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Background Ulcerative colitis (UC) is a chronic inflammatory condition affecting the colonic epithelium, with potential roles for the inflammasome, complement activation, T cells, and the microbiome in pathogenesis. We applied an established method of microarray-based gene expression analysis to a set of 128 UC biopsies (from 113 patients), to elucidate the molecular changes associated with active UC. Aims Our aim was to describe the molecules most associated with UC disease activity (the endoscopic Mayo score) and to annotate these molecules into biological processes. Methods 128 UC colonic biopsies were collected at the University of Alberta Hospital (Edmonton, Alberta) and Cedars-Sinai Hospital (Los Angeles, California) during standard of care colonoscopy. Biopsies were processed using Affymetrix microarrays. Gene expression data from the population was visualized using volcano plots (showing fold change and association between genes and endoscopic Mayo score), and heatmaps (showing expression of the top 30 genes in a previously established cell panel). Overexpression of top genes was analyzed using Gene Ontology and KEGG pathways. Results The volcano plot (Figure 1A) showed strong associations between the endoscopic Mayo score and components of innate immunity, e.g. complement factor B (CFB), C1-inhibitor (also known as SERPING1), chitinase 3-like 1 (CHI3L1), and inflammasome genes (ZBP1 and PIM2). Moderate associations with calprotectin (S100A8 and S100A9), other inflammasome components (CASP1 and NLRP3), and T cell transcripts (i.e. CTLA4, PDL1) were observed. Targets of biologic therapy (TNFA, ITGA4/B7, IL12B) were weakly associated with the endoscopic Mayo score. Expression of the top genes in a cell panel (Figure 1B) showed primary expression in monocytes, macrophages, dendritic cells, and polymorphonucleocytes, with some expression in colon epithelial and endothelial cells. Minimal expression was found in CD4/CD8 T cells or NK cells. Pathway analysis represented extracellular matrix remodeling, complement regulation, and TNFA signaling, but revealed no pathways associated with adaptive immunity (Table 1). Conclusions UC disease activity, as assessed by the endoscopic Mayo score, was strongly associated with tissue remodeling and molecules of innate immunity that were largely found in myeloid cells, colon epithelium, and endothelium. Cognate T cells were not dominant features of UC disease activity. These data suggest that the driver of ongoing UC activity is independent of the cognate T cell response. Funding Agencies None

Background Eosinophilic esophagitis (EoE) is a complex, chronic, allergic disease that commonly presents as dysphagia in young adults. Co-occurring allergic or atopic disease, including food allergies and asthma are seen in approximately 70% of cases. Allergy to house dust mite (HDM) tropomyosin, Der p 10, and cross-reactivity to shrimp has been well described. We discuss a presentation of EoE in the setting of positive HDM skin prick testing that subsequently improved with dietary elimination of shrimp, that has never been described in the literature. Purpose To highlight an underlying mechanism in EoE and the importance of a multidisciplinary approach to this disease. Method A 45-year-old male with a medical history significant for ulcerative colitis (diagnosed two years prior and maintained in deep endoscopic remission with adalimumab) and asthma (with seasonal, rare usage of budesonide and formoterol inhaler) was seen by his outpatient gastroenterologist following three weeks of new-onset dysphagia and subjective intermittent food bolus impaction. The patient was pre-emptively started on daily proton pump inhibitor prior to endoscopy, but discontinued this within less than two weeks as he felt like it induced loose bowel movements. Esophagogastroduodenoscopy (EGD) was performed and revealed proximal esophageal furrows. Histology of esophageal biopsies was compatible with EoE: distal esophagus >100 eosinophils/hpf with eosinophil degranulation, mid and proximal esophagus >25 eosinophils/hpf with eosinophil degranulation. The patient self-identified that his episodes of dysphagia and food bolus impaction were associated with shrimp ingestion, thus he eliminated shrimp from his diet. Result(s) Two-month clinical follow-up demonstrated symptomatic remission despite no other active treatment or additional food elimination. Consultation with an allergist demonstrated the patient had positive skin prick testing to HDM (Dermatophagoides pteronyssinus and farina) but negative testing to shrimp, despite clinical improvement with dietary shrimp elimination. Thus his EoE was attributed to HDM cross-reactivity, specifically to the Der p 10 antigen. Follow-up EGD and biopsy to confirm endoscopic and histologic remission with shrimp elimination is scheduled in two months. Conclusion(s) This is the first case description of a patient with new onset EoE attributed to Der p 10, in the setting of positive skin prick to HDM and negative skin prick to shrimp, with subsequent symptomatic resolution of EoE following dietary shrimp elimination. Shrimp and HDM share a protein, Der p 10. Der p 10 is commonly the culprit antigen in patients that have allergic reactions to HDM and (or) shrimp, but often only demonstrate positive skin prick testing to HDM (with negative testing to shrimp). This case demonstrates a role for involvement of an allergist and skin prick testing in select cases of EoE, as this may result in a relatively simple food elimination and avoidance of further therapeutic interventions. Please acknowledge all funding agencies by checking the applicable boxes below None Disclosure of Interest None Declared

Background Ulcerative colitis (UC) is a chronic inflammatory condition affecting the colonic epithelium. We used an established microarray-based system to analyze a set of 128 UC biopsies (113 patients), assessing gene expression associated with the colon’s response to injury in UC. Aims Our aim was to describe the burden of injury in UC biopsies and to explore molecular heterogeneity across disease activity, as assessed by the endoscopic Mayo score. Methods 128 UC colon biopsies were collected at the University of Alberta Hospital (Edmonton, AB) and Cedars-Sinai Hospital (Los Angeles, CA) during standard of care colonoscopy and processed using Affymetrix microarrays. Principal component analysis (PCA) and archetypal analysis (AA) visualized relationships between biopsies and previously annotated injury-associated transcript sets. AA assigned each biopsy to one of three groups, and scores to each biopsy relating it to all three groups. Results Spearman correlations (Table 1A) were highest between the endoscopic Mayo score and the injury-repair-associated transcripts (IRRAT, 0.64, P=4.7x10-16), immunoglobulin transcripts highly associated with chronic injury and fibrosis (IGT, 0.63, P=3.0x10-15), endothelial transcripts (ENDAT, 0.61, P=1.8x10-14), and parenchymal dedifferentiation i.e. epithelial solute carrier loss (CT2, -0.60, P=6.5x10-14). PCA separated injury from no injury in PC1 (Figure 1A). T cell transcripts (QCATs), interferon-gamma inducible transcripts (GRITs) and targets of biologics (IL12, TNFA, ITGA4/B7) separated from injury transcripts in PC2. We assigned three AA groups and visualized biopsies in PCA (Figure 1B, colored by AA membership). Group 1 (grey, N=44) biopsies had little parenchymal dedifferentiation and low expression of injury-associated transcripts. Groups 2 (red, N=44) and 3 (blue, N=40) had increased expression of injury-associated transcript sets and dedifferentiation compared to Group 1 (Table 1). Although Group 3 was endoscopically similar to Group 1 (P>0.05), Group 3 showed elevated injury-associated transcript set expression (e.g. IRRAT) and increased parenchymal dedifferentiation (CT2). Conclusions Assessment of UC biopsies using AA and previously annotated injury-associated gene sets reveals two groups of biopsies that are endoscopically similar though one group has increased molecular abnormalities, thus revealing heterogeneity unrelated to the Mayo score. A molecular system based around PCA and AA could enhance and refine UC disease assessment by allowing for quantitation and qualification of injury in biopsies obtained at endoscopy i.e. a level of resolution beyond conventional endoscopic scoring. Funding Agencies None

BACKGROUND: The assessment of patients with ulcerative colitis (UC) remains a challenge despite rapidly evolving medical therapy. Current assessment with endoscopic scoring and histopathology lacks the granularity to correlate strongly with response to therapy. AIMS: Utilizing a microarray based system for colonic epithelial assessment we looked for stratification of endoscopically similar UC biopsies using molecularly heterogeneous archetypes. METHODS: Molecular data from 71 UC biopsies (from 61 patients) was obtained from microarray analysis. The top 300 genes correlating with the endoscopic Mayo score (2/3 vs 0/1) were used for an unsupervised analytical method called archetypal analysis, and grouped the biopsies into three distinct clusters. Logistic regression modeling was used to compare archetype scores or cluster membership to endoscopic Mayo score and PC1 in predicting mucosal healing. A contingency table was generated to show evidence of mucosal healing within each of the archetype clusters. We then assessed a subset of biopsies from the original set of 71 (selected due to the availability of biopsies before and after therapy, all on TNF therapy) plus one IBDU case. Patients were classified as ‘responders’ (Mayo 2/3 score to Mayo 0/1 score by last obtained biopsy or scope) or ‘non-responders’ (Mayo 2/3 score that did not decrease to 0/1 by last obtained biopsy or scope). RESULTS: We found three unique groups of biopsies using archetypal analysis (A1: lack of inflammation, A2: inflammation and response to wounding, A3: inflammation). Logistic regression showed that the only models with statistically significant predictive value (p-value < 0.05) were those that contained archetype scores or cluster membership. Response rates differed between archetype clusters with statistical significance (Table 1), while the mayo score distribution within these clusters was not statistically different. In our subset of serial biopsies, the majority of initial biopsies were found to have an A2 archetype, moving to an A1 archetype in follow-up that mirrored response to treatment (Figure 1). CONCLUSIONS: This archetypal analysis suggests there is potentially important heterogeneity in UC biopsies that is not accessible by endoscopic Mayo score. Serial biopsies showed dynamic shifts in the archetype composition between biopsies. This may be a useful tool for both initailly prognosticating patients and assessing response to treatment over time with increased granularity and reliablity. FUNDING AGENCIES: None

BACKGROUND: Ulcerative colitis (UC) is a chronic, idiopathic inflammatory condition affecting the colonic epithelium, with the inflammasome, T cells, complement activation, and microbiome dysbiosis contributing to pathogenesis. AIMS: We applied a previously established method of microarray molecular analysis to a set of 71 UC biopsies (from 61 patients), to elucidate the molecular changes associated with active UC, specifically comparing UC to T-cell mediated rejection (TCMR), as a prototype of a sterile, T-cell mediated disease. METHODS: 71 for-cause UC colonic biopsies were collected at the U of A Hospital in Edmonton, AB and Cedars-Sinai Hospital in LA, California. These biopsies were processed using Affymetrix GeneChip microarrays and the data analyzed in R programming language. Gene expression data was displayed using volcano plots (showing the fold change and association between the genes and endoscopic Mayo score) and heatmaps (showing expression of the top 30 genes in a cell panel). We then analyzed overexpression of the top genes using the DAVID tool(1), and compared the results to similar results for top genes overexpressed in TCMR. RESULTS: The volcano plot (Figure 1) showed strong associations between the endoscopic Mayo score and decay accelerating factor (CD55), and moderate associations with calprotectin genes (S100A8/S100A9), with lesser associations for effector T cell transcripts (i.e. CTLA4, interferon gamma (IFNG), and chemokine ligand (CXCL13)), many IFNG inducible transcripts, inflammasome transcripts (CASP1), and toll-like receptors (TLR5). NLRP3 (incriminated in mouse UC models) did not pass the IQR filter and was not significant. Expression of the top genes in a cell panel showed primary expression in monocytes, macrophages, and dendritic cells, with some expression in epithelial and endothelial cells, while minimal expression was found in CD4/CD8 T cells, or in NK cells. Pathway analysis showed major differences between pathway terms. CONCLUSIONS: Our findings show that while transcripts associated with cognate T cell inflammatory processes (TCMR) are expressed in UC, there are substantial differences between the pathogenesis of a pure T cell-mediated disease and UC. In our cohort, the top genes associated with the endoscopic Mayo score in UC were not those associated with effector T cells: T cell-associated transcripts were only moderately associated with the Mayo score, and pathway analysis showed significant differences between TCMR and UC, which is much more an inflammatory environment with strong associations to CD55. This suggests that cognate T cell recognition is present in UC but supplemented by a second source of inflammation. REFERENCES: 1. Huang et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols (2009). FUNDING AGENCIES: None