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 two lists of genes from "ND vs HD Up" and "HD vs HA Down", 245 genes were 140 shown to be down-regulated in the presence of apocynin (Fig. 1D ). By overlapping three lists of genes 141 from "ND vs HD Up", "HD vs HA Down" and "ND vs HA Up", 55 genes out of the 245 genes were 142 present in all three lists (Fig. 1E ), indicating that these 55 genes were significantly inhibited by 143 apocynin but to a level that was still significantly higher than that in uninfected cells. The 55 genes 144 include those involved in influenza A immunity (hsa05164; DDX58, IFIH1, IFNB1, MYD88, PML, 145 STAT2), Jak-STAT signaling (hsa04630; IFNB1, IL15RA, IL22RA1, STAT2), cytokine-cytokine 146 receptor interaction (hsa04060; CX3CL1, IFNB1, IL15RA, IL22RA1) and RIG-I-like receptor 147 signaling (hsa04622; DDX58, IFIH1, IFNB1) (Table S3 and S4) . Therefore, critical immune responses 148 induced following H5N1 infection were not dampened following apocynin treatment. The remaining 149 190 of 245 genes excluded from the "ND vs HA Up" list were those significantly inhibited by apocynin 150 to a level that was similar to uninfected control cells (Fig. 1E ). The 190 genes that were reduced by 151 apocynin to basal levels were those involved in PI3K-Akt signaling (hsa04151; CCND1, GNB4, 152 IL2RG, IL6, ITGA2, JAK2, LAMA1, MYC, IPK3AP1, TLR2, VEGFC), cytokine-cytokine receptor 153 interaction (hsa04060; VEGFC, IL6, CCL2, CXCL5, CXCL16, IL2RG, CD40, CCL5, CCL7, IL1A), 154 TNF signaling (hsa04668; CASP10, CCL2, CCL5, CFLAR, CXCL5, END1, IL6, TRAF1, VEGFC) 155 and apoptosis (hsa04210; BAK1, CASP10, CFLAR, CTSO, CTSS, PARP3, TRAF1) (Table S3 and 156 S4) . This is consistent with the role of apocynin in reducing inflammation and apoptosis (29).