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

（PQ

基本信息

批准号：
10373046
负责人：
John Karijolich
金额：
$ 42.46万
依托单位：
VANDERBILT UNIVERSITY MEDICAL CENTER
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-04-01 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10373046
关键词：
Acquired Immunodeficiency Syndrome Address Affect Area B-Lymphocytes Bioinformatics Biology CRISPR interference CRISPR screen Cancer Etiology Carcinogens Cells Cellular biology Chromatin Communicable Diseases DNA Transposable Elements DNA Viruses Data Disease Disease Progression Disease remission Elements Endothelial Cells Enhancers Environment Etiology Family Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Genome Genomic Segment Gold Grant HIV Herpesviridae Infections Human Herpesvirus 8 Infection Introns Kaposi Sarcoma Laboratories Literature Location Lymphoma cell Lytic Lytic Phase Maintenance Malignant Neoplasms Mammalian Cell Maps Mediating Non-Hodgkin&apos s Lymphoma Oncogenic Outcome Pathogenesis Pathway interactions Patients Persons Phase Phenotype Play Population Primary Lesion Process Production Proteins Publishing RNA RNA Polymerase II Regulation Regulator Genes Regulatory Element Resolution Retrotransposon Risk Role Series Stress Techniques Technology Testing Time Transcript Transcription Initiation Transcription Initiation Site Transcriptional Regulation Untranslated Regions Viral Viral Genes Virion Virus antiretroviral therapy chromatin modification effective therapy experimental study genetic analysis genetic element genome-wide insight latent infection primary effusion lymphoma promoter stem cell biology targeted treatment therapeutic development transcription factor transcriptional reprogramming transcriptome transcriptome sequencing tumorigenesis virus host interaction

项目摘要

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.

人类免疫缺陷病毒 (PLWH) 感染者罹患获得性免疫缺陷综合症 (AIDS) 与许多不同恶性肿瘤的风险增加有关。其中最常见的癌症人群包括卡波西肉瘤 (KS) 和非霍奇金淋巴瘤，例如原发性渗出性淋巴瘤（PEL）。 KS 是内皮细胞来源的病变，而 PEL 是 B 细胞来源的。 KS 和 PEL 的病原体是致癌 DNA 病毒，卡波西肉瘤相关疱疹病毒 (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，两者都是进展到和维持 KSHV 相关癌症。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裂解阶段的进展中发挥重要作用。因此，破译 KSHV 感染期间运行的基因调控机制将识别肿瘤发生过程 PLWH 以及确定治疗开发的潜在目标。转座元件 (TE) 是基因序列可以或曾经可以在基因组中从一个位置移动到另一个位置，并且最近对哺乳动物细胞遗传调控景观的分析揭示了 TE 在广泛的功能中发挥作用。一系列的调控过程，包括转录调控。而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等领域获得了认可，例如在 PLWH 中的情况尚不清楚。我们的研究调查了这个未知数，这是提出挑衅性问题的基础 2（PQ#2）。利用 5' 端 RNA 测序技术，我们绘制了转录起始图谱潜伏和裂解 PEL 细胞，并已鉴定出 TE 的广泛转录。此外，我们还发现了 TE 从注释的基因调控元件（例如增强子和基因启动子）内转录，并且一些转录的 TE 与主要 KSHV 编码的转录因子 RTA 结合。值得注意的是，有针对性的 CRISPR 筛选鉴定出 RTA 结合的 TE 衍生增强子，可显着影响 KSHV 裂解再激活在 PEL 中。与科学文献中的观察结果一起，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宿主与 KSHV 战斗的相关性，并且它们的调节对于发病机制至关重要。为了检验这个假设，我们提出了一系列综合实验，旨在确定 TE 和 KSHV 之间的相互作用。瞄准 1，我们将确定 PEL 中 RTA 绑定 TE 的功能。在目标 2 中，我们将确定 KSHV 感染如何内皮细胞影响 TE 表达以及 TE 衍生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。预计完成这些研究确定 TE 如何导致 PLWH 中的 KSHV 相关癌症。我们的研究结果将代表根本性的关于致癌 DNA 病毒如何利用细胞遗传调控景观导致疾病的新见解。