Phone: 0032 (0)16 34 42 18 @ibdleuven @TARGID_KULEUVEN @bverstockt @SareVerstockt @gmatteoli1978 @JoaoPGSabino @ICleynen @saeedfc ABSTRACT 28 Patients with IBD are considered immunosuppressed, but do not seem more vulnerable for Nevertheless, intestinal inflammation has shown an important risk factor for SARS-CoV-2 infection and 30 prognosis. Therefore, we investigated the effect of intestinal inflammation on the viral intestinal entry 31 mechanisms, including ACE2, in IBD. 32We collected (un)inflamed mucosal biopsies from CD (n=193) and UC (n=158) patients, and 51 matched 33 non-IBD controls for RNA sequencing, differential gene expression and co-expression analysis. Organoids 34 from UC patients were subjected to an inflammatory mix and processed for RNA sequencing. Transmural 35 ileal biopsies were processed for single-cell (sc) sequencing. Publicly available colonic sc-RNA sequencing 36 data, and microarrays from tissue pre/post anti-TNF therapy, were analyzed. 37In inflamed CD ileum, ACE2 was significantly decreased compared to control ileum (p=4.6E-07), whereas 38 colonic ACE2 expression was higher in inflamed colon of CD/UC compared to control (p=8.3E-03; p=1.9E-39 03). Sc-RNA sequencing confirmed this ACE2 dysregulation, and exclusive epithelial ACE2 expression. 40Network analyses highlighted HNF4A as key regulator of ileal ACE2, while pro-inflammatory cytokines and 41 interferon regulating factors regulated colonic ACE2. Inflammatory stimuli upregulated ACE2 in UC 42 organoids (p=1.7E-02), not in non-IBD controls (p=9.1E-01). Anti-TNF therapy restored colonic ACE2 43 dysregulation in responders. 44Intestinal inflammation alters SARS-CoV-2 coreceptors in the intestine, with opposing effects in ileum and 45 colon. HNF4A, an IBD susceptibility gene, is an important upstream regulator of ACE2 in ileum, whereas 46 interferon signaling dominates in colon. Our data support the importance of adequate control of IBD in order 47 to reduce risk of (complicated) 49