In 2013, a novel reassortant influenza A virus (H7N9) of avian origin emerged in the south of China caused 800 human infections with a mortality of 40%. Although the first epidemic has subsided, the presence of a natural reservoir and the disease severity highlight the need to evaluate its risk for human public health and to understand the possible pathogenesis mechanism. Host factors might play a critical role in the development of severe complications. Normal human bronchial epithelial (NHBE) cell cultures have been an effective model to assess the viral-host interaction. In this study, we aimed to assess host differentially expressed gene signatures in respiratory tract epithelial cells after influenza A virus pdmH1N1 or H7N9 infection.

To gain global and dynamic gene expression profiles, the NHBE cells cultured from a 24 year old donor were challenged by 3.0 m.o.i. avian H7N9 virus (A/Taiwan/4-CGMH/2014), H1N1pdm virus (A/California/07/2009), or mock control. After 12 hours and 36 hours incubation, the cell pellets were collected for transcriptome analysis on the GeneChip HTA 2.0 array (Affymetrix platform) and the bioinformatic software were used for results evaluation. All results were run in duplicate.

The PCA analysis results showed that after 12 and 36 hours infection, there are significant different transcriptome profiling pattern between pdmH1N1 and H7N9. A total of 44,699 transcripts can be detected on the HTA chip, gene expression was quantified and compared between the control and the virus-infected groups, and differentially expressed genes (DEGs) with a q-value <0.05 were identified. The number of upregulated genes was larger than the numbers of downregulated genes in both groups of virus-infected NHBE cells at both time points.

After 12 hours infection, 2313(5.40%) transcripts in pdmH1N1 infected NHBE cells, and 7125(15.94%) transcripts in H7N9 infected cells showed significant differences. Interestingly, the differentially expressed transcripts in pdmH1N1 infected NHBE cells decreased (986, 2.21%) 36 hours after infection, but the differentially expressed transcripts in H7N9 infected NHBE cells increased (8882, 19.87%). Gene expression analysis reveals that cellular repair pathway related genes, which include the cytoskeleton remodeling and keratin filaments pathways, were significantly inhibited in the H7N9 infected NHBE cells; ATP12A, KRT4, and CEACAM5 gene expression decreased 1273-540 fold 36 hours after H7N9 infection. Furthermore, canonical signaling pathway analysis results showed that the interferon signaling and apoptosis pathways were highly activated in avian H7N9 infected NHBE cells compared with the pdmH1N1 infected cells.

There are significantly different gene expression patterns between pdmH1N1 and H7N9 infected NHBE cells. H7N9 virus infection induced strong immune response, however cellular repair mechanisms were inhibited at the same time. Differential expression of specific factors observed between avian H7N9 and pdmH1N1 influenza virus strains could explain the variation in disease pathogenicity. These findings provide a framework for future studies examining the molecular mechanisms underlying the pathogenicity of avian H7N9 virus. The study results provide valuable viral-host interaction between H7N9 and NHBE cells, which improves our understanding of the pathogenic mechanisms that lead to severe complications. Collectively, our data provide new insight into the underlying mechanisms of the differential pathogenicity of avian influenza viruses.


  1. Gao R, Cao B, Hu Y, Feng Z, Wang D, Hu W, Chen J, Jie Z, Qiu H, Xu K, Xu X, Lu H, Zhu W, et al. Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med. 2013; 368:1888-97. NEJMoa1304459.
  2. Huang CG, Lee LA, Wu YC, Hsiao MJ, Horng JT, Kuo RL, Huang CH, Lin YC, Tsao KC, Chen MC, Chen TC, Shih SR. A pilot study on primary cultures of human respiratory tract epithelials to predict patients’ response to H7N9 infection. Oncotarget. 2018 Feb 20;9(18):14492-14508. doi: 10.18632/oncotarget.24537. eCollection 2018 Mar 6.
  3. Kuo RL, Chen CJ, Tam EH, Huang CG, Li LH, Li ZH, Su PC, Liu HP, Wu CC. Interactome Analysis of NS1 Protein Encoded by Influenza A H7N9 Virus Reveals an Inhibitory Role of NS1 in Host mRNA Maturation. J Proteome Res. 2018 Apr 6;17(4):1474-1484.
  4. Chen GW, Kuo SM, Yang SL, Gong YN, Hsiao MR, Liu YC, Shih SR, Tsao KC. Genomic signatures for avian H7N9 viruses adapting to humans. PLoS One. 2016; 11:e0148432.