Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1

Siying Ye; Chris Cowled; Cheng-Hon Yap; John Stambas

By overlapping the three lists of genes from "ND vs HD Up", "HD vs HA Down" and "ND vs 158 HA Down", eleven genes were found in all three comparisons. This suggests that these 11 genes are 159 upregulated following H5N1 infection and are significantly reduced by apocynin treatment to a level 160 lower than that observed in uninfected control cells (Fig. 1F ). Among these were inflammatory 161 cytokines/chemokines genes, including CXCL5, IL1A, AXL (a member of the TAM receptor family of 162 receptor tyrosine kinases) and TMEM173/STING (Stimulator of IFN Genes) ( Table S4) . and qRT-PCR analysis (Fig. 2E ). Apocynin treatment further increased SOCS1 mRNA expression (Fig. 172 2E) . Although HiSeq analysis did not detect a statistically significant increase of SOCS1 following 173 apocynin treatment, the Log2 fold-changes in SOCS1 gene expression were similar between the HD 174 and HA groups (4.8-fold vs 4.0-fold) (Fig. 2E) . SOCS3 transcription was also found to be significantly 175 increased following H5N1 infection alone following HiSeq analysis and was further increased after 176 apocynin treatment (Fig. 2F ). In contrast, SOCS3 mRNA was only slightly increased when samples 177 were analyzed by qRT-PCR (Fig. 2F) . 178