Genome-scale CRISPR screen reveals inhibitory factors as regulatory module of HIV
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE185343 | GEO | 2022/06/04
REPOSITORIES: GEO
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Project description:Genome-scale CRISPR screen reveals inhibitory factors as regulatory module of HIV
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Project description:Interferon (IFN) inhibits HIV replication by inducing an array of antiviral effectors. Here we describe a novel CRISPR knockout screening approach to identify the ensemble of these HIV restriction factors. We assembled a CRISPR sgRNA library specific for Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomes in trans into budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. We identify a small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5 which together explain the inhibitory effects of IFN on the HIV-1 LAI strain in THP-1 cells. Further, we identify novel HIV dependency factors, including SEC62 and TLR2. The ability of IFN-induced restriction factors to inhibit an HIV strain to replicate in human cells suggests that these human restriction factors are incompletely antagonized.
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Project description:Very little is known about the role of macrophages as immune mediators during natural HIV infection. Humanized mice are a highly valuable in vivo model to study HIV pathogenesis. Still, the presence of murine mononuclear phagocytes in these models represents a significant limitation for the study of their human counterpart. Therefore, we generated a novel humanized mouse model for the selective depletion of human myeloid cells at a time point of our choosing. These inducible human myeloid cell depletion (iHMD) mice showed specific human myeloid cell depletion with no adverse events for the animals. We used this model to demonstrate that human mononuclear phagocytes restrict HIV replication in vivo by secreting antiviral cytokines and chemokines. These in vivo data were validated by a co-culture assay, showing soluble factors are at the basics of macrophage-mediated restriction of HIV. Transcriptomic data confirmed macrophages restrict HIV replication via upregulation of antiviral cytokines and chemokines. RNA sequencing CD4+ T-cells showed cellular activation, up-regulation of HIV restriction factors and the downregulation of DNA transcription and RNA translation in the presence of macrophages. This work describes a novel role of macrophages as effector cells acting against HIV replication and disease progression.
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