scholarly journals Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening

2018 ◽  
Author(s):  
Robert C. Orchard ◽  
Meagan E. Sullender ◽  
Bria F. Dunlap ◽  
Dale R. Balce ◽  
John G. Doench ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
World Wide ◽  
Human Cells ◽  
Gene Promoters ◽  
Murine Norovirus ◽  
Individual Gene ◽  
Genome Wide ◽  
Host Genes ◽  
Crispr Activation

AbstractNoroviruses (NoVs) are a leading cause of gastroenteritis world-wide, yet host factors that restrict NoV replication are not well understood. Here, we use a CRISPR activation (CRISPRa) genome-wide screening to identify host genes that can inhibit murine norovirus (MNoV) replication in either mouse or human cells. Our screens identified with high confidence 57 genes that can inhibit MNoV infection when overexpressed. A significant number of these genes are in interferon and immune regulation signaling networks, but surprising, the majority of the genes identified are not associated with innate or adaptive immunity nor with any antiviral activity. Confirmatory studies of eight of the genes in validate the initial screening data. Mechanistic studies on TRIM7 demonstrated a conserved role of the molecule in mouse and human cells in restricting MNoV in a step of infection after viral entry. Furthermore, we demonstrate that two isoforms of TRIM7 have differential antiviral activity. Taken together these data provide a resource for understanding norovirus biology and demonstrate a robust methodology for identifying new antiviral molecules across cell types and species.Author SummaryNorovirus is one of the leading causes of foodborne illness world-wide. Despite its prevalence, our understanding of norovirus biology is limited due to the difficulty in growing human norovirus in vitro and a lack of an animal model. Murine norovirus (MNoV) is a model norovirus system because MNoV replicates robustly in cell culture and in mice. To identify host genes that can restrict norovirus replication when overexpressed we performed genome-wide CRISPR activation (CRISPRa) screens to induce gene overexpression at the native locus through recruitment of transcriptional activators to individual gene promoters. We found 57 genes could block murine norovirus replication in either mouse or human cells. Several of these genes are associated with classical immune signaling pathways, while many of the molecules we identified have not been previously associated with antiviral activity. Our data is a resource for those studying norovirus and we provide a robust approach to identify novel antiviral genes.

scholarly journals Identification of Antinorovirus Genes in Human Cells Using Genome-Wide CRISPR Activation Screening

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Robert C. Orchard ◽  
Meagan E. Sullender ◽  
Bria F. Dunlap ◽  
Dale R. Balce ◽  
John G. Doench ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Viral Entry ◽  
Human Cells ◽  
Gene Promoters ◽  
Murine Norovirus ◽  
Individual Gene ◽  
Genome Wide ◽  
Host Genes ◽  
Crispr Activation

ABSTRACT Noroviruses (NoVs) are a leading cause of gastroenteritis worldwide, yet host factors that restrict NoV replication are not well understood. Here, we use a CRISPR activation genome-wide screening to identify host genes that can inhibit murine norovirus (MNoV) replication in human cells. Our screens identified with high confidence 49 genes that can inhibit MNoV infection when overexpressed. A significant number of these genes are in interferon and immune regulation signaling networks, but surprisingly, the majority of the genes identified are neither associated with innate or adaptive immunity nor associated with any antiviral activity. Confirmatory studies of eight of the genes validate the initial screening data. Mechanistic studies on TRIM7 demonstrated a conserved role of the molecule in mouse and human cells in restricting MNoV in a step of infection after viral entry. Furthermore, we demonstrate that two isoforms of TRIM7 have differential antiviral activity. Taken together, these data provide a resource for understanding norovirus biology and demonstrate a robust methodology for identifying new antiviral molecules. IMPORTANCE Norovirus is one of the leading causes of food-borne illness worldwide. Despite its prevalence, our understanding of norovirus biology is limited due to the difficulty in growing human norovirus in vitro and a lack of an animal model. Murine norovirus (MNoV) is a model norovirus system because MNoV replicates robustly in cell culture and in mice. To identify host genes that can restrict norovirus replication when overexpressed, we performed genome-wide CRISPR activation screens to induce gene overexpression at the native locus through recruitment of transcriptional activators to individual gene promoters. We found 49 genes that could block murine norovirus replication in human cells. Several of these genes are associated with classical immune signaling pathways, while many of the molecules we identified have not been previously associated with antiviral activity. Our data are a resource for those studying noroviruses, and we provide a robust approach to identify novel antiviral genes.

scholarly journals Inhibition of the replication of SARS-CoV-2 in human cells by the FDA-approved drug chlorpromazine

2020 ◽  
Author(s):  
Marion Plaze ◽  
David Attali ◽  
Matthieu Prot ◽  
Anne-Cécile Petit ◽  
Michael Blatzer ◽  
...  
Keyword(s):  
Health Care ◽  
Side Effects ◽  
Antiviral Activity ◽  
Health Care Professionals ◽  
Human Cells ◽  
Clinical Routine ◽  
Infected People ◽  
Typical Antipsychotics ◽  
Urgent Action

AbstractUrgent action is needed to fight the ongoing COVID-19 pandemic by reducing the number of infected people along with the infection contagiousness and severity. Chlorpromazine (CPZ), the prototype of typical antipsychotics from the phenothiazine group, is known to inhibit clathrin-mediated endocytosis and acts as an antiviral, in particular against SARS-CoV-1 and MERS-CoV. In this study, we describe the in vitro testing of CPZ against a SARS-CoV-2 isolate in monkey and human cells. We evidenced an antiviral activity against SARS-CoV-2 with an IC50 of ∼10μM. Because of its high biodistribution in lung, saliva and brain, such IC50 measured in vitro may translate to CPZ dosage used in clinical routine. This extrapolation is in line with our observations of a higher prevalence of symptomatic and severe forms of COVID-19 infections among health care professionals compared to patients in psychiatric wards. These preclinical findings support the repurposing of CPZ, a largely used drug with mild side effects, in COVID-19 treatment.

scholarly journals Suppression of Viral RNA Recombination by a Host Exoribonuclease

2006 ◽  
Vol 80 (6) ◽  
pp. 2631-2640 ◽  
Author(s):  
Chi-Ping Cheng ◽  
Elena Serviene ◽  
Peter D. Nagy
Keyword(s):  
Rna Virus ◽  
Viral Rna ◽  
Rna Turnover ◽  
Rna Recombination ◽  
Viral Rnas ◽  
Yeast Strains ◽  
Genome Wide ◽  
Host Genes

ABSTRACT RNA viruses of humans, animals, and plants evolve rapidly due to mutations and RNA recombination. A previous genome-wide screen in Saccharomyces cerevisiae, a model host, identified five host genes, including XRN1, encoding a 5′-3′ exoribonuclease, whose absence led to an ∼10- to 50-fold enhancement of RNA recombination in Tomato bushy stunt virus (E. Serviene, N. Shapka, C. P. Cheng, T. Panavas, B. Phuangrat, J. Baker, and P. D. Nagy, Proc. Natl. Acad. Sci. USA 102:10545-10550, 2005). In this study, we found abundant 5′-truncated viral RNAs in xrn1Δ mutant strains but not in the parental yeast strains, suggesting that these RNAs might serve as recombination substrates promoting RNA recombination in xrn1Δ mutant yeast. This model is supported by data showing that an enhanced level of viral recombinant accumulation occurred when two different 5′-truncated viral RNAs were expressed in the parental and xrn1Δ mutant yeast strains or electroporated into plant protoplasts. Moreover, we demonstrate that purified Xrn1p can degrade the 5′-truncated viral RNAs in vitro. Based on these findings, we propose that Xrn1p can suppress viral RNA recombination by rapidly removing the 5′-truncated RNAs, the substrates of recombination, and thus reducing the chance for recombination to occur in the parental yeast strain. In addition, we show that the 5′-truncated viral RNAs are generated by host endoribonucleases. Accordingly, overexpression of the Ngl2p endoribonuclease led to an increased accumulation of cleaved viral RNAs in vivo and in vitro. Altogether, this paper establishes that host ribonucleases and host-mediated viral RNA turnover play major roles in RNA virus recombination and evolution.

scholarly journals Papaya Fruit Pulp and Resulting Lactic Fermented Pulp Exert Antiviral Activity against Zika Virus

2020 ◽  
Vol 8 (9) ◽  
pp. 1257
Author(s):  
Juliano G. Haddad ◽  
Victoria Carcauzon ◽  
Omar El Kalamouni ◽  
Philippe Desprès ◽  
Cyrielle Garcia ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Zika Virus ◽  
Human Cells ◽  
Host Cells ◽  
Dependent Manner ◽  
Bacterial Strains ◽  
Lactic Fermentation ◽  
Papaya Pulp ◽  
Leuconostoc Pseudomesenteroides

There are a several emerging and re-emerging RNA viruses that are prevalent around the world for which there are no licensed vaccines or antiviral drugs. Zika virus (ZIKV) is an example of an emerging virus that has become a significant concern worldwide because of its association with severe congenital malformations and neurological disorders in adults. Several polyphenol-rich extracts from plants were used as nutraceuticals which exhibit potent in vitro antiviral effects. Here, we demonstrated that the papaya pulp extracted from Carica papaya fruit inhibits the infection of ZIKV in human cells without loss of cell viability. At the non-cytotoxic concentrations, papaya pulp extract has the ability to reduce the virus progeny production in ZIKV-infected human cells by at least 4-log, regardless of viral strains tested. Time-of-drug-addition assays revealed that papaya pulp extract interfered with the attachment of viral particles to the host cells. With a view of preserving the properties of papaya pulp over time, lactic fermentation based on the use of bacterial strains Weissella cibaria 64, Lactobacillus plantarum 75 and Leuconostoc pseudomesenteroides 56 was performed and the resulting fermented papaya pulp samples were tested on ZIKV. We found that lactic fermentation of papaya pulp causes a moderate loss of antiviral activity against ZIKV in a bacterial strain-dependent manner. Whereas IC50 of the papaya pulp extract was 0.3 mg/mL, we found that fermentation resulted in IC50 up to 4 mg/mL. We can conclude that papaya pulp possesses antiviral activity against ZIKV and the fermentation process has a moderate effect on the antiviral effect.

scholarly journals The Adenosine Analogue NITD008 has Potent Antiviral Activity against Human and Animal Caliciviruses

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 496
Author(s):  
Daniel Enosi Tuipulotu ◽  
Tulio M. Fumian ◽  
Natalie E. Netzler ◽  
Jason M. Mackenzie ◽  
Peter A. White
Keyword(s):  
Antiviral Activity ◽  
Well Being ◽  
Model Systems ◽  
Murine Norovirus ◽  
Substantial Impact ◽  
Antiviral Compounds ◽  
Adenosine Analogue ◽  
Health And Well Being

The widespread nature of calicivirus infections globally has a substantial impact on the health and well-being of humans and animals alike. Currently, the only vaccines approved against caliciviruses are for feline and rabbit-specific members of this group, and thus there is a growing effort towards the development of broad-spectrum antivirals for calicivirus infections. In this study, we evaluated the antiviral activity of the adenosine analogue NITD008 in vitro using three calicivirus model systems namely; feline calicivirus (FCV), murine norovirus (MNV), and the human norovirus replicon. We show that the nucleoside analogue (NA), NITD008, has limited toxicity and inhibits calicivirus replication in all three model systems with EC50 values of 0.94 μM, 0.91 µM, and 0.21 µM for MNV, FCV, and the Norwalk replicon, respectively. NITD008 has a similar level of potency to the most well-studied NA 2′-C-methylcytidine in vitro. Significantly, we also show that continual NITD008 treatment effectively cleared the Norwalk replicon from cells and treatment with 5 µM NITD008 was sufficient to completely prevent rebound. Given the potency displayed by NITD008 against several caliciviruses, we propose that this compound should be interrogated further to assess its effectiveness in vivo. In summary, we have added a potent NA to the current suite of antiviral compounds and provide a NA scaffold that could be further modified for therapeutic use against calicivirus infections.

scholarly journals In vitro antiviral activity of dieckol and phlorofucofuroeckol-A isolated from edible brown alga Eisenia bicyclis against murine norovirus

ALGAE ◽  
2015 ◽  
Vol 30 (3) ◽  
pp. 241-246 ◽  
Author(s):  
Sung-Hwan Eom ◽  
Sun-Young Moon ◽  
Dae-Sung Lee ◽  
Hyo-Jung Kim ◽  
Kunbawui Park ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Brown Alga ◽  
Murine Norovirus ◽  
Eisenia Bicyclis

scholarly journals Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis

2018 ◽  
Author(s):  
Kwan-Wood Gabriel Lam ◽  
Kevin Brick ◽  
Gang Cheng ◽  
Florencia Pratto ◽  
R. Daniel Camerini-Otero
Keyword(s):  
Meiotic Prophase ◽  
Genetic Recombination ◽  
Gene Promoters ◽  
Recombination Hotspots ◽  
Genome Wide ◽  
Cell Type Specific ◽  
Genome Wide Survey ◽  
Meiotic Recombination Hotspots

AbstractMeiosis is the specialized cell division during which parental genomes recombine to create genotypically unique gametes. Despite its importance, mammalian meiosis cannot be studied in vitro, greatly limiting mechanistic studies. In vivo, meiocytes progress asynchronously through meiosis and therefore the study of specific stages of meiosis is a challenge. Here, we describe a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic sub-stages. Interrogating the H3K4me3 landscape revealed dynamic chromatin transitions between sub-stages of meiotic prophase I, both at sites of genetic recombination and at gene promoters. We also leveraged this method to perform the first comprehensive, genome-wide survey of histone marks in meiotic prophase, revealing a heretofore unappreciated complexity of the epigenetic landscape at meiotic recombination hotspots. Ultimately, this study presents a straightforward, scalable framework for interrogating the complexities of mammalian meiosis.

scholarly journals Unbiased investigation of specificities of prime editing systems in human cells

2020 ◽  
Vol 48 (18) ◽  
pp. 10576-10589 ◽  
Author(s):  
Do Yon Kim ◽  
Su Bin Moon ◽  
Jeong-Heon Ko ◽  
Yong-Sam Kim ◽  
Daesik Kim
Keyword(s):  
Amplicon Sequencing ◽  
Human Cells ◽  
Specific Method ◽  
Vitro Assay ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
Target Sites ◽  
Human Genomic

Abstract Prime editors (PEs) enable targeted precise editing, including the generation of substitutions, insertions and deletions, in eukaryotic genomes. However, their genome-wide specificity has not been explored. Here, we developed Nickase-based Digenome-seq (nDigenome-seq), an in vitro assay that uses whole-genome sequencing to identify single-strand breaks induced by CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) nickase. We used nDigenome-seq to screen for potential genome-wide off-target sites of Cas9 H840A nickase, a PE component, targeted to nine human genomic sites. Then, using targeted amplicon sequencing of off-target candidates identified by nDigenome-seq, we showed that only five off-target sites showed detectable PE-induced modifications in cells, at frequencies ranging from 0.1 to 1.9%, suggesting that PEs provide a highly specific method of precise genome editing. We also found that PE specificity in human cells could be further improved by incorporating mutations from engineered Cas9 variants, particularly eSpCas9 and Sniper Cas9, into PE.

scholarly journals Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells

PLoS Genetics ◽  
2016 ◽  
Vol 12 (2) ◽  
pp. e1005901 ◽  
Author(s):  
Xinlei Lian ◽  
Jiahui Guo ◽  
Wei Gu ◽  
Yizhi Cui ◽  
Jiayong Zhong ◽  
...  
Keyword(s):  
Human Cells ◽  
Translation Elongation ◽  
Individual Gene ◽  
Genome Wide ◽  
Gene Level ◽  
Experimental Resolution

Phenolic Compounds Present in Medicinal Mushroom Extracts Generate Reactive Oxygen Species in Human Cells In Vitro

2008 ◽  
Vol 10 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Song Wei ◽  
Johannes P. F. G. Helsper ◽  
L. J. L. D. Van Griensven
Keyword(s):  
Reactive Oxygen Species ◽  
Phenolic Compounds ◽  
Reactive Oxygen ◽  
Human Cells ◽  
Oxygen Species ◽  
Medicinal Mushroom ◽  
Mushroom Extracts
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