A CRISPR Activation Screen Identifies Genes That Protect against Zika Virus Infection

Abstract

Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barré syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection, we used a genomescale CRISPR activation screen. Our highly ranking hits included a short list of interferon-stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted interferon lambda 2 (IFN-2) and interferon alpha-inducible protein 6 (IFI6) as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing single guide RNAs (sgRNAs) for both of these genes displayed lower levels of cell death than did the controls. Furthermore, the identified genes were significantly induced in ZIKV-infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiate CRISPR activation screens as a tool to identify host factors impeding pathogen infection. IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barré syndrome, neuropathy, and myelitis. Vertical transmission of ZIKV can cause fetus demise, stillbirth, or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome-wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide a better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.

Bat-borne virus diversity, spillover and emergence

“…Compared to more well-studied viruses with a zoonotic origin, such as influenza A virus and HIV, there is still much to uncover for post-entry species barriers of emergent, bat-derived viral pathogens. Large-scale CRISPR-Cas9-mediated knockout and activation screens in human cells have recently identified specific host factors that are essential to flaviviruses [128][129][130] , HIV 131 , Epstein-Barr virus 132 and influenza A virus 133,134 but such data have not yet been generated for bat-derived viruses.…”

The Molecular Interactions of ZIKV and DENV with the Type-I IFN Response

“…IFI6 is a 13 kDa protein that is known to be involved in cell survival and counteracting viral-mediated apoptosis [ 68 ]. Increased expression of IFI6 was shown to reduce ZIKV replication and prevented ZIKV mediated cell death in the Huh7 (liver origin) cell line [ 69 ]. In this study, IFI6 localized to the ER near ZIKV RCs suggesting that it may play a role in inhibiting viral replication or virion production.…”

Chasing Intracellular Zika Virus Using Proteomics

“…The recent technological revolution allows acquiring knowledge on biological processes at incredible speed. Several systematic and unbiased genetic approaches to identify host factors involved in flavivirus replication have been conducted to date [14,15,16,17,18,19,20,21]. For instance, next generation sequencing (NGS) became an affordable and widely used technology to unearth underrepresented sequences or estimate the abundance of RNA transcripts in complex mixtures.…”