長(zhǎng)鏈非編碼RNA在肝細(xì)胞肝癌的發(fā)病機(jī)制中作用及其診斷價(jià)值研究
本文選題:肝細(xì)胞肝癌 + 長(zhǎng)鏈非編碼RNA; 參考:《南京醫(yī)科大學(xué)》2016年博士論文
【摘要】:肝細(xì)胞性肝癌(Hepatocellular carcinoma, HCC)是我國(guó)最常見(jiàn)的惡性腫瘤之一,其死亡率位列癌癥相關(guān)腫瘤死亡率第三位。HCC具有起病隱匿、惡性程度高、進(jìn)展迅速、易轉(zhuǎn)移、病死率高、總體預(yù)后不佳等特點(diǎn),嚴(yán)重危害人類健康。因此,探索肝癌發(fā)生以及其早期轉(zhuǎn)移的具體機(jī)制對(duì)于肝癌早期診斷及提高患者預(yù)后具有重要價(jià)值。既往針對(duì)于肝癌發(fā)生發(fā)展的機(jī)制研究多集中于傳統(tǒng)的蛋白編碼基因,主要涉及遺傳學(xué),表觀遺傳學(xué)以及相關(guān)信號(hào)通路的調(diào)控。隨著高通量測(cè)序技術(shù)發(fā)展,研究者已經(jīng)揭示在人類基因組中非編碼RNA (Non-coding RNA, ncRNA)比例占據(jù)了95%以上,蛋白編碼RNA以及功能性非編碼RNA間復(fù)雜相互作用在肝癌的發(fā)生發(fā)展中具有重要的作用。長(zhǎng)鏈非編碼RNA (long non-coding RNA, lncRNA)作為ncRNA的重要組成成分之一,也越來(lái)越受到重視。目前已經(jīng)揭示lncRNA可以通過(guò)多種途徑參與表觀遺傳,基因轉(zhuǎn)錄及轉(zhuǎn)錄后水平的調(diào)控并且具有作為早期疾病診斷標(biāo)記物的潛力。生物信息學(xué)研究發(fā)現(xiàn)具有特殊位置關(guān)系的蛋白編碼基因以及長(zhǎng)鏈非編碼RNA間具有潛在的順式調(diào)控關(guān)系,該現(xiàn)象被稱為FlanklOkb模式,即在同一染色體基因座中,在某一蛋白編碼基因的側(cè)翼10kb之內(nèi)存在長(zhǎng)鏈非編碼RNA,則該lncRNA具有潛在調(diào)控該蛋白編碼基因的能力。既往研究表明,角蛋白19 (Keratin 19, KRT19)是膽管/肝臟祖細(xì)胞(Hepatic progenitor cell, HPC)的重要標(biāo)記物,但在肝細(xì)胞性肝癌中表達(dá)時(shí)提示其預(yù)后較差,目前推測(cè)可能與KRT19介導(dǎo)的腫瘤細(xì)胞轉(zhuǎn)移相關(guān),但具體機(jī)制尚不清楚。本研究主要基于生物信息學(xué)理論聚焦于KRT19上游25kb處lncRNA (Linc00974),探索其是否能夠介導(dǎo)KRT19參與對(duì)肝細(xì)胞性肝癌的發(fā)生發(fā)展的調(diào)控及其具體機(jī)制。此外,KRT19外周循環(huán)可溶性片段目前已作為肺癌的腫瘤標(biāo)記物在臨床應(yīng)用,但因在肝癌中靈敏性及特異性不高而未用于肝癌相關(guān)診斷,F(xiàn)有傳統(tǒng)的生物標(biāo)志物對(duì)于肝癌的早期發(fā)現(xiàn)及進(jìn)展具有有明顯的局限性。因此,本研究擬通過(guò)高通量芯片技術(shù),探索在HCC患者外周血漿中是否存在具有肝癌發(fā)生發(fā)展相關(guān)差異lncRNA,并探索其作為生物標(biāo)記物的潛能。本研究中我們利用生物信息學(xué)分析、表達(dá)譜芯片結(jié)合經(jīng)典分子生物學(xué)技術(shù)等,在分子水平、細(xì)胞水平、實(shí)驗(yàn)動(dòng)物水平以及臨床樣本中探索由表觀遺傳所介導(dǎo)的長(zhǎng)鏈非編碼RNALinc00974對(duì)KRT19異常表達(dá)的肝癌生物學(xué)行為的影響。研究發(fā)現(xiàn):較癌旁組織而言,Linc00974在肝癌中呈現(xiàn)明顯高表達(dá)狀態(tài)。鑒于Linc00974尚未在人類疾病中報(bào)道,在證實(shí)Linc00974缺乏蛋白編碼能力并可穩(wěn)定存在于HCC相關(guān)細(xì)胞株基礎(chǔ)上,通過(guò)胞漿胞核RNA分離提取的方式,進(jìn)一步確認(rèn)Linc00974主要定位于細(xì)胞漿中,為后續(xù)研究Linc00974具體調(diào)控機(jī)制提供了理論基礎(chǔ)。結(jié)合生物信息學(xué)分析與已發(fā)表文獻(xiàn),我們發(fā)現(xiàn)異常表達(dá)的長(zhǎng)鏈非編碼RNA通常由其啟動(dòng)子區(qū)異常甲基化進(jìn)而影響其轉(zhuǎn)錄水平表達(dá)。通過(guò)生物信息學(xué)預(yù)測(cè)我們發(fā)現(xiàn),在Linc00974上游啟動(dòng)子區(qū)存在明顯富集的CpG島(CpG island),提示Linc00974的異常表達(dá)可能由于其上游CpG島的異常甲基化引起,經(jīng)亞硫酸氫鹽測(cè)序法檢測(cè)發(fā)現(xiàn),在Linc00974異常高表達(dá)的肝癌組織中呈現(xiàn)明顯甲基化抑制水平。隨后我們?cè)?50例經(jīng)臨床病理確診為HCC患者的癌及癌旁組織中通過(guò)實(shí)時(shí)熒光定量PCR (Quantitative Real-time PCR, qRT-PCR)免疫印跡、免疫組織化學(xué)檢測(cè)KRT19表達(dá)水平,研究發(fā)現(xiàn),在肝癌患者中存在27例為KRT19陽(yáng)性表達(dá),123例為陰性表達(dá),Pearson相關(guān)性分析提示,在肝癌人群中,Linc00974與KRT19表達(dá)呈現(xiàn)明顯一致的正相關(guān)。結(jié)合肝癌患者相關(guān)臨床信息分析同樣提示該長(zhǎng)鏈非編碼RNA與肝癌患者腫瘤生長(zhǎng),TNM分期以及腫瘤轉(zhuǎn)移密切相關(guān)。進(jìn)一步通過(guò)體外細(xì)胞功能研究發(fā)現(xiàn),異常表達(dá)的Linc00974在KRT19特異性表達(dá)的肝癌相關(guān)細(xì)胞株中可以明顯通過(guò)上調(diào)KRT19表達(dá)促進(jìn)細(xì)胞增殖以及侵襲能力并伴隨細(xì)胞凋亡抑制以及細(xì)胞周期阻滯,而對(duì)KRT19陰性的肝癌細(xì)胞株則無(wú)明顯影響。利用上述KRT19特異性表達(dá)肝癌細(xì)胞株進(jìn)行裸鼠皮下原位荷瘤以及尾靜脈注射肺定植模型,發(fā)現(xiàn)Linc00974既可促進(jìn)肝癌細(xì)胞的體內(nèi)生長(zhǎng),又能促進(jìn)肝癌細(xì)胞侵襲入血,引起腫瘤遠(yuǎn)期轉(zhuǎn)移,并且該效應(yīng)依賴于KRT19表達(dá)。為進(jìn)一步探索Linc00974對(duì)KRT19具體調(diào)控機(jī)制,我們首先利用RNA免疫共沉淀技術(shù)(RNA Immunoprecipitation, RIP)探索Linc00974是否可以通過(guò)直接綁定KRT19蛋白進(jìn)而影響其功能及相關(guān)效應(yīng)產(chǎn)生。RIP研究顯示Linc00974無(wú)法直接與KRT19蛋白結(jié)合。結(jié)合Linc00974亞細(xì)胞定位及incRNA相關(guān)調(diào)控機(jī)制報(bào)道,通過(guò)運(yùn)用生物信息學(xué)預(yù)測(cè),研究組發(fā)現(xiàn),在Linc00974與KRT19間存在潛在共同綁定miRNA(miR-624),進(jìn)一步通過(guò)熒光素酶報(bào)告基因?qū)嶒?yàn)結(jié)合表達(dá)譜芯片及后期大數(shù)據(jù)信號(hào)通路富集發(fā)現(xiàn),miR-624可以作為“橋梁樣”作用,與Linc00974、KRT19形成內(nèi)源性競(jìng)爭(zhēng)性RNA環(huán)路(competing endogenous RNA loop,ceRNA loop)。通過(guò)體外試驗(yàn)證實(shí),在miR-624存在的肝癌細(xì)胞中,Linc00974通過(guò)吸附miR-624而發(fā)揮內(nèi)源性“海綿樣”作用,誘導(dǎo)KRT19表達(dá),并進(jìn)一步活化NOTCH及TGF-p信號(hào)通路。最終研究表明Linc00974可通過(guò)KRT19依耐性信號(hào)通路促進(jìn)肝癌細(xì)胞生長(zhǎng)以及侵襲-轉(zhuǎn)移級(jí)聯(lián)反應(yīng),證明Linc00974在肝癌的發(fā)生發(fā)展中發(fā)揮著重要作用。既往研究發(fā)現(xiàn),AFP作為傳統(tǒng)的肝癌診斷標(biāo)記物,在診斷早期肝癌以及肝癌早期轉(zhuǎn)移過(guò)程中其特異性相對(duì)較低,因此,探索具有更高特異性及靈敏性的微創(chuàng)肝癌術(shù)前標(biāo)記物對(duì)肝癌早期診斷以及早期轉(zhuǎn)移預(yù)或AFP陰性肝癌患者的補(bǔ)充診斷具有重要的臨床意義。在本研究中,我們首先基于前期KRT19及Linc00974相關(guān)臨床檢測(cè)及分析,進(jìn)一步探索Linc00974是否可以作為肝癌診斷相關(guān)血漿標(biāo)記物;其次,通過(guò)運(yùn)用高通量長(zhǎng)鏈非編碼RNA轉(zhuǎn)錄組芯片技術(shù)在肝癌患者術(shù)前/術(shù)后血漿樣本進(jìn)行篩選,在嚴(yán)密質(zhì)控基礎(chǔ)上,對(duì)差異表達(dá)的血漿lncRNA在隨機(jī)臨床樣本中進(jìn)行定量驗(yàn)證,通過(guò)風(fēng)險(xiǎn)評(píng)分方法、受試者工作特征曲線(Receiver operating characteristic curve, ROC)分析結(jié)合曲線下積分及聚類分析來(lái)評(píng)估血漿lncRNA對(duì)肝癌的診斷能力。研究發(fā)現(xiàn):1.在肝癌患者血漿中,Linc00974僅以片段方式存在。Linc00974血漿特異性片段(Linc00974 Fraction 1,Linc00974F-1)在肝癌患者術(shù)前呈現(xiàn)明顯高表達(dá),腫瘤切除后,血漿Linc00974F-1表達(dá)顯著下降。結(jié)合KRT19血漿可溶性片段CYFRA21-1分別進(jìn)行ROC曲線分析及聚類分析顯示,聯(lián)合Linc00974F-1與CYFRA21-1診斷肝癌其曲線下面積僅為0.764。而聯(lián)合兩者指標(biāo)在預(yù)測(cè)腫瘤生長(zhǎng)尤其在區(qū)分是否為小肝癌水平以及預(yù)測(cè)腫瘤是否發(fā)生轉(zhuǎn)移時(shí)其曲線下面積分別為0.834及0.866,提示聯(lián)合兩者指標(biāo)可明顯聯(lián)合Linc00974F-1及CYFRA21-1可作為潛在預(yù)測(cè)早期肝癌以及肝癌轉(zhuǎn)移相關(guān)的生物標(biāo)記物。2.與健康對(duì)照相比,肝癌患者術(shù)前血漿中存在明顯異常的lncRNA表達(dá)譜系。聯(lián)合肝癌患者術(shù)后血漿lncRNA表達(dá)譜分析,篩選出13條滿足潛在肝癌術(shù)前診斷標(biāo)記物特征的lncRNA進(jìn)行后續(xù)驗(yàn)證;陔S機(jī)選擇標(biāo)準(zhǔn),設(shè)定20對(duì)肝癌患者及健康對(duì)照作為測(cè)試組及147/180例(肝癌患者/健康對(duì)照)樣本作為驗(yàn)證組。采用風(fēng)險(xiǎn)分層結(jié)合ROC曲線分析發(fā)現(xiàn):最終篩選出的RP11-160H22.5, XLOC_014172及LOC149086可穩(wěn)定表達(dá)于肝癌患者及健康對(duì)照血漿中并且在肝癌患者術(shù)前呈現(xiàn)明顯高表達(dá)狀態(tài),而在腫瘤切除后可顯著下降并且在肝硬化、慢性肝炎患者中無(wú)異常表達(dá)。聯(lián)合三者進(jìn)行肝癌術(shù)前診斷其曲線下面積可達(dá)0.896,其診斷靈敏度和特異度分別為91%/92%。進(jìn)一步分析三者指標(biāo)與肝癌患者臨床信息關(guān)聯(lián)發(fā)現(xiàn),XLOC_014172及LOC149086聯(lián)合可作為潛在肝癌早期轉(zhuǎn)移標(biāo)記物,其ROC曲線下面積可達(dá)0.934,靈敏度和特異度分別為90%/90%。少數(shù)肝癌患者的術(shù)后血漿RP11-160H22.5, XLOC_014172及LOC149086反常性升高,結(jié)合臨床信息統(tǒng)計(jì)及相關(guān)文獻(xiàn)報(bào)道分析,其升高可能與患者術(shù)前腫瘤早期轉(zhuǎn)移,通過(guò)相關(guān)載體諸如外泌小體等引起的繼發(fā)性升高相關(guān)。綜上所述,我們的研究對(duì)原發(fā)性肝癌發(fā)生發(fā)展,特別是腫瘤生長(zhǎng)及轉(zhuǎn)移中功能性非編碼RNA參與的表觀遺傳調(diào)控作用進(jìn)行了深入而廣泛的探討,為進(jìn)一步理解該過(guò)程中紛繁復(fù)雜的信號(hào)通路提供了新的思路和視角,同時(shí),通過(guò)高通量檢測(cè)結(jié)合現(xiàn)有腫瘤標(biāo)記物為肝癌的早期診斷以及早期轉(zhuǎn)移預(yù)警提供了新的靶點(diǎn)。
[Abstract]:Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China. The mortality rate of cancer related cancer mortality is third.HCC, which has the characteristics of insidious onset, high malignancy, rapid progression, easy metastasis, high mortality and poor overall prognosis. The specific mechanism of its early metastasis is of great value for the early diagnosis of liver cancer and the improvement of the prognosis of the patients. Previous studies on the mechanism of the development of liver cancer mainly focus on the traditional protein coding genes, mainly involving genetics, epigenetics and related signaling pathways. With the development of high throughput sequencing technology, researchers It has been revealed that the proportion of non coded RNA (Non-coding RNA, ncRNA) occupies more than 95% in the human genome. The complex interaction between protein encoded RNA and functional non coded RNA plays an important role in the development and development of liver cancer. Long chain non coded RNA (long non-coding RNA, lncRNA) is one of the important components of ncRNA. More attention has been made. It has been revealed that lncRNA can participate in epigenetic, gene transcription and post transcriptional regulation and have potential as a marker for early diagnosis of disease through a variety of pathways. Bioinformatics studies have found that a protein encoding gene with a special location and a potential for long chain uncoded RNA The phenomenon is known as the FlanklOkb model, that is, in the same chromosome loci, the memory of the flanking 10KB of a protein encoding gene is in the long chain non coding RNA, then the lncRNA has the potential to regulate the gene encoding the protein. Previous studies have shown that keratin 19 (Keratin 19, KRT19) is a bile duct / liver progenitor cell (Hepat). IC progenitor cell, HPC) is an important marker, but the expression in HCC indicates a poor prognosis. It is presumed that it may be associated with KRT19 mediated tumor cell metastasis, but the specific mechanism is not clear. This study focuses on the bioinformatics theory focusing on lncRNA (Linc00974) at 25KB in the upstream of KRT19, to explore whether it can be found. Mediating the involvement of KRT19 in the regulation of the development of hepatocellular carcinoma and its specific mechanism. In addition, the KRT19 peripheral circulating soluble fragment is currently used as a tumor marker for lung cancer, but it is not used for the diagnosis of liver cancer because of the low sensitivity and specificity in the liver cancer. The existing traditional biomarkers for liver cancer In this study, we use high throughput chip technology to explore the existence and development of lncRNA in the peripheral plasma of HCC patients and explore its potential as a biomarker. In this study, we use bioinformatics analysis, expression spectrum chip to combine classic Molecular biology techniques, in the molecular level, cell level, experimental animal level and clinical samples, explore the effects of epigenetic long chain non coding RNALinc00974 on the biological behavior of liver cancer with abnormal expression of KRT19. The study shows that Linc00974 is highly expressed in liver cancer compared with the paracancerous tissue. Linc00974 has not been reported in human disease. On the basis of confirming the coding ability of Linc00974 deficiency protein and stable on the basis of HCC related cell lines, it is further confirmed that Linc00974 is mainly located in the cytoplasm through the separation and extraction of cytoplasmic nucleus RNA, which provides a theoretical basis for subsequent research on the specific regulation mechanism of Linc00974. It is found that the abnormal expression of long chain non coding RNA is usually based on the abnormal methylation of its promoter region and then affects its transcriptional level. By bioinformatics, we found that there is an obvious enrichment of CpG Island (CpG Island) in the promoter region of the upstream of Linc00974, suggesting that the abnormal expression of Linc00974 can be expressed. Due to the abnormal methylation of the CpG island in the upper reaches of its upstream, it was detected by the hydrogen sulfite sequencing method and showed significant methylation inhibition in the abnormal high expression of Linc00974 in the liver cancer tissues. Then we passed real-time fluorescent quantitative PCR (Quantitative Real-time P) in 150 cases of HCC patients with clinicopathological diagnosis of cancer and para cancer. CR, qRT-PCR) immunoblotting and immunohistochemical detection of KRT19 expression. It was found that there were 27 cases of KRT19 positive expression and 123 negative expression in patients with liver cancer. Pearson correlation analysis suggested that the expression of Linc00974 and KRT19 showed a positive correlation in the liver cancer population. It is suggested that the long chain noncoding RNA is closely related to tumor growth, TNM staging and tumor metastasis in patients with liver cancer. Further through in vitro cell function study, it is found that abnormal expression of Linc00974 in the hepatocellular carcinoma related cell lines with KRT19 specific expression can be obviously promoted by up regulation of KRT19 to promote cell proliferation and invasiveness. The inhibition of apoptosis and cell cycle arrest, but no obvious effect on KRT19 negative liver cancer cell lines. Using the KRT19 specific expression of hepatoma cell lines in nude mice in situ tumor bearing tumor and tail vein injection lung colonization model, it is found that Linc00974 can promote the growth of liver cancer cells in vivo, and promote the invasion of hepatoma cells. In order to further explore the specific regulation mechanism of Linc00974 to KRT19, we first use RNA immunoprecipitation (RNA Immunoprecipitation, RIP) to explore whether Linc00974 can directly bind KRT19 protein and then affect its function and related effects to produce.RIP research, in order to further explore the specific regulation mechanism of KRT19. It was shown that Linc00974 could not be directly associated with KRT19 protein. Combined with Linc00974 subcellular localization and incRNA related regulatory mechanism, the research group found that there was a potential CO binding miRNA (miR-624) between Linc00974 and KRT19 by using bioinformatics prediction, and further through the fluorescein reporter gene experiment combined with the expression spectrum chip and the later stage. The enrichment of large data signal pathway shows that miR-624 can act as a "bridge like" function and form endogenous competitive RNA loop (competing endogenous RNA loop, ceRNA loop) with Linc00974 and KRT19. Induction of KRT19 expression and further activation of NOTCH and TGF-p signaling pathways. The final study shows that Linc00974 can promote the growth of hepatoma cells and the invasion and metastasis cascade reaction through the KRT19 impatience signaling pathway. It is proved that Linc00974 plays an important role in the development of liver cancer. Previous studies have found that AFP is a diagnostic marker for the traditional liver cancer. The specificity is relatively low in the diagnosis of early liver cancer and the early metastasis of liver cancer. Therefore, it is important to explore the early diagnosis of liver cancer with higher specificity and sensitivity to the early diagnosis of liver cancer and the supplementary diagnosis of early metastasis or AFP negative liver cancer. In the previous KRT19 and Linc00974 related clinical tests and analysis, we further explore whether Linc00974 can be used as a plasma marker for the diagnosis of liver cancer; secondly, screening the plasma samples before and after operation by high throughput long chain non coded RNA transcriptional chip technology on the basis of strict quality control. The plasma lncRNA was quantified in a randomized clinical sample. By the risk scoring method, the Receiver operating characteristic curve (ROC) analysis combined with the curve integral and cluster analysis to evaluate the diagnostic ability of plasma lncRNA to liver cancer. The study found that 1. in the plasma of the liver cancer patients, Linc00974 only The.Linc00974 plasma specific fragment (Linc00974 Fraction 1, Linc00974F-1) was highly expressed before operation in the patients with liver cancer. After tumor resection, the expression of Linc00974F-1 in plasma was significantly decreased. The ROC curve analysis and cluster analysis of KRT19 plasma soluble fragment CYFRA21-1, respectively, showed that Linc00974F-1 and CYFRA21- were combined with CYFRA21-. 1 the area under the curve of the diagnosis of liver cancer is only 0.764. and the combination of the two indexes is 0.834 and 0.866 respectively in predicting the growth of tumor, especially whether it is small liver cancer and whether the tumor has metastasize. It is suggested that the combination of the two indexes can be combined with Linc00974F-1 and CYFRA21-1 as a potential predictor of early liver disease. .2. related biomarkers associated with metastasis of cancer and liver cancer compared with healthy controls, there was a significant abnormal lncRNA expression pedigree in the plasma of the patients with liver cancer. The plasma lncRNA expression profile of the patients with liver cancer after operation was analyzed, and 13 lncRNA were screened for subsequent validation of the characteristics of the diagnostic markers for the potential hepatocellular carcinoma. 20 cases of liver cancer patients and healthy controls were set as test groups and 147/180 cases (liver cancer patients / health control) samples were used as validation groups. The risk stratification combined with ROC curve analysis showed that the final screening of RP11-160H22.5, XLOC_014172 and LOC149086 could be stably expressed in liver cancer patients and healthy control plasma and in patients with liver cancer. There was a significant state of high expression before the resection and no abnormal expression in the patients with liver cirrhosis and chronic hepatitis after the tumor resection. The area under the curve for the diagnosis of liver cancer was up to 0.896 in the three cases, and the sensitivity and specificity of the diagnosis were 91%/92%. further analysis of the correlation between the three indexes and the clinical information of the patients with liver cancer. It is found that the combination of XLOC_014172 and LOC149086 can be used as an early metastasis marker for potential liver cancer. The area under the ROC curve is up to 0.934. The sensitivity and specificity are respectively the increase of RP11-160H22.5, XLOC_014172 and LOC149086 in the postoperative plasma of a few 90%/90%. patients with 90%/90%.. The early metastasis of the tumor may be associated with the secondary elevation caused by the related vector, such as the external secretory body. To sum up, our study has carried out a thorough and extensive discussion on the epigenetic regulation of the development of primary liver cancer, especially the functional non coded RNA involved in tumor growth and metastasis. It provides new ideas and perspectives in understanding the complex signal pathways in the process, and provides new targets for early diagnosis of liver cancer and early warning of early metastasis by high throughput detection combined with existing tumor markers.
【學(xué)位授予單位】:南京醫(yī)科大學(xué)
【學(xué)位級(jí)別】:博士
【學(xué)位授予年份】:2016
【分類號(hào)】:R735.7
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