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Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

使用 RNA-seq 评估特发性肺纤维化中的病毒 RNA

  • 影响因子:2.40
  • DOI:10.1186/s12890-020-1114-1
  • 作者列表:"Qinyan Yin","Michael J. Strong","Yan Zhuang","Erik K. Flemington","Naftali Kaminski","Joao A. de Andrade","Joseph A. Lasky
  • 发表时间:2020-04-03
Abstract

Abstract Background Numerous publications suggest an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports have employed immunohistochemistry, in situ hybridization and/or PCR, which are susceptible to specificity artifacts. Methods We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K). Results We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. Conclusions To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.

摘要

【摘要】背景: 大量的文献报道提示疱疹病毒感染与特发性肺纤维化 (IPF) 之间存在关联。这些报告采用免疫组织化学、原位杂交和/或 PCR,易受特异性伪影影响。方法我们使用新一代测序研究了 IPF 和病毒 RNA 表达之间的可能关联,这有可能提供高度的敏感性和特异性。我们在 28 例 IPF 患者肺活检样本和 20 例对照中定量了 740 种病毒的病毒 RNA 表达。使用选择病毒 (EBV 、 HCV 、疱疹病毒 saimiri 和 HERV-K) 的 实时RT-PCR 确认关键 RNA-seq 结果。结果在 IPF 和对照肺之间,我们在肺组织标本中发现了病毒感染的零星低水平证据,但没有发现任何病毒表达的统计学差异,包括 EBV,疱疹病毒 saimiri 和 HERV-K。结论据我们所知,这是第一份采用 RNA-seq 评估病毒感染是否与 IPF 发病机制相关的出版物。我们的结果没有解决病毒感染在 IPF 急性加重中的作用,然而,这项分析显然不支持疱疹病毒检测和 IPF 之间的关联。

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影响因子:4.40
发表时间:2020-01-01
DOI:10.1007/s00262-019-02431-8
作者列表:["Shibaki, Ryota","Murakami, Shuji","Matsumoto, Yuji","Yoshida, Tatsuya","Goto, Yasushi","Kanda, Shintaro","Horinouchi, Hidehito","Fujiwara, Yutaka","Yamamoto, Nobuyuki","Kusumoto, Masahiko","Yamamoto, Noboru","Ohe, Yuichiro"]

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影响因子:4.04
发表时间:2020-01-25
来源期刊:New biotechnology
DOI:10.1016/j.nbt.2019.08.006
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