The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication

ABSTRACTThe positions of host factors required for viral replication within a human protein-protein interaction (PPI) network can be exploited to identify drug targets that are robust to drug-mediated selective pressure. Host factors can physically interact with viral proteins, be a component of virus-regulated pathways (where proteins do not interact with viral proteins), or be required for viral replication but unregulated by viruses. Here, we demonstrate a method of combining human PPI networks with virus-host PPI data to improve antiviral drug discovery for influenza viruses by identifying target host proteins. Analysis shows that influenza virus proteins physically interact with host proteins in network positions significant for information flow, even after the removal of known abundance-degree bias within PPI data. We have isolated a subnetwork of the human PPI network that connects virus-interacting host proteins to host factors that are important for influenza virus replication without physically interacting with viral proteins. The subnetwork is enriched for signaling and immune processes distinct from those associated with virus-interacting proteins. Selecting proteins based on subnetwork topology, we performed an siRNA screen to determine whether the subnetwork was enriched for virus replication host factors and whether network position within the subnetwork offers an advantage in prioritization of drug targets to control influenza virus replication. We found that the subnetwork is highly enriched for target host proteins—more so than the set of host factors that physically interact with viral proteins. Our findings demonstrate that network positions are a powerful predictor to guide antiviral drug candidate prioritization.IMPORTANCEIntegrating virus-host interactions with host protein-protein interactions, we have created a method using these established network practices to identify host factors (i.e., proteins) that are likely candidates for antiviral drug targeting. We demonstrate that interaction cascades between host proteins that directly interact with viral proteins and host factors that are important to influenza virus replication are enriched for signaling and immune processes. Additionally, we show that host proteins that interact with viral proteins are in network locations of power. Finally, we demonstrate a new network methodology to predict novel host factors and validate predictions with an siRNA screen. Our results show that integrating virus-host proteins interactions is useful in the identification of antiviral drug target candidates.

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Genome-Wide RNAi Screening to Identify Human Host Factors Crucial for Influenza Virus Replication

Advances in Delivery Science and Technology - RNA Interference from Biology to Therapeutics ◽

10.1007/978-1-4614-4744-3_12 ◽

2012 ◽

pp. 243-257

Author(s):

Katharina Ahrens ◽

Alexander Karlas

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Host Factors ◽

Rnai Screening ◽

Human Host ◽

Genome Wide ◽

Influenza Virus Replication ◽

Human Host Factors

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Network-Guided Discovery of Influenza Virus Replication Host Factors

10.1101/344861 ◽

2018 ◽

Cited By ~ 1

Author(s):

Emily E. Ackerman ◽

Eiryo Kawakami ◽

Manami Katoh ◽

Tokiko Watanabe ◽

Shinji Watanabe ◽

...

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Drug Targets ◽

Antiviral Drug ◽

Viral Proteins ◽

Host Factors ◽

Host Protein ◽

Ppi Network ◽

Host Proteins ◽

Influenza Virus Replication

ABSTRACTThe position of host factors required for viral replication within a human protein-protein interaction (PPI) network can be exploited to identify drug targets that are robust to drug-mediated selective pressure. Host factors can physically interact with viral proteins, be a component of pathways regulated by viruses (where proteins themselves do not interact with viral proteins) or be required for viral replication but unregulated by viruses. Here, we demonstrate a method of combining a human PPI network with virus-host protein interaction data to improve antiviral drug discovery for influenza viruses by identifying target host proteins. Network analysis shows that influenza virus proteins physically interact with host proteins in network positions significant for information flow. We have isolated a subnetwork of the human PPI network which connects virus-interacting host proteins to host factors that are important for influenza virus replication without physically interacting with viral proteins. The subnetwork is enriched for signaling and immune processes. Selecting proteins based on network topology within the subnetwork, we performed an siRNA screen to determine if the subnetwork was enriched for virus replication host factors and if network position within the subnetwork offers an advantage in prioritization of drug targets to control influenza virus replication. We found that the subnetwork is highly enriched for target host proteins – more so than the set of host factors that physically interact with viral proteins. Our findings demonstrate that network positions are a powerful predictor to guide antiviral drug candidate prioritization.IMPORTANCEIntegrating virus-host interactions with host protein-protein interactions, we have created a method using these established network practices to identify host factors (i.e. proteins) that are likely candidates for antiviral drug targeting. We demonstrate that interaction cascades between host proteins that directly interact with viral proteins and host factors that are important to influenza replication are enriched for signaling and immune processes. Additionally, we show that host proteins that interact with viral proteins are in network locations of power. Finally, we demonstrate a new network methodology to predict novel host factors and validate predictions with an siRNA screen. Our results show that integrating virus-host proteins interactions is useful in the identification of antiviral drug target candidates.

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Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

Nature ◽

10.1038/nature08760 ◽

2010 ◽

Vol 463 (7282) ◽

pp. 818-822 ◽

Cited By ~ 473

Author(s):

Alexander Karlas ◽

Nikolaus Machuy ◽

Yujin Shin ◽

Klaus-Peter Pleissner ◽

Anita Artarini ◽

...

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Rnai Screen ◽

Host Factors ◽

Human Host ◽

Genome Wide ◽

Influenza Virus Replication ◽

Human Host Factors

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Genomewide RNAi-based screen for host factors required for influenza virus replication

Science-Business eXchange ◽

10.1038/scibx.2010.129 ◽

2010 ◽

Vol 3 (4) ◽

pp. 129-129

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Host Factors ◽

Influenza Virus Replication

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Human host factors required for influenza virus replication

Nature ◽

10.1038/nature08699 ◽

2009 ◽

Vol 463 (7282) ◽

pp. 813-817 ◽

Cited By ~ 557

Author(s):

Renate König ◽

Silke Stertz ◽

Yingyao Zhou ◽

Atsushi Inoue ◽

H. -Heinrich Hoffmann ◽

...

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Host Factors ◽

Human Host ◽

Influenza Virus Replication ◽

Human Host Factors

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ANP32 Proteins Are Essential for Influenza Virus Replication in Human Cells

Journal of Virology ◽

10.1128/jvi.00217-19 ◽

2019 ◽

Vol 93 (17) ◽

Cited By ~ 16

Author(s):

Ecco Staller ◽

Carol M. Sheppard ◽

Peter J. Neasham ◽

Bhakti Mistry ◽

Thomas P. Peacock ◽

...

Keyword(s):

Influenza Virus ◽

Virus Replication ◽

Influenza A ◽

Polymerase Activity ◽

Human Cells ◽

Host Factors ◽

Influenza B Virus ◽

Influenza B ◽

B Virus ◽

Influenza Virus Replication

ABSTRACT ANP32 proteins have been implicated in supporting influenza virus replication, but most of the work to date has focused on the ability of avian Anp32 proteins to overcome restriction of avian influenza polymerases in human cells. Using a CRISPR approach, we show that the human acidic nuclear phosphoproteins (ANPs) ANP32A and ANP32B are functionally redundant but essential host factors for mammalian-adapted influenza A virus (IAV) and influenza B virus (IBV) replication in human cells. When both proteins are absent from human cells, influenza polymerases are unable to replicate the viral genome, and infectious virus cannot propagate. Provision of exogenous ANP32A or ANP32B recovers polymerase activity and virus growth. We demonstrate that this redundancy is absent in the murine Anp32 orthologues; murine Anp32A is incapable of recovering IAV polymerase activity, while murine Anp32B can do so. Intriguingly, IBV polymerase is able to use murine Anp32A. We show, using a domain swap and point mutations, that the leucine-rich repeat (LRR) 5 region comprises an important functional domain for mammalian ANP32 proteins. Our approach has identified a pair of essential host factors for influenza virus replication and can be harnessed to inform future interventions. IMPORTANCE Influenza virus is the etiological agent behind some of the most devastating infectious disease pandemics to date, and influenza outbreaks still pose a major threat to public health. Influenza virus polymerase, the molecule that copies the viral RNA genome, hijacks cellular proteins to support its replication. Current anti-influenza drugs are aimed against viral proteins, including the polymerase, but RNA viruses like influenza tend to become resistant to such drugs very rapidly. An alternative strategy is to design therapeutics that target the host proteins that are necessary for virus propagation. Here, we show that the human proteins ANP32A and ANP32B are essential for influenza A and B virus replication, such that in their absence cells become impervious to the virus. We map the proviral activity of ANP32 proteins to one region in particular, which could inform future intervention.

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