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

项目摘要/摘要：基因组不稳定是预后不良的最重要特征 在许多癌症中。但是，尽管这是人类癌症的一个几乎普遍的特征，我们对如何 缺乏基因组不稳定性启动和促进肿瘤的发展。因为它的广泛存在和 与侵袭性肿瘤密切相关，洞察基因组可能的机制和后果 在寻找新的、有针对性的癌症治疗和诊断方法时，不稳定是至关重要的。 在这里，提出了一个新的模型，并得到了重要的初步发现的支持，用于维持基因组 通过顺式作用的长非编码RNA(LncRNA)元件调节大规模的多方面稳定性 染色体功能。该项目的主要假设是最近发现的顺式作用的ASAR LncRNAs(异步复制常染色体RNA)，由正常细胞在所有常染色体上表达，以 调节基本的染色体行为，如DNA复制时机、单等位基因表达、3- 空间染色体定位和有丝分裂染色体凝聚，但经常在 癌症导致基因组不稳定。ASAR家族的前两个成员(ASAR6， ASAR15)分别是6号和15号染色体稳定所必需的，并且任一条lncRNA的中断都会导致 通过增加复制分叉的停滞和染色体的错误分离而导致染色体的异常。 这项研究的长期目标是识别人类常染色体上的所有ASAR，验证它们的功能 在基因组稳定性中的作用，并将ASARs用作了解并最终识别和治疗癌症的工具 基因组不稳定。在目标1中，将在全基因组范围内搜索可能的ASARs的表达 利用单细胞衍生的、单倍型分辨的人类原代细胞模型系统，随后评估 用核苷酸测序法测定DNA复制对潜在ASARS的功能性质 时间、等位基因特异性RNA表达和3D染色体定位。为了探索潜在的影响 ASARs对人类健康的影响，在约10,000例人类肿瘤数据集中寻找ASARs的显著干扰 样本将会被执行。 这项研究将作为涉及高级技能发展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，公共演讲和网络等专业发展，并将 在奈特癌症研究所由癌症生物学家组成的广泛的知识社区内进行 俄亥俄州立大学分子和医学遗传学家以及计算生物学家。博士后研究 DIRECTION将把染色体生物学的知识和基因组学中开发的技能 博士前研究人类非蛋白质编码生殖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提供了新的见解，基因组不稳定性是癌症中的一种常见异常。

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.