Role of novel cis-acting long non-coding RNAs in DNA replication timing and chromosome stability in cancer

新型顺式作用长非编码RNA在癌症DNA复制计时和染色体稳定性中的作用

• 批准号: 10013156
• 负责人: Michael B Heskett
• 金额: $ 4.55万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-09 至 2021-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10013156
• 关键词: 3-Dimensional; Affect; Alleles; Back; Behavior; Bioinformatics; Biological Assay; Biological Models; Biology; Biometry; Cancer Diagnostics; Cancer Model; Cell Line; Cell model; Cells; Chromatin; Chromatin Structure; Chromosomal Loss; Chromosomal Rearrangement; Chromosomal Stability; Chromosome 15; Chromosome 6; Chromosome Condensation; Chromosome Deletion; Chromosome Structures; Chromosome abnormality; Chromosomes; Clone Cells; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Communities; DNA Replication Timing; DNA biosynthesis; DNA replication fork; Data Set; Development; Elements; Event; Family; Fluorescent in Situ Hybridization; Future; Gene Expression; Genes; Genetic Nondisjunction; Genetic Transcription; Genome; Genome Stability; Genomic Instability; Genomics; Haplotypes; Health; Human; Human Characteristics; Human Chromosomes; Human Cloning; In Vitro; Institutes; Knowledge; Lead; Learning; Link; Maintenance; Malignant Neoplasms; Measures; Medical; Methods; Mitotic; Mitotic Chromosome; Modeling; Molecular; Names; Normal Cell; Nucleotides; Operative Surgical Procedures; Patient-Focused Outcomes; Phase; Phenotype; Physical condensation; Population; Postdoctoral Fellow; Progress Reports; Proteins; Public Speaking; RNA; Regulator Genes; Research; Role; Route; Sampling; Single Nucleotide Polymorphism; Testing; The Cancer Genome Atlas; Tissues; Training; Transcript; Translating; Untranslated RNA; Work; articular cartilage; autosome; cancer cell; cancer genome; cancer risk; cancer type; chromosome conformation capture; chromosome missegregation; clinically significant; genome wide association study; genome-wide; insight; interest; lymphoblastoid cell line; member; novel; novel diagnostics; novel therapeutic intervention; novel therapeutics; outcome forecast; pre-doctoral; progenitor; programs; risk variant; skill acquisition; stem cells; targeted cancer therapy; therapy development; tool; tumor; tumor progression; virtual

Project Summary/Abstract: Genome instability is the most significant feature associated with poor prognosis in many cancers. But despite being a near-universal characteristic of human cancer, our knowledge of how genome instability initiates and contributes to tumor development is lacking. Because of its wide presence and close association with aggressive tumors, insight into the possible mechanisms and consequences of genome instability is crucial in the search for new and targeted cancer therapies and diagnostics. Here a new model is proposed, backed by significant preliminary findings, for the maintenance of genomic stability by cis-acting long non-coding RNA (lncRNA) elements that regulate multiple aspects of large-scale chromosome function. The main hypothesis of this project is that the recently discovered, cis-acting ASAR lncRNAs (ASynchronously Replicating Autosomal RNA), are expressed by normal cells on all autosomes to regulate fundamental chromosome behavior such as DNA replication timing, monoallelic gene expression, 3- dimensional chromosome localization, and mitotic chromosome condensation, but are frequently disrupted in cancer leading to genomic instability. Expression of the first two members of the ASAR family (ASAR6, ASAR15) is required for stability on chromosome 6 and 15 respectively, and disruption of either lncRNA leads to aberrant chromosomes through increased stalling of replication forks and mis-segregation of chromosomes. The long-term objective of this research is to identify all ASARs on human autosomes, validate their functional role in genome stability, and use ASARs as a tool to understand and ultimately identify and treat cancers with genomic instability. In Aim 1 a genome wide search for expression of putative ASARs will be performed utilizing a single-cell derived, haplotype-resolved human primary cell model system, followed by assessment of the functional qualities of potential ASARS with nucleotide sequencing assays that measure DNA replication timing, allele specific RNA expression, and 3D chromosome localization. To probe the potential effects of ASARs on human health, a search for significant disruption of ASARs in a dataset of ~10,000 human tumor samples will be performed. The research will be conducted as part of a comprehensive training plan involving advanced skill development in bioinformatics and biostatistics, professional development such as public speaking and networking, and will take place within an extensive intellectual community composed of cancer biologists at the Knight Cancer Institute, molecular and medical geneticists, and computational biologists at OHSU. The post-doctoral research direction will translate the knowledge of chromosome biology and skillsets in genomics developed during the pre-doctoral period to study the mechanisms of action of non protein-coding germline risk loci in human cancer. The successful results of the proposed research will reveal basic functions of chromosomes and provide new insight towards understanding genomic instability, a common abnormality in cancer.

项目摘要/摘要：基因组不稳定性是与预后不良相关的最重要特征 在许多癌症中。但是，尽管是人类癌症的几乎全世界的特征，但我们的了解 缺乏基因组不稳定性并导致肿瘤发展。因为它的存在很广 与侵略性肿瘤密切关联，洞悉基因组的可能机制和后果 不稳定性对于寻找新的和有针对性的癌症疗法和诊断至关重要。 在这里，提出了一个新模型，并得到了重要的初步发现的支持，以维持基因组 顺式作用长的非编码RNA（lncRNA）元素的稳定性，这些元素调节了大规模的多个方面 染色体功能。该项目的主要假设是最近发现的，顺式作用ASAR lncRNA（异步复制常染色体RNA），由正常细胞在所有常染色体上表达 调节基本染色体行为，例如DNA复制时机，单相基因表达，3- 尺寸染色体定位和有丝分裂染色体凝结，但经常被干扰 导致基因组不稳定的癌症。 ASAR家族的前两个成员的表达（Asar6， ASAR15）分别在6和15染色体上稳定性需要，并破坏任何LNCRNA铅 通过增加复制叉的失速和染色体的错误分离来使异常的染色体。 这项研究的长期目的是确定所有关于人类常染色体的ASAR，验证其功能 在基因组稳定性中的作用，并使用ASAR作为一种工具来理解和最终识别和治疗癌症 基因组不稳定性。在目标1中，将进行基因组广泛的搜索推定ASAR的表达 利用单细胞得出的单倍型分辨的人类原代细胞模型系统，然后评估 用核苷酸测序测定测量DNA复制的潜在ASAR的功能质量 定时，等位基因特异性RNA表达和3D染色体定位。探究 关于人类健康的ASAR，寻找约10,000个人类肿瘤数据集中的ASAR的大幅破坏 样品将进行。 该研究将作为涉及高级技能开发的综合培训计划的一部分进行 在生物信息学和生物统计学方面，专业发展，例如公开演讲和网络，将 发生在一个由骑士癌症的癌症生物学家组成的广泛的知识分子社区中 OHSU的研究所，分子和医学遗传学家以及计算生物学家。博士后研究 方向将转化有关在此期间开发的基因组学中染色体生物学和技能集的知识 研究前时期，研究非蛋白质编码种系风险基因座的作用机制 癌症。拟议研究的成功结果将揭示染色体的基本功能和 为理解基因组不稳定性，这是癌症常见异常的新见解。