Salmonella enterica serovar Typhimurium SPI-1 and SPI-2 shape the transcriptional landscape of epithelial cells in a human intestinal organoid model system
Authors: Lawrence Anna-Lisa E. , Abuaita Basel H. , Berger Ryan P. , Hill David R. , Huang Sha , Yadagiri Veda K. , Bons Brooke , Fields Courtney , Wobus Christiane E. , Spence Jason R. , Young Vincent B. , O’Riordan Mary X. 
Published: October 2020

AbstractThe intestinal epithelium is a primary interface for engagement of the host response by foodborne pathogens, likeSalmonella entericaserovar Typhimurium (STm). While interaction of STm with the mammalian host has been well studiedin vitroin transformed epithelial cell lines or in the complex intestinal environmentin vivo, few tractable models recapitulate key features of the intestinal epithelium. Human intestinal organoids (HIOs) contain a polarized epithelium with functionally differentiated cell subtypes, including enterocytes and goblet cells. HIOs contain luminal space that supports bacterial replication and are more amenable to experimental manipulation than animals while more reflective of physiological epithelial responses. Here we use the HIO model to define transcriptional responses of the host epithelium to STm infection, also determining host pathways dependent onSalmonellaPathogenicity Island-1 (SPI-1) and -2 (SPI-2) encoded Type 3 secretion systems (T3SS). Consistent with prior findings, we find that STm strongly stimulates pro-inflammatory gene expression. Infection-induced cytokine gene expression was rapid, transient and largely independent of SPI-1 T3SS-mediated invasion, likely due to continued luminal stimulation. Notably, STm infection led to significant down-regulation of host genes associated with cell cycle and DNA repair, an effect that required SPI-1 and SPI-2 T3SS. The transcriptional profile of cell cycle-associated target genes implicates multiple miRNAs as likely mediators of STm-dependent cell cycle suppression. These findings from Salmonella-infected HIOs delineate common and distinct contributions of SPI-1 and SPI-2 T3SSs in inducing early host responses during enteric infection and reveal host cell cycle as a potential target during STm intracellular infection.ImportanceSalmonella entericaserovar Typhimurium (STm) causes a significant health burden worldwide, yet host responses to initial stages of intestinal infection remain poorly understood. Due to differences in infection outcome between mice and humans, evaluating physiological host responses driven by major virulence determinants ofSalmonellahave been difficult to date. Here we use the 3D human intestinal organoid model to define early responses to infection with wildtype STm and mutants defective in the SPI-1 or SPI-2 Type 3 secretion systems. Both secretion system mutants show defects in a mouse model of oralSalmonellainfection but the specific contributions of each secretion system are less well understood. We show that STm upregulates pro-inflammatory pathways independently of either secretion system while downregulation of host cell cycle pathways is dependent on both SPI-1 and SPI-2. These findings lay the groundwork for future studies investigating how SPI-1- and SPI-2-driven host responses affect infection outcome and show the potential of this model to study host-pathogen interactions with other serovars to understand how initial interactions with the intestinal epithelium may affect pathogenesis.