Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES
Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES
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DOI：
10.1128/jvi.06717-11
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发表时间：
2012-03-01
影响因子：
5.4
通讯作者：
Flemington, Erik K.
中科院分区：
文献类型：
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作者：
Lin, Zhen;Puetter, Adriane;Flemington, Erik K.
许多通常用于生物学研究的细胞系都被发现含有外源性病毒，如人类肿瘤病毒EB病毒和人乳头状瘤病毒。然而，以前还没有广泛的、公正的方法在全球范围内评估细胞模型系统中异位生物的存在。我们认为，高通量测序应该为组织培养细胞系统的微生物群提供无与伦比的洞察力。在这里，我们使用了我们的RNA-Seq分析管道，Parses(RNA-Seq外源序列分析管道)，来调查EBV研究人员常用的两个EBV阳性B细胞系中异位生物的存在。来自Akata和JY B细胞系的测序数据集被发现包含EBV的读数，并且JY数据集被发现也包含从小鼠白血病病毒(MuLV)的读数。进一步的研究表明，MuLV在JY细胞中的转录活性很高。我们还鉴定了一些MuLV选择性剪接事件，并发现了APOBEC3G(载脂蛋白B mRNA编辑酶，催化多肽样3G)依赖DNA编辑的证据。最后，逆转录-聚合酶链式反应分析显示，在其他三个人类B细胞株(DG75、Ramos和P3HR1Cl.13)中存在MuLV，这是Epstein-Barr病毒领域的研究人员通常使用的。我们认为，使用RNA-seq/parses类方法对组织培养微生物群进行彻底检查对于在生物学研究中适当利用这些系统至关重要。
Many cell lines commonly used for biological studies have been found to harbor exogenous agents such as the human tumor viruses Epstein-Barr virus (EBV) and human papillomavirus. Nevertheless, broad-based, unbiased approaches to globally assess the presence of ectopic organisms within cell model systems have not previously been available. We reasoned that high-throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell systems. Here we have used our RNA-seq analysis pipeline, PARSES (Pipeline for Analysis of RNA-Seq Exogenous Sequences), to investigate the presence of ectopic organisms within two EBV-positive B-cell lines commonly used by EBV researchers. Sequencing data sets from both the Akata and JY B-cell lines were found to contain reads for EBV, and the JY data set was found to also contain reads from the murine leukemia virus (MuLV). Further investigation revealed that MuLV transcription in JY cells is highly active. We also identified a number of MuLV alternative splicing events, and we uncovered evidence of APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G)-dependent DNA editing. Finally, reverse transcription-PCR analysis showed the presence of MuLV in three other human B-cell lines (DG75, Ramos, and P3HR1 Cl.13) commonly used by investigators in the Epstein-Barr virus field. We believe that a thorough examination of tissue culture microbiomes using RNA-seq/PARSES-like approaches is critical for the appropriate utilization of these systems in biological studies.