Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses

Abstract

Acute gastroenteritis (AGE) has a significant disease burden on society. Noroviruses, rotaviruses, and astroviruses are important viral causes of AGE but are relatively understudied enteric pathogens. Recent developments in novel biomimetic human models of enteric disease are opening new possibilities for studying human-specific host–microbe interactions. Human intestinal enteroids (HIE), which are epithelium-only intestinal organoids derived from stem cells isolated from human intestinal biopsy tissues, have been successfully used to culture representative norovirus, rotavirus, and astrovirus strains. Previous studies investigated host–virus interactions at the intestinal epithelial interface by individually profiling the epithelial transcriptional response to a member of each virus family by RNA sequencing (RNA-seq). Despite differences in the tissue origin, enteric virus used, and hours post infection at which RNA was collected in each data set, the uniform analysis of publicly available datasets identified a conserved epithelial response to virus infection focused around “type I interferon production” and interferon-stimulated genes. Additionally, transcriptional changes specific to only one or two of the enteric viruses were also identified. This study can guide future explorations into common and unique aspects of the host response to virus infections in the human intestinal epithelium and demonstrates the promise of comparative RNA-seq analysis, even if performed under different experimental conditions, to discover universal and virus-specific genes and pathways responsible for antiviral host defense.

Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

“…Last, we wanted to explore whether this model would also provide insights in viral-host interactions and to this end, we performed an RNA sequencing analysis. Previous studies on enteric virus infection of enteroids unequivocally showed a signature dominated by interferon and innate immune pathways (7). Usually, interferon responses are initiated by infected cells but mostly amplified by bystander cells (6).…”

“…The induction of the host innate response plays an essential role in the suppression of pathogen infection. In the case of enteric pathogens, interferon responses are highly upregulated in vivo and in vitro (6,7). We previously reported that human astrovirus VA1, another enteric virus and causative agent of viral gastroenteritis, induces interferon and interferon-stimulated genes (ISG) in the HIE system but not in an immortalized cell line, the Caco2 cells (8).…”

Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids

“…Transcription factor enrichment analysis of HNoV GII.4-infected HIEs identified STAT1 and STAT2 binding sites as highly enriched in the promoter regions of genes whose levels of expression were significantly upregulated following infection (41). Similarly, HNoV GII.4 infection of HIEs stimulates a robust innate response involving predominately a type III IFN response and the induction of ISGs including ISG15 and ISG45 (28,42). Targeted profiling of immunological genes associated with HNoV replication in HIEs suggests that the two most upregulated immune-related genes with viral replication are ISGs CXCL10 and IFI44L (43-45).…”

“…The understanding of HAstV pathogenesis has evolved with the development of relevant models for replication in cell lines (21,(70)(71)(72). Additionally, the recent identification of murine astrovirus (muAstV) as an endemic virus in mouse facilities (71) and HIE culturing methods for HAstVs have resulted in important advancements in HAstV pathobiology (21,28,73). MuAstV preferentially replicates in the small intestine and chronically infects immunocompromised mice (21,22,71), and some strains have been found to induce chronic antiviral signaling via type III IFN, supporting important interactions between AstVs and IFN signaling.…”

“…While mouse models have implicated IFNs as critical for the regulation of murine enteric viruses such as murine norovirus, murine rotavirus, and murine astrovirus, the roles of IFNs in the regulation of human enteric viruses have been less carefully explored (21)(22)(23)(24)(25)(26)(27). A recent comparison of RNA-sequencing datasets identified shared transcriptional changes involving the innate immune response upon infection of HIEs with multiple human enteric viruses, including genes associated with Toll-like receptors, IFN receptors (IFNAR, IFNGR, IFNLR), IFN-stimulated genes, and IFN-associated chemokines (28). Virus-specific transcriptional changes were also observed.…”