Noncoding RNAs in gamma-Herpesvirus Biology and AIDS Malignancies

摘要 这一P01提案的统一假设是KSHV、EBV和MHV68的比较研究将 加速发现受长非编码RNA(LncRNAs)调控的途径，这些RNAs有助于 伽马疱疹病毒潜伏期与肿瘤发生。具体地说，我们假设A)疱疹病毒利用 调节病毒和宿主基因表达的lncRNAs，以及B)病毒lncRNAs和/或病毒干扰 宿主lncRNAs直接参与病毒相关的艾滋病恶性病变的发生。要解决这些问题 假设我们提出了三个高度集成的项目，目标是从功能上分析LncRNAs和 它们的作用机制。项目1由雷恩博士(佛罗里达大学)领导，将研究KSHV- HIV相关KSHV中编码的lncRNA和宿主lncRNA表达的变化 恶性肿瘤。由弗莱明顿博士(杜兰大学)领导的项目2将询问Epstein-Barr病毒lncRNAs 以及在HIV相关EBV恶性肿瘤的背景下宿主LncRNA表达的变化。项目3由 Tibbetts博士(UF)将研究MHV68 lncRNAs的功能和宿主lncRNAs在 一种简便易行的小鼠模型中的潜伏期和淋巴肿大。重要的是，所有的项目都有强大的小说支持 初步数据，包括使用新的多平台发现新的伽马疱疹病毒lncRNAs 基因组学方法，并暗示其中一些lncRNAs在病毒生物学和发病机制中的作用。这口井- 有组织的行政核心(核心A，核心领导：罗尔夫·雷恩)将保持监督和组织 该计划，包括生物统计咨询和遵守重复性和透明度标准。 另外两个已经建立并且非常高效的服务核心将支持排序， 生物信息学和重组病毒生成需要跨越三个项目：病毒RNA-seq和 生物信息学核心将保留在杜兰大学(核心B，核心领导：埃里克·弗莱明顿)。这个 重组病毒核心是在2009年由NCI资助的RC2奖建立的，将保持在 UF(核心C，核心领导者：罗尔夫·雷恩)。此外，领导NIH的帕森斯博士(新奥尔良LSUHSC)- 支持LSUHSC/LCRC艾滋病毒临床和生物检验库，将促进获得有价值的 来自HIV感染者的卡波西肉瘤(KS)和淋巴瘤肿瘤标本。我们的建议意义重大 和极具创新性的研究领域--《了解病毒和宿主lncRNA在 伽马疱疹病毒肿瘤发生“-以及在所有三个领域应用大量最先进的技术 项目。最后，研究与发病相关的组织培养和动物模型，并辅之以 分析EBV和KSHV相关恶性肿瘤的人类肿瘤组织，将大大增加我们的 在艾滋病恶性疾病的背景下对病毒和宿主的lncRNA的理解。

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.