Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency
Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency
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DOI：
10.1186/s12977-019-0494-x
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发表时间：
2019-11-11
期刊：
影响因子：
3.3
通讯作者：
Yukl, Steven A.
中科院分区：
文献类型：
--
作者：
Telwatte, Sushama;Moron-Lopez, Sara;Yukl, Steven A.
背景HIV感染细胞系被广泛用于研究HIV潜伏感染，潜伏感染被认为是HIV治愈的主要障碍。我们假设，这些细胞系彼此不同，也不同于HIV感染者的细胞，其潜伏期的机制不同。结果为了量化在HIV转录的不同阶段阻断HIV表达的程度，我们使用了最近描述的一组RT-ddPCR方法来测量在大量潜伏感染(U1，ACH-2，J-Lat)和生产性感染(8E5，激活的J-Lat)细胞系中7种HIV转录本(“通读”、启动的、5‘延长的、中期转录/未剪接的[Pol]、远端转录的[Nef]、多腺化的和多切片的[Tat-Rev])的水平。为了评估单细胞变异和研究与艾滋病毒转录阻断相关的细胞基因，我们建立了一个新的多重qPCR小组，并定量检测了7个艾滋病毒靶标和细胞转录物在潜伏感染和生产性感染细胞系中的单细胞水平。大细胞HIV转录图谱在细胞系和ART抑制个体的细胞之间有很大的不同。与ART抑制个体的细胞相比，潜伏细胞系表现出较低的HIV转录启动水平和较高的多聚腺苷化和剪接水平。ACh-2和J-Lat细胞表现出不同形式的转录干扰，而U1细胞则表现出伸长障碍。单细胞研究表明，在HIV转录本、T细胞表型标记、抗病毒因子和潜伏期相关基因的表达方面，细胞系之间/细胞内的表达存在显著差异。多剪接HIV TAT-Rev的表达与参与激活、组织保留、T细胞转录和凋亡/生存的细胞基因的表达有关。结论HIV感染细胞株之间以及不同于ART治疗个体的细胞株在控制HIV潜伏感染的机制上有所不同。在评估特定细胞系对未来艾滋病毒研究的适合性时，必须考虑病毒和细胞基因表达的这些差异。与此同时，在不同的细胞系之间也有一些共同的特征，比如抗病毒防御基因的低表达，以及生产性感染和参与生存的基因之间的关系。这些特征可能导致HIV在体内的潜伏期或持久性，值得使用新的单细胞分析方法进行进一步研究，如本文中描述的那些。
Background HIV-infected cell lines are widely used to study latent HIV infection, which is considered the main barrier to HIV cure. We hypothesized that these cell lines differ from each other and from cells from HIV-infected individuals in the mechanisms underlying latency. Results To quantify the degree to which HIV expression is inhibited by blocks at different stages of HIV transcription, we employed a recently-described panel of RT-ddPCR assays to measure levels of 7 HIV transcripts ("read-through," initiated, 5 ' elongated, mid-transcribed/unspliced [Pol], distal-transcribed [Nef], polyadenylated, and multiply-sliced [Tat-Rev]) in bulk populations of latently-infected (U1, ACH-2, J-Lat) and productively-infected (8E5, activated J-Lat) cell lines. To assess single-cell variation and investigate cellular genes associated with HIV transcriptional blocks, we developed a novel multiplex qPCR panel and quantified single cell levels of 7 HIV targets and 89 cellular transcripts in latently- and productively-infected cell lines. The bulk cell HIV transcription profile differed dramatically between cell lines and cells from ART-suppressed individuals. Compared to cells from ART-suppressed individuals, latent cell lines showed lower levels of HIV transcriptional initiation and higher levels of polyadenylation and splicing. ACH-2 and J-Lat cells showed different forms of transcriptional interference, while U1 cells showed a block to elongation. Single-cell studies revealed marked variation between/within cell lines in expression of HIV transcripts, T cell phenotypic markers, antiviral factors, and genes implicated in latency. Expression of multiply-spliced HIV Tat-Rev was associated with expression of cellular genes involved in activation, tissue retention, T cell transcription, and apoptosis/survival. Conclusions HIV-infected cell lines differ from each other and from cells from ART-treated individuals in the mechanisms governing latent HIV infection. These differences in viral and cellular gene expression must be considered when gauging the suitability of a given cell line for future research on HIV. At the same time, some features were shared across cell lines, such as low expression of antiviral defense genes and a relationship between productive infection and genes involved in survival. These features may contribute to HIV latency or persistence in vivo, and deserve further study using novel single cell assays such as those described in this manuscript.