Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response

• Published in: PLoS computational biology 2015-10, Vol.11 (10), p.e1004553-e1004553
• Main Authors: van der Lee, Robin, Feng, Qian, Langereis, Martijn A, Ter Horst, Rob, Szklarczyk, Radek, Netea, Mihai G, Andeweg, Arno C, van Kuppeveld, Frank J M, Huynen, Martijn A
• Format: Article
• Language: English
• Subjects: Antiviral agents; Cytokines - genetics; Cytokines - immunology; Data mining; Datasets; DEAD Box Protein 58; DEAD-box RNA Helicases - immunology; Distribution; Drug therapy; Experiments; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Viral - genetics; Gene Expression Regulation, Viral - immunology; Genomes; Genomics; Genomics - methods; Health aspects; Immunity, Innate - immunology; Influenza; Influenza viruses; Interferon; Proteins; Receptors, Immunologic; RNA, Viral - genetics; RNA, Viral - immunology; Studies; Systems Integration; Transcription factors; Virus Integration - genetics; Virus Integration - immunology; Viruses; Viruses - genetics; Viruses - immunology
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1004553

The RIG-I-like receptor (RLR) pathway is essential for detecting cytosolic viral RNA to trigger the production of type I interferons (IFNα/β) that initiate an innate antiviral response. Through systematic assessment of a wide variety of genomics data, we discovered 10 molecular signatures of known RLR pathway components that collectively predict novel members. We demonstrate that RLR pathway genes, among others, tend to evolve rapidly, interact with viral proteins, contain a limited set of protein domains, are regulated by specific transcription factors, and form a tightly connected interaction network. Using a Bayesian approach to integrate these signatures, we propose likely novel RLR regulators. RNAi knockdown experiments revealed a high prediction accuracy, identifying 94 genes among 187 candidates tested (~50%) that affected viral RNA-induced production of IFNβ. The discovered antiviral regulators may participate in a wide range of processes that highlight the complexity of antiviral defense (e.g. MAP3K11, CDK11B, PSMA3, TRIM14, HSPA9B, CDC37, NUP98, G3BP1), and include uncharacterized factors (DDX17, C6orf58, C16orf57, PKN2, SNW1). Our validated RLR pathway list (http://rlr.cmbi.umcn.nl/), obtained using a combination of integrative genomics and experiments, is a new resource for innate antiviral immunity research.