食管鳞状细胞癌多组学数据的整合分析及全基因组关联研究数据挖掘

发布时间：2018-05-17 12:11

本文选题：食管鳞状细胞癌 + 多组学　；参考：《北京协和医学院》2017年硕士论文

【摘要】：背景与目的:食管鳞状细胞癌(esophageal squamous cell carcinoma,ESCC)是我国特色的严重危害健康和生命的重大疾病。ESCC的发生发展机制不明,致使其疗效差,预后令人沮丧。生命体是一个复杂的调控系统,疾病的发生与发展涉及基因变异、表观遗传改变、基因表达异常以及信号通路紊乱等诸多层次的复杂调控机制,利用单一组学数据分析致病因子的局限性愈发显著。因此本研究通过对多种层次和来源的ESCC高通量组学数据的整合分析,以期阐明关键基因或网络通路及其调控的异常在ESCC发生发展中的分子机制,为ESCC的早期诊断、个体化治疗和指导用药等提供理论依据。方法:本研究运用高通量测序技术和系统生物医学的理论和技术方法,分别对94例ESCC患者的DNA和RNA进行全基因组测序和转录组测序,进行ESCC全基因组遗传变异谱、体细胞突变谱、转录组表达谱等多维度的贯穿组学研究,并结合患者的临床资料进行关联分析,建立ESCC的异常分子调控网络,阐明ESCC发生发展和转归的规律;另外采用全基因组关联研究的策略,对随访5年以上的1,088例ESCC患者外周血DNA的7,875,353个SNP与患者总生存时间进行关联分析,然后对发现的相关SNP在1,479例ESCC的独立样本中进行验证,以探索中国人群ESCC预后相关联的SNP位点和基因。结果:首先,我们在ESCC中鉴定了 6种突变谱,并发现以TC突变为特征的E4突变谱与酒精摄取和酒精代谢基因上的SNP相关。其次,我们确定了 20个频发突变的蛋白编码基因,其中包括CUL3和RBPJ,这两个基因从未有过ESCC的相关报道。同时我们还鉴定了 15个非编码区中的突变,包括NEAT1等。第三,我们确定了57个拷贝数变异的区域,其中有14个基因的拷贝数在ESCC,头颈部鳞癌(head and neck squamous cell carcinoma,HNSCC),肺鳞癌(lung squamous cell carcinoma,LUSCC)三种鳞癌中均与基因表达呈正相关。此外,我们确定了LRP1B和TTC28是ESCC中最常发生结构变异的基因。我们还发现细胞周期和PI3K/AKT信号通路在ESCC中频繁的畸变,表明这些通路可能是ESCC发生发展进程中最关键的通路。另外,通过全基因组关联研究,我们发现位于EIF4B内含子区的rs4919698TG遗传变异增加患者的死亡风险(HR=1.67;95%CI=1.32-2.12;P=2.01×10~(-6))。结论:本研究通过整合多组学数据全面地概括了 ESCC中基因组水平的改变。确定了 ESCC中的突变谱、拷贝数变异、结构变异等基因组改变。通过全基因组关联研究发现EIF4B上的rs4919698遗传变异与患者的总生存时间相关。这些结果描述了 ESCC的基因组全景,并为ESCC的早期诊断和个体化治疗提供了理论基础。
[Abstract]:Background & objective: esophageal squamous cell carcinoma (ESCC) is an important disease with serious health and life hazards in China. The mechanism of its occurrence and development is unclear, which results in poor curative effect and dismal prognosis. Life is a complex regulatory system. The occurrence and development of disease involve many levels of complex regulatory mechanisms, such as gene variation, epigenetic change, abnormal gene expression and signal pathway disorder. The limitations of using a single set of data to analyze pathogenic factors are increasingly significant. Therefore, through the integration and analysis of high-throughput ESCC data from various levels and sources, we hope to elucidate the molecular mechanism of key genes or network pathways and their regulatory abnormalities in the pathogenesis and development of ESCC, which may be the early diagnosis of ESCC. Individualized treatment and guidance of drug use to provide theoretical basis. Methods: the DNA and RNA of 94 patients with ESCC were sequenced by high throughput sequencing technique and the theory and technique of systematic biomedicine, respectively, and the whole genome genetic variation profile of ESCC was carried out. Somatic mutation profile, transcriptional expression profile, and so on, combined with the clinical data of the patients to carry out association analysis, to establish the abnormal molecular regulatory network of ESCC, to clarify the occurrence, development and outcome of ESCC. In addition, using the strategy of genome-wide association study, 7875353 SNP of peripheral blood DNA in 1088 ESCC patients who were followed up for more than 5 years were analyzed with total survival time, and the related SNP was verified in 1479 independent samples of ESCC. To explore the SNP loci and genes associated with the prognosis of ESCC in Chinese population. Results: first, we identified six mutations in ESCC, and found that E4 mutations characterized by TC mutations were associated with SNP on alcohol uptake and alcohol metabolism genes. Secondly, we identified 20 frequently mutated protein coding genes, including CUL3 and RBPJ, which have never been reported by ESCC. We also identified mutations in 15 non-coding regions, including NEAT1. Thirdly, we identified 57 copy number variant regions, 14 of which were positively correlated with gene expression in ESCC, head and neck squamous cell carcinomatous carcinoma of head and neck, lung squamous cell carcinoma LUSCC. In addition, we identified LRP1B and TTC28 as the most frequently occurring structural mutations in ESCC. We also found that cell cycle and PI3K/AKT signaling pathways were frequently distorted in ESCC, suggesting that these pathways may be the most critical pathways in the development of ESCC. In addition, through the whole genome association study, we found that the rs4919698TG genetic variation located in the intron of EIF4B increased the risk of death in patients. Conclusion: this study summarized the changes of genome level in ESCC by integrating multiple sets of data. The mutation spectrum, copy number variation and structural variation in ESCC were determined. The genetic variation of rs4919698 on EIF4B was found to be related to the total survival time of patients. These results describe the genomic panorama of ESCC and provide a theoretical basis for early diagnosis and individualized treatment of ESCC.
【学位授予单位】：北京协和医学院
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：R735.1

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