Disease map pathways affected by SARS-CoV-2 in gut organoids based on single-cell RNA-seq data

Scope: The COVID-19 disease can have gastrointestinal manifestation. The virus replicates in the gut and has potential faecal-oral transmission besides airborne transmission (Lamers et al., 2020). Intestinal organoids are a proven experimental model of the human gut and can help understand the viral infection of the gut without animal models and additional biopsies. Single-cell RNA-seq techniques can distinguish the SARS-CoV-2 replicating cells and thus help to understand how cells respond to the viral infection. With the COVID-19 disease map, cross-talk between the pathways can be uncovered in intestinal cells and compared between infected cells and bystanders.

Methodology: We used the Triana et al. single-cell RNA-seq experiment on colon and ileal organoids infected with SARS-CoV2 virus (GSE156760) (Triana et al., 2020). Samples were processed using a 10X Genomics pipeline then SEURAT (Hao et al., 2020). Cell types were assigned by visualising the expression of marker genes on uniform manifold approximation and projection plots. Cell infection status was determined by the expression level of viral transcripts. For each cell type, genes differentially expressed between infection states were determined using MAST software applying log2 fold change cut-off 0.5 and Benjmani Hochberg corrected p-value cut-off 0.05 (Finak et al., 2015). Pathways annotated by the COVID-19 disease map were downloaded and the corresponding transcripts tested for enrichment analysis with the hypergeometric test and Benjamini Hochberg correction. The background was the expressed genes in ileal or colonic organoids. The code is available here