Differential Expression Profile of Chicken Embryo Fibroblast DF-1 Cells Infected with Cell-Adapted Infectious Bursal Disease Virus

Abstract

RNA-Seq was used to unveil the transcriptional profile of DF-1 cells at the early stage of caIBDV infection. Total RNAs were extracted from virus-infected cells at 0, 6 and 12 hpi. RNA-Seq datasets of respective samples mapped to 56.5–57.6% of isoforms in the reference genome Galgal4.73. At 6 hpi, 23 isoforms underwent an elevated expression, while 128 isoforms were up-regulated and 5 were down-regulated at 12 hpi in the virus-infected group. Besides, 10 isoforms were exclusively expressed in the virus-infected cells. Though no significant change was detected in cytokine and interferon expression levels at the first 12 hours of infection, modulations of the upstream regulators were observed. In addition to the reported regulatory factors including EIF2AK2, MX, OAS*A, GBP7 and IFIT, IBDV infection also triggered a IFIT5-IRF1/3-RSAD5 pathway in the DF-1 cells which potentially restricted the viral replication cycle in the early infection stage. Over-expression of LIPA and CH25H, together with the suppression of STARD4, LSS and AACS genes implied a modulation of membrane fluidity and lipid raft arrangement in the infected cells. Alternative splicing of the EFR3 homolog A gene was also through to be involved in the lipid membrane regulation, and these cumulative responses projected an inhibition of viral endocytosis. Recognition of viral RNA genomes and intermediates was presumably enhanced by the elevated levels of IFIH1, DHX58 and TRIM25 genes which possess properties on detecting viral dsRNA. On the other hand, the caIBDV arrested the host's apoptotic process by inducing the expression of apoptosis inhibitors including NFKBIA/Z, TNFAIP2/3 and ITA at the first 12 hours of infection. In conclusion, the differential expression landscape demonstrated with RNA-Seq provides a comprehensive picture on the molecular interactions between host cells and virus at the early stage of infection.

Differential gene expression in chicken primary B cells infected ex vivo with attenuated and very virulent strains of infectious bursal disease virus (IBDV)

“…This is consistent with a study by Hui et al, which characterized the gene expression of DF-1 cells infected with the D78 strain [35]. Twenty-two of the genes that we identified as being differentially expressed in D78-infected chicken primary B cells were similarly differentially expressed following D78 infection of DF-1 cells.…”

“…Twenty-two of the genes that we identified as being differentially expressed in D78-infected chicken primary B cells were similarly differentially expressed following D78 infection of DF-1 cells. Notably, Hui et al identified that D78 triggered an IFIT5-IRF1/3-Viperin pathway in infected DF-1 cells [35]. In our study, D78 infection also led to the significant up-regulation of IFIT5, IRF1, IRF7 and RSAD2 (Viperin), suggesting that this pathway is also triggered in chicken primary B cells infected with D78.…”

“…It is therefore difficult to interpret how the infected B cells respond to IBDV. To address this, some research groups have characterized the transcriptional response of cells infected with IBDV in culture [35][36][37][38][39]. These studies have the advantage of well-defined multiplicities of infection (MOIs) and time points p.i., and as transcriptional responses are from one cell population, they are not confounded by multiple cell types found in vivo.…”

“…These studies have the advantage of well-defined multiplicities of infection (MOIs) and time points p.i., and as transcriptional responses are from one cell population, they are not confounded by multiple cell types found in vivo. However, until recently it was not possible to culture chicken primary B cells ex vivo, so the transcriptome has typically been characterized in either fibroblast cells [35,36,39] or dendritic cells [37]. While providing some insight into host cell-IBDV interactions, vv IBDV strains will not replicate in fibroblast cells without prior adaptation and, as infection of B cells is crucial to the pathogenesis of IBDV, the relevance of the data should not be over-interpreted.…”

Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

“…Moreover, the recognition of IBDV is important for cells to activate their surface markers. Raymond [28] found that chicken DF-1 cells may enhance levels of IFIH1, DHX58, and TRIM25, which possess properties for detecting viral dsRNA.…”