Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids

Authors: Duan et al.

Link to paper: https://doi.org/10.1101/2020.05.02.073320

Journal/ Pre-Print: BioRxiv

Tags: Bioinformatics, Cell Biology, Drug discovery/Drug repurpose, Gut, Molecular biology

Research Highlights

1. SARS-CoV-2 pseudo virus can infect human pluripotent stem cell-derived colonic organoids (hPSC-CO) (as well as hPSC-COs transplanted under the kidney capsule of NOD scid IL2Rgnull mice), which results in the reduction of the KRT20+ enterocyte and ACE2+ intestinal epithelial cell population

2. High throughput compound screen with hPSC-CO identifies four drugs that reduce SARS-Cov-2 infection: mycophenolic acid (MPA), quinacrine dihydrochloride (QNHC), chloroquine and resveratrol

3. hPSC-COs can be infected by SARS-CoV-2 virus, which is reduced by pre-treatment with MPA and QNHC

Summary 

The authors aim to evaluate the usage of hPSC-CO for studying SARS-CoV-2 infection of intestinal epithelial cells. Single cell RNAseq shows ACE2 and TMPRSS2 expression of hPSC-CO. The authors show that SARS-CoV-2 pseudo virus as well as SARS-COV-2 virus is able to infect hPSC-CO and that infection leads to a decrease in the enterocyte population. HPSC-CO xenografts were also infected by SARS-CoV-2 pseudo virus. HPSC-CO were further utilised to screen a compound library and four drugs were shown to reduce SARS-CoV-2 virus infection: mycophenolic acid (MPA), quinacrine dihydrochloride (QNHC), chloroquine and resveratrol.

Impact for SARS-CoV2/COVID19 research efforts

Understand the virology and/or cell biology of SARS-CoV2

Inhibit of SARS-CoV2 transmission

Treat of SARS-CoV2 positive individuals

Study Type

· In silico study / bioinformatics study

· In vitro study

· In vivo study (mouse)

Strengths and limitations of the paper

Novelty: 1. Study uses human pluripotent stem cell-derived colonic organoids (hPSC-CO) to study SARS-CoV-2 infection of intestinal epithelial cells

2. hPSC-CO were used to screen a large compound library for inhibition of SARS-CoV-2 infection

3. Authors identify four compounds that specifically reduce SARS-CoV-2 infection of hPSC-CO: mycophenolic acid (MPA), quinacrine dihydrochloride (QNHC), chloroquine and resveratrol

Standing in the field: Co-expression of TMPRSS2 and ACE2 on enterocytes might be controversial (not supported by the following publication: https://doi.org/10.1101/2020.04.21.054015, but supported by https://doi.org/10.1101/2020.04.24.059667)

Appropriate statistics: Authors describe how many biological replicates they used for this study and which statistical tests they perform

Viral model used: SARS-CoV-2 Pseudo entry virus (rVSV expressing SARS-CoV-2 spikes) and SARS-CoV-2 (isolate USA WA1/2020 (NR-52281))

Translatability: The drugs MPA and QNHC could be considered for clinical trials of COVID-19 therapy

Main limitations: 1. Labelling of the UMAP plots isn’t accurate: Muc2 should define goblet cells and CHGA should define NE cells

2. Immunofluorescence staining of organoids could benefit from an overall image of the organoid and then an enlarged area of interest, to allow better evaluation of the staining

3. In the methods description of SARS-CoV-2 pseudo virus infection the authors describe the centrifugation of hSPC-CO inoculated with pseudo virus for 1h at 1200g, which in our understanding could lead to the disruption of the hPSC-CO

4. In the evaluation of the inhibition of pseudo virus entry into hPSC-CO (see Fig. 3k) it isn’t clear whether the quantification of Luc+ cells was performed relative to all cells on each slide or whether only Luc+ cells were counted