Virus Expression Database

GSE154613

Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds

Submitted by Avi Ma'ayan (Icahn School of Medicine at Mount Sinai, USA) on Jul 16 2020

Platform: ngs – Illumina NextSeq 500 (Homo sapiens)

Pubmed: None listed

Summary The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed a significant burden on the human population. To understand the virus and the disease it causes we sought to interfere with the transcriptional response of the infected host. Utilizing the expression pattern of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures (LINCS). Here we demonstrate the successful identification of compounds that display efficacy in blocking SARS-CoV-2 replication based on their ability to counteract the virus-induced transcriptional landscape. These compounds were found to potently reduce viral load despite having no impact on viral entry or modulation of the host antiviral response in the absence of virus. RNA-Seq profiling implicated the induction of the cholesterol biosynthesis pathway as the underlying mechanism of inhibition and suggested that targeting this aspect of host biology may significantly reduce SARS-CoV-2 viral load.

66 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM4675736 Organoids_Amlodipine-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated
GSM4675737 Organoids_Amlodipine-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated
GSM4675738 Organoids_Amlodipine-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated
GSM4675739 Organoids_Berbamine-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated
GSM4675740 Organoids_Berbamine-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated
GSM4675741 Organoids_Berbamine-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated
GSM4675742 Organoids_DMSO-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus
GSM4675743 Organoids_DMSO-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus
GSM4675744 Organoids_DMSO-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus
GSM4675745 Organoids_Loperamide-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated
GSM4675746 Organoids_Loperamide-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated
GSM4675747 Organoids_Loperamide-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated
GSM4675748 Organoids_MOCK-1 pancreatic cell line  Mock Uninfected
GSM4675749 Organoids_MOCK-2 pancreatic cell line  Mock Uninfected
GSM4675750 Organoids_MOCK-3 pancreatic cell line  Mock Uninfected
GSM4675751 Organoids_RS504393-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated
GSM4675752 Organoids_RS504393-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated
GSM4675753 Organoids_RS504393-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated
GSM4675754 Organoids_Terfenadine-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated
GSM4675755 Organoids_Terfenadine-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated
GSM4675756 Organoids_Terfenadine-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated
GSM4675757 Organoids_Trifluoperazine-1 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazine treated
GSM4675758 Organoids_Trifluoperazine-2 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazine treated
GSM4675759 Organoids_Trifluoperazine-3 pancreatic cell line  SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazine treated
GSM4675760 ACE2-A549-Amlodipine-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675761 ACE2-A549-Amlodipine-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675762 ACE2-A549-Amlodipine-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675763 ACE2-A549-Amoldipine-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675764 ACE2-A549-Amoldipine-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675765 ACE2-A549-Amoldipine-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Amlodopine treated; ACE2 overexpressed
GSM4675766 ACE2-A549-Berbamine-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675767 ACE2-A549-Berbamine-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675768 ACE2-A549-Berbamine-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675769 ACE2-A549-Berbamine-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675770 ACE2-A549-Berbamine-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675771 ACE2-A549-Berbamine-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Berbamine treated; ACE2 overexpressed
GSM4675772 ACE2-A549-DMSO-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
ACE2 overexpressed
GSM4675773 ACE2-A549-DMSO-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
ACE2 overexpressed
GSM4675774 ACE2-A549-DMSO-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
ACE2 overexpressed
GSM4675775 ACE2-A549-Loperamide-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675776 ACE2-A549-Loperamide-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675777 ACE2-A549-Loperamide-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675778 ACE2-A549-Loperamide-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675779 ACE2-A549-Loperamide-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675780 ACE2-A549-Loperamide-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Loperamide treated; ACE2 overexpressed
GSM4675781 ACE2-A549-Mock-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
ACE2 overexpressed
GSM4675782 ACE2-A549-Mock-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
ACE2 overexpressed
GSM4675783 ACE2-A549-Mock-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
ACE2 overexpressed
GSM4675784 ACE2-A549-RS504393-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675785 ACE2-A549-RS504393-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675786 ACE2-A549-RS504393-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675787 ACE2-A549-RS504393-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675788 ACE2-A549-RS504393-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675789 ACE2-A549-RS504393-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
RS504393 treated; ACE2 overexpressed
GSM4675790 ACE2-A549-Terfenadine-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675791 ACE2-A549-Terfenadine-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675792 ACE2-A549-Terfenadine-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675793 ACE2-A549-Terfenadine-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675794 ACE2-A549-Terfenadine-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675795 ACE2-A549-Terfenadine-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Terfenadine treated; ACE2 overexpressed
GSM4675796 ACE2-A549-Trifluoperazine-COV2-1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazone treated; ACE2 overexpressed
GSM4675797 ACE2-A549-Trifluoperazine-COV2-2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazone treated; ACE2 overexpressed
GSM4675798 ACE2-A549-Trifluoperazine-COV2-3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 Severe acute respiratory syndrome-related coronavirus Extra interventions
Trifluoperazone treated; ACE2 overexpressed
GSM4675799 ACE2-A549-Trifluoperazone-drugonly-1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Trifluoperazone treated; ACE2 overexpressed
GSM4675800 ACE2-A549-Trifluoperazone-drugonly-2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Trifluoperazone treated; ACE2 overexpressed
GSM4675801 ACE2-A549-Trifluoperazone-drugonly-3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
Trifluoperazone treated; ACE2 overexpressed