Microbial and Host Factors in the Progression to Celiac Disease

PROJECT SUMMARY Celiac disease (CeD) is an immune-mediated enteropathy that occurs when genetically susceptible individuals consume gluten. CeD affects >1% of the US population, and its prevalence is rising. HLA-DQ2 and/or DQ8 haplotypes are necessary for the development of CeD. However, only ~3% of individuals with these risk alleles

develop CeD, suggesting a role for environmental factors and gene-by-environment interactions in the initiation and pathogenesis of this disease. Diagnosis of this lifelong disease obligates strict adherence to a restrictive diet, which markedly reduces quality of life. Potential celiac disease (PCeD) is used to describe individuals with

HLA-DQ2/HLA-DQ8 risk alleles and circulating antibodies to tissue transglutaminase and endomysium, and yet normal duodenal villous architecture. PCeD can progress to CeD (PCeD-P), revert to seronegativity, or remain persistently seropositive without abnormal small bowel histology (PCeD that is static (PCeD-S)). The PCeD

population provides a unique ability to define the cascade of microbial and host factors culminating in CeD. Insight into the mechanisms that lead to the loss of gluten tolerance and resulting tissue injury will provide reliable markers of disease progression, aid in case management, and offer an opportunity to prevent the progression

to mucosal injury. To do this, we will recruit children with suspected CeD based on positive serology and children with negative celiac serology undergoing upper endoscopy at Washington University and University of Alabama. This will allow us to compare paired plasma, stool, duodenal biopsies, duodenal fluid aspirates, and clinical

metadata from four gluten consuming groups (newly diagnosed treatment naïve CeD, PCeD-P, PCeD-S, and non-CeD controls). To determine if there are transcriptomic signatures in children with PCeD who subsequently develop histologically proven CeD (PCeD-P), we will perform spatial transcriptomics on biopsies from PCeD

participants and sex, age, and race matched CeD and non-CeD controls. Previously, we demonstrated that a subset of CD8+ T cells expressing killer cell immunoglobulin-like receptors (KIR) are increased in frequency in the blood and duodenum of adults with CeD and suppress pathogenic gliadin specific CD4+ T cells. We will

determine the frequency of KIR+CD8+ T cells, gliadin specific CD4+ T cells, and the ratio of these cells among CeD, PCeD, and non-CeD controls. Additionally, we will determine the transcriptomic and TCR clonality shifts within KIR+CD8+ T cells and associate these to CeD progression. Understanding the interplay between CD4+

T cells and CD8+ T cells will help in assessing the contribution of adaptive immune system in CeD progression in children. We do not know if microbial differences drive small bowel CeD inflammation, or vice-versa. By systematically comparing the gut (small bowel and stool) bacterial microbiome and virome of children with biopsy

confirmed CeD, PCeD-P, PCeD-S, and non-CeD controls we will define the microbial cascade of events leading to progression in susceptible individuals. This prospective interrogation of CeD at a uniquely instructive point in the disease process will provide novel and informative insight into the evolution of tissue injury in CeD.