Summary of Study ST001921

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001212. The data can be accessed directly via it's Project DOI: 10.21228/M81X3N This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001921
Study TitleAn Airway Organoid-Based Screen Identifies a Role for the HIF1α-Glycolysis Axis in SARS-CoV-2 Infection
Study SummarySARS-CoV-2 causes the COVID-19 pandemic. It is urgent to develop disease models to dissect mechanisms regulating SARS-CoV-2 infection. Here, we derive airway organoids from human pluripotent stem cells (hPSC-AOs). The hPSC-AOs, particularly ciliated-like cells, are permissive to SARS-CoV-2 infection. Using this platform, we perform a high content screen and identify GW6471, which blocks SARS-CoV-2 infection. GW6471 can also block infection of the B.1.351 SARS-CoV-2 variant. RNA-seq analysis suggests that GW6471 blocks SARS-CoV-2 infection at least in part by inhibiting HIF1α, which is further validated by chemical inhibitor and genetic perturbation targeting HIF1α. Metabolic profiling identifies decreased rates of glycolysis upon GW6471 treatment, consistent with transcriptome profiling. Finally, xanthohumol, 5-(Tetradecyloxy)-2-furoic acid, and ND-646, three compounds that suppress fatty acid biosynthesis, also block SARS-CoV-2 infection. Together, a high content screen coupled with transcriptome and metabolic profiling reveals a key role of the HIF1α-glycolysis axis in mediating SARS-CoV-2 infection of human airway epithelium.
Institute
Weill Cornell Medicine
Last NameChen
First NameShuibing
AddressA 827B, 1300 York Ave
Emailshc2034@med.cornell.edu
Phone2127465431
Submit Date2021-09-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailGC-MS
Release Date2021-10-20
Release Version1
Shuibing Chen Shuibing Chen
https://dx.doi.org/10.21228/M81X3N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001212
Project DOI:doi: 10.21228/M81X3N
Project Title:An Airway Organoid-Based Screen Identifies a Role for the HIF1α-Glycolysis Axis in SARS-CoV-2 Infection
Project Type:MS
Project Summary:SARS-CoV-2 causes the COVID-19 pandemic. It is urgent to develop disease models to dissect mechanisms regulating SARS-CoV-2 infection. Here, we derive airway organoids from human pluripotent stem cells (hPSC-AOs). The hPSC-AOs, particularly ciliated-like cells, are permissive to SARS-CoV-2 infection. Using this platform, we perform a high content screen and identify GW6471, which blocks SARS-CoV-2 infection. GW6471 can also block infection of the B.1.351 SARS-CoV-2 variant. RNA-seq analysis suggests that GW6471 blocks SARS-CoV-2 infection at least in part by inhibiting HIF1α, which is further validated by chemical inhibitor and genetic perturbation targeting HIF1α. Metabolic profiling identifies decreased rates of glycolysis upon GW6471 treatment, consistent with transcriptome profiling. Finally, xanthohumol, 5-(Tetradecyloxy)-2-furoic acid, and ND-646, three compounds that suppress fatty acid biosynthesis, also block SARS-CoV-2 infection. Together, a high content screen coupled with transcriptome and metabolic profiling reveals a key role of the HIF1α-glycolysis axis in mediating SARS-CoV-2 infection of human airway epithelium.
Institute:Weill Cornell Medical College
Department:Surgery
Last Name:Chen
First Name:Shuibing
Address:A 827B, 1300 York Ave, New York, NY, 10065, USA
Email:shc2034@med.cornell.edu
Phone:2127465431

Subject:

Subject ID:SU001999
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA177907GW+SARS_CoV_2_3GW+SARS_CoV_2
SA177908GW+SARS_CoV_2_2GW+SARS_CoV_2
SA177909GW+SARS_CoV_2_1GW+SARS_CoV_2
SA177914Mock2mock
SA177915Mock3mock
SA177916Mock4mock
SA177917Mock1mock
SA177910SARS_CoV_2_4SARS_CoV_2
SA177911SARS_CoV_2_1SARS_CoV_2
SA177912SARS_CoV_2_3SARS_CoV_2
SA177913SARS_CoV_2_2SARS_CoV_2
SA177918shHIF1+SARS+CoV-2_2scramble shRNA+SARS+CoV-2
SA177919shHIF1+SARS+CoV-2_3scramble shRNA+SARS+CoV-2
SA177920scramble shRNA+SARS+CoV-2_3scramble shRNA+SARS+CoV-2
SA177921scramble shRNA+SARS+CoV-2_1scramble shRNA+SARS+CoV-2
SA177922scramble shRNA+SARS+CoV-2_2scramble shRNA+SARS+CoV-2
SA177923shHIF1+SARS+CoV-2_1scramble shRNA+SARS+CoV-2
Showing results 1 to 17 of 17

Collection:

Collection ID:CO001992
Collection Summary:hPSC-AOs were collected into 150 mM ammonium acetate. After centrifugation, cell pellets were collected for metabolite profiling. Metabolite extraction was performed with 200 μl of 80% methanol (20% water) with internal standards (U13C succinate, and U13C citrate, and heptadecanoate).
Sample Type:Lung organoids

Treatment:

Treatment ID:TR002011
Treatment Summary:SARS-CoV-2 variants, including USA-WA1/2020 and B.1.351, were obtained from the World Reference Center for Emerging Viruses and Arboviruses located at the University of Texas, Medical Branch via the CDC. SARS-CoV-2 was propagated in Vero E6 cells (ATCC) in EMEM supplemented with 10% FCS, 1 mM Sodium Pyruvate and 10 mM HEPES. hPSC-AOs were fragmented into small cell clusters and plated on 10% matrigel-coated plates. The infection was performed in the culture media at the indicated MOIs at 37°C. For pre-infection treatment experiments, hPSC-AOs were pretreated with DMSO (control), 10 µM GW6471 for 4 hours prior to infection. HIF1a knockdown in hPSC-AOs Two shRNAs against HIF1α and one scrambled negative control non-effective shRNA in lentiviral GFP vectors were purchased from OriGene company. The shRNA sequences are shown in Table S3. To generate lentivirus particles, shRNA vectors and lentivirus packaging vectors were co-transfected into 293T cells. The day 15 lung progenitor cells were infected with the collected lentivirus (MOI=0.5) with 8 μg/ml polybrene. To increase the infection efficiency, the cells were centrifuged at 2300 rpm for 1 hour at 30℃. At 24 hpi, the cells were selected with 1 μg/ml puromycin for an additional 72 hours. After selection, the cells were dissociated into single cells and seeded into 24 well plates at 300-400 cells/μl for 3D organoid differentiation.

Sample Preparation:

Sampleprep ID:SP002005
Sampleprep Summary:In brief, the samples were methoximized with 50 µl of methoxyamine hydrochloride (MOA, 15 mg/mL in pyridine) at 30°C for 90 minutes. The silylation step was done with 50 µl of N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA, containing 1% TMCS, Supelco, PA, USA) at 70 °C for 60 minutes. After the samples cooled to room temperature, they were analyzed by GC-TOF/MS. Separation was performed with a 30-meter DB-5MS column coupled with 10-meter guard column. Helium was used as carrier gas at a flow of 1 ml/min. The oven program is as the following: started at 60 °C for 1 minute, 10°C /min to 320 minutes and kept for 3 minutes.

Combined analysis:

Analysis ID AN003122
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column 30-meter DB-5MS
MS Type EI
MS instrument type GC-TOF
MS instrument name new
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH002307
Chromatography Summary:Separation was performed with a 30-meter DB-5MS column coupled with 10-meter guard column. Helium was used as carrier gas at a flow of 1 ml/min. The oven program is as the following: started at 60 °C for 1 minute, 10°C /min to 320 minutes and kept for 3 minutes.
Instrument Name:Agilent 7890A
Column Name:30-meter DB-5MS
Chromatography Type:GC

MS:

MS ID:MS002903
Analysis ID:AN003122
Instrument Name:new
Instrument Type:GC-TOF
MS Type:EI
MS Comments:The transfer line temperature was set to 250 °C. The data was acquired with MassLynx software (Waters). The data was collected with the scan time of 0.3 s and interscan delay of 0.1 s. The mass range was set to 35 to 650 for EI. Raw data files (.raw) generated from GC-TOF/MS were analyzed in Refiner MS (Genedata Expressionist, Basel, Switzerland) software. The output from Refiner MS contains retention time, quantification mass, and peak volume for each metabolite.
Ion Mode:POSITIVE
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