Transcriptomic analysis of Mandarin fish brain cells infected with infectious spleen and kidney necrosis virus with an emphasis on retinoic acid-inducible gene 1-like receptors and apoptosis pathways

Infectious spleen and kidney necrosis virus (ISKNV) has caused significant economic losses in the cultured Mandarin fish (Siniperca chuatsi) industry. The molecular mechanisms that underlie the pathogenesis of the viral infection remain poorly understood. In this study, deep RNA sequencing technique was used to analyze the transcriptomic profiles of Mandarin fish brain cells (CPB) at progressive time points after ISKNV infection. A total of 96,206,040 clean data from 98,235,240 sequence reads were obtained. These raw data were assembled into 66,787 unigenes. Among these unigenes, 33,225 and 29,210 had significant hit the Nr and SwissProt databases where they matched 27,537and 19,638 unique protein accessions, respectively. In the samples harvested at 24 or 72 h post of the infection, a total of 10,834 or 7584 genes were differentially expressed in infected CPB cells compared to non-infected cells, including 5445 or 3766 up-regulated genes and 5389 or 3818 down-regulated genes, respectively. In addition, 12 differentially expressed genes (DEGs) were validated by quantitative PCR. These DEGs were involved in many pathways of viral pathogenesis. Further analysis of the major DEGs genes involved in the RLRs and apoptosis pathways revealed some interesting findings. In the RLRs pathway, ISKNV infection inhibited the activation of NF-κB via over expression of the IKKB-α and IKKB-β and lessened expression of interleukin-1 receptor-associated kinase 4 (IRAK4). In the apoptosis pathway, ISKNV infection could induce apoptosis mainly via tumor necrosis factor (TNF) mediated extrinsic pathway. The cellular apoptosis induced by ISKNV infection was confirmed using annexinV-FITC/PI and DAPI staining methods.