Systems Biology Analysis of Innate Resistance to Avian Influenza Virus Infection in Two Genetically Distinct Chicken Inbred Lines

Avian influenza virus (AIV) infection can cause significant economic losses to the poultry industry, and raise a great public health threat due to potential host jump from animals to humans. To develop more effective intervention strategies, it is essential to elucidate molecular mechanisms of host response to AIV infection in chickens. Systems biology approach provides a great opportunity in improving our understanding complex “OMIC” data. The objective of this study was to identify genes and signal pathways associated with AIV infection in two genetically distinct, highly inbred chicken lines (Fayoumi, resistant to AIV infection, and Leghorn, susceptible to AIV infection) by RNA-Seq integrated systems biology analysis.

    Three-week old chickens were inoculated with 10⁷ EID₅₀of low pathogenic H5N3 AIV, and lungs were harvested one day post inoculation. Eight cDNA libraries (2 libraries from individual bird within each 4 line × infection groups (infected and non-infected Leghorn and infected and non-infected Fayoumi)) were prepared and sequenced by Illumina HiSeq 2000, which yielded a total of 490 million 100 bp paired-end reads. Gene expression levels of all annotated chicken genes were analyzed using CLC Genomics Workbench. DESeq was used to identify differentially expressed transcripts between infected and non-infected birds (FDR < 0.05 and fold-change > 2). The RNA-Seq data were imported into the computational systems biology pipeline to identify significantly activated or deactivated signal pathways.

    Totally there were 79.92% annotated chicken genes identified in Leghorn and 78.52% chicken genes identified in Fayoumi birds. With AIV infection, there were 1232 and 145 genes up-regulated and 836 and 50 genes down-regulated, in Leghorn and Fayoumi birds, respectively. A list of signaling pathways has been identified by the systems biology analysis basing on differentially expressed genes. These pathways responded differently with AIV infection in different chicken lines and tissues. Natural killer cell mediated cytotoxicity, RIG-I like receptor and Toll like receptor signaling pathways were significantly activated in both Leghorn and Fayoumi birds in both lungs and trachea. B and T cell receptor signaling pathways were deactivated in both genetic lines in lungs. While in trachea, T cell receptor signaling pathway was deactivated in both lines and B cell receptor signaling pathway was deactivated in Fayoumi birds and activated in Leghorn birds. Further investigation of the roles of these differentially expressed mRNAs and pathways in the regulation of host-AIV interaction can expedite breakthroughs in functional genomics/proteomic discovery and lead new directions for the development of anti-viral drugs or vaccines in poultry.