Dissecting Host/Pathogen Interactions in the Gastrointestinal Epithelium

Human intestinal epithelial cells (hIECs) are arranged as a monolayer of cells and provide the first line of defense against invading pathogens. Upon viral infection hIECs upregulate type I and III interferons to control the infection. These interferons lead to the induction of hundreds of interferon stimulated genes (ISGs) that aid in the clearance of the virus and protection of uninfected cells. Upon infection hIECs preferentially upregulate type III interferons to clear the infection. We and others have shown that when added in trans both type I and type III interferons act as key antiviral cytokines, however they achieve their antiviral results using unique patterns of ISGs. Importantly, while hundreds of ISGs have been described using mainly enterocyte models, whether all cell types in the human gastrointestinal tract upregulate the same ISGs following enteric virus infection has yet to be addressed. Using human intestinal mini-gut organoids and both multiplex RNA FISH and single cell RNA sequencing (scRNA-Seq) following virus infection, we have been able to determine the cell type specific response to virus infection. Our analysis showed that each cell type in the human gastrointestinal tract upregulated a unique pattern of ISGs to combat enteric virus infection. Interestingly, we could also show that each cell type in the human ileum also expressed cell-type specific basal ISGs. Together our results illustrate that each individual cell type has a unique ISG pattern that can help us understand virus tropism and virus clearance mechanisms used by hIECs.

Learning Objectives:

1. Develop a basic knowledge of interferon response to viral infection.
2. Describe methods used to evaluate viral response at the single cell level.
3. Describe methods to determine virus infection and propagation in vitro.