Abstract
We have previously demonstrated that IL-27 is a novel anti-HIV cytokine, which inhibits HIV replication in CD4 T cells and macrophages as interferon (IFN)-α does. To further understand the mechanism of the antiviral effect, we performed Affymetrix DNA microarray and gene functional annotation analysis using DAVID (the Database for Annotation, Visualization, and Integrated Discovery). DAVID is a web-based bioinformatics application that systematically identifies enriched biology associated with large gene list(s) derived from high-throughput genomic experiments, such as microarray. The enriched annotation terms identified by DAVID will give important insights into understanding the biological themes under study. Having used the DAVID bioinformatics tools, we have shown that IL-27 differentially regulates the gene expression between T cells and macrophages. IL-27 significantly induces IFN-inducible genes including antiviral genes in macrophages as does IFN-α, suggesting that IL-27 inhibits HIV replication in macrophages via a mechanism similar to that of IFN-α.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Pflanz, S., Timans, J.C., Cheung, J., Rosales, R., Kanzler, H., Gilbert, J., Hibbert, L., Churakova, T., Travis, M., Vaisberg, E., Blumenschein, W.M, Mattson, J.D., Wagner, J. L., To, W., Zurawski, S., McClanahan, T.K., Gorman, D.M., Bazan J.F., de Waal Malefyt, R., Rennick, D., Kastelein, R.A. (2002) IL-27, a heterodimeric cytokine composed of EBI3 and p28 protein, induces proliferation of naive CD4 (+) T cells. Immunity 16: 779–790.
Hunter, C.A. (2005) New IL-12-family members: IL-23 and IL-27, cytokines with divergent functions. Nat. Rev. Immunol. 5: 521–531.
Foli, A., Saville, M.W., Baseler, M.W., Yarchoan, R. (1995) Effects of the Th1 and Th2 stimulatory cytokines interleukin-12 and interleukin-4 on human immunodeficiency virus replication. Blood 85: 2114–2123.
Fakruddin, J. M., Lempicki, R.A., Gorelick, R.J., Yang, J., Adelsberger, J.W., Garcia-Pineres, A.J., Pinto, L.A., Lane, H.C., Imamichi, T. (2007) Noninfectious papilloma virus-like particles inhibit HIV-1 replication: implications for immune control of HIV-1 infection by IL-27. Blood 109: 1841–1849.
Imamichi, T., Yang, J., Huang, D.W., Brann, T.W., Fullmer, B.A., Adelsberger, J.W., Lempicki, R.A., Baseler, M.W., Lane, H.C. (2008) IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages. AIDS 22: 39–45.
Langer, J.A., Cutrone, E.C., Kotenko, S. (2004) The class II cytokine receptor (CRF2) family: overview and patterns of receptor-ligand interactions. Cytokine Growth Factor Rev. 15: 33–48.
Pestka, S., Langer, J.A., Zoon, K.C., Samuel, C.E. (1987) Interferons and their actions. Annu. Rev. Biochem. 56: 727–777.
Galligan, C.L., Murooka, T.T., Rahbar, R., Baig, E., Majchrzak-Kita, B., Fish, E.N. (2006) Interferons and viruses: signaling for supremacy. Immunol. Res. 35: 27–40.
Samuel, C.E. (2001) Antiviral actions of interferons. Clin. Microbiol. Rev. 14: 778–809.
Dennis, G. Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., Lempicki, R.A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4: R60.
Huang, D.W., Sherman, B.T., Tan, Q., Kir, J., Liu, D., Bryant, D., Guo, Y., Stephens, R., Baseler, M.W., Lane, H.C., Lempicki, R.A. (2007) DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35: W169–W175.
Huang, D.W., Sherman, BT., Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37: 1–13.
Lim, W.K., Wang, K., Lefebvre, C., Califano, A. (2007) Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 23: i282–i288.
Harr, B., Schlötterer, C. (2006) Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res. 34: e8.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Imamichi, T., Yang, J., Huang, D.W., Sherman, B., Lempicki, R.A. (2012). Interleukin-27 Induces Interferon-Inducible Genes: Analysis of Gene Expression Profiles Using Affymetrix Microarray and DAVID. In: De Ley, M. (eds) Cytokine Protocols. Methods in Molecular Biology, vol 820. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-439-1_3
Download citation
DOI: https://doi.org/10.1007/978-1-61779-439-1_3
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-438-4
Online ISBN: 978-1-61779-439-1
eBook Packages: Springer Protocols