Ng Wah. / Thesis submitted in: August 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 101-113). / Abstracts in English and Chinese. / ABSTRACT --- p.II / 摘要 --- p.IV / ACKNOWLEDGEMENT --- p.VI / TABLE OF CONTENTS --- p.VII / LIST OF TABLES --- p.X / LIST OF FIGURES --- p.XI / ABBREVIATIONS --- p.XII / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Introduction --- p.2 / Chapter 1.2 --- Etiological Factors of Hepatocellualr Carcinoma (HCC) --- p.4 / Chapter 1.2.1 --- Dietary Aflatoxins --- p.4 / Chapter 1.2.2 --- Liver Cirrhosis --- p.5 / Chapter 1.2.3 --- Alcohol Abuse --- p.6 / Chapter 1.2.4 --- Viral Hepatitis Infection --- p.6 / Chapter 1.3 --- Literature Review on the Investigations of HBV Integrants in HCC --- p.16 / Chapter 1.3.1 --- Affected Host Junctions --- p.17 / Chapter 1.3.2 --- Viral Junctions --- p.18 / Chapter 1.4 --- Restriction Site Polymerase Chain Reaction (RS-PCR) --- p.19 / Chapter 1.5 --- Aims of Thesis --- p.21 / Chapter Chapter 2 --- Materials and Methods --- p.22 / Chapter 2.1 --- Materials --- p.23 / Chapter 2.1.1 --- Chemicals --- p.23 / Chapter 2.1.2 --- Buffers --- p.24 / Chapter 2.1.3 --- Cell Cultures --- p.24 / Chapter 2.1.4 --- Nucleic Acids --- p.24 / Chapter 2.1.5 --- Enzymes --- p.25 / Chapter 2.1.6 --- Equipment --- p.25 / Chapter 2.1.7 --- Software and Web Resources --- p.26 / Chapter 2.2 --- Methods --- p.27 / Chapter 2.2.1 --- DNA Extraction --- p.27 / Chapter 2.2.2 --- RS-PCR --- p.31 / Chapter 2.2.3 --- Sequencing --- p.37 / Chapter 2.2.4 --- Spectral Karyotyping (SKY) --- p.38 / Chapter 2.2.5 --- Fluorescence In situ hybridization --- p.39 / Chapter Chapter 3 --- Investigation of HBV Integration Sites in HCC Cell lines --- p.45 / Chapter 3.1 --- Introduction --- p.46 / Chapter 3.2 --- Materials and Methods --- p.47 / Chapter 3.2.1 --- Cell Lines --- p.47 / Chapter 3.2.2 --- RS-PCR --- p.47 / Chapter 3.2.3 --- Spectral Karyotyping --- p.48 / Chapter 3.2.4 --- Tyramide Signal Amplification for HBV in FISH Analysis --- p.48 / Chapter 3.3 --- Results --- p.51 / Chapter 3.3.1 --- Identification of HBV Integration Sites in Cell Lines --- p.51 / Chapter 3.3.2 --- Evaluation of RSO Primer Efficiency --- p.52 / Chapter 3.3.3 --- SKY and FISH Analysis --- p.53 / Chapter 3.4 --- Discussion --- p.64 / Chapter 3.4.1 --- HBV Insertions in HCC Cell Lines --- p.64 / Chapter 3.4.2 --- Efficacy of RSO Primers --- p.65 / Chapter 3.4.3 --- Investigation of HBV Integration on Chromosomal Rearrangement --- p.65 / Chapter Chapter 4 --- Investigation of Hepatitis B Virus Integration Sites in Primary HCC --- p.67 / Chapter 4.1 --- Introduction --- p.68 / Chapter 4.2 --- Materials and Methods --- p.69 / Chapter 4.2.1 --- Patients --- p.69 / Chapter 4.2.2 --- RS-PCR --- p.70 / Chapter 4.3 --- Results --- p.72 / Chapter 4.3.1 --- HBV Integration Sites in Primary HCC Tumors and Adjacent Non- malignant Liver --- p.72 / Chapter 4.4 --- Discussion --- p.88 / Chapter 4.4.1 --- HBV integration Sites in Primary HCC Tumors and Adjacent Non- malignant Liver --- p.88 / Chapter 4.4.2 --- Summary on HBV Integrants Identified --- p.91 / Chapter Chapter 5 --- Proposed Future Studies --- p.98 / Chapter 5.1 --- Correlation of Structural Aberrations with HBV Integrations --- p.99 / Chapter 5.2 --- Transcriptional Expression Study on the Genes Interrupted by or Located near the Virus Host Junctions --- p.100 / Chapter Chapter 6 --- References --- p.101

丹參為雙子葉植物唇形科鼠尾草族植物的乾燥根及根莖。在中國，丹參為廣泛用於治療心血管疾病的藥用植物，而在西方，丹參也常作為一種輔助性藥物。《中國藥典2010版》收錄了35個以上含有丹參的複方或者方劑。在這些複方中，採用了富含丹酚酸和丹參酮的丹參水提物、乙醇提取物或兩者的混合物。丹參提取物具有較強的抗氧化作用，被認為在化學預防和化療的輔助治療中有一定用途。作為主要的丹參水溶性成分，熱敏感的丹酚酸在提取與加熱過程中可能會降解為其他丹酚酸。丹參水提取物的化學組成可能會在不同熱水提取溫度下有所不同，進而影響其藥理活性。在本研究中，通過加熱回流提取和在不同溫度下的微波提取（MAE-W）獲得了6種丹參水提取物，並對這些提取物進行化學成分和藥理分析，考察它們的抗氧化、抗凋亡和血管舒張作用。在這些提取物中，第三輪的微波提取物（100 oC）含有最多的丹酚酸和丹參酮，在1，1-二苯基-2-三硝基苯肼（DPPH）法和鐵還原/抗氧化能力（FRAP）法中具有最強的抗氧化活性，在2,2'-偶氮二(2-脒基丙烷)二鹽酸鹽（AAPH）誘導人血紅細胞的溶血實驗和過氧化氫誘導大鼠心肌細胞H9c2凋亡實驗中還顯示了最強的抑制作用，對大鼠腦基底動脈有最強的鬆弛效應。這些丹參水提取物的抗氧化作用與它們的血管舒張效應呈一定的線性關係（回歸係數r = 0.895 - 0.977）。通過多元線性回歸分析發現，丹參素可以作為丹參水提物的抗氧化和血管舒張功能的顯著性標記物，而丹參酮IIA則是抑制過氧化氫誘導大鼠心肌H9c2細胞凋亡的標記物。 / 作為丹參中主要的脂溶性成分，丹參酮在不同的腫瘤細胞系和荷瘤小鼠模型中展示了抗癌潛力。這些丹參酮的抗癌機制包括細胞週期阻滯，觸發半胱天冬酶（Caspase）依賴的內源性和外源性的凋亡途徑和絲裂原激活的蛋白激酶（MAPK）信號通路等。丹參新酮（miltirone）是從丹參中分離得到的松香烷型二萜醌類化合物，具有多種的藥理活性，如抗氧化，抗焦慮和抗腫瘤等。本研究評估了丹參新酮在人肝癌HepG2細胞系和P-糖蛋白（P-gp）過表達的阿霉素耐藥HepG2細胞系（R-HepG2）中的凋亡作用及其機制。丹參新酮在HepG2細胞中顯示了細胞毒性（EC₅₀值為7.06 微摩），而丹參新酮在抑制HepG2和R-HepG2細胞增殖中的濃度依賴性沒有顯著性差異。丹參新酮（1.56 - 6.25微摩）與阿霉素（DOX）對R-HepG2細胞的增殖具有協同效應，在達到50的生長抑制時，它們的聯合用藥指數為0.3至0.5。流式細胞術分析表明，丹參新酮降低了R-HepG2細胞中P-gp介導的阿霉素外排，分子對接研究表明該效果是通過抑制P-gp的藥物結合位點。在非壞死濃度（25微摩或以下），丹參新酮在HepG2和R-HepG2細胞中活化了Caspase依賴的凋亡途徑，誘導產生活性氧（ROS）和氧化應激，且觸發ROS介導的包括p38 MAPK，應激活化蛋白激酶/c-Jun氨基末端激酶（SAPK / JNK）以及細胞外調節激酶1和2在內的MAPK信號通路。綜上所述，在R-HepG2中丹參新酮是P-gp和細胞增殖的雙重抑制劑，顯示了其在治療肝癌（HCC）的潛力。 / 為了增加藥物開發的成功率，在藥物發現的早期階段應考察新化學實體（NCEs）的蛋白結合率，清除率，藥動學參數，以及藥物代謝相互作用等體內代謝參數。以往的研究已經顯示了從丹參中分離得到的四種主要丹參酮對人和大鼠的細胞色素P450酶介導的探針底物的代謝具有不同程度的抑制作用，需要注意丹參和其他藥物間的相互作用。本研究的另一目的是在人類肝微粒體中探討丹參新酮與探針底物間的細胞色素P450酶介導的代謝相關的相互作用。人肝微粒體孵育實驗結果表明丹參新酮對CYP1A2（IC₅₀值為 1.73微摩）和CYP2C9（IC₅₀值為8.61微摩）有中等強度的抑制，對CYP2D6（IC₅₀值為30.20微摩）和CYP3A4（IC₅₀值為33.88微摩）有弱的抑制。酶動力學和分子對接研究的結果進一步表明，丹參新酮為CYP1A2（Ki值為3.17微摩）的中等強度混合型抑制劑，是CYP2C9（Ki值為1.48微摩）的中等強度競爭型抑制劑，也是CYP2D6（Ki值為24.25微摩）和CYP3A4（Ki值為35.09微摩）的弱的混合型抑制劑。這些結果表明，應考慮丹參新酮與CYP1A2和CYP2C9代謝的藥物間的相互作用，但是可認為其與CYP2D6及CYP3A4代謝的藥物間幾乎不存在相互作用。 / 總之，本研究考察了不同提取方法對丹參提取物成份及其藥效的影響，確定了不同用途的丹參提取物的質控標記物。本研究還考察了丹參新酮體外抗肝癌的能力及其藥物代謝相互作用為基礎的類藥性,為其進一步的體內試驗提供了依據。 / Danshen, the dried root and rhizome of Salvia miltiorrhiza Bg. (Fam. Labiatae), is a widely used medicinal plant for the treatment of cardiovascular diseases in China and also a complementary medicine in the West. Danshen is indexed in the Pharmacopoeia of People’s Republic of China (2010 Edition), with more than 35 formulations and concoctions containing Danshen water-extracts, ethanolic extracts or their combination which are rich in phenolic acids and tanshinones with various contents. Danshen extracts have been considered for the use as an adjunct in chemoprevention and chemotherapy due to their strong antioxidant effects. Phenolic acids, the major water-soluble components in Danshen, are thermosensitive and may degrade to other phenolic acids during extractions upon heating. The chemical profiles of Danshen water-extracts may vary with different heat water extraction at different temperatures, affecting the composition and bioactivity of the extracts obtained. In this study, six water-extracts of Danshen obtained from heat reflux water extraction and microwave-assisted extraction with water (MAE-W) at different temperatures were prepared for evaluation of their composition and pharmacological effects such as antioxidant, anti-apoptosis and vascular relaxation. Among these extracts obtained, the third-round MAE-W (100 °C) product, which was the last round product obtained by extracting the same crude material three times, had the highest contents of phenolic acids and tanshinones, with the strongest antioxidant activity estimated by 2, 2-diphenyl-1-(2, 4, 6-trinitrophenyl) hydrazyl (DPPH) assay and ferric reducing / antioxidant potential (FRAP) assay. This extract also possessed the strongest inhibitory effects on 2, 2'-azobis-2-amidino-propane (AAPH)-induced haemolysis in human red blood cells, hydrogen peroxide-induced apoptosis in rat heart H9c2 cells and the highest relaxation effects on rat basilar artery. The antioxidant effects of Danshen water-extracts linearly correlated to their relaxation effects (r = 0.895 to 0.977). Through multiple linear regression analysis, danshensu was found to be the most significant marker in the antioxidant and vasodilation effects of Danshen water-extract, while tanshinone IIA as the marker on hydrogen peroxide-induced apoptosis in rat heart H9c2 cells. Danshensu is, therefore, a useful marker for the quality control of Danshen water-extracts in antioxidant and vasodilation, while tanshinone IIA for anti-apoptotic potential of water-extracts. / Tanshinones, the major lipid-soluble components isolated from Danshen, have been reported for their anti-cancer potential in various cell lines and tumor-bearing mice models. Their anti-cancer mechanisms are also well-studied, mainly through cell cycle arrest, caspase-dependent apoptotic pathways and mitogen activated protein kinase (MAPK) signaling pathways. Miltirone, another abietane type-diterpene quinone isolated from Danshen, has been reported for its anti-oxidative, anxiolytic and anti-cancer effects. This study evaluated the apoptotic effect of miltirone and the underlying mechanisms in a human hepatoma HepG2 cell line and its p-glycoprotein (P-gp)-overexpressed doxorubicin-resistant counterpart (R-HepG2). Miltirone showed similar cytotoxicity in HepG2 (EC₅₀ = 7.06 μM) and R-HepG2 (EC₅₀ = 12.0 μM), demonstrated synergistic effects (1.56 - 6.25 μM) with doxorubicin (DOX) on the growth inhibition of R-HepG2 (synergism: 0.3 < CI < 0.5 at 50 % inhibition). Flow cytometric analysis showed that miltirone decreased P-gp-mediated DOX efflux in R-HepG2, and molecular docking studies illustrated that this effect was through inhibition on the active site of P-gp. At non-necrotic concentrations (25 μM or below), miltirone activated caspase-dependent apoptotic pathways, and induced the generation of reactive oxygen species (ROS) and oxidative stress which triggered ROS-mediated MAPK signaling pathways, including p38 MAPK, stress-activated protein kinase / c-Jun N-terminal kinase (SAPK/JNK) and extracellular regulated kinase 1/2, in both HepG2 and R-HepG2 cells. It is therefore concluded that miltirone is a dual inhibitor on P-gp and cell proliferation in R-HepG2 cells, with potential for the treatment of human hepatocellular carcinoma (HCC). / In order to improve the successful rates in drug development, the in vivo metabolic parameters of new chemical entities (NCEs), such as protein bindings, clearance rate, pharmacokinetic parameters and metabolism-based drug-drug interactions, should be considered at the early stage of drug discovery. Previous studies have shown that major tanshinones isolated from Danshen inhibited the metabolism of model probe substrates of human and rat CYP450 enzymes, with potential in causing herb-drug interactions. The aim of this study was to study the effect of miltirone on the metabolism of model probe substrates of CYP1A2, 2C9, 2D6 and 3A4 in pooled human liver microsomes. Miltirone showed moderate inhibition on CYP1A2 (IC₅₀ = 1.73 μM) and CYP2C9 (IC₅₀ = 8.61 μM), and weak inhibition on CYP2D6 (IC₅₀ = 30.20 μM) and CYP3A4 (IC₅₀ = 33.88 μM). Enzyme kinetic studies showed that miltirone competitively inhibited CYP2C9 (Ki = 1.48 μM), and displayed mixed type inhibitions on CYP1A2, CYP2D6 and CYP3A4 with Ki values of 3.17 μM, 24.25 μM and 35.09 μM, respectively. Molecular docking study further confirmed the ligand-binding conformations of miltirone in the active sites of human CYP450 isoforms. These findings suggested that miltirone may have potential drug-drug interactions with CYP1A2- and CYP2C9-metabolized drugs, and to a lesser extent with CYP2D6- and CYP3A4-metabolized drugs. / In conclusion, this study investigated the effects of Danshen water-extracts produced by different extraction methods on the chemical compositions and pharmacological activities, and consequently confirmed the biomarkers for the quality control of Danshen water-extracts for different medicinal uses. This study also demonstrated the anti-cancer potential of miltirone for HCC in vitro and the metabolism-based drug-drug interactions for its drug-likeness, which may provide useful and promising data for in vivo anti-cancer study of miltirone and further pre-clinical studies. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Zhou, Xuelin / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 195-224). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Abstract --- p.i / 論文摘要 --- p.v / Publications based on the work in this thesis --- p.viii / Acknowledgements --- p.x / Abbreviations --- p.xii / Table of Contents --- p.xv / Chapter Chapter 1 --- General introduction --- p.1 / Chapter 1.1 --- Reactive oxygen species and carcinogenesis --- p.1 / Chapter 1.2 --- Reactive oxygen species and tumor progression & metastasis --- p.2 / Chapter 1.3 --- Antioxidant enzymes in chemoprevention and chemotherapy --- p.3 / Chapter 1.3.1 --- Glutathione and Glutathione reductase --- p.5 / Chapter 1.3.2 --- Glutathione Peroxidase --- p.5 / Chapter 1.3.3 --- Glutathione S-transferases --- p.6 / Chapter 1.3.4 --- NAD(P)H: quinone reductase 1 --- p.7 / Chapter 1.3.5 --- Heme oxygenase-1 --- p.8 / Chapter 1.3.6 --- Thioredoxin reductase --- p.9 / Chapter 1.3.7 --- Superoxide Dismutase --- p.10 / Chapter 1.3.8 --- Catalase --- p.11 / Chapter 1.4 --- Medicinal uses of Danshen --- p.12 / Chapter 1.5 --- Analysis of Danshen and its components --- p.14 / Chapter 1.6 --- Antioxidant effects of Danshen extract and its bioactive compounds in chemoprevention and chemotherapy-related disease --- p.19 / Chapter 1.7 --- Anti-cancer effects of tanshinones isolated from Danshen --- p.21 / Chapter 1.7.1 --- Tanshinone IIA --- p.22 / Chapter 1.7.2 --- Tanshinone I --- p.26 / Chapter 1.7.3 --- Cryptotanshinone --- p.27 / Chapter 1.7.4 --- Dihydrotanshinone --- p.27 / Chapter 1.8 --- Metabolism / disposition of Danshen and its major active ingredients --- p.28 / Chapter 1.9 --- Herb-drug interactions with Danshen --- p.31 / Chapter 1.10 --- Effects of Danshen (and its major active ingredients) on model probe substrates of CYP isoforms --- p.33 / Chapter 1.11 --- CYPs induction by Danshen and its active components --- p.38 / Chapter 1.12 --- Effects of Danshen / active ingredients on drug transporter proteins --- p.40 / Chapter 1.13 --- CYP450 inhibition screening for new chemical entity --- p.42 / Chapter 1.14 --- Molecular docking analysis --- p.44 / Chapter 1.15 --- The Aim of this study --- p.45 / Chapter Chapter 2 --- Quantitative and qualitative studies to evaluate the efficiency of different heat water-extractions --- p.48 / Chapter 2.1 --- Introduction --- p.48 / Chapter 2.2 --- Materials and methods --- p.51 / Chapter 2.2.1 --- Materials and apparatus --- p.51 / Chapter 2.2.2 --- Extraction procedures --- p.51 / Chapter 2.2.3 --- HPLC analysis --- p.54 / Chapter 2.2.4 --- DPPH assay and FRAP assay --- p.54 / Chapter 2.2.5 --- Inhibition of 2,2'-azobis-2-amidinopropane (AAPH)-induced haemolysis in human red blood cells --- p.55 / Chapter 2.2.6 --- Protective effects on hydrogen peroxide-induced apoptosis in rat heart H9c2 cells --- p.56 / Chapter 2.2.7 --- Vasodilation effects on rat basilar artery --- p.57 / Chapter 2.2.8 --- Statistical analysis --- p.58 / Chapter 2.3 --- Results and Discussion --- p.59 / Chapter 2.3.1 --- Chemical profiles analyzed by HPLC analysis --- p.59 / Chapter 2.3.2 --- DPPH assay and FRAP assay --- p.63 / Chapter 2.3.3 --- Inhibition of AAPH-induced haemolysis --- p.65 / Chapter 2.3.4 --- Protective effects on hydrogen peroxide-induced apoptosis --- p.69 / Chapter 2.3.5 --- Vasodilation effects on rat basilar artery --- p.71 / Chapter 2.3.6 --- Multiple linear regression analysis --- p.76 / Chapter Chapter 3 --- Effects of miltirone on cell proliferation in a hepatoma HepG2 cell line and its doxorubicin-resistant counterpart --- p.83 / Chapter 3.1 --- Introduction --- p.83 / Chapter 3.2 --- Materials and Methods --- p.87 / Chapter 3.2.1 --- Chemicals --- p.87 / Chapter 3.2.2 --- Cell culture --- p.87 / Chapter 3.2.3 --- Cell viability test --- p.88 / Chapter 3.2.4 --- Drug-efflux study by flow cytometry --- p.89 / Chapter 3.2.5 --- Molecular docking study and Ligand-based prediction --- p.90 / Chapter 3.2.6 --- Measurement of ROS generation by confocal microscopy and flow cytometry --- p.91 / Chapter 3.2.7 --- GSH and GSSG determination for oxidative stress --- p.93 / Chapter 3.2.8 --- Apoptosis-related proteins expression detected by Western blotting analysis --- p.94 / Chapter 3.2.9 --- Data analysis --- p.96 / Chapter 3.3 --- Results --- p.97 / Chapter 3.3.1 --- Cytotoxicity in hepatoma cells --- p.97 / Chapter 3.3.2 --- Drug-efflux study by flow cytometry --- p.104 / Chapter 3.3.3 --- Molecular docking study and Ligand-based prediction --- p.108 / Chapter 3.3.4 --- ROS generation --- p.113 / Chapter 3.3.5 --- Determination of GSH/GSSG ratio --- p.117 / Chapter 3.3.6 --- Caspase-dependent apoptosis. --- p.121 / Chapter 3.3.7 --- Phosphorylation of MAPKs --- p.126 / Chapter 3.4 --- Discussion --- p.134 / Chapter Chapter 4 --- Enzyme kinetic and molecular docking studies of miltirone on major human cytochrome P450 isozymes inhibitions --- p.139 / Chapter 4.1 --- Introduction --- p.139 / Chapter 4.2 --- Material and Methods --- p.141 / Chapter 4.2.1 --- Materials and Reagents --- p.141 / Chapter 4.2.2 --- Incubation conditions --- p.142 / Chapter 4.2.3 --- Samples preparation --- p.143 / Chapter 4.2.4 --- HPLC analysis --- p.143 / Chapter 4.2.5 --- CYP inhibition and enzymatic kinetic study --- p.144 / Chapter 4.2.6 --- Molecular docking analysis --- p.145 / Chapter 4.2.7 --- Data analysis --- p.146 / Chapter 4.3 --- Results --- p.148 / Chapter 4.3.1 --- CYP inhibition and enzymatic kinetic study --- p.148 / Chapter 4.3.2 --- Molecular docking study of miltirone --- p.167 / Chapter 4.4 --- Discussions --- p.184 / Chapter Chapter 5 --- General discussion --- p.188 / References --- p.195

Xu, Jiaying. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 98-107). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

Hu Ying. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 95-122). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract (in English) --- p.ii / Abstract (in Chinese) --- p.iv / Table of contents --- p.vi / List of figures --- p.x / List of tables --- p.xi / Abbreviations --- p.vii / Chapter CHAPTER ONE: --- INTRODUCATION --- p.1 / Chapter 1.1 --- Hepatocellular Carcinoma --- p.2 / Chapter 1.1.1. --- Epidemiology of HCC --- p.2 / Chapter 1.1.2. --- The major risk factors --- p.2 / Chapter 1.1.3. --- Management of HCC --- p.3 / Chapter 1.2 --- Mechanisms of multidrug resistance (MDR) in cancer cells --- p.4 / Chapter 1.2.1. --- Major mechanisms in reduced drug accumulation --- p.5 / Chapter 1.2.1.1. --- P-glycoprotein (P-gp) --- p.6 / Chapter 1.2.1.2. --- Multidrug Resistance-associated Protein (MRP) --- p.7 / Chapter 1.2.1.3. --- Other effluxes --- p.8 / Chapter 1.2.2. --- Inhibition of apoptotic signaling pathways --- p.11 / Chapter 1.2.2.1. --- TP53 and multidrug resistance --- p.11 / Chapter 1.2.2.2. --- Anti-oncogene PTEN and drug resistance --- p.13 / Chapter 1.2.2.3. --- Influence of BCL2 family on drug resistance --- p.14 / Chapter 1.3 --- The chemotherapeutic agent of doxorubicin --- p.15 / Chapter 1.4 --- Aims of study --- p.18 / Chapter CHAPTER 2 --- MATERIALS AND METHODS --- p.20 / Chapter 2.1 --- Cell culture --- p.21 / Chapter 2.1.1 --- Cell lines and cell culture --- p.21 / Chapter 2.1.2 --- Subculture --- p.23 / Chapter 2.1.3 --- Cryopreservation --- p.23 / Chapter 2.1.4 --- Recovery of cryopreserved culture --- p.24 / Chapter 2.1.5 --- Cell number counting --- p.24 / Chapter 2.2 --- MTT experiments --- p.26 / Chapter 2.2.1 --- Determination of cell seeding density --- p.26 / Chapter 2.2.2 --- Cytotoxic assay --- p.27 / Chapter 2.3 --- Spectral Karytyping (SKY) --- p.27 / Chapter 2.3.1 --- Pretreatment of chromosome slides for SKY --- p.28 / Chapter 2.3.2 --- Hybridization --- p.28 / Chapter 2.3.3 --- Detection --- p.29 / Chapter 2.4 --- Positional expression profiling --- p.30 / Chapter 2.4.1 --- RNA extraction --- p.32 / Chapter 2.4.2 --- Reverse transcription and cDNA labling --- p.34 / Chapter 2.4.3 --- Probe purification and hybridization --- p.34 / Chapter 2.4.4 --- Image acquisition and data analysis --- p.35 / Chapter 2. 5 --- Quantitative RT-PCR --- p.37 / Chapter 2.5.1 --- RNA extraction --- p.37 / Chapter 2.5.2 --- Primer design --- p.37 / Chapter 2.5.3 --- Reverse transcription --- p.37 / Chapter 2.5.4 --- Quantitative PCR --- p.39 / Chapter 2.6. --- Statistical analysis --- p.40 / Chapter CHAPTER 3 --- RESULTS --- p.43 / Introduction --- p.44 / Chapter 3.1 --- Doxorubicin resistance in HCC cell lines --- p.44 / Chapter 3.2 --- Candidate drug resistance genes --- p.56 / Chapter 3.3 --- The roles of chromosomal instability --- p.58 / Chapter 3.4 --- Candidate resistance genes identified in chromosome 10 --- p.69 / Chapter CHAPTER 4 --- DISCUSSION --- p.75 / Introduction --- p.76 / Chapter 4.1 --- In vitro cell models facilitate drug resistance investigations --- p.11 / Chapter 4.2 --- Aneuploidy and DX resistance --- p.78 / Chapter 4.3 --- The role of known resistance genes on chromosome 10 --- p.79 / Chapter 4.4 --- Identification of novel DX resistance genes on chromosome 10 --- p.80 / Chapter 4.5 --- Common drug resistance genes --- p.83 / Chapter 4.5.1. --- The roles of classical drug resistance --- p.85 / Chapter 4.5.2. --- Inhibition of apoptosis and deregulation of cell cycle --- p.86 / Chapter CHAPTER 5 --- PROPOSED FUTURE STUDIES --- p.90 / Chapter 5.1. --- Validate significant in vitro findings by clinical trials --- p.91 / Chapter 5.2. --- Molecular mechanisms in inactivation of ECHS1 in resistant cells --- p.92 / Chapter 5.3. --- Future utilization of cDNA microarray data --- p.93 / REFERENCES --- p.95 / PUBLICATION --- p.122

Li Qian. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 102-117). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.vi / List of Abbreviations --- p.ix / List of tables and figures --- p.ix / Content --- p.x / Chapter Chapter 1: --- Introduction --- p.1 / Chapter 1.1 --- Traditional Chinese Medicine: Agrimony --- p.1 / Chapter 1.2 --- Hepatocellular carcinoma (HCC) and its risk factors --- p.4 / Chapter 1.3 --- Basic concepts relevant to cancer prevention --- p.6 / Chapter 1.3.1 --- Multistage process of carcinogenesis --- p.6 / Chapter 1.3.2 --- Chemical carcinogenesis --- p.7 / Chapter 1.3.3 --- Possible chemopreventive strategies --- p.8 / Chapter 1.3.4 --- Phase I and phase II systems in chemical carcinogenesis --- p.10 / Chapter Chapter 2 --- Materials and methods --- p.12 / Chapter 2.1 --- Preparation of aqueous extract of Agrimonia pilosa --- p.12 / Chapter 2.2 --- In vivo study --- p.13 / Chapter 2.2.1 --- Animal model for hepatocarcinogenesis --- p.13 / Chapter 2.2.1.1 --- Chemical carcinogens --- p.13 / Chapter 2.2.1.2 --- Animals --- p.16 / Chapter 2.2.1.3 --- Animal treatment and sacrifice --- p.17 / Chapter 2.2.2 --- Histological and immunohistochemical study --- p.20 / Chapter 2.2.3 --- Preparation of liver homogenates and microsomes from rat --- p.23 / Chapter 2.2.4 --- Determination of protein concentration --- p.24 / Chapter 2.2.5 --- COX-2 Activity Assay --- p.25 / Chapter 2.2.6 --- Cytochrome P450 2E1 Assay --- p.26 / Chapter 2.2.7 --- Spectrophotometry Assay for GST --- p.28 / Chapter 2.2.8 --- Isolation of total RNA from liver homogenate --- p.29 / Chapter 2.2.9 --- Semi-quantitative RT-PCR analysis --- p.32 / Chapter 2.3 --- In vitro study --- p.36 / Chapter 2.3.1 --- Cell cultures --- p.36 / Chapter 2.3.2 --- Cytotoxicity assay - Neutral Red Assay --- p.38 / Chapter 2.3.3 --- Cell cycle distribution analysis by flow cytometry --- p.39 / Chapter 2.3.4 --- DNA fragmentation --- p.40 / Chapter Chapter 3 --- Results --- p.43 / Chapter 3.1 --- In vivo study --- p.43 / Chapter 3.1.1 --- Body weight and relative liver weight --- p.43 / Chapter 3.1.2 --- Gross Morphological changes --- p.46 / Chapter 3.1.3 --- Hematoxylin & Eosin (H&E) staining for histological detection --- p.50 / Chapter 3.1.4 --- Effect of AP on DEN-CCl4-induced GST-P positive foci formation and GST-P mRNA expression --- p.60 / Chapter 3.1.5 --- Effects of AP on COX-2 --- p.72 / Chapter 3.1.6 --- Effects of AP on phase I and phase II enzymes --- p.76 / Chapter 3.2 --- In vitro study --- p.80 / Chapter 3.2.1 --- Effects of AP on proliferation of H4IIE cells detected by Neutral Red Assay --- p.80 / Chapter 3.2.2 --- Assessment of cell cycle distribution by flow cytometry --- p.82 / Chapter 3.2.3 --- DNA Fragmentation Assay --- p.88 / Chapter Chapter 4 --- Discussion --- p.90 / Chapter 4.1 --- In vivo study --- p.90 / Chapter 4.1.1 --- Morphological changes during the induction of hepatocarcinogenesis --- p.90 / Chapter 4.1.2 --- Effects of AP on GST-P foci and its mRNA --- p.91 / Chapter 4.1.3 --- Effects of AP on COX-2 enzyme activity and mRNA expression --- p.93 / Chapter 4.1.4 --- Modulation effects of AP on CYP2E1 and GST enzyme activity --- p.95 / Chapter 4.2 --- In vitro study: effects of AP on cancer cell proliferation --- p.97 / Chapter 4.3 --- Summary --- p.99 / References --- p.102

研究背景： / 肝癌是全球常見的惡性腫瘤之一，世界上每年大約有50萬死亡病例，並且呈逐年上升之勢， 是全球第3位的腫瘤死亡原因。慢性乙型和丙型肝炎病毒感染是肝癌的主要成因。肝癌惡性程度高、預後差，並且目前的治療手段非常有限，術後易復發和轉移，迄今尚無正式獲准有效治療藥物。現階段，治療肝癌的主要方法是手術切除，但是隨之引起的併發症以及較高的復發機率嚴重影響了治療的療效，大大降低肝癌病人的存活期。 / 研究目的： / 分析TDP對肝癌細胞和肝腫瘤旁細胞生長的影響；分析TDP抑癌的分子靶標蛋白及其分子機理；驗證TDP對肝癌動物模型的抑制效果。開發一種新型有效的肝癌治療藥物。 / 研究方法： / 首先用MTT法從102種來源於嶺南山竹子的純複合物中分離出了TDP,它是一種甾醇類化合物。採用MTT法檢測TDP對腫瘤細胞生長的影響；流式細胞實驗驗證TDP能否引起腫瘤細胞的凋亡；採用蛋白組學和質譜分析找出TDP抑癌的分子靶標；進一步的蛋白功能增加和缺失實驗證明Hsp27的功能和作用；生物資訊學驗證HSP27和TDP的作用結果；最後利用動物模型驗證TDP對肝腫瘤的治療效果。 / 結果： / TDP不但能效率極高的抑制肝癌細胞的生長而且可以大量誘發肝癌細胞的凋亡，而對正常的肝癌旁細胞沒有影響。二維電泳以及質譜分析TDP處理的肝癌細胞對比DMSO處理的肝癌細胞發現了具有不同表達水準的18種蛋白，Hsp27是其中一個在TDP誘導下調變化倍數較大並且與細胞凋亡有密切關係的蛋白，Hsp27的過表達以及Knock-down都充分驗證了TDP通過調節Hsp27的表達參與了依賴於caspase的線粒體凋亡途徑，在Western Blotting以及RT-PCR中得到了充分的驗證。生物資訊學預測TDP可以與Hsp27結合，實驗結果表明TDP可以誘導Hsp27的聚集並導致功能喪失。動物實驗腫瘤生長結果以及免疫組化結果證明，TDP可以在很大程度上對肝癌有抑製作用。 / 結論： / 本研究首次表明，TDP如果不是完全的,最起碼也是部分通過誘導依賴於caspase的線粒體凋亡的途徑來抑制肝癌細胞的增值和分化, 具有明顯的抗腫瘤的功效，特別是對Hsp27高表達的腫瘤細胞有比較明顯的作用，是一種值得繼續深入研究的有較高潛在價值的藥物。 / Background： / Hepatocellular carcinoma (HCC), the most common primary hepatic malignancy, is a global public health problem that accounts for approximately 500,000 deaths annually. Chronic hepatitis B and hepatitis C infections are the major risk factors for the development of HCC. Due to the high rate of these infections, the incidence of HCC remains alarmingly high globally. Although great advances have been made in HCC treatment, poor prognosis and high risk of recurrence have been major challenges to patients. Currently, surgical resection is the main treatment option for HCC patients; however, complications arising from surgery can threaten its therapeutic effect and patients’ survival. / Objectives： / To characterize the functions of 1,3,5-trihydroxy-13,13-dimethyl-2H-pyran [7,6-b]Xanthone (TDP) in cell proliferation of HepG2 cells; to discover the molecular target genes and elucidate the underlying molecular mechanism of TDP; to examine the in vivo function of TDP in a nude mouse tumor model of HCC. Finally, to investigate TDP’s potential as an anti-HCC drug candidate. / Methods and Results： / In this study, we discovered that TDP, isolated from the Chinese medicinal herb, Garcinia oblongifolia, strongly inhibited cell growth and induced caspase-dependent mitochondrial apoptosis in HCC, as evidenced from MTT assay and flow cytometry analysis. Two-dimensional gel electrophoresis and mass spectrometry-based comparative proteomics were applied to find the molecular targets of TDP in HCC cells, and eighteen proteins were identified with altered expression, with Hsp27 protein being one of the proteins most significantly down-regulated by TDP. Further Hsp27-siRNA knockdown and Lenti-Hsp27 overexpression studies found that Hsp27 was involved in TDP induced mitochondrial apoptosis, with bioinformatics predictions and biological results revealing that TDP might cause Hsp27 protein form dimer and consequent degradation via the ubiquitin-proteasome system. Finally, subcutaneously injecting cancer cells with Hsp27 expression vector into the dorsal flank of nude mice tumor model also demonstrated the suppressive effect of TDP on HCC. / Conclusions： / In summary, our study discovered that TDP, a natural xanthone, was a potent inhibitor of Hsp27 in HCC. TDP inhibited cell growth and induced apoptosis by inducing Hsp27 degradation, which stimulated mitochondrial cytochrome C release which resultantly activated caspase-3 and caspase-9. These data combined with the results of the animal model strongly supported TDP’s potential as a novel anti-cancer drug candidate, especially for cancers with an abnormally high expression of Hsp27. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Fu, Weiming. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 111-151). / Abstract also in Chinese. / Abstract (English) --- p.i / Abstract (Chinese) --- p.iiv / Acknowledgment --- p.vi / Publications --- p.viii / List of Contents --- p.ix / List of Tables --- p.xii / List of Figures --- p.xiii / List of Abbreviations --- p.xv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- General Introduction --- p.1 / Chapter 1.1.1 --- Overview of HCC --- p.1 / Chapter 1.1.2 --- Epidemiology of HCC in China and Hong Kong --- p.3 / Chapter 1.2 --- Etiology of HCC --- p.7 / Chapter 1.2.1 --- Cirrhosis --- p.8 / Chapter 1.2.2 --- HBV infection --- p.9 / Chapter 1.2.3 --- HCV infection --- p.10 / Chapter 1.2.4 --- Viral Co-Infection --- p.11 / Chapter 1.2.5 --- Fatty Liver Disease and Cryptogenic Cirrhosis --- p.12 / Chapter 1.2.6 --- Alcohol --- p.13 / Chapter 1.2.7 --- Iron --- p.13 / Chapter 1.2.8 --- Aflatoxin --- p.14 / Chapter 1.2.9 --- Others --- p.14 / Chapter 1.3 --- Diagnosis of HCC --- p.14 / Chapter 1.4 --- Prognosis of HCC --- p.17 / Chapter 1.5 --- Treatment of HCC --- p.19 / Chapter 1.5.1. --- Early stage --- p.19 / Chapter 1.5.2. --- Intermediate and advanced stage --- p.24 / Chapter 1.5.3. --- Terminal stage --- p.28 / Chapter 1.6 --- Signaling pathways in HCC --- p.28 / Chapter 1.6.1 --- Proliferation signaling pathways --- p.29 / Chapter 1.6.2 --- Signaling pathways frequently dysregulated in HCC --- p.30 / Chapter 1.6.3 --- Pathways involved in liver development and cell differentiation --- p.34 / Chapter 1.6.4 --- Inflammation pathways involved in hepatocarcinogenesis --- p.35 / Chapter 1.6.5 --- Pathways involved in neoangiogenesis --- p.37 / Chapter 1.6.6 --- The P53 tumor suppressor --- p.38 / Chapter 1.6.7 --- Heat shock proteins in HCC --- p.39 / Chapter 1.7 --- The roles of microRNAs in liver cancer progression --- p.42 / Chapter 1.8 --- TCM in the treatment of HCC --- p.45 / Chapter 1.8.1 --- Introduction --- p.45 / Chapter 1.8.2 --- Garcinia --- p.49 / Chapter 1.9 --- Objectives of the study --- p.51 / Chapter Chapter 2 --- Materials and Methods --- p.52 / Chapter 2.1 --- Preparation of the pure compounds --- p.52 / Chapter 2.2 --- Liver cell lines and tissue culture --- p.52 / Chapter 2.3 --- Human tissue samples --- p.52 / Chapter 2.4 --- Cell viability assessment with MTT assay --- p.53 / Chapter 2.5 --- Apoptosis analysis --- p.53 / Chapter 2.6 --- Two-dimensional electrophoresis (2-DE), protein visualization and image analysis --- p.54 / Chapter 2.6.1 --- Materials --- p.54 / Chapter 2.6.2 --- Protein extraction --- p.54 / Chapter 2.6.3. --- 2-DE protein profiling --- p.55 / Chapter 2.6.4. --- Gel staining and image analysis --- p.55 / Chapter 2.6.5. --- In-gel protein digestion with trypsin --- p.56 / Chapter 2.6.6. --- MALDI-TOF mass spectrometric analysis --- p.56 / Chapter 2.6.7. --- Database search --- p.57 / Chapter 2.7.1 --- Sample preparation --- p.58 / Chapter 2.7.2 --- SDS-PAGE --- p.58 / Chapter 2.7.3 --- Protein transfer --- p.58 / Chapter 2.7.4 --- Blocking --- p.59 / Chapter 2.7.5 --- Incubation with primary and secondary antibodies --- p.59 / Chapter 2.7.6 --- Proteins Visualization --- p.59 / Chapter 2.8 --- Real-time PCR --- p.60 / Chapter 2.9 --- Vector construction and lentivirus production --- p.61 / Chapter 2.9.1 --- Lenti-vector construction for Hsp27 expression --- p.61 / Chapter 2.9.2 --- Lentivirus production --- p.62 / Chapter 2.9.3 --- Lentivirus infection --- p.63 / Chapter 2.10 --- SiRNAs transfection. --- p.63 / Chapter 2.11 --- Identification of potential protein targets for TDP --- p.64 / Chapter 2.12 --- In Vivo Tumorigenesis --- p.64 / Chapter 2.13 --- Assay of chaperone activity of Hsp27 using lysozyme as substrate --- p.65 / Chapter 2.14 --- Mitochondria and cytosolic proteins preparation --- p.66 / Chapter 2.15 --- Immunohistochemistry (IHC) --- p.67 / Chapter 2.15.1 --- Preparation of paraffin tissue sections --- p.67 / Chapter 2.15.2 --- Immunostaining --- p.67 / Chapter 2.16 --- Methodology of this study --- p.68 / Chapter 2.17 --- Statistical analysis --- p.68 / Chapter CHAPTER 3 --- Results --- p.69 / Chapter 3.1 --- Introduction --- p.69 / Chapter 3.2 --- TDP significantly suppressed cell growth and induced apoptosis in HCC cells. --- p.69 / Chapter 3.2.1 --- TDP was identified from 102 pure compounds by using MTT assay --- p.69 / Chapter 3.2.2 --- TDP significantly suppressed HCC cell growth --- p.73 / Chapter 3.2.3 --- TDP induced the apoptosis of HCC cells --- p.74 / Chapter 3.3 --- Study of the molecular mechanism of TDP on HCC --- p.76 / Chapter 3.3.1 --- The comparative proteomic profiling --- p.76 / Chapter 3.3.2 --- Hsp27 was one of the molecular targets of TDP in HepG2 cells. --- p.80 / Chapter 3.3.3 --- TDP induced apoptosis through the caspase-dependent mitochondrial pathway. --- p.82 / Chapter 3.3.4 --- Hsp27 involved in the mitochondrial apoptosis induced by TDP --- p.84 / Chapter 3.3.5 --- Enforced Hsp27 overexpression rescued the mitochondrial apoptosis induced by TDP in HepG2 cells --- p.87 / Chapter 3.3.6 --- The possible regulatory signaling by TDP --- p.91 / Chapter 3.4 --- TDP directly targeted Hsp27 and destroyed its chaperone action --- p.92 / Chapter 3.5 --- Degradation of Hsp27 aggregation stimulated by TDP was mediated by ubiquitin-proteasome system (UPS) pathway --- p.96 / Chapter 3.6 --- Nude mice model demonstrated the suppressive effect of TDP on HCC --- p.97 / Chapter Chapter 4 --- Discussion and Conclusions --- p.100 / Chapter 4.1 --- Discussion --- p.100 / Chapter 4.2 --- Conclusion --- p.110 / Reference --- p.111

MicroRNA（miRNAs）是一類細小的非編碼RNA（ncRNA），能透過轉錄後機制調節靶標基因的表達。miRNA的發現，不僅提出一個嶄新的基因調節機制，更強調了小ncRNA於不同的生理和發展過程中的重要性。最近的研究更進一步展示了miRNA失調與癌症發展之間的因果關係。 / 我們此前曾利用陣列分析，發現miRNA在肝細胞癌（HCC）中的失調模式，揭示了miR-145在HCC的普遍下調。在本論文的第一部分，定量逆轉錄聚合酶鏈反應（qRT-PCR）進一步證實了miR-145在50的肝細胞癌患者（n=80）的腫瘤中出現表達下調，而且miR-145的表達下調更與較短的无病生存期相關。其中一個低內源性miR-145的肝癌腫瘤樣本被建立為細胞株─HKCI-C2。此體外模型保持低miR-145水平，並於恢復miR-145表達後，抑製細胞存活和增殖。多個計算機演算法均預測了miR-145可針對胰島素樣生長因子（IGF）信號通路中的多個基因，包括胰島素受體底物（IRS1）-1，IRS2和胰島素樣生長因子1受體。這些假定目標的蛋白表達亦被miR-145下調。熒光素酶檢測進一步驗證了miR-145和IRS1/IRS2 3'-非編碼區的直接目標關聯。隨後的分析也確定miR-145能下調 IGF信號通路下游的信號傳導，即活性β-catenin水平。 / 最近出現的深度測序技術，為研究miRNome提供了一個前所未有的平台，以識別已知和新的miRNA。此外，現代生物信息學技術可同時對不同類型的小ncRNA，如PIWI-interacting RNA（piRNAs）進行分析。在本論文的第二部分中，我們利用Illumina大規模並行測序對兩個肝癌細胞株（HKCI-4和HKCI-8）和正常肝細胞株（MIHA）的小RNA轉錄組進行研究。生物信息學和生物功能分析揭示一種新型piRNA（取名為piR-Hep1）在肝腫瘤發生中的重要角色。在73例肝癌中，qRT-PCR結果顯示piR-Hep1在47的肝癌組織出現上調。PiR-Hep1的沉默能抑制肝癌細胞存活、遷移和侵襲，同時亦減少了Akt的磷酸化。在miRNA的分析中，miR-1323被發現在肝癌組織中大量表達，並與肝硬化背景下產生的肝腫瘤相關。此外，miR-1323出現過表達的肝硬化肝癌患者的無病和整體存活率亦較差（P<0.009）。 / 總觀來說，本論文首次發現miR-145可同時抑制引致肝癌的IGF信號通路中的多個傳導因子，亦突出了piR-Hep1的功能重要性和miR-1323在肝癌患者中的預後意義。此外，本研究表明，傳統的陣列分析和新一代的測序技術均能發現重要的miRNA。新一代測序技術對轉錄組的全面分析，將對研究各種不同類型的ncRNAs在肝癌發生發展過程中的參與提供新的思路。 / MicroRNAs (miRNAs) are a class of small non-coding RNAs (ncRNA) that post-transcriptionally regulate gene expression. The discovery of miRNAs not only puts forth an alternate gene regulatory mechanism, but also underscores the importance of small ncRNAs as pivotal regulators of diverse physiological and developmental processes. Recent studies have emphasized a causal link between miRNA deregulation and cancer development. / Our group has previously reported on dysregulated miRNA pattern in hepatocellular carcinoma (HCC) by array-based profiling, which revealed common downregulation of miR-145. In the first part of this thesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) corroborated reduced miR-145 expression in 50% of tumors in a cohort of 80 HCC patients, which also correlated reduced miR-145 expression with shorter disease-free survival of patients. One HCC tumor analyzed with low endogenous miR-145 was propagated as cell line. This in vitro model HKCI-C2 maintained low miR-145 level and upon restoration of miR-145 expression, a consistent inhibitory effect on cell viability and proliferation was readily observed. Multiple in silico algorithms predicted that miR-145 could target a number of genes along the insulin-like growth factor (IGF) signaling, including insulin receptor substrate (IRS1)-1, IRS2 and insulin-like growth factor 1 receptor. Protein expression of these putative targets was concordantly downregulated in the presence of miR-145. Luciferase reporter assay further verified direct target association of miR-145 to specific sites of IRS1 and IRS2 3’-untranslated regions. Subsequent analysis also affirmed the modulation of IGF signaling cascade by miR-145 as evident by reduction of the downstream mediator, namely, the active β-catenin level. / The recent advent of deep sequencing has provided an unprecedented platform to study the miRNome, in which both known and novel miRNAs can be identified. Moreover, bioinformatics advances have enabled different types of small ncRNAs, e.g. piwi-interacting RNAs (piRNAs), to be analyzed simultaneously. In the second part of this thesis, small RNA transcriptomes of two HCC cell lines (HKCI-4 and HKCI-8) and an immortalized hepatocyte line (MIHA) were examined using Illumina massively parallel sequencing. Combined bioinformatic and biological analyses revealed the involvement of a novel piRNA, designated as piR-Hep1, in liver tumorigenesis. piR-Hep1 was found to be up-regulated in 47% of HCC in a cohort of 73 HCC patients by qRT-PCR. Silencing of piR-Hep1 inhibited cell viability, motility and invasiveness with a concomitant reduction of Akt phosphorylation. In the analysis of miRNA, miR-1323 was found to be abundantly expressed in HCC and distinctly associated with tumors arising from a cirrhotic background. Furthermore, miR-1323 overexpression in cirrhotic-HCC correlated with poorer disease-free and overall survivals of patients (P<0.009). / Taken together, results from this thesis showed for the first time the pleiotropic effect of miR-145 on targeting multiple components of the oncogenic IGF signaling pathway in HCC. In addition, the functional importance of piR-Hep1 and the prognostic significance of miR-1323 in HCC were highlighted. Studies conducted demonstrated that important miRNAs can be discovered by both traditional array-based profiling and next-generation sequencing. Moreover, comprehensive definition of transcriptome by next-generation sequencing unveils virtually all types of ncRNAs and provides new insight into the liver carcinogenic events. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Law, Tak Yin. / "December 2012." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 180-200). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Abstracts also in Chinese. / Acknowledgements --- p.i / Publications --- p.ii / Abstract --- p.iii / 摘要 --- p.vi / Contents --- p.viii / List of Figures --- p.xiii / List of Tables --- p.xv / Abbreviations --- p.xvi / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Hepatocellular Carcinoma - One of the world’s most deadly killers --- p.2 / Chapter 1.2 --- MicroRNAs - a tiny molecule with enormous impacts --- p.10 / Chapter 1.2.1 --- Discovery of miRNAs --- p.11 / Chapter 1.2.2 --- Biogenesis and actions of miRNA --- p.13 / Chapter 1.3 --- MiRNAs and cancer --- p.16 / Chapter 1.4 --- Involvements of miRNAs in HCC etiological factors --- p.18 / Chapter 1.4.1 --- Viral hepatitis infection --- p.19 / Chapter 1.4.2 --- Chronic heavy alcohol consumption --- p.26 / Chapter 1.4.3 --- Dietary aflatoxin exposure --- p.28 / Chapter 1.4.4 --- Male gender --- p.31 / Chapter 1.4.5 --- Obesity --- p.33 / Chapter 1.5 --- Regulation of cancer-associated signaling network by microRNAs --- p.34 / Chapter 1.5.1 --- Apoptotic pathway --- p.37 / Chapter 1.5.1.1 --- Intrinsic pathway --- p.38 / Chapter 1.5.1.2 --- Extrinsic pathway --- p.39 / Chapter 1.5.2 --- Cell cycle regulators --- p.41 / Chapter 1.5.2.1 --- G₁/S transition --- p.42 / Chapter 1.5.2.2 --- G₂/M transition --- p.43 / Chapter 1.5.3 --- Receptor tyrosine kinase-mediated pathways --- p.45 / Chapter 1.5.3.1 --- c-MET-activated signaling --- p.45 / Chapter 1.5.3.2 --- PI3K-Akt --- p.47 / Chapter 1.5.3.3 --- RAS-RAF-MEK-ERK cascade --- p.48 / Chapter 1.5.4 --- TGF-ß signaling pathways --- p.50 / Chapter 1.5.5 --- Metastatic pathways --- p.52 / Chapter 1.5.5.1 --- MiRNAs with metastatic suppressing effects --- p.52 / Chapter 1.5.5.2 --- MiRNAs with metastatic promoting effects --- p.53 / Chapter 1.6 --- Clinical potentials of microRNAs - a killer or a cure? --- p.56 / Chapter 1.6.1 --- MiRNAs involvements in HCC risk prediction --- p.57 / Chapter 1.6.2 --- MiRNAs as diagnostic biomarkers --- p.59 / Chapter 1.6.3 --- MiRNAs as prognostic biomarkers --- p.60 / Chapter 1.6.4 --- Effects of miRNAs on responses to therapy --- p.61 / Chapter 1.7 --- Non-coding RNAs --- p.62 / Chapter 1.8 --- Aims of study --- p.63 / Chapter 2 --- Materials and Methods --- p.65 / Chapter 2.1 --- Quantitative reverse transcription polymerase chain reaction (qRT-PCR) --- p.66 / Chapter 2.1.1 --- Materials --- p.66 / Chapter 2.1.1.1 --- Total RNA extraction --- p.66 / Chapter 2.1.1.2 --- DNase treatment --- p.66 / Chapter 2.1.1.3 --- Reverse transcription --- p.66 / Chapter 2.1.1.4 --- Quantitative polymerase chain reaction --- p.66 / Chapter 2.1.2 --- Methods --- p.67 / Chapter 2.1.2.1 --- Total RNA extraction --- p.67 / Chapter 2.1.2.2 --- DNase treatment --- p.68 / Chapter 2.1.2.3 --- Reverse transcription --- p.69 / Chapter 2.1.2.4 --- Quantitative polymerase chain reaction --- p.69 / Chapter 2.2 --- Transfection --- p.70 / Chapter 2.2.1 --- Materials --- p.70 / Chapter 2.2.2 --- Methods --- p.70 / Chapter 2.2.2.1 --- Evaluation of HCC cells transfection efficiency --- p.70 / Chapter 2.2.2.2 --- Transfection --- p.71 / Chapter 2.3 --- In vitro functional assay --- p.72 / Chapter 2.3.1 --- Materials --- p.72 / Chapter 2.3.1.1 --- Cell viability assay --- p.72 / Chapter 2.3.1.2 --- Colony formation assay --- p.72 / Chapter 2.3.1.3 --- Cell cycle analysis --- p.72 / Chapter 2.3.1.4 --- Apoptosis assay --- p.72 / Chapter 2.3.1.5 --- Cell motility and invasion assay --- p.73 / Chapter 2.3.2 --- Methods --- p.73 / Chapter 2.3.2.1 --- Cell viability assay --- p.73 / Chapter 2.3.2.2 --- Colony formation assay --- p.74 / Chapter 2.3.2.3 --- Cell cycle analysis --- p.75 / Chapter 2.3.2.4 --- Apoptosis assay --- p.75 / Chapter 2.3.2.5 --- Cell motility and invasion assay --- p.76 / Chapter 2.4 --- Luciferase reporter assay --- p.78 / Chapter 2.4.1 --- Materials --- p.78 / Chapter 2.4.1.1 --- Cloning --- p.78 / Chapter 2.4.1.2 --- Cycle sequencing --- p.78 / Chapter 2.4.1.3 --- Luciferase reporter assay --- p.79 / Chapter 2.4.2 --- Methods --- p.79 / Chapter 2.4.1.1 --- Cloning --- p.79 / Chapter 2.4.2.2 --- Cycle sequencing --- p.81 / Chapter 2.4.2.3 --- Luciferase reporter assay --- p.82 / Chapter 2.5 --- Western blot --- p.84 / Chapter 2.5.1 --- Materials --- p.84 / Chapter 2.5.2 --- Methods --- p.85 / Chapter 2.5.2.1 --- Cell harvesting and protein quantitation --- p.86 / Chapter 2.5.2.2 --- Western blotting --- p.86 / Chapter 2.6 --- Small RNA Sequencing --- p.88 / Chapter 2.6.1 --- Materials --- p.88 / Chapter 2.6.2 --- Methods --- p.88 / Chapter 2.6.2.1 --- Sample preparation --- p.88 / Chapter 2.6.2.2 --- Cluster generation by bridge amplification --- p.88 / Chapter 2.6.2.3 --- Sequencing by synthesis --- p.89 / Chapter 2.7 --- Northern blot analysis --- p.94 / Chapter 2.7.1 --- Materials --- p.94 / Chapter 2.7.2 --- Methods --- p.94 / Chapter 2.7.2.1 --- Polyacrylamide gel electrophoresis (PAGE) --- p.94 / Chapter 2.7.2.2 --- Probe preparation --- p.95 / Chapter 2.7.2.3 --- Hybridization, stringency washes and signal detection --- p.95 / Chapter 3 --- Conventional miRNA profiling reveals miR-145 as a tumor suppressor in HCC --- p.97 / Chapter 3.1 --- Introduction --- p.98 / Chapter 3.2 --- Materials and Methods --- p.102 / Chapter 3.2.1 --- Patients --- p.102 / Chapter 3.2.2 --- qRT-PCR --- p.104 / Chapter 3.2.3 --- Cell line --- p.105 / Chapter 3.2.4 --- Transfection --- p.106 / Chapter 3.2.5 --- In vitro functional assay --- p.107 / Chapter 3.2.5.1 --- Cell viability assay --- p.107 / Chapter 3.2.5.2 --- Colony formation assay --- p.107 / Chapter 3.2.5.3 --- Flow cytometry assay --- p.107 / Chapter 3.2.6 --- miRNA target prediction --- p.109 / Chapter 3.2.7 --- Luciferase reporter assay --- p.110 / Chapter 3.2.8 --- Western blot --- p.112 / Chapter 3.2.9 --- Immunohistochemistry --- p.113 / Chapter 3.2.10 --- Statistical analysis --- p.114 / Chapter 3.3 --- Results --- p.115 / Chapter 3.3.1 --- Down-regulation of miR-145 in primary HCC --- p.115 / Chapter 3.3.2 --- Re-expression of miR-145 induced G₂-M arrest and apoptosis --- p.119 / Chapter 3.3.3 --- IRS1, IRS2 and IGF1R expressions --- p.124 / Chapter 3.3.4 --- miR-145 targeted both IRS1 and IRS2 and elicited IGF signaling --- p.126 / Chapter 3.4 --- Discussion --- p.131 / Chapter 4 --- Small RNA Deep sequencing reveals novel non-coding RNAs in HCC --- p.134 / Chapter 4.1 --- Introduction --- p.135 / Chapter 4.2 --- Materials and Methods --- p.136 / Chapter 4.2.1 --- Cell lines --- p.136 / Chapter 4.2.2 --- Patients --- p.137 / Chapter 4.2.3 --- Small RNA Sequencing --- p.139 / Chapter 4.2.4 --- Bioinformatics analysis --- p.140 / Chapter 4.2.4.1 --- Sequence mapping and ncRNA identification --- p.140 / Chapter 4.2.4.2 --- Putative miRNA prediction --- p.140 / Chapter 4.2.4.3 --- Putative piRNA identification --- p.140 / Chapter 4.2.4.4 --- Differentially-expressed ncRNAs identification --- p.141 / Chapter 4.2.5 --- qRT-PCR --- p.142 / Chapter 4.2.6 --- Northern blot analysis --- p.143 / Chapter 4.2.7 --- Transfection --- p.144 / Chapter 4.2.8 --- In vitro functional assays --- p.145 / Chapter 4.2.8.1 --- Cell viability assay --- p.145 / Chapter 4.2.8.2 --- Cell motility and invasion assay --- p.145 / Chapter 4.2.9 --- Western blot analysis --- p.147 / Chapter 4.2.10 --- Statistical analysis --- p.148 / Chapter 4.3 --- Results --- p.149 / Chapter 4.3.1 --- Small RNA Sequencing --- p.149 / Chapter 4.3.2 --- Up-regulation of putative piR-Hep1 in HCC --- p.155 / Chapter 4.3.3 --- piR-Hep1 silencing reduced cell viability and invasiveness --- p.159 / Chapter 4.3.4 --- Novel miR-1323 overexpression in HCC --- p.162 / Chapter 4.4 --- Discussion --- p.171 / Chapter 5 --- Concluding remarks and future perspectives --- p.175 / Chapter 6 --- References --- p.179

Tang Wan-yee. / "July 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 192-212). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

Hepatocellular carcinoma (HCC) is a highly malignant tumor that is prevalent in Southeast Asia and China, where hepatitis B viral (HBV) infection is the main etiologic factor. Despite a high incidence of HCC developing in patients with HBV-induced liver cirrhosis, the molecular events underlying the malignant liver progression remain largely unclear. In an effort to characterize the genetic abnormalities involved in the HBV-related liver carcinogenesis, genome-wide exploration by metaphase comparative genomic hybridization (CGH) was performed on 100 cirrhotic HCC tumors that were derived from chronic hepatitis B carriers. CGH analysis indicated chromosomal instability in both early and advanced stage tumors where common genomic copy gains on 1q, 8q and 17q, and deletions on 4q, 8p, 13q, 16q and 17p found in both groups are suggestive of early events in hepatocarcinogenesis. Nevertheless, a combined univariate and multivariate statistical analyses highlighted for the first time preferential regional 3q26-q28, 7q21-q22 and 7q34-q36 gains in association with advanced stage HCC. The novel aberrant gains identified here thus formed basis for further mapping analysis for causative genes related to HCC progression in this thesis. / Near 50% of the advanced stage HCC manifested copy gains of chr 7q21-q22. High resolution mapping analysis by cDNA microarray-based CGH nominated 13 amplified candidates within the region 7q21-q22 Analysis on the mRNA expresson levels of these genes in a cohort of primary HCC compared to paired adjacent non-tumorous liver tissues by quantitative RT-PCR (qRT-PCR) indicated the up-regulation of the PFTK1 (PFTAIRE protein kinase 1) gene as the only candidate that demonstrated a close association with advanced metastatic tumors. The effects of PFTK1 on cell proliferation, migration and invasive phenotypes were further studied to substantiate its role in HCC progression. Upon gene suppression of PFTK1 in vitro by RNA interference (RNAi), a significant reduction in chemotactic migration, cellular invasion and an inhibition on cell motility were indicated, albeit cell proliferation remained unaffected. / Sub-cellular localization study of translated PFTK1 protein indicated protein localization in both the nucleus and cytoplasm. This has led to the further investigations of potential PFTK1 function at both the transcriptional and protein levels. (Abstract shortened by UMI.) / Sy Ming Hui. / "July 2005." / Advisers: Winnie Yeo; Nathalie Wong. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3571. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 124-139). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

In summary, the genome-wide miRNA analyses on HCC tumors, adjacent non-malignant livers and cell lines revealed distinct differential miRNA expressions. In particular, the findings of deregulated miR-223 and miR-222 underscore the potential role for these microRNAs in the development of HCC. / In the functional examinations of miR-222, inhibition of miR-222 expression in Hep3B and HKCI-9 exerted no effect on cell viability. However, significant retardations on cell migration were observed in both Hep3B (64.5%, p=0.008) and HKCI-9 (52.5%, p=0.048). In Hep3B cells, functional knockdown of miR-222 was further shown to impede filopodia formation (p=0.0273). Coupling expression profiling from functional knockdown of miR-222 in Hep3B and HKCI-9 with pathway analysis, a number of miR-222 modulated pathways was suggested. Examination of such pathways, AKT and JAK/STAT, by Western blot analysis suggested profound decrease of total AKT and STAT3 protein in both Hep3B and HKCI-9. A corresponding diminution of phosphorylated AKT was also shown in both cell lines. In the examination of JAK/STAT pathway, reductions of phosphorylated STAT3 proteins were demonstrated in Hep3B and HKCI-9 following functional knockdown of miR-222. Parallel quantitative RT-PCR analysis did not suggest transcriptional changes of AKT and STAT3 mRNA between miR-222 inhibited cells and mock controls in Hep3B and HKCI-9. This in turn would be suggestive of a post-transcriptional repression of AKT and STAT3 proteins by miR-222 knockdown. Based on the functional characterization of miR-222, it would suggest the likelihood of miR-222 induction on HCC cell motility through modulation of the AKT and JAK/STAT signalling pathways. / MicroRNAs (miRNAs) are an abundant class of small, 19-25 nucleotides, non-coding RNAs with significant roles in transcriptional silencing and translational suppression. Recent studies have emphasized on a causative link between miRNA deregulations and cancer development. However, such information remains minimal in Hepatocellular Carcinoma (HCC). In an effort to characterize differentially expressed miRNAs in HCC development, global expression analyses on HCC tumors, paired adjacent non-malignant livers and HCC cell fines were carried out. Distinct miRNA expression pattern that was able to distinguish HCC tumors from non-malignant cirrhotic livers was suggested. Based on a comprehensive screening, 96 miRNAs showed differential expressions in HCC tumors, within which over 60% of miRNAs displayed increased expressions. / Six top ranked differentially expressed miRNAs, namely down-regulated miR-223, miR-126 and miR-122a, and up-regulated miR-222, miR-221 and miR-31 were subjected to further Northern blot validations. Amongst these verified candidates, miR-223 and miR-222 showed the most consistent expression changes that allowed unequivocal differentiation between HCC and non-tumoral liver (p&le;0.002). The potential functional roles of miR-223 and miR-222 were subsequently investigated. Ectopic expression of miR-223 in 3 HCC cell fines, Hep3B, HKCI-C3 and HKCI-10, revealed a consistent growth inhibitory effect of 21-44% (p&le;0.01). In an attempt to define potential downstream targets of miR-223, an integrative analysis of overexpressed genes from mRNA array with in-silico predictions was utilized. This approach allowed streamline of 386 targets to a candidate gene, Stathmin1 (STMN1). A significant inverse correlation between STMN1 mRNA and miR-223 expressions was demonstrated (p=0.006). At the protein level, restoration of miR-223 expressions in HCC cell lines resulted in substantial reduction of STMN1. Furthermore, miR-223 could repress the luciferase activity in reporter construct containing the putative recognition site at the STMN1 3'UTR. / Wong, Wing Lei. / Adviser: Nathalie Wong. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3450. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 163-171). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.