Noncoding RNAs in gamma-Herpesvirus Biology and AIDS Malignancies

项目总结 卡波西肉瘤相关疱疹病毒(KSHV)是一种人类伽玛疱疹病毒，是艾滋病的病原体 恶性疾病，如KS和原发性渗出性淋巴瘤(PEL)。近年来，致病性变得越来越明显 包括EBV、KSHV和MHV68在内的疱疹病毒表达大量的长非编码RNA(LncRNAs)，其中许多 它们与蛋白质编码转录本处于反义定向。这些RNAs的功能和结构如下 很大程度上是未知的。此外，这些病毒还表达microRNAs(MiRNAs)。在描述KSHV的同时 使用一种改进的杂交(QClash)交联法和测序方法，我们鉴定了miRNA靶体 数百个宿主细胞中的lncRNAs可能是miRNA的靶标。这些数据强烈表明，KSHV和KSHV 编码的蛋白质和miRNAs参与了宿主lncRNAs的失调。重要的是，34个lncRNA是 报道了KSHV感染后的扰动，包括MALAT1，HotTip，ANRIL，Meg3，UCA1和GAS-5 与人类癌症有关。我们还将mrna和lncRNA靶标与癌症标志联系起来。 表型，如增殖、迁移、血管生成和葡萄糖代谢，并开始识别 作为KS模型的人内皮细胞中受KSHV miRNAs干扰的信号通路。我们也 异常剪接被确定为另一种癌症标志表型。在这里，我们建议扩展我们的研究范围 通过整合QClash、RNAseq和miRNAseq数据中的多个组学数据集来综合分析 KSHV感染的内皮细胞中miRNA调控的基因调控网络。此外，我们还建议验证 我们在大量人类肿瘤样本中的发现，并通过产生第一个KS肿瘤miRNA 由QClash提供的Target ome。这些研究将与项目2和项目3进行比较 此外，还将由核心B、C和D支持。此外，我们正在从功能上研究 反义LANA转录本(ALT)，我们已经用高度的 创新的RNA下拉试验。此外，我们还将研究一类新发现的病毒环状RNA的作用。 它已经被这个程序发现了。总而言之，这个项目的目标是描绘病毒的作用 在艾滋病恶性肿瘤中受病毒感染干扰的lncRNA和宿主细胞lncRNAs。

PROJECT SUMMARY Kaposi's sarcoma-associated herpesvirus (KSHV), a human gamma-herpesvirus, is the causative agent of AIDS malignancies like KS and primary effusion lymphomas (PEL). In recent years it became clear that pathogenic herpesviruses including EBV, KSHV, and MHV68 express numerous long non-coding RNAs (lncRNAs) many of which are in antisense orientation to protein coding transcripts. The function and structure of these RNAs is largely unknown. In addition, these viruses express microRNAs (miRNAs). While characterizing the KSHV miRNA targetomes using a modified Crosslinking and Sequencing of Hybrids (qCLASH) protocol, we identified several hundred host cellular lncRNAs as putative miRNA targets. These data strongly suggest that both KSHV encoded proteins and miRNAs contribute to dysregulation of host lncRNAs. Importantly, 34 lncRNAs that are perturbed following KSHV infection, including MALAT1, HOTTIP, ANRIL, Meg3, UCA1 and GAS-5 are reported to be associated with human cancers. We also linked both mRNA and lncRNA targets to cancer hallmark phenotypes such as proliferation, migration, angiogenesis, and glucose metabolism, and started to identify signaling pathways that are perturbed by KSHV miRNAs in human endothelial cells as a model for KS. We also identified aberrant splicing as an additional cancer hallmark phenotype. Here we propose to extend our studies by integrating multi-omics data sets from qCLASH, RNAseq and miRNAseq data to comprehensively analyze miRNA-regulated gene regulatory networks in KSHV infected endothelial cells. Moreover, we propose to validate our findings in a significant number of human tumor samples and by generating the first KS tumor miRNA targetome by qCLASH. These studies will be performed in a comparative fashion with Projects 2 and 3 and furthermore will be supported by Cores B, C, and D. In addition, we are functionally studying the role of the antisense LANA transcript (ALT) for which we have identified 81 putative binding proteins using a highly innovative RNA-pulldown assay. Moreover, we will study the role of a newly identified class of viral circular RNAs that has been discovered by this program. In summary, the goal of this project is to delineate the role of viral lncRNAs and host cellular lncRNAs that are perturbed by viral infection in AIDS malignancies.