膀胱尿路上皮腫瘤發病率在泌尿道腫瘤中排第二位，它具有高複發性的特點。目前，有創性尿道膀胱鏡檢查是診斷的金標準。儘管先後有很多血液或尿液中的分子被先後用於診斷膀胱癌的診斷研究，但到目前為止尚未有任何一種方法可以取代膀胱鏡檢查。有證據表明在膀胱上皮腫瘤組織中有很多異常表達的microRNA，但是內在機制的有關研究相對缺乏。在本研究中，我們利用在尿液上清中異常表達的microRNA來評估它們在膀胱癌診斷中的價值。而且，我們揭示了其潛在的調控機理。通過microRNA基因芯片，我們結合并對比來自膀胱腫瘤病人和正常對照患者的9個尿液上清樣本，以及4對腫瘤組織及臨近正常黏膜上皮中microRNA的表達，初步篩選出10個異常的microRNA。然後我們使用定量RT-PCR的方法在另外獨立的18對腫瘤組織和正常黏膜中進一步驗證芯片結果。最後我們就6個被帥選出來的microRNA在71例的膀胱癌患者和正常對照組的尿液上清中進行檢測並評估其診斷效能。我們發現，miR-125b和miR-99a的表達在膀胱癌患者的尿液上清中明顯下調。另外，它們下調程度與腫瘤的病理分級相關。結合miR-125b和miR-99b兩者作為診斷膀胱癌的指標，靈敏度達86.7%，特異度達81.1%，同時有陽性預測值達91.8%。當作為腫瘤分級指標，miR-125b具有81.4%的敏感度，87.0%的特異度，陽性預測值達93.4%。膀胱腫瘤切除之後，和術前比較，兩個microRNA的表達水平再度上升。我們將miR-99轉染到三個膀胱腫瘤細胞株中（T24，UMUC3和J82）。我們發現miR-99a對UMUC3細胞具有輕微的抗增殖功能。同時，miR-99a在3個細胞株中顯示均顯示具有抗遷移和抗侵襲能力。為尋找miR-99a的目標mRNA，我們結合數據庫算法預測，在Western blot中驗證到miR-99a能顯著下調VLDLR蛋白。隨後我們將帶有VLDLR的3'UTR質粒轉染進入細胞中并證實VLDLR mRNA是miR-99a直接作用的目標。另外，當VLDLR siRNA被轉入3個細胞株之後，我們觀察到相似的抗遷移和抗侵襲的現象。最後我們發現N-cadherin是該通路中的下游抑制遷移和侵襲的分子。本項研究證實研究尿液上清中的microRNA是可行的。MiR-125b和miR-99a是膀胱腫瘤的診斷和分級的有效指標。此外，miR-99a能夠通過和VLDLR mRNA直接結合從而抑制膀胱腫瘤遷移和侵襲功能。 / Urothelial carcinoma of the bladder (UCB) is the second most common malignancy in the urological system with high recurrence rate. Current gold standard examination for diagnosis is urethrocystoscopy, which is an invasive procedure. Although numerous molecular markers in blood or urine have been proposed as diagnostic biomarkers for bladder cancer, none of them could replace urethrocystoscopy in clinical practice. There are accumulating evidences suggesting microRNA dysregulation might be related to the pathogenesis of UCB. However, the exact functions of these microRNAs in UCB remain unknown. In this thesis, the role of selected microRNAs in urine supernatant was investigated in the diagnosis of UCB and also the carcinogenesis of UCB. / In brief, a high-throughput microarray was carried out on nine supernatants of urine from UCB and normal subjects, and also four pairs of tissue from UCB and normal mucosa. Ten microRNA candidates were then identified. Quantitative RT-PCR was used to validate these microRNAs on a set of 18 pairs of tumor tissue and normal mucosa. Eventually, six potential candidate microRNAs were selected and then validated as diagnostic tools on the samples of urine supernatants from 71 patients (50 of known UCB and 21 of normal subjects). The expression levels of these selected microRNAs were further evaluated in the urine supernatants of 20 patients after tumors resections. MiR-125b and miR-99a were the two most significantly down-regulated microRNAs in the urine supernatants of patients with UCB. Moreover, the degree of down-regulation was associated with the pathological grade of the tumor. A combined index of miR-125b and miR-99a in urine supernatant had a sensitivity of 86.7%, specificity of 81.1%, and a positive predicted value of 91.8% for diagnosing UCB. When used to discriminate high-grade from low-grade UCB, miR-125b alone had a sensitivity of 81.4%, specificity of 87.0% and PPV of 93.4%. After transurethral resections, the expression levels of both microRNAs were significantly increased compared to pre-operative levels. / In further studies on the role of microRNAs on the development of UCB, miR-99a was selected for further studies. The precursor of miR-99a was temporally transfected into 3 bladder cancer cell lines: T24, UMUC3 and J82. The proliferation ability was noticed to be suppressed mildly in UMUC3, but not the other. Meanwhile, migration and invasion abilities were inhibited by miR-99a in the all 3 cell lines. Potential targets of miR-99a were predicted from several prediction databases. Subsequently, in Western Blot study, the protein level of very low density lipoprotein receptor (VLDLR) was showed to be down-regulated by miR-99a. Thereafter, a plasmid constructed with 3’UTR of VLDLR was transfected into cytoplasm, which confirmed VLDLR mRNA was a direct target of miR-99a. All 3 cells lines showed the same effect on suppression of migration and invasion after knockdown of VLDLR. N-cadherin was identified as a down-stream molecule responsible for the migration and invasion suppression in this pathway. / This study confirmed microRNA expression in urine supernatants was a feasible approach for the assessment of biomarkers, and miR-125b and miR-99a showed promising results in the diagnosis and grading of UCB. Furthermore, we showed that miR-99a suppressed tumor migration and invasion by directly targeting VLDLR. / Detailed summary in vernacular field only. / Zhang, Dingzuan. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 107-131). / Abstract and appendix also in Chinese. / Abstract --- p.I / 摘要 --- p.III / Acknowledgments --- p.V / Abbreviations --- p.VII / List of figures --- p.IX / List of Tables --- p.XI / Content --- p.XII / Chapter Chapter I: --- General Introduction / Chapter 1.1 --- Bladder cancer --- p.1 / Chapter 1.1.1 --- The incidence of bladder cancer / Chapter 1.1.2 --- The burden of bladder cancer to the health care system / Chapter 1.1.3 --- Risk factors for bladder cancer / Chapter 1.1.4 --- Pathology grading system in bladder cancer / Chapter 1.1.5 --- Current diagnostic methods and treatment for bladder cancer / Chapter 1.2 --- Biomarkers for bladder cancer --- p.7 / Chapter 1.2.1 --- The advantages of biomarkers in blood and urine for the diagnosis of bladder cancer / Chapter 1.2.2 --- Biomarkers in blood for bladder cancer / Chapter 1.2.3 --- Biomarkers in the urine for bladder cancer / Chapter 1.2.4 --- Current concerning problems with biomarkers / Chapter 1.3 --- MicroRNAs and bladder cancer --- p.11 / Chapter 1.3.1 --- Post-trancriptional function of microRNAs / Chapter 1.3.2 --- The function of microRNAs in tumor / Chapter 1.3.3 --- Prospects of detecting microRNA in cell-free fluid in tumor / Chapter 1.4 --- MicroRNA target identification --- p.15 / Chapter 1.4.1 --- Prediction of microRNA target / Chapter 1.4.2 --- Validation of microRNA target / Chapter 1.4.3 --- Validation of direct interaction between microRNA and target RNA / Chapter 1.4.4 --- Validation of direct binding of microRNA and mRNA in vivo / Chapter 1.5 --- Migration and invasion of bladder cancer --- p.19 / Chapter 1.5.1 --- The biological process of migration in bladder cancer / Chapter 1.5.2 --- Epithelial to mesenchymal transition in bladder cancer / Chapter 1.6 --- Objectives of this study --- p.21 / Chapter Chapter II --- MicroRNAs in urine supernatant: potential useful markers for bladder cancer screening / Chapter 2.1 --- Introduction --- p.23 / Chapter 2.2 --- Materials and methods --- p.26 / Chapter 2.2.1 --- Ethics Statement / Chapter 2.2.2 --- Patients and samples / Chapter 2.2.3 --- RNA extraction / Chapter 2.2.4 --- MicroRNA microarray / Chapter 2.2.5 --- Quantitative real-time polymerase chain reaction (RT-PCR) / Chapter 2.2.6 --- Statistical methods / Chapter 2.3 --- Results --- p.31 / Chapter 2.3.1 --- MicroRNA screening by microRNA microarray / Chapter 2.3.2 --- Independent validation of the ten selected microRNAs by qRT-PCR on tissue / Chapter 2.3.3 --- Verification of the six validated microRNAs in urine supernatants as tumor markers / Chapter 2.3.4 --- MiR-125b and miR-99a in urine supernatants were useful for the diagnosis of bladder cancer / Chapter 2. --- 3.5 MiR-125b and miR-99a were two highly correlated microRNAs / Chapter 2.3.6 --- Expression levels of miR-125b and miR-99a increased after tumor resection / Chapter 2.4 --- Discussion --- p.47 / Chapter Chapter III: --- MiR-99a suppresses migration and invasion in bladder cancer by targeting VLDLR / Chapter 3.1 --- Introduction --- p.53 / Chapter 3.2 --- Materials and methods --- p.56 / Chapter 3.2.1 --- Human tissue samples and bladder cancer cell lines / Chapter 3.2.2 --- RNA extraction and Polymerase Chain Reaction / Chapter 3.2.3 --- MicroRNA and plasmid transfection / Chapter 3.2.4 --- Western Immunoblotting / Chapter 3.2.5 --- Agarose gel electrophoresis / Chapter 3.2.6 --- Luciferase assay / Chapter 3.2.7 --- MTT proliferation assay / Chapter 3.2.8 --- Apoptosis assay / Chapter 3.2.9 --- Cell cycle analysis / Chapter 3.2.10 --- Cell migration Assay / Chapter 3.1.11 --- Cell invasion assay: / Chapter 3.2.12 --- Statistical methods: / Chapter 3.3 --- Results --- p.67 / Chapter 3.3.1 --- MiR-99a was significantly down-regulated in bladder cancer / Chapter 3.3.2 --- Precursor microRNA was successfully transfected into bladder cancer cell lines / Chapter 3.3.3 --- MiR-99a had little effect on cell proliferation / Chapter 3.3.4 --- MiR-99a had little effect on cell apoptosis and cell cycle / Chapter 3.3.5 --- Over-expression of miR-99a suppressed cell migration in bladder cancer / Chapter 3.3.6 --- Over-expression of miR-99a also suppressed invasion ability in bladder cancer / Chapter 3.3.7 --- Target prediction for miR-99a using 8 target prediction databases / Chapter 3.3.8 --- Protein level of VLDLR was down-regulated by miR-99a in bladder cancer / Chapter 3.3.9 --- VLDLR was a direct target of miR-99a / Chapter 3.3.10 --- VLDLR mRNA was not down-regulated correspondingly by miR-99a / Chapter 3.3.11 --- MiR-99a suppressed down-stream protein of VLDLR in Reelin pathway / Chapter 3.3.12 --- Knockdown of VLDLR also suppressed cell migration and invasion / Chapter 3.3.13 --- N-cadherin was the down-stream protein responsible for the suppression of migration and invasion in miR-99a/VLDLR pathway / Chapter 3.4 --- Discussion --- p.93 / Chapter Chapter IV: --- Conclusion and prospective --- p.101 / Appendix --- p.105 / Reference --- p.107

Yang, Ling. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 222-244). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Awards and Presentations --- p.ii / Abstract in English --- p.iii / Abstract in Chinese --- p.vii / Table of Contents --- p.x / List of Tables --- p.xv / List of Figures --- p.xvii / List of Abbreviations --- p.xx / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Gliomas --- p.1 / Chapter 1.1.1 --- Oligodendroglial tumors (OTs) --- p.3 / Chapter 1.1.2 --- Glioblastoma multiforme (GBM) --- p.3 / Chapter 1.1.3 --- Molecular pathology of gliomas --- p.4 / Chapter 1.1.3.1 --- Genetic alterations in OTs --- p.4 / Chapter 1.1.3.2 --- Prognostic and predictive factors in OTs --- p.7 / Chapter 1.1.3.3 --- Genetic alterations in GBM --- p.8 / Chapter 1.1.3.4 --- Prognostic and predictive factors in GBM --- p.10 / Chapter 1.2 --- microRNA(miRNA) --- p.13 / Chapter 1.2.1 --- miRNA biogenesis and function --- p.13 / Chapter 1.2.2 --- miRNA involvement in cancer --- p.17 / Chapter 1.2.2.1 --- Dysregulation of miRNAs in human malignancies --- p.17 / Chapter 1.2.2.2 --- Function and potential application of miRNAs --- p.17 / Chapter 1.2.3 --- Role of miRNAs in glioma --- p.19 / Chapter 1.2.3.1 --- miRNAs in OTs --- p.19 / Chapter 1.2.3.2 --- miRNAs in GBM --- p.20 / Chapter 1.3 --- miR-137 --- p.30 / Chapter 1.3.1 --- Biology of miR-137 --- p.30 / Chapter 1.3.2 --- Role of miR-137 in carcinogenesis --- p.33 / Chapter 1.3.2.1 --- Deregulation of miR-137 in cancer --- p.33 / Chapter 1.3.2.2 --- Regulation of miR-137 expression in cancer --- p.33 / Chapter 1.3.2.3 --- Biological functions of miR-137 in cancer --- p.37 / Chapter 1.3.3 --- Role of miR-137 in differentiation and neurogenesis --- p.39 / Chapter CHAPTER 2 --- AIMS OF STUDY --- p.43 / Chapter CHARPTER 3 --- MATERIALS AND METHODS --- p.45 / Chapter 3.1 --- Tumor samples --- p.45 / Chapter 3.2 --- Cell lines and culture conditions --- p.48 / Chapter 3.3 --- Fluorescence in situ hybridization (FISH) --- p.49 / Chapter 3.4 --- Cell transfection --- p.52 / Chapter 3.4.1 --- Transfection of oligonucleotides --- p.52 / Chapter 3.4.1.1 --- Oligonucleotide preparation --- p.52 / Chapter 3.4.1.2 --- Optimization of transfection condition --- p.52 / Chapter 3.4.2 --- Cotransfection of plasmids and miRNA mimic --- p.53 / Chapter 3.4.2.1 --- Optimization of transfection condition --- p.53 / Chapter 3.4.2.2 --- Procedure of transfection --- p.54 / Chapter 3.5 --- Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) --- p.55 / Chapter 3.5.1 --- RNA extraction from frozen tissues and cell lines --- p.55 / Chapter 3.5.2 --- qRT-PCR for miR-137 --- p.56 / Chapter 3.5.3 --- qRT-PCR for CSE1L and ERBB4 transcripts --- p.57 / Chapter 3.6 --- 5-aza-2'-deoxycytidine (5-aza-dC) and Trichostatin A (TSA) treatment --- p.61 / Chapter 3.7 --- Western blotting --- p.62 / Chapter 3.7.1 --- Preparation of cell lysate --- p.62 / Chapter 3.7.2 --- Measurement of protein concentration --- p.62 / Chapter 3.7.3 --- Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) --- p.63 / Chapter 3.7.4 --- Electroblotting of proteins --- p.67 / Chapter 3.7.5 --- Immunoblotting --- p.67 / Chapter 3.8 --- Dual-luciferase reporter assay --- p.70 / Chapter 3.8.1 --- Construction of reporter plasmids --- p.70 / Chapter 3.8.1.1 --- Experimental outline --- p.70 / Chapter 3.8.1.2 --- PCR Amplification of MREs --- p.70 / Chapter 3.8.1.3 --- TA cloning --- p.71 / Chapter 3.8.1.4 --- Transformation --- p.72 / Chapter 3.8.1.5 --- Blue/white screening and validation of recombinants --- p.72 / Chapter 3.8.1.6 --- Subcloning of 3'UTR fragments into pMIR-reproter vector --- p.73 / Chapter 3.8.2 --- Site-directed mutagenesis --- p.74 / Chapter 3.8.3 --- Plasmid and miRNA mimic cotransfection --- p.76 / Chapter 3.8.4 --- Determination of luciferase activity --- p.76 / Chapter 3.9 --- Functional assays : --- p.79 / Chapter 3.9.1 --- Cell growth and proliferation assay --- p.79 / Chapter 3.9.1.1 --- "3-(4，5-Dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay" --- p.79 / Chapter 3.9.1.2 --- Cell counting --- p.80 / Chapter 3.9.1.3 --- 5-Bromo-2'-deoxyuridine (BrdU) incorporation assay --- p.80 / Chapter 3.9.2 --- Apoptosis assay --- p.82 / Chapter 3.9.3 --- Anchorage-independent growth assay --- p.82 / Chapter 3.9.4 --- Wound healing assay --- p.83 / Chapter 3.9.5 --- Matrigel invasion assay --- p.84 / Chapter 3.9.6 --- Cell differentiation assay --- p.85 / Chapter 3.10 --- Immunohistochemical analysis --- p.86 / Chapter 3.10.1 --- H&E staining --- p.86 / Chapter 3.10.2 --- Detection of Ki-67 expression --- p.87 / Chapter 3.10.3 --- Detection of CSE1L expression --- p.87 / Chapter 3.10.4 --- Scoring methods --- p.88 / Chapter 3.11 --- Bioinformatic analysis --- p.90 / Chapter 3.12 --- Statistical analysis --- p.92 / Chapter CHAPTER 4 --- RESULTS --- p.93 / Chapter 4.1 --- Expression of miR-137 in glioma cells and clinical significance --- p.93 / Chapter 4.1.1 --- Description of 36 OT samples --- p.93 / Chapter 4.1.2 --- miR-137 level in oligodendroglial tumors and glioma cells --- p.102 / Chapter 4.1.3 --- "Association of miR-137 expression with clinicopathological features, lp/19q status and Ki-67 expression" --- p.104 / Chapter 4.2 --- miR-137 levels in glioma cells after demethylation treatment --- p.113 / Chapter 4.3 --- Biological effects of miR-137 overexpression in glioma cells --- p.118 / Chapter 4.3.1 --- Cell growth --- p.118 / Chapter 4.3.1.1 --- Cell viability --- p.118 / Chapter 4.3.1.2 --- Cell number --- p.123 / Chapter 4.3.1.3 --- Cell cycle analysis : --- p.127 / Chapter 4.3.2 --- Anchorage-independent cell growth --- p.130 / Chapter 4.3.3 --- Cell apoptosis --- p.134 / Chapter 4.3.4 --- Cell motility --- p.136 / Chapter 4.3.5 --- Cell differentiation : --- p.142 / Chapter 4.4 --- Identification of miR-137 targets --- p.144 / Chapter 4.4.1 --- In silico prediction of potential miR-137 targets --- p.144 / Chapter 4.4.2 --- Experimental validation of miR-137 targets by dual-luciferase reporter assay --- p.147 / Chapter 4.4.3 --- "Expression of miR-137 candidate targets, CSE1L and ERBB4 in glioma cells" --- p.152 / Chapter 4.4.4 --- Effects of miR-137 on CSE1L transcript and protein levels --- p.154 / Chapter 4.5 --- Expression of CSE1L in OTs --- p.156 / Chapter 4.5.1 --- CSE1L expression in OTs by qRT-PCR and IHC --- p.156 / Chapter 4.5.2 --- Correlation of CSE1L expression with clinicopathological features --- p.165 / Chapter 4.6 --- Effects of CSE1L knockdown in glioma cells --- p.168 / Chapter 4.6.1 --- Cell growth --- p.170 / Chapter 4.6.1.1 --- Cell viability --- p.170 / Chapter 4.6.1.2 --- Cell number --- p.173 / Chapter 4.6.1.3 --- Cell cycle analysis --- p.176 / Chapter 4.6.2 --- Anchorage-independent cell growth --- p.179 / Chapter 4.6.3 --- Cell apoptosis --- p.182 / Chapter 4.6.4 --- Cell motility --- p.184 / Chapter CHAPTER 5 --- DISCUSSION --- p.190 / Chapter 5.1 --- Expression of miR-137 transcript level in OTs and glioma cell lines --- p.190 / Chapter 5.2 --- Association of miR-137 expression with OT clinical and molecular parameters --- p.192 / Chapter 5.3 --- Prognostic significance of clinical features and miR-137 expression in OTs --- p.194 / Chapter 5.4 --- Inactivation mechanisms of miR-137 in glioma --- p.196 / Chapter 5.5 --- Biological effects of miR-137 overexpression in glioma cells --- p.198 / Chapter 5.6 --- CSE1L is a novel miR-137 target in glioma --- p.200 / Chapter 5.7 --- Expression of CSE1L in glioma --- p.203 / Chapter 5.8 --- Intracellular distribution of CSElL in OTs --- p.206 / Chapter 5.9 --- Correlation of CSE1L expression with clinicopathological and molecular features in OTs --- p.208 / Chapter 5.10 --- CSE1L mediates effects of miR-137 in glioma cells --- p.210 / Chapter 5.11 --- Biological roles of CSE1L in glioma cells 226}0Ø. --- p.212 / Chapter 5.11.1 --- CSE1L in glioma cell proliferation --- p.212 / Chapter 5.11.2 --- CSE1L in glioma cell apoptosis --- p.213 / Chapter 5.11.3 --- CSE1L in glioma cell invasion --- p.215 / Chapter CHAPTER 6 --- CONCLUSIONS --- p.216 / Chapter CHAPTER 7 --- FUTURE STUDIES --- p.219 / Chapter 7.1 --- Expression Molecular mechanisms for miR-137 inactivation in glioma --- p.219 / Chapter 7.2 --- Identification of more miR-137 targets in glioma --- p.219 / Chapter 7.3 --- Role of miR-137 and CSE1L in drug-induced apoptosis in glioma --- p.220 / Chapter 7.4 --- Deciphering dysregulated and clinical relevant miRNAs in glioma --- p.220 / Chapter 7.5 --- Effects of miR-137 in vivo and the therapeutic potential in glioma treatment --- p.221 / REFERENCES --- p.222

雖然錯誤調控微小核糖核酸 (miRNA) 引起肝細胞癌 (HCC) 發生發展的生物途徑得到了廣泛的研究，但是對於上游的調控機制卻知之甚少。以往的研究表明，組蛋白甲基化轉移酶 (EZH2) 介導的組蛋白3上27位賴氨酸三甲基化（H3K27me3）是一類通過沉默腫瘤抑制基因而誘發癌症的機制，並且與脫氧核糖核酸 (DNA) 啟動子甲基化機制獨立存在。另一方面，基因抑制也與 H3K27和DNA甲基化相關聯。盡管如此，miRNA沉默機制，特別是在肝癌中，仍然是知之甚少。 / 在這項研究中，我們使用整合全基因組定位和表達分析方法，以探討在肝癌細胞中miRNA表達的表觀遺傳和轉錄控制。通過染色質免疫沉澱偶聯人類啟動子芯片的方法，我們發現在Hep3B和HKCI - 8肝癌細胞中分別有8.4和12.2%的審問miRNA有豐富的H3K27me3。另一方面，在甲基結合域捕捉偶聯芯片實驗中，我們發現在Hep3B和HKCI-8肝癌細胞中分別有15.5和14.7% 的miRNA出現DNA超甲基化。與以往的蛋白質編碼基因結果相同，大多數 H3K27me3豐富的miRNA沒有被檢測到DNA超甲基化，並且反之亦然。 敲除EZH2基因引起H3K27me3水平廣泛下降,並且恢復 H3K27me3抑制的 miRNA表達，而DNA去甲基化劑5-氮雜 -2'-脫氧胞苷 (5-aza-dC) 卻不能重新啟動他們的表達，進一步顯示EZH2基因介導的H3K27me3引發miRNA沉默的機制是獨立存在的。然而，一些過往研究證明有腫瘤抑制功能的miRNA，包括 miR-9-1，miR-9-2和 miR-9-3 被發現同時被 H3K27me3和DNA甲基化調節。我們進一步發現，在肝瘤細胞中，miR-9 特異性調控致癌性的基因結合核因 (NF-κB) 信號通路，並且與配對的非腫瘤肝組織相比，miR-9 的表達在大約一半的原發性肝癌腫瘤（五十九分之三十零）中顯著被壓抑。 / 為了調查在H3K27me3介導的miRNA基因沉默中參與的轉錄因子，我們應用轉錄因子結合位點分析的方法檢查H3K27me3結合蛋白編碼和miRNA基因的調控區域。在包括miR-9亞型的miRNA中，滎陽 1（YY1）的結合位點在這些調控區域中反覆出現並有很高的代表性。定量芯片聯合聚合酶鏈反應結果顯示，在Hep3B細胞中，敲除YY1不僅大大降低了自身的結合力，同時在 miR-9-1，miR-9-2和 miR-9-3 的啟動子中，EZH2基因和H3K27me3結合也大大降低了。尤其重要的是，敲除YY1可以顯著地重新激活他們的表達，表明在肝癌細胞中YY1在EZH2基因介導的的miR-9 表觀遺傳沉默中發揮重要作用。功能研究證明，下調YY1能夠抑制肝癌細胞的增殖，增加細胞凋亡和減少體內的腫瘤生長。定量實時聚合酶鏈反應進一步證實在miR-9 被下調的子集肝癌腫瘤中，有超過85的樣本顯示YY1和EZH2基因同時過量表達，表明我們的研究結果具有臨床相關性。 / 總之，我們完整的分析表明miRNA的調控在肝癌上的獨特表觀遺傳模式。 H3K27me3介導的miRNA沉默可由擁有致癌功能的YY1誘發，它亦可能代表一個可能公認的肝癌癌基因。綜合表觀遺傳和miRNA表達的轉錄控制的結果，能夠提高我們對肝癌發生發展的認識和闡明利用表觀遺傳方法針對性治療肝癌的新的發展方向。 / Although the biological pathways by which mis-regulated microRNAs (miRNAs) contribute to the development of hepatocellular carcinoma (HCC) have been extensively investigated, little is known about the upstream regulatory mechanisms. Previous studies demonstrated that EZH2-mediated histone H3 lysine 27 trimethylation (H3K27me3) is a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation. On the other hand, gene repression can be associated with both H3K27 and DNA methylation. However, the mechanisms underlying miRNA silencing, particularly in HCC, are poorly understood. / In this study, we used an integrated genome-wide location and expression analysis to investigate the epigenetic and transcriptional controls of miRNA expression in HCC cells. Chromatin immunoprecipitation (ChIP) coupled with human promoter microarrays revealed that 8.4 and 12.2% of the interrogated miRNA were enriched with H3K27me3 in Hep3B and HKCI-8 HCC cells, respectively. On the other hand, Methyl-binding domain capture coupled with microarray (MethylCap-chip) uncovered that 15.5 and 14.7% of miRNA were hypermethylated in Hep3B and HKCI-8 HCC cells, respectively. Consistent with previous observation on protein-coding genes, most of the miRNAs enriched with H3K27me3 had no detectable DNA hypermethylation and vice versa. Knockdown of EZH2 decreased global H3K27me3 level and restored expression of the H3K27me3-targeted miRNAs while the DNA demethylating agent 5-aza-2’-deoxycytidine (5-aza-dC) did not reactivate their expression, further suggesting the independence of EZH2-mediated H3K27me3 in miRNA silencing. Nevertheless, a few miRNAs reported to exhibit tumor-suppressive functions including miR-9-1, miR-9-2 and miR-9-3 were found to be regulated by both H3K27me3 and DNA methylation. We further found that miR-9 targeted the oncogenic NF-κB signaling pathway in HCC cells and were significantly repressed in approximately half of the primary HCC tumors (30/59) compared to the paired non-tumor liver tissues. / To investigate the involvement of transcription factors in H3K27me3-mediated gene silencing of miRNAs, the regulatory regions of H3K27me3-bound protein-coding and miRNA genes were submitted to transcription factor binding site analysis. The binding sites for Ying Yang 1 (YY1) were recurrently over-represented in these loci including the miR-9 isoforms. Quantitative ChIP-PCR demonstrated that knockdown of YY1 in Hep3B cells not only significantly reduced its own binding, but also the EZH2 and H3K27me3 promoter occupancy at miR-9-1, miR-9-2 and miR-9-3. Importantly, their expression levels were significantly reactivated by YY1 knockdown, suggesting that YY1 plays part in the EZH2-mediated epigenetic silencing of miR-9 in HCC cells. Functionally, down-regulation of YY1 was shown to inhibit HCC cell proliferation, increase cell apoptosis and reduce tumor growth in vivo. Quantitative RT-PCR further demonstrated that YY1 and EZH2 were concordantly over-expressed in over 85% of the same subset of HCC tumors that exhibited miR-9 down-regulation, demonstrating the clinical relevance of our findings. / In conclusion, our integrated analysis demonstrated differential epigenetic patterns of miRNA regulation in HCC. H3K27me3-mediated silencing of miRNAs may be initiated by YY1, which possesses oncogenic functions and may represent a putative HCC oncogene. The findings of combinatorial epigenetic and transcriptional control of miRNA expression enhance our understanding of hepatocarcinogenesis and shed light on the development of novel epigenetic targeted therapy of HCC. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Tsang, Pui Fong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 111-121). / Abstracts also in Chinese. / Abstract (English version) --- p.i / Abstract (Chinese version) --- p.iv / Acknowledgements --- p.vi / table of contents --- p.vii / List of tables --- p.x / List of Figures --- p.xi / Abbreviations --- p.xiii / Chapter CHAPTER 1 --- INTRODUCTION4 / Chapter 1.1 --- Hepatocellular carcinoma --- p.1 / Chapter 1.1.1 --- Epidemiology --- p.1 / Chapter 1.1.2 --- Etiology --- p.2 / Chapter 1.2 --- Epigenetic mechanisms --- p.3 / Chapter 1.2.1 --- Epigenetic silencing by DNA hypermethylation --- p.3 / Chapter 1.2.2 --- Epigenetic silencing by Polycomb group protein --- p.5 / Chapter 1.2.3 --- Interplay between H3K27me3 and DNA hypermethylation --- p.7 / Chapter 1.3 --- microRNA --- p.10 / Chapter 1.3.1 --- Transcriptional gene silencing by miRNA --- p.11 / Chapter 1.3.2 --- miRNA and cancers --- p.12 / Chapter 1.3.3 --- miRNA and liver cancer --- p.13 / Chapter 1.4 --- Signal transduction pathway and cancers --- p.14 / Chapter 1.5 --- Aims of study --- p.15 / Chapter CHAPTER 2 --- MATERIALS AND METHODS / Chapter 2.1 --- Cell lines --- p.16 / Chapter 2.2 --- Clinical samples --- p.16 / Chapter 2.3 --- Plasmid DNA transfection --- p.16 / Chapter 2.4 --- Small interfering RNA transfection --- p.17 / Chapter 2.5 --- Extraction of total RNA --- p.19 / Chapter 2.6 --- Western blot analysis --- p.19 / Chapter 2.7 --- Quantitative RT-PCR --- p.20 / Chapter 2.8 --- miRNA Real Time RT-PCR --- p.22 / Chapter 2.9 --- ChIP-chip assay --- p.24 / Chapter 2.10 --- MethylCap-chip --- p.27 / Chapter 2.11 --- miRNA microarray --- p.28 / Chapter 2.12 --- ChIP Assay and Quantitative ChIP-PCR Assay --- p.28 / Chapter 2.13 --- Colony formation assay --- p.33 / Chapter 2.14 --- Cell proliferation assay --- p.33 / Chapter 2.15 --- Annexin V apoptosis assay --- p.34 / Chapter 2.16 --- Cancer 10-pathway reporter array --- p.34 / Chapter 2.16.1 --- Transfection of siEZH2 with 5-aza-dC treatment --- p.34 / Chapter 2.16.2 --- Transfection of siYY1 and pcDNA3-miR9 plasmid --- p.35 / Chapter 2.16.3 --- Luciferase reporter array --- p.35 / Chapter 2.17 --- Animal Studies --- p.36 / Chapter 2.18 --- Statistical Analysis --- p.36 / Chapter CHAPTER 3 --- Results / Chapter 3.1 --- Occupancy of miRNA genes by epigenetic marks in HCC cells --- p.37 / Chapter 3.1.1 --- Identification of H3K27me3-occupied miRNAs --- p.37 / Chapter 3.1.2 --- Identification of DNA methylation-occupied miRNAs --- p.41 / Chapter 3.1.3 --- Relationship between H3K27me3 and DNA methylation occupancy of miRNAs in HCC cells --- p.45 / Chapter 3.2 --- Regulation of miRNA expression by H3K27me3 and DNA methylation in HCC cells --- p.51 / Chapter 3.3 --- Epigenetic regulation and molecular function of miR-9 in HCC cells --- p.56 / Chapter 3.3.1 --- Confirmation of H3K27me3 and DNA methylation occupancy in miR-9 genes --- p.59 / Chapter 3.3.2 --- Synergistic reactivation of miR-9 upon removal of epigenetic marks --- p.62 / Chapter 3.3.3 --- Effect of miR-9 re-expression on NFKB1 (p50) expression and NF-κB signaling in HCC cells --- p.66 / Chapter 3.4 --- Role of the transcription factor YY1 in the epigenetic regulation of miR-9 --- p.72 / Chapter 3.4.1 --- Identification of transcription factors involved in the regulation of H3K27me3-bound genes --- p.72 / Chapter 3.4.2 --- Occupancy of YY1 on miR-9 in HCC cells --- p.75 / Chapter 3.4.3 --- Effects of YY1 on EZH2/H3K27me3 occupancy and expression of miR-9 --- p.78 / Chapter 3.4.4 --- Effects of YY1 on p50/p65 expression and NF-κB signaling in HCC cells --- p.81 / Chapter 3.5 --- Functional significance of YY1 in HCC --- p.84 / Chapter 3.5.1 --- Effect of YY1 on HCC cell growth --- p.84 / Chapter 3.5.2 --- Effect of YY1 on HCC cell apoptosis --- p.87 / Chapter 3.5.3 --- Effect of YY1 on HCC cell growth in vivo --- p.90 / Chapter 3.5.4 --- Expressions of YY1, EZH2 and miR-9 on clinical HCC samples --- p.92 / Chapter CHAPTER 4 --- DISCUSSION / Chapter 4.1 --- Independence of EHZ2-mediated H3K27me3 and DNA methylation --- p.97 / Chapter 4.2 --- Concordant H3K27 and DNA methylation-mediated silencing of miR-9 --- p.101 / Chapter 4.3 --- Ectopic expression of miR-9 inhibits NF-kB signaling in HCC cells --- p.102 / Chapter 4.4 --- YY1 is involved in the regulation of H3K27me3-bound genes --- p.103 / Chapter 4.5 --- Knockdown of YY1 inhibits NF-kB signaling in HCC --- p.105 / Chapter 4.6 --- Clinical relevance and therapeutic significance of miR-9 silencing by YY1-mediated recruitment of EZH2 --- p.106 / Chapter 4.7 --- Limitations and future studies --- p.109 / REFERENCES --- p.111 / PUBLICATION --- p.122

Ng, Wing Chi Linda. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 120-142). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgement --- p.iv / Publications --- p.v / Abbreviations --- p.vi / Table of Contents --- p.viii / List of Tables --- p.xiii / List of Figures --- p.xiv / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Stem Cells --- p.1 / Chapter 1.1.1 --- Definition of Stem Cells --- p.1 / Chapter 1.1.2 --- Different Origins of Stem Cells --- p.2 / Chapter 1.1.3 --- Challenges and Importance of Stem Cell Research --- p.5 / Chapter 1.2 --- Adult Mesenchymal Stem Cells --- p.7 / Chapter 1.2.1 --- Characteristics of Adult Mesenchymal Stem Cells --- p.7 / Chapter 1.2.2 --- Adipose Tissue as an Alternate Source of MSCs --- p.8 / Chapter 1.2.3 --- Adipose Tissue Versus Bone Marrow as a Source of MSCs --- p.10 / Chapter 1.3 --- Adipose Tissue-derived Stem Cells (ATSCs) --- p.11 / Chapter 1.3.1 --- Cell Surface Marker Characteristic of ATSCs --- p.11 / Chapter 1.3.2 --- Global Gene Expression Profile of ATSCs --- p.14 / Chapter 1.3.3 --- Immunomodulatory Effect of ATSCs --- p.15 / Chapter 1.3.4 --- Proliferation Capacity of ATSCs --- p.17 / Chapter 1.3.5 --- Multilineage Differentiation of ATSCs --- p.18 / Chapter 1.3.5.1 --- Differentiation Capability of ATSCs : Adipogenesis --- p.18 / Chapter 1.3.5.2 --- Osteogenesis --- p.19 / Chapter 1.3.5.3 --- Skeletal and Smooth Muscle Myogenesis --- p.21 / Chapter 1.3.5.4 --- Cardiomyogenesis --- p.23 / Chapter 1.3.5.5 --- Chondrogenesis --- p.24 / Chapter 1.3.5.6 --- Neurogenesis --- p.27 / Chapter 1.4 --- Signaling Pathways in Stem Cells --- p.31 / Chapter 1.4.1 --- Wnt Signaling --- p.31 / Chapter 1.4.2 --- Notch Signaling --- p.33 / Chapter 1.4.3 --- Signaling Pathway of the TGF-β Superfamily --- p.34 / Chapter 1.5 --- Pathways Controlling Chondrogenesis --- p.36 / Chapter 1.6 --- MicroRNA --- p.39 / Chapter 1.6.1 --- MicroRNA - A Novel Gene Regulator --- p.39 / Chapter 1.6.2 --- Biogenesis of MicroRNAs --- p.40 / Chapter 1.6.3 --- Post-transcriptional Repression by MicroRNAs --- p.43 / Chapter 1.6.4 --- Role of MicroRNAs in Development --- p.45 / Chapter 1.6.5 --- MicroRNAs in Stem Cell Differentiation --- p.46 / Chapter 1.6.5.1 --- MicroRNA Expression Profile in ESCs --- p.46 / Chapter 1.6.5.2 --- Lineage Differentiation --- p.47 / Chapter 1.7 --- Project Aims --- p.52 / Chapter 1.8 --- Significance of Study --- p.53 / Chapter Chapter 2 --- Materials and Methods --- p.54 / Chapter 2.1 --- Sample Collection --- p.54 / Chapter 2.2 --- Isolation and Culture of ATSCs --- p.54 / Chapter 2.3 --- Measurement of Cell Growth --- p.55 / Chapter 2.4 --- Effect of Estrogen Treatment on ATSC Proliferation --- p.55 / Chapter 2.5 --- Multilineage Differentiation of ATSCs --- p.55 / Chapter 2.5.1 --- Chondrogenic Differentiation --- p.56 / Chapter 2.5.2 --- Neural Differentiation --- p.56 / Chapter 2.6 --- Immunocytochemical Analysis of Surface Markers and Lineage Specific Markers --- p.57 / Chapter 2.7 --- Alcian Blue Staining --- p.58 / Chapter 2.8 --- RNA Extraction --- p.58 / Chapter 2.9 --- Reverse Transcription --- p.59 / Chapter 2.10 --- Quantitative Real-time Polymerase Chain Reaction --- p.59 / Chapter 2.11 --- Statistical Analysis of Real-time PCR Data --- p.61 / Chapter 2.12 --- MicroRNA Profiling --- p.61 / Chapter 2.12.1 --- Reverse Transcription --- p.62 / Chapter 2.12.2 --- Quantitative Real-time Polymerase Chain Reaction --- p.62 / Chapter 2.13 --- mRNA Target Prediction of MicroRNA --- p.63 / Chapter 2.14 --- MicroRNA Knockdown Assay --- p.63 / Chapter 2.15 --- MicroRNA Over-expression Assay --- p.64 / Chapter 2.15.1 --- Vector Amplification --- p.64 / Chapter 2.15.1.1 --- Transformation --- p.64 / Chapter 2.15.1.2 --- Purification of Plasmid DNA --- p.65 / Chapter 2.15.1.3 --- Confirmation of Construct Insertion --- p.66 / Chapter 2.15.2 --- Transfection of Plasmid and Establishment of MicroRNA Precursor Expressing Cell Lines --- p.66 / Chapter 2.16 --- Gene Expression Microarry --- p.67 / Chapter 2.16.1 --- Preparation of Amplification and Labeling Reaction --- p.67 / Chapter 2.16.2 --- Purification of the Labeled/Amplified RNA --- p.68 / Chapter 2.16.3 --- RNA Fragmentation --- p.68 / Chapter 2.16.4 --- Hybridization --- p.69 / Chapter 2.16.5 --- Array Washing and Scanning --- p.69 / Chapter 2.16.6 --- Statistical Analysis of Microarray Data --- p.69 / Chapter CHAPTER 3 --- RESULTS --- p.71 / Chapter 3.1 --- Isolation and Characterization of ATSCs --- p.71 / Chapter 3.2 --- ATSCs Exhibited Multilineage Differentiation --- p.75 / Chapter 3.2.1 --- Chondrogenic Differentiation --- p.75 / Chapter 3.2.2 --- Expression of Chondrogenic Markers --- p.76 / Chapter 3.2.3 --- Neural Differentiation --- p.80 / Chapter 3.2.4 --- Expression of Neural Markers --- p.83 / Chapter 3.3 --- Effect of Donor's Reproductive Status on the Proliferation and Differentiation Capacity of ATSCs --- p.83 / Chapter 3.3.1 --- Expression of Stem Cell Makers --- p.86 / Chapter 3.3.2 --- Cell Proliferation Assay --- p.86 / Chapter 3.3.3 --- Differentiation Capacity of ATSCs --- p.89 / Chapter 3.4 --- Effect of E2 Treatment on the Proliferation Rate of ATSCs --- p.89 / Chapter 3.5 --- MicroRNA --- p.91 / Chapter 3.5.1 --- MicroRNA Expression Profile of Undifferentiated and Chondrogenic Differentiated ATSCs --- p.91 / Chapter 3.5.2 --- Clustering Analysis Identified MicroRNAs Segregate with ATSCs --- p.91 / Chapter 3.5.3 --- Identification of Differentially Expressed MicroRNAs in Chondrogenic-induced ATSCs --- p.95 / Chapter 3.5.4 --- mRNA Target Prediction for miR-199a --- p.97 / Chapter 3.6 --- Correlating MicroRNA Expression and mRNA Levels: Clues to MicroRNA Function --- p.97 / Chapter 3.6.1 --- Effect ofmiR-199a RNAi in Phenotypic Changes of Chondrogenic-induced ATSCs --- p.97 / Chapter 3.6.2 --- Identification of Potential Target Genes by Microarray Analysis of ATSCs with miR-199a Over-expression and Knockdown --- p.102 / Chapter CHAPTER 4 --- DISCUSSION --- p.104 / Chapter CHAPTER 5 --- CONCLUSIONS --- p.115 / APPENDICES --- p.117 / REFERENCES --- p.120

Prostate cancer is one of the leading causes of death among males in the United States. In this study, we hypothesized that an activated PKC-iota-dependent anti-apoptotic pathway, drives the cell cycle proliferation and survival of prostate cancer cells. We investigated the role of atypical PKC-iota (PKC-ι) in androgen- independent prostate DU-145 carcinoma, androgen-dependent prostate LNCaP carcinoma compared to transformed non-malignant prostate RWPE-1 cells. Western blotting and immunoprecipitations demonstrated that PKC-ι is associated with cyclin-dependent activating kinase (CAK/Cdk7) in androgen-dependent, RWPE-1 and LNCaP cells but not in androgen-independent DU-145 cells. Treatment of prostate RWPE-1 cells with PKC-ι silencing RNA (siRNA) decreased cell proliferation, cell cycle accumulation at G2/M phase and decreased phosphorylation of Cdk7 and cdk2. In addition, PKC-ι siRNA treatment provoked a decrease in phosphorylation of Bad and increased Bad/Bcl-xL heterodimerization, leading to cell apoptosis. In DU-145 cells, PKC-ι is anti-apoptotic and still required for cell survival. Treatment with PKC-ι siRNA blocked an increase in cell number, and inhibited G1/S transition. In addition to cell cycle arrest, both RWPE-1 cells and DU-145 cells underwent apoptosis via mitochondria dysfunction and activating apoptosis cascades such as release of cytochrome c, activation of caspase-7, and poly-(ADP-ribose) polymerase (PARP) cleavage. Mechanistic pathways involving aPKCs in the NF-κB survival pathway were established using pro-inflammatory cytokine, tumor necrosis factor alpha (TNFα). Results demonstrated that RWPE-1 cells and DU-145 cells are insensitive to TNFα whereas LNCaP cells are sensitive to TNFα treatment and undergo apoptosis. In DU-145 cells, TNFα induced PKC-ι activation of IκB kinase, IKKα/ß, while in RWPE-1 cells, PKC-ζ activates IKKα/ß. Both RWPE-1 and DU-145 show degradation of IκBα allowing NF-κB/p65 translocation to the nucleus. In LNCaP cells, the upstream kinase activation IKKα/ß was not observed, although there have been reports that LNCaP cells weakly activate IKKα and have NF-κB activation. In vivo kinase assay demonstrates that PKC-ι is the substrate of IKKα/ß. A putative PKC-ι inhibitor (ICA-1) inhibited activation of IKKα/ß in vivo. Hence, PKC-ι is an antiapoptotic protein and this suggests that anti-PKC-ι therapy may be a viable option for prostate carcinoma cells.

published_or_final_version / Surgery / Master / Master of Philosophy

published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / Pathology / Master / Master of Medical Sciences

published_or_final_version / Chinese Medicine / Master / Master of Philosophy