Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and regulation of noncoding RNA expression in a CD4+ T cell line.
Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and regulation of noncoding RNA expression in a CD4+ T cell line.
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作者：
Chang ST;Sova P;Peng X;Weiss J;Law GL;Palermo RE;Katze MG
下一代测序（NGS）能够对整个转录组进行高灵敏度测量。我们报告的第一个应用程序，我们的知识，这种技术的分析RNA从CD 4 + T细胞系感染完整的HIV。我们对感染细胞的总mRNA进行测序，并检测宿主和病毒mRNA表达的差异。病毒读段占总映射测序读段的很大一部分：感染后12 h（hpi）约为20%，24 hpi约为40%。我们还检测到一个小的，但显着的抑制T细胞活化相关基因在12 hpi。这种抑制持续存在，并扩大了24 hpi，病毒诱导的T细胞细胞病理学提供了新的可能的标志物。到24 hpi时，超过50%的可检测宿主基因座的表达也发生了改变，这表明宿主过程（包括RNA加工、剪接和运输）发生了广泛的改变，其程度此前尚未报道。此外，下一代测序提供了对替代病毒RNA剪接事件和非编码RNA（包括microRNA宿主基因）表达的深入了解。测序技术的最新进展现在允许有效地测量细胞中的所有RNA。这种方法对于研究病毒感染模型特别有用，因为它允许同时测量宿主和病毒RNA。使用下一代测序（NGS），我们测量了HIV感染的T细胞系中总mRNA的变化。据我们所知，这是该技术首次应用于调查涉及完整HIV的HIV-宿主相互作用。我们直接测量了感染细胞中病毒mRNA的量，并检测到新的病毒RNA剪接变体和非编码RNA种类宿主表达的变化。我们还在病毒复制的早期阶段检测到T细胞活化和其他宿主过程的微小变化，这些变化在病毒复制的峰值附近增加，提供了T细胞死亡的新候选生物标志物。
Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4+ T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. Recent advances in sequencing technology now allow the measurement of effectively all the RNA in a cell. This approach is especially useful for studying models of virus infection, as it allows the simultaneous measurement of both host and viral RNA. Using next-generation sequencing (NGS), we measured changes in total mRNA from a HIV-infected T cell line. To our knowledge, this is the first application of this technology to the investigation of HIV-host interactions involving intact HIV. We directly measured the amount of viral mRNA in infected cells and detected novel viral RNA splice variants and changes in the host expression of noncoding RNA species. We also detected small changes in T cell activation and other host processes during the early stages of viral replication that increased near the peak of viral replication, providing new candidate biomarkers of T cell death.