对结直肠癌基因表达与基因组修饰异常的综合分析

发布时间：2018-05-09 20:21

  本文选题：结直肠癌 + 长链非编码RNA　； 参考：《南方医科大学》2017年硕士论文

【摘要】：结直肠癌为消化道常见的恶性肿瘤之一,是继肺癌、胃癌和肝癌之后的第四大癌症死亡原因。近年来,我国人民结直肠癌的发生率呈现升高趋势。癌症的表观基因组表现为全局性的DNA甲基化的缺失和局部超甲基化。越来越多的实验证明,特异性的长链非编码RNA可以经过和染色质修饰复合体的相互作用,进而改变染色质的DNA甲基化状态来调控基因的表达,是重要的基因表达调控元素,与肿瘤的发生发展密切相关。但关于长链非编码RNA在结直肠癌中的研究却只是冰山一角,进一步研究这其中的分子机制将很有必要。另外,不同的癌细胞所处的分化阶段不同,关于不同分化程度的癌细胞之间在转录组学和表观遗传组学上的差异性的研究却很少。本研究对12个不同分化程度(高分化、中分化,低分化)的结直肠癌组织样本以及3个正常的结直肠组织样本进行MeDIP-seq以及RNA-seq测序,并对测序数据分别进行质量控制、比对、组装、差异及功能富集分析、加权基因共表达和共甲基化网络分析等,通过将癌症的转录组学和DNA甲基化组测序数据进行联合分析,以揭示不同分化程度的结直肠癌组织中差异表达的长链非编码RNA与其靶基因的差异甲基化状态之间的关系。通过本研究,我们识别了 1095个新的长链非编码RNA转录本;筛选出了不同分化程度的结直肠癌组织与正常结直肠组织相比差异表达的116个长链非编码RNA、1656个蛋白编码基因和3994个差异DNA甲基化的位点。其中差异表达的长链非编码RNA在GO Biological Process层面主要富集在消化道以及肺的形态发生中,差异表达的蛋白质基因主要富集在两种与癌症侵袭、发生有关的信号通路中,即AGE-RAGE信号传导通路以及Wnt信号传导通路。与差异DNA甲基化片段所关联的基因大部分都有和结直肠癌相关的报道。我们还识别出2个与结直肠癌显著相关的加权基因共表达网络(文中分别称为green-yellow模块和red模块),其中green-yellow模块与结直肠癌正相关,而red模块与结直肠癌负相关。另外我们找到3个差异表达长链非编码RNA(分别是 RP11-288I21.1,RP11-35609.1,RP11-74M11.2),其所对应的 3 个潜在靶基因(CLCNKA,TTC6,RNPS1P1)也是差异表达的,而且其靶基因的启动子区域发生了差异DNA甲基化。我们的结果显示,癌症组样本和正常组样本之间表现出了明显的差异性,但中分化癌症组与正常组之间的差异性并非如我们所预想的介于高分化癌症组和低分化癌症组之间,这可能提示着,癌细胞的分化状态与基因表达的改变之间并无直接的关系。另外结直肠癌患者与正常个体相比,其基因组发生了广泛的DNA甲基化的缺失,这与之前的很多报道都是一致的。结直肠癌的表达谱和甲基化谱联合分析显示,长链非编码RNA及其靶基因同时差异表达的结果有很多,而其靶基因的启动子区域却鲜少呈现出差异DNA甲基化的状态,这可能提示着,蛋白编码基因启动子区域错误的DNA甲基化并非结直肠癌细胞中异常表观基因组修饰的关键特征。
[Abstract]:Colorectal cancer is one of the most common malignant tumors in the digestive tract. It is the fourth major cause of cancer death after lung cancer, gastric cancer and liver cancer. In recent years, the incidence of colorectal cancer in our country is increasing. The epigenetic genome of cancer is the loss of global DNA methylation and local hypermethylation. More and more experiments have proved that The specific long chain non coding RNA can interact with chromatin modified complex, and then change the DNA methylation status of chromatin to regulate gene expression. It is an important regulatory element of gene expression, which is closely related to the development of tumor. However, the study of long chain noncoding RNA in colorectal cancer is only an ice mountain. It is necessary to further study the molecular mechanisms of this. In addition, the differentiation stages of different cancer cells are different. There are few studies on the differences in the transcriptional and epigenetic components between different differentiated cancer cells. This study is a direct study of 12 different degrees of differentiation (high differentiation, middle differentiation, and low differentiation). Colorectal cancer tissue samples and 3 normal colorectal tissue samples were carried out by MeDIP-seq and RNA-seq sequencing, and the quality control, comparison, assembly, difference and functional enrichment analysis, weighted gene co expression and co methylation network analysis were performed on the sequencing data, by combining the transcriptional and DNA methylation data of the carcinoma. In this study, 1095 new long chain non coded RNA transcripts were identified, and 1095 colorectal cancer tissues with different differentiation range and normal colorectal tissues were screened by this study. Compared with 116 long chain non coding RNA, 1656 protein coding genes and 3994 different DNA methylation sites, the differentially expressed long chain non coding RNA was mainly enriched in the digestive tract and lung morphogenesis at the GO Biological Process level, and the differentially expressed protein genes were mainly enriched in two species and cancer invasion, The AGE-RAGE signal transduction pathway and the Wnt signal transduction pathway occur in the related signaling pathways. Most of the genes associated with differential DNA methylation fragments are related to colorectal cancer. We also identified 2 weighted gene co expression networks associated with colorectal cancer, which are called green-yellow module and R, respectively. Ed module), in which the green-yellow module is positively related to colorectal cancer, and the red module is negatively related to colorectal cancer. In addition, we find 3 differentially expressed long chain non coded RNA (RP11-288I21.1, RP11-35609.1, RP11-74M11.2), and the corresponding 3 potential target genes (CLCNKA, TTC6, RNPS1P1) are also differentially expressed, and their target genes are also expressed. The difference between the cancer group and the normal group showed a distinct difference between the cancer group and the normal group, but the difference between the differentiated cancer group and the normal group was not as between the highly differentiated cancer group and the low differentiated cancer group, which may suggest that the cancer cells are DNA. There is no direct relationship between the differentiation state and the changes in gene expression. In addition, colorectal cancer patients have extensive DNA methylation loss compared with normal individuals, which are consistent with many previous reports. Colorectal cancer expression and methylation analysis show that long chain non coded RNA and its target gene are identical. There are a lot of differences in time difference expression, but few of the promoter regions of the target gene show a state of differential DNA methylation, which may suggest that DNA methylation in the promoter region of the protein coding gene is not the key feature of abnormal epigenetic modification in colorectal cancer cells.

【学位授予单位】：南方医科大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：R735.34
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本文编号：1867289