Exon level transcriptomic profiling of HIV-1-infected CD4(+) T cells reveals virus-induced genes and host environment favorable for viral replication.
Exon level transcriptomic profiling of HIV-1-infected CD4(+) T cells reveals virus-induced genes and host environment favorable for viral replication.
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DOI：
10.1371/journal.ppat.1002861
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发表时间：
2012
期刊：
影响因子：
6.7
通讯作者：
Tremblay MJ
中科院分区：
文献类型：
--
作者：
Imbeault M;Giguère K;Ouellet M;Tremblay MJ
HIV-1是非常特化的，因为即使在CD4+ T淋巴细胞（其在外周血中的主要天然储存库）中，病毒也只能在激活状态下有效感染一小部分细胞。由于hiv -1感染细胞的比例非常低，迄今为止，大多数研究都未能在对病毒感染高度敏感的细胞的全基因组尺度上获得精确的转录组谱。利用Affymetrix外显子阵列技术和一种允许对HIV-1感染细胞进行磁分离的报告病毒，我们描述了最有利于病毒建立和复制的宿主细胞因子，以及病毒诱导的宿主基因表达变化仅发生在HIV-1有效感染的靶细胞中。我们还证实，在激活的CD4+ T细胞群体中，HIV-1在感染后的早期时间点对未感染的旁观者细胞的转录组没有可检测到的影响。本研究收集的数据为hiv -1感染的CD4+ T细胞的生物学提供了独特的见解，并鉴定了被认为在病毒与其宿主之间的相互作用中起决定性作用的基因。此外，它提供了在HIV-1有效感染的原发人CD4+ T细胞中发现的选择性剪接事件的第一个目录。先前的一些研究已经监测了hiv -1在各种宿主细胞靶点和组织中诱导的基因表达，但有效感染细胞和未感染的旁观者细胞之间的区别是一个尚未解决的技术挑战。因此，数据解释一直偏向于大多数未感染的旁观者细胞的转录反应，这些细胞暴露于病毒感染细胞释放的可溶性因子。在设计了一种独特和创新的分子工具来识别有效感染HIV-1的细胞，并描述了一种有效的基于磁珠的技术来将它们与未感染的旁观者细胞分离，我们接受了这一挑战，并对HIV-1感染和未感染的旁观者CD4+ T细胞进行了首次全基因组转录组学和大规模蛋白质组学分析。我们在此证明HIV-1感染和未感染的旁观者细胞显示出独特的转录组特征，这可能允许识别新的易感性和抗性因素。
HIV-1 is extremely specialized since, even amongst CD4+ T lymphocytes (its major natural reservoir in peripheral blood), the virus productively infects only a small proportion of cells under an activated state. As the percentage of HIV-1-infected cells is very low, most studies have so far failed to capture the precise transcriptomic profile at the whole-genome scale of cells highly susceptible to virus infection. Using Affymetrix Exon array technology and a reporter virus allowing the magnetic isolation of HIV-1-infected cells, we describe the host cell factors most favorable for virus establishment and replication along with an overview of virus-induced changes in host gene expression occurring exclusively in target cells productively infected with HIV-1. We also establish that within a population of activated CD4+ T cells, HIV-1 has no detectable effect on the transcriptome of uninfected bystander cells at early time points following infection. The data gathered in this study provides unique insights into the biology of HIV-1-infected CD4+ T cells and identifies genes thought to play a determinant role in the interplay between the virus and its host. Furthermore, it provides the first catalogue of alternative splicing events found in primary human CD4+ T cells productively infected with HIV-1. Some previous studies have monitored HIV-1-induced gene expression in various host cell targets and tissues but the discrimination between productively infected cells and uninfected bystander cells represents a technical challenge yet to be solved. Consequently, data interpretation has always been biased towards the transcriptional response of a majority of uninfected bystander cells that were exposed to soluble factors released by virus-infected cells. Following the design of a unique and innovative molecular tool to identify cells productively infected with HIV-1 and the description of an efficient magnetic beads-based technique to separate them from uninfected bystander cells, we undertake this challenge and perform the first comparative whole-genome transcriptomic and large-scale proteomic profiling of both HIV-1-infected and uninfected bystander CD4+ T cells. We demonstrate herein that HIV-1- infected and uninfected bystander cells display distinctive transcriptomic signatures which might permit to identify new susceptibility and resistance factors.
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