A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

Abstract

BackgroundThe 2014–2016 Ebola virus (EBOV) outbreak in West Africa highlighted the need for improved therapeutic options against this virus. Approaches targeting host factors/pathways essential for the virus are advantageous because they can potentially target a wide range of viruses, including newly emerging ones and because the development of resistance is less likely than when targeting the virus directly. However, systematic approaches for screening host factors important for EBOV have been hampered by the necessity to work with this virus at biosafety level 4 (BSL4).MethodsIn order to identify host factors involved in the EBOV life cycle, we performed a genome-wide siRNA screen comprising 64,755 individual siRNAs against 21,566 human genes to assess their activity in EBOV genome replication and transcription. As a screening platform, we used reverse genetics-based life cycle modelling systems that recapitulate these processes without the need for a BSL4 laboratory.ResultsAmong others, we identified the de novo pyrimidine synthesis pathway as an essential host pathway for EBOV genome replication and transcription, and confirmed this using infectious EBOV under BSL4 conditions. An FDA-approved drug targeting this pathway showed antiviral activity against infectious EBOV, as well as other non-segmented negative-sense RNA viruses.ConclusionsThis study provides a minable data set for every human gene regarding its role in EBOV genome replication and transcription, shows that an FDA-approved drug targeting one of the identified pathways is highly efficacious in vitro, and demonstrates the power of life cycle modelling systems for conducting genome-wide host factor screens for BSL4 viruses.Electronic supplementary materialThe online version of this article (10.1186/s13073-018-0570-1) contains supplementary material, which is available to authorized users.

The anti-viral facet of anti-rheumatic drugs: Lessons from COVID-19

“…Martin et al reported preliminary effect on several RNA viruses such us Newcastle disease virus, Rabies virus and Influenza A virus [116]. BK polyomavirus is a DNA virus member of polyomaviridae family and causative agent of infectious hemorrhagic cystitis in transplant recipients and of polyomavirus-associated nephropathy (PVAN), a potentially dreadful complication after kidney transplantation.…”

The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression

“…These data suggest a mechanism of action that may be conserved among several cytoplasmically replicating negative-stranded RNA viruses (NSVs) that share commonalties in their replication cycles, such as replication in cytoplasmic inclusion bodies [10,[21][22][23][24]. Importantly, we also could show that NXF1 is important for the life cycle of EBOV in context of infectious virus [19]. However, the precise function of NXF1 in the EBOV life cycle remained unclear.…”

“…Expression plasmids for the RNP proteins, the T7 polymerase and the T7-driven monocistronic minigenomes (pT7-1cis-vRNA-rLuc, pT7-1cis-vRNA-nLuc) have been previously described [19,41]. Plasmids for the expression of N-terminally flag/HA-tagged constructs were generated by insertion of the respective genes (NXF1, p15, NP) into a pCAGGS-flag/HA vector.…”

“…To obtain a comprehensive picture of the pro-and anti-viral factors that are important for EBOV RNA synthesis (i.e., genome replication and transcription) and/or protein expression, we recently performed a genome-wide siRNA screen [19]. As primary readout we used a minigenome assay (reviewed in [20]).…”

Current status of small molecule drug development for Ebola virus and other filoviruses

“…The anti-EBOV activity of DHODH inhibitors such as GSK983 and brequinar is related to depletion of pyrimidine pools [65]. Interestingly, a genetic screen also identified de novo pyrimidine biosynthesis as critical for EBOV replication [67]. Although DHODH inhibitors have been used clinically for other applications, in vivo studies have not demonstrated convincing antiviral activity, possibly because uracil is available systemically in vivo to feed the salvage pathway, overcoming the block to the de novo pyrimidine synthesis pathway [68][69][70].…”