Transcribed Ultra Conserved Regions in Glioblastoma

胶质母细胞瘤中转录的超级保守区域

• 批准号: 10377434
• 负责人: Roger Abounader
• 金额: $ 20.19万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10377434
• 关键词: Astrocytes; Binding; Bioinformatics; Brain; Brain Neoplasms; Cell Line; Cell Proliferation; Cells; Code; Data; Data Analyses; Databases; Development; Evolution; Genes; Genomics; Glioblastoma; Goals; Human; Human Genome; Immunocompetent; Knowledge; Lead; Light; Liquid Chromatography; Location; Malignant Neoplasms; Malignant neoplasm of brain; Nucleic Acid Binding; Nucleic Acid Regulatory Sequences; Nucleic Acids; Patients; Play; Protein Analysis; Proteins; Publishing; RNA; Research; Research Personnel; Resistance; Role; Sampling; The Cancer Genome Atlas; Time; Tissues; Transcript; Untranslated RNA; Variant; Work; base; chromatin isolation by RNA purification sequencing; differential expression; experimental study; in vivo; knock-down; migration; mouse model; overexpression; stem cell differentiation; stem cells; tandem mass spectrometry; transcriptome sequencing; tumor; tumor growth

ABSTRACT Glioblastoma (GBM) is the most common and deadliest primary malignant brain tumor. Most GBM research has focused on protein-coding genes and less on non-coding transcripts that make up 98% of cellular RNA. Transcribed Ultra-Conserved Regions (TUCRs) are a group of 481 transcripts that are 100% conserved across multiple species. They are highly resistant to variation and are commonly deregulated in cancer, suggesting regulatory and functional importance. Some evidence suggests that most TUCRs are long non-coding RNAs (lncRNAs) that are highly conserved, unlike most other lncRNAs that are usually poorly conserved. TUCRs are largely understudied in cancer and not at all in GBM. As of the date of submission of this R21 application, there were no published studies on TUCRs in GBM. In preliminary work, we performed the first analysis of TUCR expression in GBM using The Cancer Genome Atlas (TCGA) RNA-Seq data and identified 194 TUCRs that are differentially expressed relative to normal brain. Many of these TUCRs correlated with patient survival. This project aims to identify and characterize TUCRs that are differentially expressed in GBM and to uncover their functions and mechanisms of action. We propose three specific aims. In Aim 1, we will identify and characterize TUCRs that are differentially expressed in GBM. Candidate TUCRs will be identified from TCGA RNA-Seq data analyses and prioritized based on their differential expression and correlation with survival. Their full transcript sequences will be uncovered and their lncRNA status verified. In Aim 2, we will uncover the functions of select TUCR lncRNAs in GBM. The top 20 ranked TUCR lncRNAs from aim 1 will be used for this aim. TUCR lncRNAs will be overexpressed and knocked down/out in GBM cell lines and stem cells. The effects of the TUCRs on cell proliferation, survival, invasion, migration and stem cell differentiation as well as on in vivo tumor growth in an RCAS/Tva immune competent mouse model of GBM will be analyzed. In Aim 3, we will identify the mechanism of action for select TUCR lncRNAs in GBM. TUCRs that exert regulatory effects on GBM malignancy as determined in aim 2 will be prioritized. We will identify the subcellular localization of each TUCR lncRNA and use a multipronged approach consisting of bioinformatics and experimental determination of protein and nucleic acid binding partners followed by functional rescue experiments to uncover the mechanisms of action of TUCR lncRNAs. Successful completion of this project would represent the first comprehensive analysis of TUCRs in GBM and generate new knowledge on the mechanisms of GBM malignancy.

抽象的 胶质母细胞瘤（GBM）是最常见，最致命的原发性恶性脑肿瘤。大多数GBM研究都有 侧重于蛋白质编码基因，而较少于占细胞RNA 98％的非编码转录本。 转录的超保存区域（TUCR）是一组481个成绩单，在整个方面100％保守 多种物种。它们对变异具有高度抵抗力，通常在癌症中放松管制，这表明 监管和功能重要性。一些证据表明，大多数TUCR是长的非编码RNA （LNCRNA）是高度保守的，与大多数其他通常保守性不佳的LNCRNA不同。 Tucr是 在很大程度上研究了癌症，而根本不研究GBM。截至提交此R21申请的日期， 没有关于GBM中TUCR的发表研究。在初步工作中，我们进行了TUCR的首次分析 使用癌症基因组图集（TCGA）RNA-seq数据中的GBM表达，并确定了194个TUCR 相对于正常大脑的差异表达。这些TUCR中的许多与患者的生存有关。这 项目旨在识别和表征在GBM中差异表达并揭示其的TUCR 作用的功能和机制。我们提出了三个具体目标。在AIM 1中，我们将确定并 表征在GBM中差异表达的TUCR。候选TUCR将从 TCGA RNA-seq数据分析并根据其差异表达和与生存的相关性进行了优先排序。 他们的完整成绩单序列将被发现并验证其LNCRNA状态。在AIM 2中，我们将发现 GBM中选择的TUCR LNCRNA的功能。将使用AIM 1的前20名TUCR LNCRNA 为此目标。 TUCR LNCRNA将过表达并在GBM细胞系和干细胞中击倒/撞倒。这 TUCR对细胞增殖，生存，侵袭，迁移和干细胞分化以及对 将分析RCAS/TVA免疫胜任小鼠GBM小鼠模型中的体内肿瘤生长。在AIM 3中，我们 将确定GBM中选择的TUCR LNCRNA的作用机理。发挥调节作用的TUCR AIM 2中确定的GBM恶性肿瘤将得到优先级。我们将确定每个的亚细胞定位 tucr lncRNA，并使用由生物信息学和实验确定的多收益方法 蛋白质和核酸结合伴侣，然后进行功能救援实验，以发现机制 tucr lncrnas的作用。成功完成该项目将代表第一个综合 GBM中TUCR的分析，并产生有关GBM恶性肿瘤机制的新知识。