Systems-biology Approaches to Discover Anti-viral Effectors of the Human Innate Immune Response

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2011 Oct 14

PMID 21994773

Citations 7

Authors

Carsten Munk

Andreas F R Sommer

Renate Konig

Affiliations

Soon will be listed here.

Abstract

Virus infections elicit an immediate innate response involving antiviral factors. The activities of some of these factors are, in turn, blocked by viral countermeasures. The ensuing battle between the host and the viruses is crucial for determining whether the virus establishes a foothold and/or induces adaptive immune responses. A comprehensive systems-level understanding of the repertoire of anti-viral effectors in the context of these immediate virus-host responses would provide significant advantages in devising novel strategies to interfere with the initial establishment of infections. Recent efforts to identify cellular factors in a comprehensive and unbiased manner, using genome-wide siRNA screens and other systems biology "omics" methodologies, have revealed several potential anti-viral effectors for viruses like Human immunodeficiency virus type 1 (HIV-1), Hepatitis C virus (HCV), West Nile virus (WNV), and influenza virus. This review describes the discovery of novel viral restriction factors and discusses how the integration of different methods in systems biology can be used to more comprehensively identify the intimate interactions of viruses and the cellular innate resistance.

Citing Articles

Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects.

Kannan A, Suomalainen M, Volle R, Bauer M, Amsler M, Trinh H Viruses. 2022; 14(7).

PMID: 35891387 PMC: 9322957. DOI: 10.3390/v14071407.

Facilitating Antiviral Drug Discovery Using Genetic and Evolutionary Knowledge.

Xu X, Zhang Q, Chu X, Quan Y, Lv B, Zhang H Viruses. 2021; 13(11).

PMID: 34834924 PMC: 8626054. DOI: 10.3390/v13112117.

RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications.

Tan K, Andiappan A, Lee B, Yan Y, Liu J, Tang S Cells. 2019; 8(9).

PMID: 31461941 PMC: 6770044. DOI: 10.3390/cells8090986.

Influenza-Omics and the Host Response: Recent Advances and Future Prospects.

Powell J, Waters K Pathogens. 2017; 6(2).

PMID: 28604586 PMC: 5488659. DOI: 10.3390/pathogens6020025.

Human genome-wide RNAi screen identifies an essential role for inositol pyrophosphates in Type-I interferon response.

Pulloor N, Nair S, McCaffrey K, Kostic A, Bist P, Weaver J PLoS Pathog. 2014; 10(2):e1003981.

PMID: 24586175 PMC: 3937324. DOI: 10.1371/journal.ppat.1003981.

References

Douglas J, Viswanathan K, McCarroll M, Gustin J, Fruh K, Moses A . Vpu directs the degradation of the human immunodeficiency virus restriction factor BST-2/Tetherin via a {beta}TrCP-dependent mechanism. J Virol. 2009; 83(16):7931-47. PMC: 2715753. DOI: 10.1128/JVI.00242-09. View

Chiu Y, Greene W . The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol. 2008; 26:317-53. DOI: 10.1146/annurev.immunol.26.021607.090350. View

Konig R, Zhou Y, Elleder D, Diamond T, Bonamy G, Irelan J . Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008; 135(1):49-60. PMC: 2628946. DOI: 10.1016/j.cell.2008.07.032. View

Sadler A, Williams B . Interferon-inducible antiviral effectors. Nat Rev Immunol. 2008; 8(7):559-68. PMC: 2522268. DOI: 10.1038/nri2314. View

Schoggins J, Wilson S, Panis M, Murphy M, Jones C, Bieniasz P . A diverse range of gene products are effectors of the type I interferon antiviral response. Nature. 2011; 472(7344):481-5. PMC: 3409588. DOI: 10.1038/nature09907. View

Van Damme N, Goff D, Katsura C, Jorgenson R, Mitchell R, Johnson M . The interferon-induced protein BST-2 restricts HIV-1 release and is downregulated from the cell surface by the viral Vpu protein. Cell Host Microbe. 2008; 3(4):245-52. PMC: 2474773. DOI: 10.1016/j.chom.2008.03.001. View

Wu X, Anderson J, Campbell E, Joseph A, Hope T . Proteasome inhibitors uncouple rhesus TRIM5alpha restriction of HIV-1 reverse transcription and infection. Proc Natl Acad Sci U S A. 2006; 103(19):7465-70. PMC: 1464362. DOI: 10.1073/pnas.0510483103. View

Gardy J, Lynn D, Brinkman F, Hancock R . Enabling a systems biology approach to immunology: focus on innate immunity. Trends Immunol. 2009; 30(6):249-62. DOI: 10.1016/j.it.2009.03.009. View

Konig R, Chiang C, Tu B, Yan S, DeJesus P, Romero A . A probability-based approach for the analysis of large-scale RNAi screens. Nat Methods. 2007; 4(10):847-9. DOI: 10.1038/nmeth1089. View

10.

Sheehy A, Gaddis N, Choi J, Malim M . Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002; 418(6898):646-50. DOI: 10.1038/nature00939. View

11.

Karlas A, Machuy N, Shin Y, Pleissner K, Artarini A, Heuer D . Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature. 2010; 463(7282):818-22. DOI: 10.1038/nature08760. View

12.

Suspene R, Aynaud M, Koch S, Pasdeloup D, Labetoulle M, Gaertner B . Genetic editing of herpes simplex virus 1 and Epstein-Barr herpesvirus genomes by human APOBEC3 cytidine deaminases in culture and in vivo. J Virol. 2011; 85(15):7594-602. PMC: 3147940. DOI: 10.1128/JVI.00290-11. View

13.

Kumar H, Kawai T, Akira S . Pathogen recognition by the innate immune system. Int Rev Immunol. 2011; 30(1):16-34. DOI: 10.3109/08830185.2010.529976. View

14.

Shapira S, Hacohen N . Systems biology approaches to dissect mammalian innate immunity. Curr Opin Immunol. 2010; 23(1):71-7. PMC: 3746755. DOI: 10.1016/j.coi.2010.10.022. View

15.

Sabin L, Hanna S, Cherry S . Innate antiviral immunity in Drosophila. Curr Opin Immunol. 2010; 22(1):4-9. PMC: 2831143. DOI: 10.1016/j.coi.2010.01.007. View

16.

Ringrose J, Jeeninga R, Berkhout B, Speijer D . Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. J Virol. 2008; 82(9):4320-30. PMC: 2293043. DOI: 10.1128/JVI.01819-07. View

17.

Harris R, Bishop K, Sheehy A, Craig H, Petersen-Mahrt S, Watt I . DNA deamination mediates innate immunity to retroviral infection. Cell. 2003; 113(6):803-9. DOI: 10.1016/s0092-8674(03)00423-9. View

18.

Li Q, Brass A, Ng A, Hu Z, Xavier R, Liang T . A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc Natl Acad Sci U S A. 2009; 106(38):16410-5. PMC: 2752535. DOI: 10.1073/pnas.0907439106. View

19.

Peng X, Gralinski L, Armour C, Ferris M, Thomas M, Proll S . Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. mBio. 2010; 1(5). PMC: 2962437. DOI: 10.1128/mBio.00206-10. View

20.

Lu J, Pan Q, Rong L, He W, Liu S, Liang C . The IFITM proteins inhibit HIV-1 infection. J Virol. 2010; 85(5):2126-37. PMC: 3067758. DOI: 10.1128/JVI.01531-10. View