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Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells

机译：血液和淋巴内皮细胞初次感染后KSHV转录组的定量分析

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The transcriptome of the Kaposi’s sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters. Similar patterns of KSHV expression were detected in BCBL-1 cells undergoing long-term latent infections and in primary latent infections of both BEC and LEC cultures. High expression levels of poly-adenylated nuclear (PAN) RNA and spliced and unspliced transcripts encoding the K12 Kaposin B/C complex and associated microRNA region were detected, with an elevated expression of a large set of lytic genes in all latently infected cultures. Quantitation of non-overlapping regions of transcripts across the complete KSHV genome enabled for the first time accurate evaluation of the KSHV transcriptome associated with viral latency in different cell types. Hierarchical clustering applied to a gene correlation matrix identified modules of co-regulated genes with similar correlation profiles, which corresponded with biological and functional similarities of the encoded gene products. Gene modules were differentially upregulated during latency in specific cell types indicating a role for cellular factors associated with differentiated and/or proliferative states of the host cell to influence viral gene expression.
机译：使用RNAseq分析人血液（BEC），淋巴（LEC）和永生化（TIME）内皮细胞的原发性潜伏感染后卡波西氏肉瘤相关疱疹病毒（KSHV / HHV8）的转录组，并将其与BCBL中的长期潜伏期进行比较-1淋巴瘤细胞。无需人工诱导即可获得天然表达的转录本，并确定了KSHV基因组的全面注释。开发了一套独特的编码序列（UCDS）功能和解决重叠转录物的方法，以准确地定量来自特定启动子的转录物水平。在经历长期潜伏感染的BCBL-1细胞和BEC和LEC培养物的原发潜伏感染中，发现了类似的KSHV表达模式。检测到高表达水平的聚腺苷酸化核（PAN）RNA以及编码K12 Kaposin B / C复合体和相关microRNA区域的剪接和非剪接转录本，在所有潜伏感染的培养物中大量裂解基因的表达升高。完整的KSHV基因组中转录本的非重叠区域的定量分析首次实现了与不同细胞类型中病毒潜伏期相关的KSHV转录组的首次准确评估。应用于基因相关矩阵的层次聚类可确定具有相似相关配置文件的共调控基因的模块，这些模块与编码基因产物的生物学和功能相似性相对应。基因模块在特定细胞类型的潜伏期差异上调，表明与宿主细胞的分化和/或增殖状态相关的细胞因子对病毒基因表达的影响。

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