Prospective Multi-Omic Analysis of At-Risk infants to Model Celiac Disease Pathogenesis

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Project Summary Globally there is a tremendous rise in the incidence of autoimmune disease including celiac disease (CD). CD is unique among autoimmune disorders in that the genetic predisposition, specific human leukocyte antigen (HLA), auto antibodies produced, and trigger, gluten, are known. However, more than 30% of the population carry the predisposing genes and are exposed to gluten, yet only 2-3% of these individuals develop CD even decades after gluten exposure, suggesting a critical role for additional environmental factors. This finding highlights the crucial gap in knowledge of the earliest steps in CD pathogenesis that occur following the exposure to gluten leading to the loss of tolerance and subsequent development of autoimmunity. To understand the complex interactions involved in the development of disease, detailed data collection and multi-omic analysis must begin before the onset of disease, through the development of disease, and into remission. I have access to a unique prospective longitudinal birth cohort to accomplish this. My work has shown that environmental factors alter the gut microbiome composition and function with potential implications for increasing susceptibility to CD in at-risk infants. My preliminary data suggest that gut microbiome alterations at the species level are present prior to the loss of tolerance to gluten and onset of CD. Therefore, I propose to investigate the role of the gut microbiome as a factor that may play a key role in early steps involved in the onset of the disease. I hypothesize that HLA genetics in combination with environmental factors (delivery mode, diet, and antibiotic exposure) can affect the microbiome composition and function ultimately causing epigenetic changes in immune cells leading to the switch from tolerance to immune response to gluten in genetically predisposed individuals. With guidance from my mentoring team, during this 5 year K23 mentored career development award, my objective is gain expertise in microbiome analysis, immunology, and computational analysis to create integrative models that can identify biologic pathways and clinical factors that contribute to loss of tolerance in children genetically at risk of autoimmunity with the goal of personalized prevention of CD. The proposed project has three major aims. Aim 1 I will identify metagenomic alterations before and after the loss of tolerance to gluten and in relation to environmental factors in infants with CD and controls. In aim 2 I will determine alterations in gene expression of circulating monocytes using single cell RNA sequencing before and after the development of CD and compared to controls. Aim 3 will utilize the multi-omic data to build a integrative models to identify biological pathways that contribute to and may predict CD development in at-risk children. This work will lay the scientific framework to launch my career as an NIH-funded independent clinical investigator who can blend expertise in translational investigation, with clinical expertise in CD, immunology, and bioinformatics, to develop computational models and eventually programs for personalized medicine for patients at risk for autoimmune disease.