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OP14 Extracellular RNAs as liquid biopsy non-invasive biomarker in IBD

Verstockt., B.(1,2);Verstockt, S.(2);Sabino, J.(1,2);Ferrante, M.(1,2);Vermeire, S.(1,2)

(1)University Hospitals Leuven, Dpt. Gastroenterology and Hepatology, Leuven, Belgium;(2)KU Leuven, Dpt. Chronic Diseases- Metabolism and Ageing- TARGID-IBD, Leuven, Belgium

Background

Extracellular RNAs (exRNAs) are RNA species present outside of the cells in which they were transcribed. They are found in human serum, though the exact role of circulating exRNAs remains to be established, especially in inflammatory bowel diseases (IBD). Besides their potential help in our pathophysiological understanding of disease, they might serve as liquid biopsies or non-invasive biomarkers.  We characterised exRNAs in serum from IBD patients, and questioned their potential in separating ulcerative colitis (UC) from Crohn’s disease (CD).

Methods

We carried out SILVER-seq (Small Input Liquid Volume Extracellular RNA-sequencing) on serum droplets (5-7ml) from a cross-sectional cohort of 26 IBD patients (15 UC, 11 CD) with active endoscopic disease (Mayo endoscopic sub score  or Simple Endoscopic Score for Crohn’s disease ) (Table 1). Normalization and differential expression were done using DESeq2 R package, co-expression network analyses performed using WGCNA (FDR adjusted p ≤0.05). Using randomized generalized linear modelling (RGLM), a diagnostic exRNA marker was designed to separate UC from CD samples (15 UC, 11 CD). 

Results

We detected 60,675 exRNAs in serum from IBD patients, capturing 76.1% of all genes expressed in intestinal tissue, and including highly abundant intestinal genes (e.g MUC2) and intestinal barrier genes (e.g claudin 8, occludin and RETNLB). Co-expression network analysis identified 69 clusters of which 1 significantly correlated with the distinction between CD and UC (FDR p=0.003, r=-0.70). One of the hub genes within this module (consisting of 148 genes, upregulated in UC) was GNA12 (p=2.3E-4, r=0.66 for correlation with the module eigengene), encoding for a membrane bound GTPase that plays a key role in tight junction assembly and has previously been identified as UC-specific SNP in GWAS (Figure 1). Serum GNA12 expression was not associated with faecal calprotectin (p=0.55, r=0.12), disease duration (p=0.24, r=0.25), age (p=0.43, r=0.16) or gender (p=1.0), but did correlate with other UC-specific genes including TNFRSF14 (p=0.04, r=0.4), HNF4A (p=0.04, r=-0.4) and CAMK2A (p=0.004, r=0.54). Through machine learning within the UC-specific module (containing 148 genes), we identified an 8-gene exRNA panel, including GNA12, that could accurately discriminate between UC and CD patients (accuracy 96.2%).

Figure 1: Visualisation of the identified exRNA network including GNA12

Conclusion

Liquid biopsies are a novel non-invasive tool in IBD biomarker development. Although larger in-depth studies are required to further validate, explore and characterise the potential of serum exRNAs in the field of IBD, the current pilot project identified a new non-invasive tool to accurately distinguish CD from UC patients.

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