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| Status |
Public on Apr 15, 2024 |
| Title |
Replication-competent HIV-1 gRNA Constructs for CRISPR/Cas9-based Discovery of Antiviral Factors |
| Organism |
Human immunodeficiency virus 1 |
| Experiment type |
Other
|
| Summary |
Innate cellular defense mechanisms and viral countermeasures govern the outcome of pathogen exposure but the complex virus-host interplay remains poorly understood. Here, we developed a virus-guided technology platform where the pathogen itself reveals its cellular opponents. To accomplish this, we engineered replication-competent HIV-1 expressing single guide RNAs (sgRNAs) targeting potential antiviral genes in Cas9 expressing CD4+ T cells. Screening of HIV-1 constructs targeting >500 potential antiviral genes revealed that sgRNAs against GRN, CIITA, EHMT2, CEACAM3, CC2D1B, RHOA and HMOX1 provide significant advantages for viral replication. We verified that GRN and CIITA inhibit HIV-1 in primary CD4+ T cells by reducing viral transcription. Lack of the accessory nef gene increased selection for sgRNAs targeting SERINC5 and IFI16. Functional analyses demonstrated that Nef counteracts the inhibitory effects of IFI16. Altogether, we established a highly versatile, effective and robust approach that forces HIV-1 to reveal its cellular opponents.
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| Overall design |
RNA from virus was reverse transcribed and a cassette containing a sgRNA was amplified to sequence the sgRNA
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| Contributor(s) |
Bozzo CP, Laliberté A, Krebs S, Graf A, Blum H, Sparrer KM, Kirchhoff F |
| Citation(s) |
38714682 |
| |
| Submission date |
Oct 16, 2023 |
| Last update date |
Jul 15, 2024 |
| Contact name |
Konstantin MJ Sparrer |
| E-mail(s) |
Konstantin.Sparrer@uni-ulm.de
|
| Organization name |
Ulm University Medical Center
|
| Department |
Institute of Molecular Virology
|
| Street address |
Meyerhofstr. 1
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL33848 |
NextSeq 2000 (Human immunodeficiency virus 1) |
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| Samples (49)
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| Relations |
| BioProject |
PRJNA1028668 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE245526_Counts_CH077_in_CEMM7.xlsx |
242.5 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Counts_NL4.3_in_CEMM7_N_1-3.xlsx |
575.8 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Counts_NL4.3_in_SupT1.xlsx |
155.7 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Counts_dNef_vs_WT.xlsx |
423.7 Kb |
(ftp)(http) |
XLSX |
| GSE245526_RAW.tar |
14.4 Mb |
(http)(custom) |
TAR (of XLSX) |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_10_dpi_IFN.xlsx |
58.7 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_10_dpi_untreated.xlsx |
59.0 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_15_dpi_IFN.xlsx |
59.4 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_15_dpi_untreated.xlsx |
59.6 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_20_dpi_IFN.xlsx |
59.3 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_20_dpi_untreated.xlsx |
59.5 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_NL4.3_in_CEMM7_N_1-2_5_dpi_untreated.xlsx |
58.9 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_sgRNA_NL4.3_CEMM7_15dpi_IFN_vs_input_N_1-3.xlsx |
216.2 Kb |
(ftp)(http) |
XLSX |
| GSE245526_Test_sgRNA_NL4.3_CEMM7_15dpi_untreated_vs_input_N_1-3.xlsx |
217.8 Kb |
(ftp)(http) |
XLSX |
| GSE245526_gRNA_list_by_gene.tab.gz |
17.8 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
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