"Project 1" KSHV short and long noncoding RNAs and alteration of host IncRNA expression

“项目 1”KSHV 短非编码 RNA 和长非编码 RNA 以及宿主 IncRNA 表达的改变

基本信息

批准号：
10865781
负责人：
ROLF F RENNE
金额：
$ 4.3万
依托单位：
UNIVERSITY OF FLORIDA
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-01 至 2027-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10865781
关键词：
AIDS related cancer Acceleration Acquired Immunodeficiency Syndrome Address B-Cell Lymphomas B-Lymphocytes Binding Proteins Biological Assay Biology CRISPR interference Cells Code Collaborations Comparative Study Complement Complex Data Data Analyses Data Set Development Endothelial Cells Experimental Designs Funding Generations Genes Genetic Genetic Transcription Global Change Goals Growth Herpesviridae Herpesviridae Infections Human Human Herpesvirus 4 Human Herpesvirus 8 Hybrids In Vitro Investigation Kaposi Sarcoma Knock-out Laboratories Link Lymphoproliferative Disorders MALAT1 gene Malignant Neoplasms Messenger RNA Methods MicroRNAs Modeling Multiomic Data Mus Pathogenicity Pathway interactions Phenotype Proliferating Proteins Protocols documentation Publications Publishing RNA RNA Splicing Regulator Genes Reporting Role Sampling Signal Pathway South Africa Specimen Structure System Techniques Transcript Treatment Protocols Tumor Suppressor Proteins Universities Untranslated RNA Validation Viral Viral Pathogenesis Virus Virus Diseases Work Xenograft procedure angiogenesis bioinformatics pipeline circular RNA comparative crosslink density gammaherpesvirus gene regulatory network glucose metabolism in vivo in vivo Model innovation lytic replication migration multiple omics mutant novel novel therapeutic intervention primary effusion lymphoma programs success tissue culture transcriptome transcriptome sequencing transcriptomics tumor tumorigenesis viral RNA viral interferon regulatory factor virus genetics

项目摘要

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.

项目摘要 Kaposi的肉瘤相关疱疹病毒（KSHV）是人类γ-HEPESVIRUS，是AIDS的病因药物 KS和原发性淋巴瘤（PEL）等恶性肿瘤。近年来，很明显病原体包括EBV，KSHV和MHV68在内与蛋白质编码转录本的反义取向。这些RNA的功能和结构是在很大程度上未知。另外，这些病毒表达microRNA（miRNA）。在描述KSHV的同时 miRNA靶标使用杂种（QClash）方案的修改的交联和测序，我们确定了数百个宿主细胞LNCRNA作为推定的miRNA靶标。这些数据强烈表明两个KSHV 编码的蛋白质和miRNA导致宿主LNCRNA的失调。重要的是，34个lncrnas 据报道，KSHV感染后受到干扰，包括Malat1，Hottip，Anril，Meg3，UCA1和Gas-5 与人类癌症相关。我们还将mRNA和lncRNA靶标连接到癌症标志诸如增殖，迁移，血管生成和葡萄糖代谢等表型，并开始鉴定人体内皮细胞中KSHV miRNA扰动的信号通路是KS的模型。我们也是鉴定出异常的剪接是额外的癌症标志表型。在这里我们建议扩展我们的研究通过整合QClash，RNASEQ和Mirnaseq数据的多摩斯数据集以全面分析 MiRNA调节的KSHV感染内皮细胞中的基因调节网络。而且，我们建议验证我们在大量人类肿瘤样品中的发现，并通过产生第一个KS肿瘤miRNA Qclash的Targetome。这些研究将以比较的方式与项目2和3进行。此外，核心B，C和D将支持D 反义LANA转录本（ALT），我们已经使用高度确定了81个推定的结合蛋白创新的RNA-Pulldown分析。此外，我们将研究新鉴定的一类病毒循环RNA的作用这是该程序发现的。总而言之，该项目的目的是描述病毒的作用 lncRNA和宿主细胞LNCRNA在艾滋病恶性肿瘤中受到病毒感染的影响。