Yuan Junfa, Yang Yi, Nie Huihui, Li Lijuan, Gu Wangang, Lin Li, Zou Min, Liu Xueqin, Wang Min, Gu Zemao
Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
BMC Genomics. 2014 Oct 25;15(1):935. doi: 10.1186/1471-2164-15-935.
Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.
A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.
Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.
鲤春病毒血症病毒（SVCV）已被确认为鲤春病毒血症（SVC）的病原体，它给养殖的鲤鱼（Cyprinus carpio）产业造成了重大损失。该疾病发病机制的分子机制仍知之甚少。在本研究中，利用深度RNA测序分析了SVCV感染后不同时间点EPC细胞的转录组和基因表达谱。本研究探讨了病毒与细胞相互作用的复杂性，并增加了有助于理解SVCV的知识。
从3600万个序列读数中获得了总共33849764条清洁数据，平均读长为100 bp。这些原始数据被组装成88772个重叠群。在这些重叠群中，19642个和25966个在NR和Uniprot数据库中有显著匹配，分别匹配了17642个和13351个独特的蛋白质登录号。在SVCV感染后24小时（感染复数为1.0），与未感染细胞相比，EPC细胞中共有623个基因差异表达，其中包括288个上调基因和335个下调基因。这些调控基因主要参与细胞凋亡、氧化应激和干扰素系统途径，所有这些都可能与病毒发病机制有关。此外，通过定量PCR验证了8个差异表达基因（DEG）。
我们的研究结果表明，在体外与SVCV感染相关的基因转录存在以前未被认识到的变化，并且本研究中确定的许多潜在级联反应显然值得进一步的实验研究。我们的数据为EPC细胞中病毒易感性的机制提供了新的线索。
