Background and Aims The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication within enterocytes. Methods Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation and IBD treatment. Results A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and non-biologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. Additionally, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. Conclusions These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19.

Background & Aims Severe forms of inflammatory bowel disease (IBD) that develop in very young children can be caused by variants in a single gene. We performed whole-exome sequence (WES) analysis to identify genetic factors that might cause granulomatous colitis and severe perianal disease, with recurrent bacterial and viral infections, in an infant of consanguineous parents. Methods We performed targeted WES analysis of DNA collected from the patient and her parents. We validated our findings by a similar analysis of DNA from 150 patients with very early onset IBD not associated with known genetic factors analyzed in Toronto, Oxford, and Munich. We compared gene expression signatures in inflamed vs. non-inflamed intestinal and rectal tissues collected from patients with treatment-resistant Crohn's disease who participated in a trial of ustekinumab. We performed functional studies of identified variants in primary cells from patients and cell culture. Results We identified a homozygous variant in the tripartite motif containing 22 gene (TRIM22) of the patient, as well as in 2 patients with a disease similar phenotype. Functional studies showed that the variant disrupted the ability of TRIM22 to regulate nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and NF-κB. Computational studies demonstrated a correlation between the TRIM22–NOD2 network and signaling pathways and genetic factors associated very early onset and adult-onset IBD. The network also associated with antiviral and mycobacterial effectors and markers of inflammation such as fecal calprotectin, c-reactive protein, and Crohn's disease activity index scores. Conclusion In WES and targeted exome sequence analyses of an infant with severe IBD, characterized by granulomatous colitis and severe perianal disease, we identified a homozygous variant of TRIM22 that affect the ability of its product to regulate NOD2. Combined computational and functional studies showed that the TRIM22–NOD2 network regulates antiviral and anti-bacterial signaling pathways that contribute to inflammation. Further study of this network could lead to new disease markers and therapeutic targets for patients with very early and adult-onset IBD.

Immune dysregulation and cytokine release syndrome have emerged as pathological hallmarks of severe Coronavirus Disease 2019 , leading to the evaluation of cytokine antagonists as therapeutic agents. A number of immune-directed therapies being considered for COVID-19 patients are already in clinical use in chronic inflammatory conditions like inflammatory bowel disease (IBD). These considerations led us to systematically examine the intersections between COVID-19 and the GI tract during health and intestinal inflammation. We have observed that IBD medications, both biologic and nonbiologic, do not significantly impact ACE2 and TMPRSS2 expression in the uninflamed intestines.Additionally, by comparing SARS CoV2-induced epithelial gene signatures with IBD-associated genes, we have identified a shared molecular subnetwork between COVID-19 and IBD. These data generate a novel appreciation of the confluence of COVID-19-and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19. nearest neighbor. The most connected subnetworks were then extracted to generate model-specific SARS-CoV-2 infection-; IBD inflammation-; or drug-response associated subnetworks. Genes common between these networks were determined and tested for enrichment to various genesets using the Fisher's exact test and p-values were adjusted using Benjamini-Hochberg (BH) procedure. Pathway and geneset enrichment analysis of subnetworks:Gene subnetworks were tested for functional enrichment using a Fisher's exact test with BH multiple test correction on a collection of gene sets. The collection of gene sets included i) Reactome pathways sourced from Enrichr 31 , i) genesets from Smillie et al 32 , ii) Huang et al 33 , iii) various macrophage perturbations (e.g. cytokines) 34 , iv) ACE2 co-expressed genes 35 and v) reported IBD GWAS genes (see supplementary methods). Key driver gene analysis:7 Key driver analysis (KDA) identifies key or "master" driver genes for a given gene set in a given BGRN. We used a previously described KDA algorithm 36 which is summarized in supplementary methods.Genesets for KDA included those associated with NHBE-COVID-19 infection or IBD inflammation. Key driver genes (KDGs) were summarized by frequency across the networks/genesets tested. Geneset variation analysis of SARS-CoV-2-infection gene expression signatures:We employed the epithelial model-COVID-19 response gene signatures (adjusted p value <0.05) in a gene set variation analysis (GSVA) using gene expression data from MSCCR and CERTIFI cohorts. For each gene set (up or down-regulated), GSVA was used to obtain a sample-wise enrichment score, that were then used for hypothesis testing with respect to phenotype information.

Aims Fibromuscular dysplasia (FMD) is a poorly understood disease that predominantly affects women during middle-life, with features that include stenosis, aneurysm, and dissection of medium-large arteries. Recently, plasma proteomics has emerged as an important means to understand cardiovascular diseases. Our objectives were: (i) to characterize plasma proteins and determine if any exhibit differential abundance in FMD subjects vs. matched healthy controls and (ii) to leverage these protein data to conduct systems analyses to provide biologic insights on FMD, and explore if this could be developed into a blood-based FMD test. Methods and results Females with ‘multifocal’ FMD and matched healthy controls underwent clinical phenotyping, dermal biopsy, and blood draw. Using dual-capture proximity extension assay and nuclear magnetic resonance-spectroscopy, we evaluated plasma levels of 981 proteins and 31 lipid sub-classes, respectively. In a discovery cohort (Ncases = 90, Ncontrols = 100), we identified 105 proteins and 16 lipid sub-classes (predominantly triglycerides and fatty acids) with differential plasma abundance in FMD cases vs. controls. In an independent cohort (Ncases = 23, Ncontrols = 28), we successfully validated 37 plasma proteins and 10 lipid sub-classes with differential abundance. Among these, 5/37 proteins exhibited genetic control and Bayesian analyses identified 3 of these as potential upstream drivers of FMD. In a 3rd cohort (Ncases = 506, Ncontrols = 876) the genetic locus of one of these upstream disease drivers, CD2-associated protein (CD2AP), was independently validated as being associated with risk of having FMD (odds ratios  = 1.36; P = 0.0003). Immune-fluorescence staining identified that CD2AP is expressed by the endothelium of medium-large arteries. Finally, machine learning trained on the discovery cohort was used to develop a test for FMD. When independently applied to the validation cohort, the test showed a c-statistic of 0.73 and sensitivity of 78.3%. Conclusion FMD exhibits a plasma proteogenomic and lipid signature that includes potential causative disease drivers, and which holds promise for developing a blood-based test for this disease.