Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA623281: Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

Source: NCBI / GSE148113
Submission Date: Apr 06 2020
Release Date:
Update Date: Dec 11 2020

Summary: The SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens.

Overall Design: We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry.

GEN Datasets:
GEND000478
Strategy:
Species:
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Protocol
Growth Protocol: hESC cultures were maintained in an undifferentiated state at 37 in a 5% CO2/air environment until stem cells reached about 90% confluence.
Treatment Protocol: hPSC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Life Technologies) supplemented with 1N2 (Life Technologies), 1B27 (Life Technologies), 50 g/ml ascorbic acid, 2 mM Glutamax (Gibco), 0.4 monothioglycerol, 0.05% BSA at 37 in a 5% CO2/5% O2/95% N2 environment. hPSCs were treated with Accutase and plated onto low attachment 6-well plates (Corning), re-suspended in endoderm induction medium containing 10 Y-27632, 0.5 ng/ml human BMP4 (R&D Systems), 2.5 ng/ml human bFGF, 100 ng/ml human Activin A (R&D Systems), for 72-76 hours dependent on the formation rates of endoderm cells. On day 3 or 3.5, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,00050,000 cells/well). For induction of anterior foregut endoderm, the endoderm cells were cultured in SFD medium supplemented with 1.5 dorsomorphin dihydrochloride (R&D Systems) and 10 SB431542 (R&D Systems) for 36 hours, and then switched to 36 hours of 10 SB431542 and 1 IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 65), the resulting anterior foregut endoderm was treated with 3 CHIR99021 (CHIR, Stem-RD), 10 ng/ml human FGF10, 10 ng/ml human KGF, 10 ng/ml human BMP4 and 50-60 nM all-trans retinoic acid (ATRA), in SFD medium for day 80. The day 105 culture was maintained in a 5% CO2/air environment. On days 15 and 16, the lung field progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing 3 CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, 10 ng/ml human BMP4, and 50 nM ATRA. Day 165 cultures of late stage lung progenitor cells were maintained in SFD media containing 3 CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55) in 3D culture, cultures were re-plated and embedded in 90% Matrigel after brief trypsinization in SFD media containing maturation components containing 3 CHIR99021, 10 ng/ml human FGF10; 10 ng/ml human KGF, 50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione, Sigma Aldrich).
Extract Protocol: -
Library Construction Protocol: Library was constructed according to the user manual of Chromium Single Cell 3Library & Gel Bead Kit v2
Sequencing
Molecule Type: Poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
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Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Identification of SARS-CoV-2 inhibitors using lung and colonic organoids.
Nature . 2020-10-28 [PMID: 33116299]