A genome wide RNA interference screening method to identify host factors that modulate Influenza A virus replication

Chin, Christopher R.; Brass, Abraham L.

doi:10.1016/j.ymeth.2012.09.009

Cited by 9 publications

(7 citation statements)

References 24 publications

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“…Genes encoding V‐ATPase subunits and accessory components were widely represented in genome‐wide RNAi screens aiming to identify host genes critical for influenza virus infection. In fact, ATP6V0D1 , 222,223 as well as ATP6AP1 , ATP6V0B , ATP6V1G1 , ATP6V0E were found to be crucial for viral replication, 224 while ATP6V1A , ATP6V1B2 , ATP6V0B , ATP6V0C , ATP6V0D1 , ATP6AP1 , and ATP6AP2 knockouts reduced viral infection in a human cell line. ATP6V0C was identified in a screening designed to identify host factors essential for the pH‐dependent virus entry 225 .…”

Section: V‐atpases: Attractive Targets For a Multitude Of Human Diseasesmentioning

confidence: 97%

Emerging insights on the role of V‐ATPase in human diseases: Therapeutic challenges and opportunities

Santos-Pereira

Rodrigues

Côrte‐Real

2021

Medicinal Research Reviews

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The control of the intracellular pH is vital for the survival of all organisms. Membrane transporters, both at the plasma and intracellular membranes, are key players in maintaining a finely tuned pH balance between intra‐ and extracellular spaces, and therefore in cellular homeostasis. V‐ATPase is a housekeeping ATP‐driven proton pump highly conserved among prokaryotes and eukaryotes. This proton pump, which exhibits a complex multisubunit structure based on cell type‐specific isoforms, is essential for pH regulation and for a multitude of ubiquitous and specialized functions. Thus, it is not surprising that V‐ATPase aberrant overexpression, mislocalization, and mutations in V‐ATPase subunit‐encoding genes have been associated with several human diseases. However, the ubiquitous expression of this transporter and the high toxicity driven by its off‐target inhibition, renders V‐ATPase‐directed therapies very challenging and increases the need for selective strategies. Here we review emerging evidence linking V‐ATPase and both inherited and acquired human diseases, explore the therapeutic challenges and opportunities envisaged from recent data, and advance future research avenues. We highlight the importance of V‐ATPases with unique subunit isoform molecular signatures and disease‐associated isoforms to design selective V‐ATPase‐directed therapies. We also discuss the rational design of drug development pipelines and cutting‐edge methodological approaches toward V‐ATPase‐centered drug discovery. Diseases like cancer, osteoporosis, and even fungal infections can benefit from V‐ATPase‐directed therapies.

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Section: V‐atpases: Attractive Targets For a Multitude Of Human Diseasesmentioning

confidence: 97%

Emerging insights on the role of V‐ATPase in human diseases: Therapeutic challenges and opportunities

Santos-Pereira

Rodrigues

Côrte‐Real

2021

Medicinal Research Reviews

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“…Methods for performing an arrayed siRNA library screen have been reviewed by us and others in detail elsewhere (Barrows et al, 2014;Chin & Brass, 2013;Panda & Cherry, 2015). Briefly, the project begins with optimizations of both siRNA transfection and infection conditions in the plate format chosen for the screen, with 384-well plates being strongly preferred due to lower amounts of siRNA library needed and the decreased costs and work load using this smaller scale.…”

Section: Arrayed Rnai Screeningmentioning

confidence: 99%

Functional Genomic Strategies for Elucidating Human–Virus Interactions

Perreira

Meraner

Brass

2016

Advances in Virus Research

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Over the last several years a wealth of transformative human-virus interaction discoveries have been produced using loss-of-function functional genomics. These insights have greatly expanded our understanding of how human pathogenic viruses exploit our cells to replicate. Two technologies have been at the forefront of this genetic revolution, RNA interference (RNAi) and random retroviral insertional mutagenesis using haploid cell lines (haploid cell screening), with the former technology largely predominating. Now the cutting edge gene editing of the CRISPR/Cas9 system has also been harnessed for large-scale functional genomics and is poised to possibly displace these earlier methods. Here we compare and contrast these three screening approaches for elucidating host-virus interactions, outline their key strengths and weaknesses including a comparison of an arrayed multiple orthologous RNAi reagent screen to a pooled CRISPR/Cas9 human rhinovirus 14-human cell interaction screen, and recount some notable insights made possible by each. We conclude with a brief perspective on what might lie ahead for the fast evolving field of human-virus functional genomics.

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“…Vacuolar ATPase (v-ATPase) activity, which is responsible for pumping protons into endosomal compartments, has been identified as a requirement for influenza virus replication in previous studies (Guinea and Carrasco, 1995;Muller et al, 2011;Perez and Carrasco, 1994). V-ATPase-encoding genes have also been identified in several genome-wide screens for host factors regulating influenza virus replication, and the knockdown of v-ATPase subunits has been shown to result in significant inhibition of influenza virus replications (Chin and Brass, 2012;Hao et al, 2008;Karlas et al, 2010;Konig et al, 2010;Mehle and Doudna, 2010). Blocking v-ATPase activity, therefore, presents an opportunity to impede influenza infection by preventing the low pH-dependent membrane fusion between endosomes and virions.…”

Section: Introductionmentioning

confidence: 99%

Inhibitory and combinatorial effect of diphyllin, a v-ATPase blocker, on influenza viruses

Chen

Cheng

Liu³

et al. 2013

Antiviral Research

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An influenza pandemic poses a serious threat to humans and animals. Conventional treatments against influenza include two classes of pathogen-targeting antivirals: M2 ion channel blockers (such as amantadine) and neuraminidase inhibitors (such as oseltamivir). Examination of the mechanism of influenza viral infection has shown that endosomal acidification plays a major role in facilitating the fusion between viral and endosomal membranes. This pathway has led to investigations on vacuolar ATPase (v-ATPase) activity, whose role as a regulating factor on influenza virus replication has been verified in extensive genome-wide screenings. Blocking v-ATPase activity thus presents the opportunity to interfere with influenza viral infection by preventing the pH-dependent membrane fusion between endosomes and virions. This study aims to apply diphyllin, a natural compound shown to be as a novel v-ATPase inhibitor, as a potential antiviral for various influenza virus strains using cell-based assays. The results show that diphyllin alters cellular susceptibility to influenza viruses through the inhibition of endosomal acidification, thus interfering with downstream virus replication, including that of known drug-resistant strains. In addition, combinatorial treatment of the host-targeting diphyllin with pathogen-targeting therapeutics (oseltamivir and amantadine) demonstrates enhanced antiviral effects and cell protection in vitro.

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A genome wide RNA interference screening method to identify host factors that modulate Influenza A virus replication

Cited by 9 publications

References 24 publications

Emerging insights on the role of V‐ATPase in human diseases: Therapeutic challenges and opportunities

Emerging insights on the role of V‐ATPase in human diseases: Therapeutic challenges and opportunities

Functional Genomic Strategies for Elucidating Human–Virus Interactions

Inhibitory and combinatorial effect of diphyllin, a v-ATPase blocker, on influenza viruses

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