RNA-seq analysis of astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape
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ABSTRACT:
PROVIDER: PRJEB35458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3671290.fastq.gz | Fastqsanger.gz | |||
| ERR3671300.fastq.gz | Fastqsanger.gz | |||
| ERR3671291.fastq.gz | Fastqsanger.gz | |||
| ERR3671301.fastq.gz | Fastqsanger.gz | |||
| ERR3671292.fastq.gz | Fastqsanger.gz |
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Project description:The host response of the primary intestinal epithelium to human astrovirus (HAstV infection has not been elucidated to date. In order to characterize the global effects of AstV infection on human intestinal tissue, we performed transcriptional profiling of VA1-infected human intestinal enteroids (HIE) by RNAseq. We used the D124 line for our studies since AstV infections are typically symptomatic in very young children, and our prior infection studies indicated rapid infection in D124. D124 HIE were mock-infected or infected with VA1 (MOI = 1) and harvested at 0 hpi (i.e., 1h post-adsorption), 12 hpi, and 24 hpi (Fig 4A). To monitor viral replication, VA1 genome copies were detected by RT-qPCR, revealing an approximately 1 and 2 log increase at 12 and 24 hpi, respectively (Fig 4B). Cellular RNA was extracted and analyzed by RNAseq. Genome copies as determined by RT-qPCR were correlated to the proportion of viral transcripts in the pool of sequenced RNA collected from the same HIE cultures, revealing an exceptionally strong correlation between the two measures of viral replication (r2 = 0.98, P = 2.5 x 10^-14. VA1 genome reads contributed 0.05 ± 0.02 x% of total RNAseq reads at 24 hpi, further confirming robust infection. Differential expression analysis was performed to identify genes associated with the HIE host response to VA1 infection. A total of 23,220 genes were detected. Differential expression of genes at each timepoint was graphed in a volcano plot. The log2 fold change in normalized expression (transcripts per million reads [TPM]) of all expressed host genes in VA1-infected HIEs relative to mock-infected HIE is shown on the x-axis. The -log10 transformed P-value is given on the y-axis. Genes that are significantly up-regulated (adjusted P < 0.05) in VA1-infected D124 HIE relative to mock-infected HIE are colored red, while significantly down-regulated genes are colored blue. Overall, after a 1 hour adsorption (0 hpi), 110 genes were significantly upregulated and 136 genes were downregulated , indicating changes due to viral attachment to cells. This number was reduced at 12 hpi, with 8 significantly upregulated and 5 downregulated genes. At 24 hpi, 154 upregulated and 49 downregulated genes compared to the mock-infected control were identified. We next identified the top 15 significantly up- and down-regulated genes at 24 hpi. This group of genes was used to generated a heatmap of the mean scaled fold-change (Z-score) in expression of each of them in virus-infected HIE relative to mock-infected HIE at each timepoint (Fig 4D). Most of the upregulated genes at 24 hpi were involved in type I and type III interferon (IFN) signaling. Of the IFN genes, IFNL1 was highly upregulated, with IFNA1 and IFNB1 upregulation being slightly lower (Fig S4B). No upregulation was observed for the genes encoding IFN-γ, or the type I and III IFN receptors (data not shown). The top 12 IFN-stimulated genes (ISGs) also positively correlated with VA1 infection (Fig S4C). Conversely, the top 12 downregulated genes, including fermitin family member 1 (FERMT1), signal peptide peptidase like 3 (SPPL3), and tetratricopeptide repeat domain 19 (TTC19) negatively correlated with VA1 infection (Fig S4D). Next, we evaluated lists of the top 100 up- and down-regulated genes at 24 hpi using an over-abundance test to identify significantly over-represented REACTOME pathways in these lists. These data revealed that the top four significantly enriched pathways among upregulated genes were all related to innate antiviral signaling (Fig 4E), which will be investigated in more detail below. For downregulated genes, the top two pathways were “neurexins and neuroligins”, which play signaling roles in synapse development, and “protein-protein interactions at synapses”. The biological significance of synapses during astrovirus infection remains to be elucidated. In order to evaluate the potential for coordinated and directional activation of genes in known signaling pathways, we applied gene set enrichment analysis (GSEA) to our RNAseq differential expression data. Based on the strong dominance of IFN signaling pathways, we focused our GSEA analysis on immune signaling (Fig 4F). During the adsorption phase, nucleic acid pattern recognition receptor signaling pathways (TLRs, STING) were upregulated, consistent with their early role in virus recognition and induction of IFN signaling. At 24 hpi, these early signaling events had been largely replaced by the later phase of IFN signaling and expression of ISGs. Taken together, these data indicate that VA1 infection predominantly elicited antiviral IFN signaling in HIE-derived fetal duodenum at the transcript level.
2019-10-31 | E-MTAB-8527 | biostudies-arrayexpress
Project description:Human astroviruses (HAstV) are understudied positive-strand RNA viruses that cause gastroenteritis mostly in children and the elderly. Three clades of astroviruses, classic, MLB-type and VA-type have been reported in humans. One limitation towards a better understanding of these viruses has been the lack of a physiologically relevant cell culture model that supports growth of all clades of HAstV. Herein, we demonstrate infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts. A detailed investigation of infection of VA1, a member of the non-canonical HAstV-VA/HMO clade, showed robust replication in HIE derived from different patients and from different intestinal regions independent of the cellular differentiation status. Flow cytometry and immunofluorescence analysis revealed that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes, in HIE cultures. RNA profiling of VA1-infected HIE uncovered that the host response to infection is dominated by interferon (IFN)-mediated innate immune responses. A comparison of the antiviral host response in non-transformed HIE and transformed human colon carcinoma Caco-2 cells highlighted significant differences between these cells, including an increased magnitude of the response in HIE. Additional studies confirmed the sensitivity of VA1 to exogenous IFNs, and indicated that the endogenous IFN response of HIE to curtail the growth of strains from all three clades. Genotypic variation in the permissiveness of different HIE lines to HAstV could be overcome by pharmacologic inhibition of JAK/STAT signaling. Collectively, our data identify HIE as a universal infection model for HAstV and an improved model of the intestinal epithelium to investigate enteric virus-host interactions.
| S-EPMC6957189 | biostudies-literature
Project description:The cellular response to astrovirus infection is not well defined. We used single cell RNA sequencing (scRNA-seq) to determine cellular response to astrovirus early or late in infection.
2023-08-20 | GSE240869 | GEO
Project description:RNA-seq analysis of astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape
2020-01-10 | E-MTAB-8527 | ExpressionAtlas
Project description:Ribosome profiling (RiboSeq) is a high-throughput sequencing technique for globally mapping the positions of translating ribosomes on the transcriptome. We infected Caco2 cells with human astrovirus 1 (HAstV1). Cells were harvested at 12 hpi and either flash frozen with no pre-treatment (NT), or pre-treated with lactimidomycin for 30 minutes followed by flash freezing (LTM). These samples where then used for ribosome profiling.
2020-07-04 | E-MTAB-8045 | biostudies-arrayexpress