Noncoding RNAs in gamma-Herpesvirus Biology and AIDS Malignancies

总结 P01提案的统一假设是，KSHV、EBV和MHV 68的比较研究将 加速发现由长链非编码RNA（lncRNA）调控的途径， γ疱疹病毒潜伏期和肿瘤发生。具体来说，我们假设A）疱疹病毒利用 B）病毒lncRNA和/或病毒干扰的lncRNA， 宿主lncRNA直接导致病毒相关的AIDS恶性肿瘤的发生。解决这些 假设我们提出了三个高度集成的项目，其目标是功能分析lncRNA， 他们的行动机制。项目1由Renne博士（佛罗里达大学，UF）领导，将研究KSHV- 编码的lncRNA和HIV相关KSHV背景下宿主lncRNA表达的改变 恶性肿瘤由杜兰大学弗莱明顿博士领导的项目2将研究EB病毒lncRNA 以及HIV相关EBV恶性肿瘤中宿主lncRNA表达的改变。项目3由 博士Tibbetts（UF）将研究MHV 68 lncRNA的功能和宿主lncRNA的改变， 潜伏期和淋巴瘤发生。重要的是，所有项目都得到了强大的小说支持。 初步数据，包括使用新的多平台发现新的γ疱疹病毒lncRNA 基因组学方法，并暗示这些lncRNA中的一些在病毒生物学和发病机制。井- 有组织的行政核心（核心A，核心领导人：Rolf Renne）将维持对 该计划，包括生物医学咨询和遵守再现性和透明度标准。 另外两个已经建立的非常有成效的服务核心将支持排序， 三个项目的生物信息学和重组病毒生成需求：病毒RNA-seq和 生物信息学核心将在杜兰大学维护（核心B，核心负责人：Erik弗莱明顿）。的 重组病毒核心，这是建立了一个国家癌症研究所资助的RC 2奖在2009年，将保持在 UF（Core C，Core Leader：Rolf Renne）。此外，帕森斯博士（LSUHSC，新奥尔良），谁领导国家卫生研究院- 支持LSUHSC/LCRC HIV临床和生物标本库，将有助于获得有价值的 HIV感染患者的卡波西肉瘤（KS）和淋巴瘤肿瘤标本。我们的建议意义重大 在研究领域方面具有高度创新性-“了解病毒和宿主lncRNA在 γ疱疹病毒肿瘤发生”-并在所有三个应用众多的最先进的技术 项目最后，研究与发病机制相关的组织培养和动物模型，并辅之以 分析人类肿瘤组织的EBV和KSHV相关的恶性肿瘤，将大大增加我们的研究。 理解艾滋病恶性肿瘤中病毒和宿主lncRNA。

SUMMARY The unifying postulate of this P01 proposal is that comparative studies of KSHV, EBV, and MHV68 will accelerate the discovery of pathways regulated by long non-coding RNAs (lncRNAs) that contribute to gammaherpesvirus latency and tumorigenesis. Specifically, we hypothesize A) that herpesviruses utilize lncRNAs to regulate both virus and host gene expression, and B) that viral lncRNAs and/or virus-perturbed host lncRNAs directly contribute to the genesis of virus-associated AIDS malignancies. To address these hypotheses we propose three highly integrated projects with the goal of functionally analyzing lncRNAs and their mechanisms of action. Project 1, led by Dr. Renne (University of Florida, UF), will investigate KSHV- encoded lncRNAs and alteration of host lncRNA expression in the context of HIV-associated KSHV malignancies. Project 2, led by Dr. Flemington (Tulane University) will interrogate Epstein-Barr virus lncRNAs and alteration of host lncRNA expression in the context of HIV-associated EBV malignancies. Project 3 led by Dr. Tibbetts (UF) will investigate function of MHV68 lncRNAs and alteration of host lncRNAs in the context of latency and lymphomagenesis in a facile murine model. Importantly, all projects are supported by strong novel preliminary data, including the discovery of new gammaherpesvirus lncRNAs using a novel multi-platform genomics approach and implicating some of these lncRNAs in viral biology and pathogenesis. The well- organized Administrative core (Core A, Core Leader: Rolf Renne) will maintain oversight and organization of the program, including biostatisical consultation and adherence to reproducibility and transparency standards. Two additional service cores, which are already established and very productive, will support sequencing, bioinformatics and recombinant virus generation needs across the three projects: The Virus RNA-seq and Bioinformatics Core will be maintained at Tulane University (Core B, Core Leader: Erik Flemington). The Recombinant Virus Core, which was established with an NCI-funded RC2 award in 2009, will be maintained at UF (Core C, Core Leader: Rolf Renne). In addition, Dr. Parsons (LSUHSC, New Orleans), who leads the NIH- supported LSUHSC/LCRC HIV Clinical and Biospecimen Repository, will facilitate the acquisition of valuable Kaposi's sarcoma (KS) and lymphoma tumor specimens from HIV-infected patients. Our proposal is significant and highly innovative in terms of the field of study – “understanding virus and host lncRNA function in gammaherpesvirus tumorigenesis” – and in applying numerous state-of-the-art techniques across all three projects. Finally, studying pathogenesis-relevant tissue culture and animal models, complemented by the analysis of human tumor tissues from EBV- and KSHV-associated malignancies, will greatly increase our understanding of both viral and host lncRNAs in the context of AIDS malignancies.