Identification of differentially expressed genes in H5N1 infected chickens using meta-analysis of DNA microarray datasets

Document Type : Research Paper

Authors

1 Ph.D student, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran

2 Professor, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran

3 Associate Professor, Institute of Biotechnology, Shiraz University, Shiraz, Iran

4 Assistant Professor, Iran veterinary organization, Tehran, Iran

Abstract

During the last years, gene expression profiling has revealed specific genes which are involved in the regulation of host response to several diseases. Avian Influenza infection is one of the important diseases in poultry industry. The aim of the present study was to identify significantly involved genes in H5N1 infection using the meta-analysis of two DNA microarray datasets of host response to influenza infection. The meta-analysis revealed that STK17B, CCL4, MCM9, IRF7 and IL6 were differentially expressed using Fisher, AW and maxP methods. We used real-time PCR to validate the differential expression of identified genes. For this aim, the previously H5N1-infected samples were used. The real-time PCR results of all five genes confirmed the differential expression between infected and non-infected samples and also the type of regulation obtained from meta-analysis significantly. The genes IL6, IRF7 and CCL4 were over expressed while STK17B and MCM9 were down expressed in infected samples. The results suggested that the meta-analysis is a robust method to find differentially expressed genes which may be ignored in individual analysis. These genes may play some critical roles in host response.

Keywords

Main Subjects


Arankalle V. A., Lole K. S., Arya R. P., Tripathy A. S., Ramdasi A. Y., Chadha M. S., Sangle S. A. and Kadam D. B. 2010. Role of host immune response and viral load in the differential outcome of pandemic H5N1 (2009) influenza virus infection in Indian patients. PLoS ONE, 5: e13099.
Burggraaf S., Karpala A. J., Bingham J., Lowther S., Selleck P., Kimpton W. and Bean A. G. 2014. H5N1 infection causes rapid mortality and high cytokine levels in chickens compared to ducks. Virus Research, 185: 23-31.
Cagle C., To T. L., Nguyen T., Wasilenko J., Adams S. C., Cardona C. J., Spackman E., Suarez D. L. and Pantin-Jockwood M. J. 2011. Pekin and Muscovy ducks respond differently to vaccination with a H5N1 highly pathogenic avian influenza (HPAI) commercial inactivated vaccine. Vaccine, 29: 6549-6557.
Cameron C. M., Cameron M. J., Bermejo-Martin J. F., Ran L., Xu L., Turner P. V. et al. 2008. Gene expression analysis of host innate immune responses during lethal H5N1 infection in ferrets. Journal of Virology, 82:11308-11317.
Cilloniz C., Shinya K., Peng X., Korth M. J., Proll S. C., Aicher L. D., Carter V. S., Chang J. H., Kobasa D., Feldmann F., Strong J. E., Feldmann H., Kawaoka Y. and Katze M. G.. 2009. Lethal influenza virus infection in Macaques is associted with early dysregulation of inflammatory related genes. PloS Pathogens, 5(10): e1000604.
Cornelissen J. B. W. J., Post J., Peeters B., Vervelde L. and Rebel J. M. J. 2012. Differential innate responses of chickens and ducks to low-pathogenic avian influenza. Avian Pathology, 41: 519-529.
Cornelissen J. B. W. J., Vervelde L., Post J. and Rebel J. M. J. 2013. Differences in highly pathogenic avian influenza viral pathogenesis and associated early inflammatory response in chickens and ducks. Avian Pathology, 42: 347-364.
De Jong M. D., Simmons C. P., Thanh T. T., Hien V. M., Smith G. J., Ghau T. N., Khanh T. H., Dong V. C., Qui P. T., Cam B. V., Ha do Q., Guan Y., Peiris J. S., Chinh N. T., Hien T. T. and Farrar J. 2006. Fatal outcome of human influenza a (H5N1) is associated with high viral load and hypercytokinemia. Nature Medicine, 12: 1203-1207.
Hartford S. A., Luo Y., Southard T. L., Min I. M., Lis J. T. and Schimenti J. C. 2011. Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication but functions in germ-line stem cells and tumor suppression. PNAS, 108: 43.
Hong F. and Breitling R. 2008. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics, 24(3): 374-82.
Kim D. K., Kim C. H., Lamont S. J., Keeler J. R. and Lillehoj H. S. 2009. Gene expression profiles of two B-complex disparate, genetically inbred Fayoumi chicken lines that differ in susceptibility to Eimeria maxima. Poultry Science, 88: 1565-1579.
Kim T. H. and Zhou H. 2015. Functional analysis of chicken IRF7 in response to dsRNA analog poly (I:C) by integrating overexpression and knockdown. PLoS ONE, 10(7): e0133450.
Kobasa D., Jones S. M., Shinya K., Kash J. C., Copps J., Ebihara H., Hatta Y., Kim J. H., Halfmann P., Hatta M., Feldmann F., Alimonti J. B., Fernando L., Li Y., Katze M. G., Feldmann H. and Kawaoka Y. 2007. Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature, 445: 319-323.
Kuchipudi S. V., Tellabati M., Sebastian S., Londt B. Z., Jansen C., Vervelde L., Brookes S. M., Brown L. H., Dunham S. P. and Chang K. C. 2014. Highly pathogenic avian influenza virus infection in chickens but not ducks is associated with elevated host immune and pro-inflammatory responses. Veterinary Research, 45(118).
Kumar A., Vijayakumar P., Gandhale P. N., Ranaware P. B., Kumar H., Kulkarni D. D., Raut A. A. and Mishra A. 2017. Genome-wide gene expression pattern underlying differential host response to high or low pathogenic H5N1 avian influenza virus in ducks. Acta Virologica, 61(1):66-76.
Kumar P. V., Raut A. A., Kumar A., Chingtham S., Dutta R., Singh H., Kumar Jatawa S., Pradeep N., Sudhakar S. B., Pal Singh V. and Mishra A. 2016. Reverse engineering of Genome-wide gene regulatory networks of avian influenza infection in chicken lungs. Veterinary Research International, 4(3): 99-105.
Kuribayashi S., Sakoda Y., kawasaki T., Tanaka T., Yamamoto N., Okamatsu M., Isoda N., Tsuda Y., Sunden Y., Umemura T., Nakajima N., Hasegawa H. and Kida H. 2013. Excessive cytokine response to rapid proliferation of highly pathogenic avian influenza viruses leads to fatal systemic capillary leakage in chickens. PLoS ONE, 8: e68375.
La Gruta N. L., Kedzierska K., stambas J. and Doherty P. C. 2007. A question of self-preservation: immunopathology in influenza virus infection. Immunology and Cell Biology, 85(2): 85-92.
Lee K. Y., Im J. S., Shibata E., Park J., Handa N., Kowalczykowski S. C. and Dutta A. 2015. MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex. Nature Communications, 6: 7744.
Liang Q. L., Luo L., Zhou K., Dong J. X. and He H. X. 2011. Immune-related gene expression in response to H5N1 avian influenza virus infection in chicken and duck embryonic fibroblasts. Molecular Immunology, 48: 924-930.
Livak K. J. and Schmittgen T. D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the (-Delta Delta CT) method.
Massin P., Deleage C., Oger A., Briand F. X., Quenault H. and Blanchard Y. 2013. Differential cellular gene expression in duck trachea infected with a highly or low pathogenic H5N1 avian influenza virus. Virology Journal, 10(279).
Osterlund P. I., Pietila T. E., Veckman V., Kotenko S. V., Julkunen I. 2007. IFN regulatory factor family members differentially regulate the expression of type 4 IFN genes. The Journal of Immunology, 179: 3434-3442.
Pantin-Jackwood M. J., Smith D. M., Wasilenko J. L., Cagle C., Shepherd E., Sarmento L., Kapczynski D. R. and Afonso C. L. 2012. Effect of age on the pathogenesis and innate immune responses in Pekin ducks infected with different H5N1 highly pathogenic avian influenza viruses. Virus Research, 167: 196-206.
Ramirez-Nieto G. C. 2008. Host molecular responses in chickens infected with an avian influenza virus. Dissertation submitted to the faculty of the graduate school of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Ranaware P. B., Mishra A., Vijayakumar P., Gandhale P. N., Kumar H., Kulkarni D. D. and Raut A. 2016. Genome wide host gene expression analysis in chicken lungs infected with avian influenza viruses. PLoS ONE, 11(14): e0153671.
Reemers S. S., van Haarlem D. A., Groot Koerkamp M. J. and Vervelde L. 2009. Differential gene-expression and host-response profiles against avian influenza virus within the chicken lung due to anatomy and airflow. Journal of General Virology, 90: 2134-2146.
Reemers S. S., Groot Koerkamp M. J., Holstege F. C., van Eden W. and Vervelde L. 2009. Cellular host transcriptional responses to influenza A virus in chicken tracheal organ cultures differ from responses in in vivo infected trachea. Veterinary Immunology and Immunopathology, 132: 91-100.
Riel D. V., Munster V. J., de Wit E., Rimmelzwaan G. F., Foucheir R. A. M., Osterhaus A. D. M. E. and Kuiken T. 2007. Human and avian influenza viruses target different cells in the lower respiratory tract of humans and other mammals. Immunopathology and Infectious Disease, 171: 1215–1223.
RStudio Team. 2015. RStudio: Integrated development for R. RStudio, Inc., Boston, MA URL http://www.rstudio.com/.
Shinya K., Ebina M., Yamada S., Ono M., Kasai N. and Kawaoka Y. 2006. Avian flu: influenza virus receptors in the human airway. Nature, 440: 435–436.
Smith J., Smith N., Yu L., Patron L. R., Gutowska M. W., Forrest H. L., Danner A. F., Seiler J. P., Digard P., Webster R. G. and Burt D. W. 2015. A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance. BMC Genomics, 16(574).
Szretter K. J., Gangappa S., Lu X., Smith C., Shieh W. J., Zaki S. R., Sambhara S., Tumpey T. M. and Katz J. M. 2007. Role of host cytokine responses in the pathogenesis of avian H5N1 influenz viruses in mice. Journal of Virology, 81: 2736-2744.
Wang J., Oberley-Deegan R., Wang S., Nikrad M., Funk C. J., Hartshorn K. L. and Mason R. J. 2009. Differentiaated human alveolar type II cells secrete antiviral IL-29 in response to influenza A infection. The Journal of Immunology, 182: 1296-1304.
Wang Y., Brahmakshatriya V., Lupiani B., Reddy S. M., Soibam B., Benham A. L., Gunaratne P., Liu H., Trakooljul N., Lng N., Okimoto R. and Zhou H. 2012. Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. BMC Genomics, 13(278).
Wang Y., Brahmakshatriya V., Zhou H., Lupiani B., Reddy S. M., yoon B., Gunaratne P. H., Kim J. H., Chen R., Wang J. and Zhou H. 2009. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics, 10(512).
Wang Y., Lupiani B., Reddy S. M., Lamont S. J. and  Zhou H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Science, 93: 485-493.
Westenius V., Makela S. M., Ziegler T., Julkunen I. and Osterlund P. 2014. Efficient replication and strong induction of innate immune responses by H9N2 avian influenza virus in human dendritic cells. Virology, 471-473.
Xing Z., Cardona C. J., Li J., Dao N., Tran T. and Andrada J. 2008. Modulation of the immune responses in chickens by low-pathogenicity avian influenza virus H9N2. Journal of General Virology, 89: 1288-1299.
Yang Z., Chen Y., Fu Y., Yang Y., Zhang Y., Chen Y. and Li D. 2014. Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data. BMC Medical Genetics, 15: 80.
Zeng H., Goldsmith C., Thawatsupha P., Chittaganpitch M., Waicharoen S., Zaki S., Tumpey T. M. and Katz J. M. 2007. Highly pathogenic avian influenza H5N1 viruses elicit an attenuated type I interferon response in polarized human bronchial epithelial cells. Journal of Virology, 81(22): 12439-12449.