clinical outcome parameters (i.e. endoscopic activity (Mayo or SES-CD), inflamed intestinal region, histological activity (Geboes score), C-reactive protein level). Additionally, random forest-based feature selection, using a publicly available dataset (PRJNA774251), was carried out to select peripheral mucin RNA isoforms that accurately stratified UC patients (n=79) from controls (n=209).

Results
Overall, expression of MUC1, MUC4, MUC6, MUC12, MUC12-AS1, MUC16, MUC20, MUC20P1, and MUC20-OT1 mRNA was identified in the blood of IBD and control patients, with MUC1, MUC20 and MUC20-OT1 being abundantly present in both cohorts. At mucin RNA isoform level, 50 originated from the intestinal mucin RNA isoform landscape [1] with RNA isoforms derived from MUC20 and MUC20-OT1 classified as the top 10 most predominantly expressed isoforms. Interestingly, expression of several MUC20-OT1 RNA isoforms was decreased in UC or CD patients with moderate to severe inflammation compared to controls (Figure 1). In addition, four MUC20-OT1 isoforms and two MUC20 were correlated to the endoscopic inflammation score. Feature selection based on random forest modeling to distinguish UC patients with moderate to severe inflammation from controls unveiled a panel of 5 mucin RNA isoforms (MUC6 (ENST00000421673.7), MUC20-OT1(ENST00000429897.5), MUC4(ENST00000467235.1), MUC20-OT1(ENST00000626852.2) and MUC5AC(PB.2811.15); area under the curve of 75.7% (train set) and 60.3% (test set); Figure 2).

Conclusion
Peripheral blood mucin RNA isoform expression can be monitored in IBD patients, with MUC20-OT1 RNA isoforms as potential non-invasive biomarkers for intestinal barrier dysfunction.

References
[1]Arras, W., Breugelmans, T., Oosterlinck, B., De Man, J. G., Malhotra-Kumar, S., Abrams, S., ... & Smet, A. (2024). The intestinal mucin isoform landscape reveals region-specific biomarker panels for inflammatory bowel disease patient stratification. Journal of Crohn’s and Colitis, jjae155.