The type I interferon (IFN) response protects cells from viral infection by inducing hundreds of interferon-stimulated genes (ISGs), some of which encode direct antiviral effectors1,2,3. Recent screening studies have begun to catalogue ISGs with antiviral activity against several RNA and DNA viruses4,5,6,7,8,9,10,11,12,13. However, antiviral ISG specificity across multiple distinct classes of viruses remains largely unexplored. Here we used an ectopic expression assay to screen a library of more than 350 human ISGs for effects on 14 viruses representing 7 families and 11 genera. We show that 47 genes inhibit one or more viruses, and 25 genes enhance virus infectivity. Comparative analysis reveals that the screened ISGs target positive-sense single-stranded RNA viruses more effectively than negative-sense single-stranded RNA viruses. Gene clustering highlights the cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS, also known as MB21D1) as a gene whose expression also broadly inhibits several RNA viruses. In vitro, lentiviral delivery of enzymatically active cGAS triggers a STING-dependent, IRF3-mediated antiviral program that functions independently of canonical IFN/STAT1 signalling. In vivo, genetic ablation of murine cGAS reveals its requirement in the antiviral response to two DNA viruses, and an unappreciated contribution to the innate control of an RNA virus. These studies uncover new paradigms for the preferential specificity of IFN-mediated antiviral pathways spanning several virus families.
Subscribe to Journal
Get full journal access for 1 year
only $3.83 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Der, S. D., Zhou, A., Williams, B. R. & Silverman, R. H. Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 15623–15628 (1998)
de Veer, M. J. et al. Functional classification of interferon-stimulated genes identified using microarrays. J. Leukoc. Biol. 69, 912–920 (2001)
Schoggins, J. W. & Rice, C. M. Interferon-stimulated genes and their antiviral effector functions. Curr. Opin. Virol. 1, 519–525 (2011)
Schoggins, J. W. et al. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472, 481–485 (2011)
Liu, S. Y., Sanchez, D. J., Aliyari, R., Lu, S. & Cheng, G. Systematic identification of type I and type II interferon-induced antiviral factors. Proc. Natl Acad. Sci. USA 109, 4239–4244 (2012)
Metz, P. et al. Identification of type I and type II interferon-induced effectors controlling hepatitis C virus replication. Hepatology 56, 2082–2093 (2012)
Fusco, D. N. et al. A genetic screen identifies interferon-α effector genes required to suppress hepatitis C virus replication. Gastroenterology 144, 1438–1449 (2013)
Zhao, H. et al. A functional genomic screen reveals novel host genes that mediate interferon-alpha’s effects against hepatitis C virus. J. Hepatol. 56, 326–333 (2012)
Zhang, Y., Burke, C. W., Ryman, K. D. & Klimstra, W. B. Identification and characterization of interferon-induced proteins that inhibit alphavirus replication. J. Virol. 81, 11246–11255 (2007)
Wilson, S. J. et al. Inhibition of HIV-1 particle assembly by 2′,3′-cyclic-nucleotide 3′-phosphodiesterase. Cell Host Microbe 12, 585–597 (2012)
Schoggins, J. W. et al. Dengue reporter viruses reveal viral dynamics in interferon receptor-deficient mice and sensitivity to interferon effectors in vitro. Proc. Natl Acad. Sci. USA 109, 14610–14615 (2012)
Karki, S. et al. Multiple interferon stimulated genes synergize with the zinc finger antiviral protein to mediate anti-alphavirus activity. PLoS ONE 7, e37398 (2012)
Meng, X. et al. C7L family of poxvirus host range genes inhibits antiviral activities induced by type I interferons and interferon regulatory factor 1. J. Virol. 86, 4538–4547 (2012)
Dupuis, S. et al. Impaired response to interferon-α/β and lethal viral disease in human STAT1 deficiency. Nature Genet. 33, 388–391 (2003)
Sun, L., Wu, J., Du, F., Chen, X. & Chen, Z. J. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339, 786–791 (2013)
Wu, J. et al. Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA. Science 339, 826–830 (2013)
Kranzusch, P. J., Lee, A. S.-Y., Berger, J. M. & Doudna, J. A. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Rep. 3, 1362–1368 (2013)
Gao, P. et al. Cyclic [G(2′,5′)pA(3′,5′)p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell 153, 1094–1107 (2013)
Civril, F. et al. Structural mechanism of cytosolic DNA sensing by cGAS. Nature 498, 332–337 (2013)
Gao, D. et al. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 341, 903–906 (2013)
Li, X. D. et al. Pivotal roles of cGAS-cGAMP signaling in antiviral defense and immune adjuvant effects. Science 341, 1390–1394 (2013)
Suthar, M. S. et al. IPS-1 is essential for the control of West Nile virus infection and immunity. PLoS Pathog. 6, e1000757 (2010)
Errett, J. S., Suthar, M. S., McMillan, A., Diamond, M. S. & Gale, M., Jr The essential, non-redundant roles of RIG-I and MDA5 in detecting and controlling West Nile virus infection. J. Virol. 87, 11416–11425 (2013)
Feuer, R., Mena, I., Pagarigan, R., Slifka, M. K. & Whitton, J. L. Cell cycle status affects coxsackievirus replication, persistence, and reactivation in vitro. J. Virol. 76, 4430–4440 (2002)
Teterina, N. L., Levenson, E. A. & Ehrenfeld, E. Viable polioviruses that encode 2A proteins with fluorescent protein tags. J. Virol. 84, 1477–1488 (2010)
van den Born, E., Posthuma, C. C., Knoops, K. & Snijder, E. J. An infectious recombinant equine arteritis virus expressing green fluorescent protein from its replicase gene. J. Gen. Virol. 88, 1196–1205 (2007)
Simmons, J. D., Wollish, A. C. & Heise, M. T. A determinant of Sindbis virus neurovirulence enables efficient disruption of Jak/STAT signaling. J. Virol. 84, 11429–11439 (2010)
Brault, A. C. et al. Infection patterns of o’nyong nyong virus in the malaria-transmitting mosquito, Anopheles gambiae. Insect Mol. Biol. 13, 625–635 (2004)
Manicassamy, B. et al. Analysis of in vivo dynamics of influenza virus infection in mice using a GFP reporter virus. Proc. Natl Acad. Sci. USA 107, 11531–11536 (2010)
Zhang, L. et al. Infection of ciliated cells by human parainfluenza virus type 3 in an in vitro model of human airway epithelium. J. Virol. 79, 1113–1124 (2005)
Park, M. S. et al. Newcastle disease virus (NDV)-based assay demonstrates interferon-antagonist activity for the NDV V protein and the Nipah virus V, W, and C proteins. J. Virol. 77, 1501–1511 (2003)
Biacchesi, S. et al. Recovery of human metapneumovirus from cDNA: optimization of growth in vitro and expression of additional genes. Virology 321, 247–259 (2004)
del Valle, J. R. et al. A vectored measles virus induces hepatitis B surface antigen antibodies while protecting macaques against measles virus challenge. J. Virol. 81, 10597–10605 (2007)
Shi, X., van Mierlo, J. T., French, A. & Elliott, R. M. Visualizing the replication cycle of bunyamwera orthobunyavirus expressing fluorescent protein-tagged Gc glycoprotein. J. Virol. 84, 8460–8469 (2010)
Ebel, G. D., Carricaburu, J., Young, D., Bernard, K. A. & Kramer, L. D. Genetic and phenotypic variation of West Nile virus in New York, 2000–2003. Am. J. Trop. Med. Hyg. 71, 493–500 (2004)
Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808–D815 (2013)
Kanki, H., Suzuki, H. & Itohara, S. High-efficiency CAG-FLPe deleter mice in C57BL/6J background. Exp. Anim. 55, 137–141 (2006)
Hwang, S. et al. Nondegradative role of Atg5-Atg12/Atg16L1 autophagy protein complex in antiviral activity of interferon gamma. Cell Host Microbe 11, 397–409 (2012)
Daffis, S., Samuel, M. A., Keller, B. C., Gale, M., Jr & Diamond, M. S. Cell-specific IRF-3 responses protect against West Nile virus infection by interferon-dependent and -independent mechanisms. PLoS Pathog. 3, e106 (2007)
We thank the following investigators for contributing viral molecular clones or viral stocks: R. Cattaneo (MV), P. Collins (PIV3, HMPV, RSV), I Frolov (VEEV), M. Heise (SINV), S. Higgs (ONNV), P. Traktman (VV), J. L. Whitton (CVB). We thank E. Jouanguy and J.-L. Casanova for STAT1−/− fibroblasts. We acknowledge the support of C. Zhao, X. Wang and W. Zhang at The Rockefeller University Genomics Resource Center. We thank E. Castillo, B. Flatley, A. Webson, E. Duan and A. McLees for laboratory support, and D. Kraemalmeyer for managing mouse colonies. This work was supported in part by National Institutes of Health grants AI091707 to C.M.R., AI057158 to I. Lipkin (Northeast Biodefense Center, subcontract to C.M.R.), DK095031 to J.W.S., AI057160 to H.W.V., HHSN272200900041CU19 to M.S.D. and H.W.V., AI104972 to M.S.D., AI083025, AI095611 and CEIRS contract HHSN266200700010C to A.G-S., GM076547 and GM103511 to J.D.A. and AI057160 to W.M.Y., an investigator of the Howard Hughes Medical Institute. M.D.G. is supported by T32 AR007279. Additional funding was provided by the Greenberg Medical Research Institute, the Starr Foundation and the Ronald A. Shellow, M.D. Memorial Fund (C.M.R.).
The authors declare no competing financial interests.
Extended data figures and tables
HeLa cells were transfected with plasmids encoding ISGs and 48 h later infected with P1M (10 m.o.i.) for 16 h. Lysates were collected and viral titres determined by plaque assay on HeLa cell monolayers, as described in Methods. Plaque assays were performed in duplicate. Data represent the average of three independent experiments. Error bars represent s.d.
a–e, Analyses were performed as described in Methods. In each cluster, one or more ISGs were removed from the analysis in Fig. 3a to determine whether virus clustering is driven by a subset of one or more dominant genes. Blue and green bars underscore +ssRNA and −ssRNA viruses, respectively. f, The top 30 ISG inhibitors from the primary screens were compiled as a gene list and transformed to a binarized vector for clustering using MATLAB Statistics Toolbox (see Methods). A dendrogram was generated from the clustering analysis to show how viruses relate to each other with respect to the ISGs that target them.
ISGs were assigned a frequency on the basis of the number of times the gene appeared in a list of the 20 most inhibitory genes from 7 +ssRNA or 5 −ssRNA virus screens. A frequency of 1 indicates an occurrence of 100% across all gene lists. Co-occurrence is reflected by adjacent red and blue bars.
a, 293 cells were transduced with lentiviruses expressing ISGs, followed by transfection with an ISRE reporter plasmid expressing Fluc. Cells were assayed for Fluc activity 24 h after transfection. b, 293 cells were co-transfected with ISG-expressing plasmids and an ISRE reporter plasmid. The cells were then treated overnight with 1,000 U ml−1 interferon-α (IFN-α), followed by Fluc activity assay. Data represent the average of three independent experiments performed in triplicate. Error bars represent s.d. Statistical significance was determined by one-way ANOVA or t-test. *P < 0.05, ***P < 0.001.
a, STAT1−/− fibroblasts were transfected with individual siRNAs targeting STING. Cell lysates were processed 48 h after transfection for western blot with anti-STING- or anti-actin-specific antibodies. From these results, siRNA no. 1 was chosen for additional studies. b, Schematic of cGAS protein sequence and truncation mutants. Red box, α-helix; blue box, β-sheet. Circles denote catalytic residues E225A and D227A. c, STAT1−/− fibroblasts were transduced with lentivirus expressing control or cGAS (wild type and truncation mutants). Cells were infected 48 h after transduction with VEEV-GFP and infectivity was monitored by FACS. Data represent the mean of two independent experiments. Error bars represent s.d. Statistical significance was determined by one-way ANOVA. *P < 0.05, **P < 0.01. d, STAT1−/− fibroblasts were transduced with lentivirus expressing control or cGAS (wild type and mutants). Cells were collected 48 h after transduction and total RNA was analysed for OAS2 mRNA induction relative to RPS11 (top), or protein lysates were analysed for phospho-IRF3 and actin expression by western blot (bottom). e, STAT1−/− fibroblasts were transduced with a puromycin-selectable lentivirus expressing cGAS and placed under selection. At various passages, cells were collected and total RNA was analysed for OAS2 mRNA induction relative to RPS11 (top), or protein lysates were analysed for cGAS and actin expression by western blot (bottom). Western blot and cGAS mRNA data represent one of two independent experiments, each showing similar results. OAS2 mRNA data are presented as the average of two independent experiments, each performed in triplicate. Error bars represent s.d.
a, Mice expressing a cGas exon 2 gene-trap cassette were crossed to FlpE-expressing mice to generate conditional knockouts. These mice were then crossed to Cre-expressing mice to generate the knockout allele with a deletion of exon 2, which contains the cGAS catalytic sites. Mice were backcrossed to remove Cre, and cGas+/− mice were intercrossed to derive cGas−/− mice. b, PCR products from genomic DNA of cGas+/+, cGas+/− and cGas−/− mice using primers outlined in a. c, qRT–PCR of relative cGas expression in lungs (left) or BMMO (right) from wild-type B6 and cGas−/− mice. Data from lung represent means of three mice per group. Data from BMMO were derived from two independent experiments performed in triplicate. Error bars represent s.e.m. Statistical significance was determined by t-test. *P < 0.05, ***P < 0.001.
Wild-type or cGas−/− mice were infected with WNV and viral titres in several regions of the brain were determined by plaque assay. n = 10 mice per group. Statistical significance was determined by t-test.
a, BMMO from wild-type and cGas−/− mice were analysed for baseline expression of chemokines Ccl5 and Cxcl10 by RT–PCR. b, BMMO from wild-type and cGas−/− mice were treated with polyIC (pIC) or transfected with polyIC (Tf-pIC) and Ifnb and Ifit1 levels were determined by qRT–PCR. In both panels, gene expression levels are relative to the housekeeping gene RPS29 and normalized to mock-treated wild-type cells. Data represent two experiments performed in triplicate. Error bars represent s.d. Statistical significance was determined by t-test. *P < 0.05, **P < 0.01, ***P < 0.001.
About this article
Cite this article
Schoggins, J., MacDuff, D., Imanaka, N. et al. Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature 505, 691–695 (2014). https://doi.org/10.1038/nature12862
Cyclic GMP-AMP synthase is essential for cytosolic double-stranded DNA and fowl adenovirus serotype 4 triggered innate immune responses in chickens
International Journal of Biological Macromolecules (2020)
Infection, Genetics and Evolution (2020)
Determination of antiviral action of long non-coding RNA loc107051710 during infectious bursal disease virus infection due to enhancement of interferon production
Suppressors of Cytokine Signaling and Protein Inhibitors of Activated Signal Transducer and Activator of Transcriptions As Therapeutic Targets in Flavivirus Infections
Journal of Interferon & Cytokine Research (2020)