發(fā)布時(shí)間：2018-07-10 06:14

  本文選題：結(jié)直腸發(fā)育 + 結(jié)直腸癌癌變�。� 參考：《北京協(xié)和醫(yī)學(xué)院》2016年博士論文

【摘要】：該博士學(xué)位論文由相互聯(lián)系的兩部分工作組成,其中第一部分分為三章。第一部分：結(jié)直腸癌預(yù)后相關(guān)基因的研究第一章：利用Spearman轉(zhuǎn)移模型尋找結(jié)直腸癌預(yù)后相關(guān)的免疫相關(guān)基因免疫相關(guān)基因通過介導(dǎo)炎癥和免疫逃逸在結(jié)直腸癌發(fā)生發(fā)展過程中起到非常重要的作用。雖然人類在探求癌癥發(fā)病分子機(jī)制的過程中取得了巨大的進(jìn)步,但是腫瘤的高度異質(zhì)大大阻礙了人類對(duì)腫瘤復(fù)雜生物學(xué)進(jìn)程的探索。胚胎發(fā)育和腫瘤進(jìn)展在生物學(xué)行為及分子機(jī)制上有很多相似之處,這種相似性使胚胎發(fā)育成為一種沒有顯著異質(zhì)性卻可以研究腫瘤生物學(xué)行為的模型。本研究中我們提出造成免疫基因內(nèi)協(xié)同性失調(diào)(定義為在癌進(jìn)展中基因間共表達(dá)模式的破壞)的免疫相關(guān)基因,可能包含許多結(jié)直腸癌的預(yù)后相關(guān)信息。我們首先建立了137例人類結(jié)直腸的基因分子表達(dá)譜,樣本涵蓋了人類結(jié)直腸胚胎發(fā)育、癌前和癌的不同階段。同時(shí)利用其中的60例樣本建立miRNA基因分子表達(dá)譜。我們首次提出Spearman轉(zhuǎn)移模型來量化人類結(jié)直腸從胚胎發(fā)育到癌前到癌變的轉(zhuǎn)化過程中的協(xié)同性失調(diào),并利用miRNA-mRNA分子調(diào)控網(wǎng)絡(luò)和機(jī)器學(xué)習(xí)算法識(shí)別具有預(yù)后信息的重要基因分子。我們最終找到12個(gè)免疫基因集合,在5套獨(dú)立的公共數(shù)據(jù)中驗(yàn)證了這些基因?qū)︻A(yù)后的預(yù)測(cè)價(jià)值。利用log-rank檢驗(yàn),這12個(gè)基因集合與4套數(shù)據(jù)的總生存顯著相關(guān)(GSE17536, n=177, p=0.0054:GSE17537, n=55, p=0.0039; GSE39582, n=562, p=0.13; GSE39084, n=70, p=0.11),并且與4套數(shù)據(jù)的無病生存顯著相關(guān)(GSE17536,n=177,p=0.0018;GSE17537,n=55,p=0.016; GSE39582, n=557,p=4.4e-05; GSE14333, n=226,p=0.032)。Cox回歸的結(jié)果證實(shí)這12個(gè)基因的表達(dá)水平是預(yù)后結(jié)直腸癌總生存(危害比：1.759；95%置信區(qū)間：1.126-2.746；p=0.013)和無病生存(危害比：2.116；95%置信區(qū)間：1.324-3.380；p=0.002)的獨(dú)立因素。第二章：結(jié)直腸發(fā)育中上調(diào)的細(xì)胞周期相關(guān)基因可以預(yù)測(cè)晚期結(jié)直腸癌生存腫瘤可以被理解為在器官發(fā)育的過程中產(chǎn)生了分子生物學(xué)上的嚴(yán)重失調(diào)的一種特殊的器官。胚胎發(fā)育和癌變進(jìn)程的細(xì)胞學(xué)行為和內(nèi)在分子事件上存在著驚人的相似性。這種并非偶然的相似性提示我們,胚胎發(fā)育可以作為研究腫瘤分子生物學(xué)行為,同時(shí)規(guī)避腫瘤異質(zhì)性所帶來的干擾的一種理想模型。因此,基于全基因組分子表達(dá)譜,在胚胎發(fā)育中和癌階段同時(shí)上調(diào)的或者同時(shí)下調(diào)的基因,可能蘊(yùn)含重要的預(yù)后信息。本研究從基因表達(dá)數(shù)據(jù)庫(Gene Expression Omnibus, GEO)中下載1,539例結(jié)直腸癌樣本的表達(dá)譜數(shù)據(jù)。在660例結(jié)直腸癌和癌旁數(shù)據(jù)中利用meta分析的方法找到1,396個(gè)差異表達(dá)的探針�；谌祟惤Y(jié)直腸胚胎發(fā)育的數(shù)據(jù),我們把這些差異表達(dá)探針分為27個(gè)模塊中,然后利用基因集富集分析(gene set enrichment analysis, GSEA),我們?cè)诓町惐磉_(dá)探針中找到393個(gè)在胚胎發(fā)育和腫瘤中同時(shí)高表達(dá)的V探針和207個(gè)在胚胎發(fā)育和腫瘤中同時(shí)低表達(dá)的A探針。值得注意的是,V探針中有28個(gè)細(xì)胞周期相關(guān)的探針和Ⅲ/Ⅳ期結(jié)直腸癌患者的總生存顯著相關(guān)(GSE17536 cross validation, n=96, p=5.70e-03; GSE29621, n=36,p=1.70e-03; GSE39084, n=38,p=0.05; GSE39582, n=264,p=0.047; GSE17537, n=36, p=5.90e-03)。第三章：受異常啟動(dòng)子區(qū)甲基化和基因突變顯著影響的發(fā)育基因可以預(yù)測(cè)晚期結(jié)直腸癌的總生存癌癥的發(fā)生和發(fā)展是一個(gè)及其復(fù)雜的生物學(xué)過程,包括基因組(如基因突變,拷貝數(shù)變化)、DNA甲基化和轉(zhuǎn)錄組等很多層面的改變。因此,僅研究一個(gè)分子層面不足以解釋腫瘤復(fù)雜的分子生物學(xué)機(jī)制。利用TCGA (the Cancer Genome Atlas)公共數(shù)據(jù)庫的資源,我們對(duì)結(jié)直腸癌DNA拷貝數(shù)變化,啟動(dòng)子區(qū)域的甲基化,基因突變和基因表達(dá)等層面的數(shù)據(jù)進(jìn)行了整合研究分析。在本研究中,我們通過各個(gè)基因?qū)用嫔吓鋵?duì)的樣本找到在不同層面發(fā)生顯著變化的差異表達(dá)基因。值得注意的是,GO (gene ontology)富集的結(jié)果顯示具有差異啟動(dòng)子區(qū)甲基化的和具有基因突變的差異表達(dá)基因都可以顯著的富集到發(fā)育進(jìn)程的GO term中,暗示胚胎發(fā)育和腫瘤進(jìn)展有著密不可分的聯(lián)系。因此,利用重啟動(dòng)隨機(jī)游走(random walk with restart),我們成功找到37個(gè)顯著的發(fā)育相關(guān)基因,并在5套獨(dú)立的表達(dá)譜芯片數(shù)據(jù)中進(jìn)行驗(yàn)證。Kaplan-Meier和Cox回歸分析的結(jié)果顯示這些基因的表達(dá)水平與Ⅲ/Ⅳ期結(jié)直腸癌的總生存顯著相關(guān)。第二部分：肺鱗癌預(yù)后相關(guān)基因研究肺鱗癌目前在臨床中沒有有效的靶向藥物。因此對(duì)肺鱗癌,尤其是肺鱗癌癌前階段的分子生物學(xué)改變的研究十分必要,這可能會(huì)為尋找重要的作用靶點(diǎn)或者靶向藥物的開發(fā)起到巨大的推進(jìn)作用。另外胚胎發(fā)育和癌變階段在細(xì)胞生物學(xué)行為和分子特異性改變上有很多相似之處。腫瘤可以理解為一個(gè)在正常發(fā)育過程中出現(xiàn)嚴(yán)重異常的器官,暗示著胚胎發(fā)育可以作為一種研究腫瘤生物學(xué)行為的模型。在本研究中,我們收集了10個(gè)時(shí)間點(diǎn)人類肺組織,涵蓋了從胚胎發(fā)育到癌前到癌形成的各個(gè)階段,并建立了基因分子表達(dá)譜。我們找到癌前和癌階段一致差異表達(dá)的基因,結(jié)合基于先驗(yàn)網(wǎng)絡(luò)的貪婪搜尋算法,利用69例具有預(yù)后信息的肺鱗癌手術(shù)樣本作為訓(xùn)練樣本,成功的找出一個(gè)含有22個(gè)基因的最優(yōu)子網(wǎng)。這22個(gè)基因的表達(dá)量于肺鱗癌患者的總生存顯著相關(guān)。
[Abstract]:The doctoral thesis consists of two parts of interrelated work. The first part is divided into three chapters. Part one: Chapter 1: the first chapter of the study on the prognosis related genes of colorectal cancer: the immuno related genes associated with the prognosis of colorectal cancer by using the Spearman transfer model to mediate inflammation and immune escape in the colorectal cancer The carcinogenesis and development of cancer have played a very important role. Although great progress has been made in the process of exploring the molecular mechanisms of cancer, the high heterogeneity of the tumor greatly hinders human exploration of the complex biological processes of cancer. The development of embryos and the progression of tumors have many phases in biological behavior and molecular mechanisms. Similarly, this similarity makes the embryo develop into a model without significant heterogeneity but can study tumor biological behavior. In this study, we propose an immune related gene that causes co homosexual dysregulation within the immune gene, defined as the disruption of INTERGENE co expression patterns in cancer progression, which may contain a number of colorectal cancer prognosis. We first established 137 cases of human colorectal gene expression profiles, which covered the development of human colorectal embryos, the different stages of precancerous and cancer. At the same time, we used 60 of them to establish the molecular expression profiles of the miRNA gene. We first proposed the Spearman transfer model to quantify the human colorectal cancer from embryonic development to cancer. The synergetic disorder in the process of carcinogenesis, and the use of miRNA-mRNA molecular control networks and machine learning algorithms to identify important gene molecules with prognostic information. We finally found 12 sets of immune genes and verified the predictive value of these genes to the prognosis in 5 sets of independent public data. The use of log-rank test, 12 GSE17536, n=177, p=0.0054:GSE17537, n=55, p=0.0039; GSE39582, n=562, p=0.13; GSE39084, n=70, p=0.11) in the total survival of the 4 sets of data. The results of.Cox regression confirmed that the expression levels of these 12 genes were independent factors for the prognosis of total survival of colorectal cancer (1.759; 95% confidence interval: 1.126-2.746; p=0.013) and disease free survival (2.116; 95% confidence interval: 1.324-3.380; p=0.002). Second: the up-regulated cell cycle related groups in the development of colorectal cancer It is possible to predict that tumor survival in advanced colorectal cancer can be understood as a special organ in the process of organ development. The cytological behavior of embryonic development and the process of carcinogenesis and internal molecular events are astonishingly similar. This is not an accidental similarity that suggests us, Embryo development can be used as an ideal model to study the biological behavior of tumor molecules and to avoid the interference of tumor heterogeneity. Therefore, gene expression based on the whole genome molecular expression, up or down at the same time in the embryonic development and cancer stage may contain important prognostic information. In Gene Expression Omnibus (GEO), the expression profiles of 1539 colorectal cancer samples were downloaded. 1396 differentially expressed probes were found by meta analysis in 660 colorectal and paracancerous data. Based on the data of human colorectal embryogenesis, we divided these differential expression probes into 27 modules. Using gene set enrichment analysis (GSEA), we found 393 V probes which were simultaneously highly expressed in embryonic development and tumors and 207 A probes with low expression in embryonic development and tumor. It is worth noting that there are 28 cell cycle related probes and stage III / IV junctions in V probes. GSE17536 cross validation, n=96, p=5.70e-03; GSE29621, n=36, p=1.70e-03; GSE39084, n=38, p=0.05; Chapter third: the developmental genes which are significantly affected by the methylation of the abnormal promoter region and the gene mutation can predict the late colorectal cancer. The occurrence and development of cancer's total survival is a complex biological process, including a variety of changes in the genome (such as gene mutation, copy number change), DNA methylation and transcriptional groups. Therefore, only one molecular level is not sufficient to explain the complex molecular biological mechanism of the tumor. The use of TCGA (the Cancer Genome Atlas) In this study, we found the differentially expressed genes that have changed significantly at different levels of DNA. It is noted that the results of GO (gene ontology) enrichment show that the differentially expressed genes with differential promoter methylation and gene mutation can be significantly enriched in the GO term of the development process, suggesting that there is an inseparable relationship between the development of the embryo and the progression of the tumor. For this reason, the restarted random walk (random walk with RES) is used. Tart), we successfully found 37 significant developmental related genes and validated.Kaplan-Meier and Cox regression analysis in 5 sets of independent expression chip data. The results showed that the expression levels of these genes were significantly related to the total survival of stage III / IV colorectal cancer. Second: lung squamous cell carcinoma prognosis related genes study lung squamous cell carcinoma at present. There is no effective targeting drug in the clinic. Therefore, it is necessary to study the molecular biological changes in the pre cancerous stage of lung squamous cell carcinoma, especially the squamous cell carcinoma of the lung, which may play an important role in the development of important targets or targeted drugs. In addition, the embryonic development and cancerous stage are in cell biological behavior and molecules. There are many similarities in specific changes. The tumor can be understood as a serious abnormal organ in normal development, suggesting that embryonic development can be used as a model to study the biological behavior of cancer. In this study, we collected 10 time points of human lung tissue, covering from embryo to cancer to cancer form. The gene molecular expression profiles were established at all stages of the formation. We found genes that were identical in precancerous and cancer stages, combined with a priori network based greedy search algorithm, and used 69 cases of lung squamous cell carcinoma with prognostic information as training samples to find an optimal subnet containing 22 genes. These 22 genes were found. The expression level was significantly correlated with the overall survival of patients with lung squamous cell carcinoma.
【學(xué)位授予單位】：北京協(xié)和醫(yī)學(xué)院
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：R734.2;R735.34
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本文編號(hào)：2112397