(PQ#2) Transposable element-mediated gene regulation in KSHV-associated cancer

获得性免疫缺陷综合征（艾滋病）的人与人类免疫缺陷病毒（PLWH）的生活是 与多种不同恶性肿瘤的风险增加有关。其中最常见的癌症 人群中的卡波西肉瘤（KS）和非霍奇金淋巴瘤，如原发性渗出性淋巴瘤 （PEL）。KS是内皮细胞源性病变，而PEL是B细胞源性病变。KS和PEL的病因 卡波西肉瘤相关疱疹病毒（Kaposi's sarcoma-associated herpesvirus，KSHV）KSHV显示两种不同的 其病毒生命周期的各个阶段，潜伏期和裂解性感染，两者都是进展所必需的， KSHV相关癌症的维持。在感染过程中细胞基因表达的重塑起着重要作用， 在潜伏期的建立以及向溶解期的进展中起重要作用。因此， KSHV感染过程中的基因调控机制将确定参与肿瘤发生的过程 以及确定治疗开发的潜在靶点。转座因子（Transposable elements，TE） 基因序列可以，或者曾经可以，在基因组中从一个位置移动到另一个， 最近对哺乳动物细胞遗传调控景观的分析揭示了TEs在广泛的 一系列调控过程，包括转录调控。虽然TE调节元件的功能 在干细胞生物学，TE在传染病和癌症中的作用， 例如在PLWH中是未知的。我们的研究探讨了这个未知的基础上挑衅性的问题 2（方案问题2）。利用5 '-末端RNA测序技术，我们绘制了转录起始景观， 的潜伏性和溶解性PEL细胞，并已确定广泛的转录的TE。此外，我们发现了TE 从注释的基因调控元件如增强子和基因启动子内转录，并且 一些转录的TE被KSHV编码的主要转录因子RTA结合。值得注意的是， CRISPR筛选鉴定出显著影响KSHV裂解再活化的RTA结合的TE衍生增强子 在PEL。结合科学文献中的观察，我们未发表的数据构成了科学前提 对于拟议的研究。我们的中心假设是TE衍生的基因调控元件位于中心 的主机KSHV的战斗，他们的调制是必不可少的发病机制。为了验证这个假设，我们 提出了一个综合系列的实验，旨在确定TE和KSHV之间的相互作用。在Aim中 1，我们将确定RTA结合的TE在PEL中的功能。在目标2中，我们将确定KSHV如何感染 内皮细胞影响TE的表达和TE衍生的调节元件对病毒的影响。 生命周期以及肿瘤发生所需的细胞途径。预计这些研究的完成将 确定TE如何导致PLWH中KSHV相关癌症。我们的发现将代表 对致癌DNA病毒如何利用细胞遗传调控景观导致疾病的新见解。

Acquired immunodeficiency syndrome (AIDS) in people living with human immunodeficiency virus (PLWH) is associated with an increased risk for a number of different malignances. The most common cancers within this population are Kaposi's sarcoma (KS) and non-Hodgkin's lymphomas, such as primary effusion lymphoma (PEL). While KS is an endothelial cell-derived lesion PEL is of B cell origin. The etiological agent of KS and PEL is the oncogenic DNA virus, Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV displays two distinct phases of its viral lifecycle, latency and lytic infection, and both are required for the progression to and maintenance of KSHV-associated cancers. The remodeling of cellular gene expression during infection plays an essential role in the establishment of latency as well as progression to the lytic phase. Thus, deciphering the gene regulatory mechanisms operating during KSHV infection will identify processes involved in tumorigenesis in PLWH as well as identify potential targets for therapeutic development. Transposable elements (TEs) are genetic sequences that can, or at one time could, move around the genome from one location to another and recent analyses of the genetic regulatory landscape of mammalian cells have revealed TEs function in a wide range of regulatory processes, including transcriptional regulation. While the function of TE regulatory elements has gained appreciation in areas such as stem cell biology, the role of TEs in infectious diseases and cancer, such as in PLWH is not known. Our study investigates this unknown which is the basis of provocative question 2 (PQ#2). Leveraging 5'-end RNA sequencing technology we have mapped the transcription initiation landscape of latent and lytic PEL cells and have identified wide-spread transcription of TEs. Moreover, we discovered TEs transcribed from within annotated gene regulatory elements such as enhancers and gene promoters, and that some transcribed TEs are bound by the main KSHV-encoded transcription factor, RTA. Remarkably, a targeted CRISPR screen identified an RTA-bound TE-derived enhancer that significantly affects KSHV lytic reactivation in PEL. Together with observations from the scientific literature our unpublished data form the scientific premise for the proposed studies. Our central hypothesis is that TE-derived gene regulatory elements are at the center of the host-KSHV battle and that their modulation is essential for pathogenesis. To test this hypothesis, we propose an integrated series of experiments aimed at determining the interplay between TEs and KSHV. In Aim 1, we will determine the function of RTA-bound TEs in PEL. In Aim 2, we will determine how KSHV infection of endothelial cells influences TE expression and the consequences of TE-derived regulatory elements on the viral lifecycle as well as cellular pathways required for tumorigenesis. Completion of these studies is expected to determine how TEs contribute to KSHV-associated cancer in PLWH. Our findings will represent fundamental new insights into how oncogenic DNA viruses co-opt the cellular genetic regulatory landscape to cause disease.