Thesis submitted in fulfilment of the requirements for the degree Doctor of Technology: Biomedical Technology in the Faculty of Health and Wellness Sciences at the Cape Peninsula University of Technology 2014 / According to the World Health Organization, cancer is the leading cause of death in the developed world, while it is the second leading cause of death in the developing world. In particular, liver cancer is the fifth most commonly diagnosed cancer in men, however, it is the second most frequent cause of death, responsible for an estimated 700,000 deaths annually. General limited access to health services, including treatment and the overall management of cancer in developing countries often contribute to the increased mortality rates when compared to developed countries. For centuries, medicinal plants have been used to prevent, and to a certain extent, treat cancer as a readily available and affordable alternative. In many instances, the curative or preventative claims still remain anecdotal. However, increasing evidence suggest that polyphenolic components of plants possess antioxidant activities, which are credited with curative/beneficial properties of medicinal plants. The curative properties could either be related to the primary compounds present in the plant itself, or the bio-activation products of plant components affecting hepatic drug metabolising and antioxidant enzymes systems related to carcinogen metabolism and maintaining oxidative homeostasis, respectively. Similarly, chronic consumption of medicinal plants could also result in hepatotoxicity, either caused by the primary plant components or bio-activation products. Due to these observations it is paramount to understand the mechanisms involved in the metabolism of plant components to critically assess beneficial versus potential harmful properties associated with chronic consumption. The focus of the current study was aimed at elucidating the bio-activity of four multipurpose indigenous plants to Southern Africa, i.e. Adansonia digitata, Agathosma betulina, Siphonochilus aethiopicus and Myrothamnus flabellifolius. Traditionally, A. digitata has been used as an immunostimulant, anti-inflammatory and analgesic agent, while also as an antipyretic agent in the treatment of diarrhoea and dysentery. Similarly, traditional medicinal uses of A. betulina include treatment cholera, haematuria, calculus, kidney diseases, as well as infections of the bladder, urethra, and prostate among others. S. aethiopicus was traditionally employed to treat infections associated with pains and fevers, whereas M. flabellifolius served as treatment of conditions ranging from respiratory ailments, backache, kidney problems, haemorrhoids, chest pain, and asthma. In the first part of this study, the polyphenolic contents and antioxidant capacities of the four plants were characterised. The emphasis was placed on using different solvents, namely water, ethanol and acetone for the extraction of the plant material and different methodologies to assess the antioxidant contents and -capacities of the various extracts as both these factors can influence the outcome. When considering the antioxidant contents, total polyphenols, flavanols, and flavonols of the different solvent extracts prepared from the four plants were determined, whereas three different assays were used for the antioxidant capacities, i.e. oxygen radical absorbance capacity (ORAC), trolox equivalent antioxidant capacity (TEAC) and ferric-reducing antioxidant power (FRAP) assays. The A. digitata acetone extract had the highest (7.121 mg gallic acid equivalent (GAE)/milligram (mg) soluble solids), whereas the water extract of the same plant had the lowest total phenolic content (0.008 mg GAE/mg soluble solids). In general, the acetone extracts demonstrated the highest total polyphenol, flavanol, and flavonol contents, followed by the ethanol extracts, with the water extracts having the lowest contents. M. flabellifolius was the only distinct deviation from this rule, where the water extract demonstrated the highest total polyphenol content. Considering antioxidant capacities, the acetone extracts provided the highest antioxidant capacities for all plants when assessed using the TEAC (8.56-32.68 milimole (mmole) trolox equivalent (TE)/mg soluble solids) and FRAP (5.69-37.39 mmole ascorbic acid equivalent/mg soluble solids) antioxidant assays, with the exception of M. flabellifolius where the water extract demonstrated the highest activity (22.73 mmole ascorbic acid equivalent/mg soluble solids). Antioxidant capacity determinations with TEAC and FRAP assays followed similar patterns, which were different from capacities determined by the ORAC (0.46-533.54 mmoleTE/mg of soluble solids) assay. Corroborating the antioxidant content findings, the acetone extracts also demonstrated the highest antioxidant capacities (140.41-533.54 mmoleTE/mg of soluble solids), followed by ethanol (94.62-151.29 mmoleTE/mg of soluble solids) and water (0.46-134.02 mmoleTE/mg of soluble solids). Only M. flabellifolius (TEAC and FRAP) and S. aethiopicus (FRAP) deviated from this trend. Correlations between the polyphenolic contents and antioxidant capacities indicated that acetone and ethanol were more effective in extracting polyphenolic compounds than water, while also providing extracts with superior antioxidant activities. Furthermore, ORAC assay was the antioxidant capacity determining assay of choice for the aqueous plant extracts, whereas the TEAC and FRAP assays were more suitable when determining the antioxidant capacities of the acetone and ethanol plant extracts. These results confirm the notion that no single assay can comprehensively determine the antioxidant activities of plant extracts and that a battery of assays should be used, as the various antioxidant capacity determination techniques use different substrates with different targets for measurement. The second part of this study comprised an in vivo experimental animal model to assess the potential toxicity, antioxidant status and modulation of the hepatic phase 2 drug metabolising enzymes following chronic consumption of the various plant extracts in male Fisher rats. Rats consumed aqueous extracts of the various plants (2% and 5% (w/v)) as the sole source of drinking fluid for 90 days, and the serum chemical pathology parameters for monitoring liver and kidney function conducted. These included alkaline phosphatase (ALP), aspartate transaminase (AST), alanine transaminase (ALT), total iron (Fe), and creatinine (CREA). Parameters for blood and hepatic redox status included total polyphenols, ORAC, reduced glutathione (GSH), oxidised glutathione (GSSG), their ratio (GSH:GSSG), conjugated dienes (CD) and thiobarbituric acid reactive substances (TBARS). Assessment of the phase 2 hepatic xenobiotic metabolising enzymes included glutathione S-transferase (GST)  and activity in the cytosolic fraction and, UDP-glucuronosyltransferase (UDP-GT) activity in liver microsomes. When considering the liver and kidney function none of the plant extracts induced any significant toxicity, while 2% A. digitata significantly increased serum Fe. When considering the redox status, the whole blood and liver samples yielded similar results, with significant decreases in oxidised glutathione (GSSG) in rats consuming the 2% M. flabellifolius (82.76 mole/L) and 5% A. digitata (90.42 mole/L) with a resultant significant increase in the glutathione redox status (GSH:GSSG ratio of 5.69 and 5.64, respectively) when compared to rats consuming water (4.77). The GSH:GSSG ratio was also significantly increased by consumption of 2% A. betulina (8.45) and 5% S. aethiopicus (5.99). The consumption of all plant extracts, except 5% A. betulina and M. flabellifolius, significantly increased lipid peroxidation in the plasma CDs assay. These results indicated an increased antioxidant capacity in the liver with/without an associated reduced cellular oxidative stress status, which could be interpreted as a reduced susceptibility to oxidative damage. When considering the phase 2 hepatic enzymes, none of the plant extracts caused any significant changes in GST, GST or UDP-GT activities. The third part investigated the chemoprotective properties against cancer promotion in the liver utilising diethylnitrosamine (DEN) as cancer initiator and maize culture material of Fusarium verticillioides, containing the fumonisin B mycotoxins, as promoters in male Fischer rats. The rats consumed 2% (w/v) aqueous extracts of A. digitata, A. betulina, and S. aethiopicus over 28 days after cancer initiation and liver sections subjected to glutathione-S-transferase placental form positive GSTP+ staining and pre-cancerous liver foci categorised according to size. In addition, blood and liver analyses were done as described in the chronic feeding study above. Consumption of the A. digitata and, to a certain extent, S. aethiopicus extracts, altered the oxidative stress status in the liver as indicated by the increased lipid peroxidation, as determined by significantly increased liver CDs and the decreased GSH:GSSG ratio in the blood. This can be related to a subchronic toxicity due to the high total polyphenol intake as mentioned above. These underlying sub chronic toxic effects of A. digitata and S. aethiopicus are likely to be responsible for the observed inhibitory effect on the proliferation of GSTP+ minifoci in the liver. Hepatic phase 2 metabolising enzyme activities were not significantly altered by A. digitata and S. aethiopicus consumption, while GST activity was significantly increased by A. betulina treatment. Based on the findings of the current study, aqueous extracts of A. digitata, A. betulina, and S. aethiopicus may serve as hepatoprotectors with a potential to modulate liver carcinogenesis, specifically cancer promotion. To our knowledge, no other studies have attempted to describe the possible chemoprevention mechanisms of these indigenous medicinal plants. Assessments of phase 1 hepatic enzymes and other antioxidant enzymes are suggested for future studies to further describe biochemical and molecular mechanisms associated with consumption of these extracts. Additionally, identifying main compounds present in the plant extracts could culminate in development of drugs and novel nutraceuticals. It is also recommended that increasing concentrations of the plant extracts and/or the ethanol extracts to be used in future studies to better describe dose-responses of the different plants in liver carcinogenesis.

Le stress oxydatif peut conduire à la sénescence, à l'apoptose et à la mutagenèse. Les cellules cancéreuses peuvent développer un avantage prolifératif sur les cellules normales dans un environnement de stress oxydatif, qui de ce fait, participe à la progression tumorale. Nous émettons l'hypothèse que MK2, une cible directe de la p38 MAPK, pourrait conférer aux cellules de cancer du foie une résistance au stress oxydatif. Dans quatre lignées cellulaires tumorales hépatobiliaires, l'inhibition pharmacologique de MK2, MK2i, augmente la mort cellulaire induite par le stress oxydatif par une diminution de l'activité de Hsp27 et une augmentation du niveau du suppresseur de tumeur p53. MK2 favorise la survie cellulaire via l'activation de la réponse anti-oxydante Nrf2 et de la voie d'HB-EGF/EGFR. MK2 est également responsable de la production d'Il-8 induite par le stress oxydatif. Cette augmentation semble dépendre de Hsp27. De plus, nous avons identifié la protéine d'échafaudage EBP50 comme une nouvelle protéine de liaison de MK2. Dans les cellules cancéreuses hépatobiliaires, EBP50 contribue à la régulation de la voie MK2/Hsp27. La déplétion d'EBP50 provoque une diminution de la phosphorylation de Hsp27, de la survie cellulaire ainsi qu'une baisse des taux d'ARNm de HB-EGF et d'IL-8. Dans les échantillons de tissus humains, l'expression de MK2, de Hsp27 et d'EBP50 est augmentée dans le carcinome hépatocellulaire par rapport au tissu hépatique non tumoral. En résumé, ces données fournissent la preuve d'un rôle prépondérant de l'axe MK2/EBP50/Hsp27 dans la progression du cancer du foie en conférant aux cellules tumorales hépatobiliaires une résistance au stress oxydatif. / Oxidative stress leads to senescence, apoptosis and mutagenesis. Cancer cells can develop a proliferative advantage over normal cells in an environment of oxidative stress, which thereby, participates in tumor progression. We hypothesized that MK2, a direct target of p38 MAPK, could mediate the resistance of liver cancer cells to oxidative stress. In four hepatocellular and biliary cancer cell lines, pharmacological inhibition of MK2 by MK2i enhanced oxidative stress-induced cell death through a decrease in Akt and Hsp27 activity and an increase in tumor suppressor p53 level. MK2 promoted cell survival via activation of the anti-oxidant Nrf2 response and the EGFR pathway. The expression of the EGFR agonist, Hb-EGF, increased in response to oxidative stress. In turn, Hb-EGF induced Hsp27 phosphorylation that was down-regulated by MK2i in liver cancer cells, indicating that EGFR activation by Hb-EGF is a potent activator of MK2. MK2 also increased oxidative stress-induced IL-8 production that depends on Hsp27. Furthermore, we found that MK2 was a binding partner of the scaffolding protein EBP50. In liver cancer cells, EBP50 contributed to up-regulate the MK2/Akt/Hsp27 pathway. Silencing of EBP50 by siRNA in these cells caused a decrease in the phosphorylation of Akt/Hsp27 and in the mRNA levels of Hb-EGF and IL-8. In human tissue samples, MK2, Hsp27 and EBP50 expressions were found to be increased in hepatocellular carcinoma compared with the matched non-tumor liver tissue. Overall, these data provide evidence for a preponderant role of MK2/EBP50/Akt/Hsp27 axis in liver cancer progression by mediating oxidative stress resistance in liver tumor cells.

Each year liver cancer kills more than half a million people, making it the third leading cause of cancer-related death worldwide. Annual incidence continues to rise steadily, both domestically and globally, increasing the burden of this disease. Advancements in the ability to obtain detailed molecular profiles of tumors have led to the successful development of targeted therapies for a number of different cancers. Unfortunately, however, the molecular pathogenesis of liver cancer is poorly understood relative to many other types of malignancies. Thus, the identification of factors contributing to the development and progression of liver tumors is a major goal of current research. In pursuit of this goal, I have utilized the Sleeping Beauty (SB) transposon system as a tool for forward genetic mutagenesis screening in mice. The SB system recapitulates the kinetics of spontaneous tumor development in humans by providing a stepwise accumulation of mutations. Micro-evolutionary processes within a developing tumor lead to the selective expansion of cells harboring mutations that confer some kind of selective advantage. By identifying the most prevalent mutation events within a specific tumor type across a large number of independent samples, a list of genes implicated as being involved in tumorigenesis can be generated. Using this approach, the Dlk1-Dio3 imprinted domain was identified as a site of frequent mutation in SB-induced hepatocellular carcinomas (HCCs). I discovered that the mechanistic basis for recurrent selection of transposon insertion within this domain in liver tumors involved activated expression of Retrotransposon-like 1 (Rtl1). I also found that RTL1 activation is a common event in human HCC, suggesting that it could potentially be beneficial as a therapeutic target in a subset of patients. Etiological factors related to liver cancer development are varied, but are linked by the fact that each provides a chronic liver injury stimulus that promotes the development of hepatic fibrosis. In fact, ˜ 90% of human HCC occurs in this context, and yet the majority of mouse liver cancer models fail to account for this important environmental component of the disease. I have conducted a screen for genetic drivers of liver cancer in the presence or absence of hepatic fibrosis. Comparison of mutation profiles between fibrotic and non-fibrotic tumors revealed largely non-overlapping sets of candidate genes, indicative of a differential selective pressure for mutations depending on the fibrotic context of the liver. Driver mutations identified preferentially in the presence of liver fibrosis have a high likelihood of relevance to human disease, given the similarities in environmental context and kinetics of mutation acquisition. Consistent with this idea, multiple genes with well-established roles in human HCC were found to be preferentially mutated in SB-induced tumors developed in a fibrotic liver. Before a candidate cancer gene identified in an animal model system can have an impact on human disease, its proposed role in tumorigenesis must be validated. Existing techniques for validation of putative liver cancer genes suffer from significant limitations including high cost, low throughput, and a level of complexity that prohibits widespread utilization. I have contributed to the generation of a novel tool for in vivo validation of candidate genes that is not subject to these limitations. By combining elements of recombinant adenoviral vectors and the piggyBac transposition system, we have generated a highly flexible gene delivery system with significant advantages over existing techniques. The Ad-PB system has broad accessibility and applicability, making it a valuable tool for advancing efforts to improve cancer therapies.

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Microsatellites (MSTs) are short tandem repeats of motifs, 1 — 6 nucleotide in length, and are considered mutational 'hot-spots' and show a greater degree of somatic variability and population polymorphisms than surrounding DNA sequences. MSTs provide for a unique computational alignment problem for many commonly used algorithms, and therefore required software tools to be developed to specifically address these issues. For this work we developed a novel approach to extract MSTs from next-gen sequencing data that can robustly detect signatures of MST mutation bias and somatic variation occurring in next-gen data including a high frequency of in-phase indels. Somatic variability, novel genomic polymorphisms that arise within a cell population not found in the progenitors, plays a critical role in cellular reprogramming leading to the development and progression of cancer. MST mutation rates are between 10 and 1000 time higher than that of surrounding DNA. MSTs are found ubiquitously throughout the genome including in nearly all transcribed regions and 10-20% of coding genomic regions. Currently the only established DNA repair defect that that has been directly linked to MST instability is replication coupled mismatch repair (MMR). An initial analysis of the utility of the software was conducted with DNA repair impaired cell lines. The results demonstrated the utility in identifying the consequences of DNA repair impairments on genomic stability. There were major objectives of the finding including 1) complimenting genomics of matched DNA samples with in-sample quantification of variation and 2) demonstrating that DNA repair proficient cells and those with different defects in DNA repair can have different somatic MST variability (SMV) profiles that may be potential markers for these defects. DNA repair disorders are debilitating conditions that result in physical and neurological abnormalities robbing the individual of a normal quality of life and life span. The various conditions that fall into this class are known as progeroid disorders and they provide a very important glimpse into the aging process on a genomic level. The conditions for four cohorts analyzed here were; Cockayne's syndrome, caused by the loss of the ERCC8 gene, also known as CSA; xeroderma pigmentosum, caused by the loss of the XPA or XPB genes; Werner syndrome, caused by the loss of the RecQL2 gene; and Rothmond-Thomson syndrome, caused by the loss of the RecQL4 gene. The goal of this project was to determine if impaired excision repair genes CSA or global XPA and B or excision repair supporting helicases BLM or RecQL4 leads to MST destabilization. Comparing cohorts from excision repair disorders with a co-sequenced normal cohort we found that CSA both RecQ helicases had an effect on the exome somatic variability of MSTs. On the other hand the effects of XPA/B were inconclusive. MST instability (MSI), defined as acquired/lost primary alleles in tumors for a small set of microsatellite loci, has been implicated and is a clinically relevant marker for colorectal cancer. Conversely, no clinically actionable genetic markers have been found for liver cancer, a cancer with a very high mortality rate. Here we explore the use SMV defined as the presence of minor alleles at MST loci, as a complementary measure of MSI as a genetic marker for colorectal and liver cancer by analyzing Illumina sequenced genomes from The Cancer Genome Atlas. Our data shows that SMV may distinguish a subpopulation of African American patients with colorectal cancer, ~33% of the population in this study. Further, for liver cancer, a higher rate of SMV may be indicative of earlier age of onset. In conclusion, the work presented here suggests that MSI should be expanded to include SMV, not only instability. / Ph. D.

Hu, Baoguang. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 121-143). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Cheung Hoi Hung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 151-166). / Abstracts in English and Chinese. / ACKNOWLEDGEMENT --- p.I / ABSTRACT --- p.II / ABBREVIATIONS --- p.IV / LIST OF FIGURES --- p.VII / LIST OF TABLES --- p.IX / CONTENTS --- p.X / Chapter CHAPTER ONE: --- GENERAL INTRODUCTION / Chapter 1.1 --- Non-coding RNAs in transcriptional output --- p.2 / Chapter 1.2 --- Diverse functions of non-coding RNAs --- p.5 / Chapter 1.3 --- HI9: imprinted non-coding RNA --- p.6 / Chapter 1.4 --- Objective --- p.7 / Chapter CHAPTER TWO: --- The ROLE OF H19 RNA IN MDR1 EXPRESSION OF HUMAN HEPATOCELLULAR CARCINOMA HepG2 CELLS / Chapter 2.1 --- Introduction / Chapter 2.1.1 --- H19-Igf2 locus as a model for genomic imprinting --- p.10 / Chapter 2.1.2 --- HI9 as a non-protein coding regulatory RNA --- p.12 / Chapter 2.1.3 --- Controversial roles of H19 RNA --- p.13 / Chapter 2.1.4 --- Novel role of H19 RNA in drug resistance --- p.15 / Chapter 2.2 --- Materials and methods / Chapter 2.2.1 --- Materials --- p.17 / Chapter 2.2.2 --- Methods / Chapter 2.2.2.1 --- Cell culture --- p.19 / Chapter 2.2.2.2 --- Plasmid construction and stable cell transfection --- p.19 / Chapter 2.2.2.3 --- Transient gene transfection --- p.20 / Chapter 2.2.2.4 --- RNA isolation and RT-PCR --- p.21 / Chapter 2.2.2.5 --- MTT drug sensitivity assay --- p.22 / Chapter 2.2.2.6 --- Western blot analysis --- p.22 / Chapter 2.3 --- Results / Chapter 2.3.1 --- Differential expression of H19 RNA in different human cancer cell lines --- p.24 / Chapter 2.3.2 --- R-HepG2 cells over-expressed P-glycoprotein and H19 RNA --- p.24 / Chapter 2.3.3 --- Development of H19-silenced cell lines in HepG2 cells by RNA interference --- p.26 / Chapter 2.3.4 --- Altered drug sensitivity in H19-silenced cells --- p.28 / Chapter 2.3.5 --- Expression of P-glycoprotein in H19-silenced cells --- p.31 / Chapter 2.3.6 --- Overexpression of H19 RNA in HepG2 cells --- p.34 / Chapter 2.3.7 --- Induction of H19 RNA and MDR1 in HepG2 cells --- p.34 / Chapter 2.4 --- Discussion / Chapter 2.4.1 --- H19 regulation of MDR1 associated drug resistance --- p.38 / Chapter 2.4.2 --- The puzzle of riboregulation in drug resistance --- p.40 / Chapter CHAPTER THREE: --- The ROLES OF PTB AND IMP1 IN H19-RELATED MDR1 EXPRESSION OF HUMAN HEPATOCELLULAR CARCINOMA HepG2 CELLS / Chapter 3.1 --- Introduction / Chapter 3.1.1 --- H19 RNA binding proteins --- p.43 / Chapter 3.2 --- Materials and methods / Chapter 3.2.1 --- Materials --- p.46 / Chapter 3.2.2 --- Methods / Chapter 3.2.2.1 --- Cell culture --- p.48 / Chapter 3.2.2.2 --- Plasmid construction and stable cell transfection --- p.48 / Chapter 3.2.2.3 --- RNA extraction and RT-PCR --- p.48 / Chapter 3.2.2.4 --- MTT drug sensitivity assay --- p.48 / Chapter 3.2.2.5 --- Western blot analysis --- p.48 / Chapter 3.2.2.6 --- Real-time PCR analysis of gene expression --- p.49 / Chapter 3.2.2.7 --- DOX efflux assay --- p.49 / Chapter 3.3 --- Results / Chapter 3.3.1 --- PTB knockdown increased P-glycoprotein expression --- p.51 / Chapter 3.3.2 --- IMP1 knockdown decreased MDR1 /P-glycoprotein expression --- p.54 / Chapter 3.3.3 --- Altered drug sensitivity in IMP 1 -knockdown cells --- p.60 / Chapter 3.4 --- Discussion / Chapter 3.4.1 --- Antagonistic effect of PTB and IMP1 on H19/MDR1 expressions --- p.64 / Chapter 3.4.2 --- Complexity of riboregulation --- p.65 / Chapter CHAPTER FOUR: --- IDENTIFICATION OF H19 RNA BINDING PROTEINS FROM HUMAN HEPATOCELLULAR CARCINOMA HepG2 CELLS / Chapter 4.1 --- Introduction / Chapter 4.1.1 --- Overview of RNA-protein interactions --- p.69 / Chapter 4.1.2 --- Methodology in the study of RNA-protein interactions --- p.71 / Chapter 4.1.3 --- Identification of RNA-binding proteins --- p.72 / Chapter 4.2 --- Materials and methods / Chapter 4.2.1 --- Materials --- p.75 / Chapter 4.2.2 --- Methods / Chapter 4.2.2.1 --- Screening of H19 cDNA from human placenta cDNA library --- p.78 / Chapter 4.2.2.2 --- Preparation of nuclear and cytoplasmic extracts from HepG2 cells / Chapter 4.2.2.3 --- In vitro RNA transcription and RNA labeling --- p.80 / Chapter 4.2.2.4 --- RNA electrophoretic mobility shift assay --- p.81 / Chapter 4.2.2.5 --- In vitro UV-crosslinking assay --- p.82 / Chapter 4.2.2.6 --- Preparation of RNA-affinity column and isolation of RNA binding proteins --- p.83 / Chapter 4.2.2.7 --- In-gel digestion and MALDI-TOF mass spectrometry --- p.84 / Chapter 4.3 --- Results / Chapter 4.3.1 --- Screening of H19 cDNA and preparation ofH19 RNA --- p.86 / Chapter 4.3.2 --- Electrophoretic mobility shift analysis of H19 RNA with HepG2 cytoplasmic extract --- p.87 / Chapter 4.3.3 --- UV-crosslinking of H19 RNA with HepG2 nuclear and cytoplasmic extract --- p.90 / Chapter 4.3.4 --- Isolation of H19 RNA binding proteins by RNA-affmity chromatography --- p.94 / Chapter 4.3.5 --- Confirmation of PTB and IMP1 as H19 RNA binding protein --- p.96 / Chapter 4.3.6 --- MALDI-TOF mass spectrometric analysis of isolated H19 RNA binding proteins --- p.96 / Chapter 4.4 --- Discussion / Chapter 4.4.1 --- RNA-protein interactions: an initial step for mechanistic study --- p.99 / Chapter 4.4.2 --- In vitro and in vivo methods for isolation of RNA binding proteins --- p.101 / Chapter 4.4.3 --- Novel role of hnRNP M protein in H19 RNA binding --- p.103 / Chapter CHAPTER FIVE: --- THE ROLE OF PTB IN APOPTOSIS / Chapter 5.1 --- Introduction / Chapter 5.1.1 --- Overview of polypyrimidine tract-binding protein in RNA processing and post-transcriptional gene regulation --- p.106 / Chapter 5.1.2 --- Evidences of polyrimidine-tract binding protein in the regulation of apoptosis --- p.108 / Chapter 5.2 --- Materials and methods / Chapter 5.2.1 --- Materials --- p.111 / Chapter 5.2.2 --- Methods / Chapter 5.2.2.1 --- Cell culture --- p.114 / Chapter 5.2.2.2 --- Stable cell transfection in A431 cells --- p.114 / Chapter 5.2.2.3 --- Western Blot analysis --- p.114 / Chapter 5.2.2.4 --- MTT drug sensitivity assay --- p.114 / Chapter 5.2.2.5 --- DNA fragmentation assay --- p.115 / Chapter 5.2.2.6 --- Flow cytometry analysis of apoptosis --- p.115 / Chapter 5.2.2.7 --- Caspase activity assay --- p.116 / Chapter 5.3 --- Results / Chapter 5.3.1 --- Taxol as an apoptosis inducer in HepG2 cells --- p.117 / Chapter 5.3.2 --- PTB was cleaved during Taxol-induced apoptosis --- p.118 / Chapter 5.3.3 --- PTB knockdown increased Taxol cytotoxicity and apoptosis --- p.118 / Chapter 5.3.4 --- Effect of PTB knockdown on drug sensitivity of cells --- p.121 / Chapter 5.3.5 --- Effect of PTB knockdown on other drug-induced apoptosis --- p.121 / Chapter 5.3.6 --- Effect of PTB knockdown on the basal expressions of genes in apoptosis pathway --- p.126 / Chapter 5.3.7 --- The role of caspase-9 activation in PTB-regulated apoptosis --- p.129 / Chapter 5.3.8 --- The effect of PTB knockdown on pro-caspase-9 expression and Taxol-induced apoptosis in A431 cells --- p.133 / Chapter 5.3.9 --- The role of PTB in the regulation of intrinsic apoptosis pathway --- p.136 / Chapter 5.4 --- Discussion / Chapter 5.4.1 --- The role of PTB in intrinsic apoptosis pathway --- p.138 / Chapter 5.4.2 --- PTB in regulation of pro-caspase-9 expression --- p.139 / Chapter CHAPTER SIX: --- GENERAL DISCUSSION AND CONCLUSION / Chapter 6.1 --- H19 as a potential target in anti-cancer gene therapy --- p.143 / Chapter 6.2 --- Conclusion --- p.144 / Chapter 6.3 --- Unanswered questions and future work --- p.145 / Chapter 6.4 --- A proposed model for H19 pathway --- p.148 / REFERENCES --- p.151

Ho Kar Fai, William. / Thesis submitted in: July 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 121-129). / Abstracts in English and Chinese. / Abstract --- p.I / Acknowledgement --- p.V / Table of Contents --- p.VI / Abbreviations --- p.VIII / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- The recent situation of hepatitis B infection and HBV-induced HCC in Hong Kong / Chapter 1.2 --- Natural history of HBV infection in human / Chapter 1.3 --- The genomic organization of HBV / Chapter 1.4 --- Potential oncogenic mechanism of HBV-induced hepatocarcinogenesis / Chapter 1.5 --- Aim of the present study / Chapter Chapter 2 --- Materials and methods --- p.16 / Chapter 2.1 --- Transformation in E.coli for subtracted normal-counterpart library / Chapter 2.2 --- PCR amplification of subtracted clones / Chapter 2.3 --- Sequencing of subtracted clones with dye-terminator cycle sequencing technology / Chapter 2.4 --- Sequence analysis and database construction / Chapter 2.5 --- Molecular cloning and characterization of novel gene / Chapter 2.6 --- In silico structural and functional analysis of Z313 / Chapter 2.7 --- Cloning and sequencing analysis of zinc finger protein 313 (Z313) / Chapter 2.7.1 --- PCR amplification of target gene -Z313 / Chapter 2.7.2 --- Mini-preparation of plasmid DNA / Chapter 2.7.3 --- Cycle sequencing of cloned cDNA -Z313 with dye-primer technology / Chapter 2.8 --- Multiple Tissue Northern (MTN) blot hybridisation / Chapter 2.9 --- RT-PCR analysis of Z313 / Chapter 2.10 --- Subcellular localization study of Z313 by Green Fluorescent Protein (GFP) / Chapter 2.10.1 --- Directional cloning of Z313 into pEGFP-Cl / Chapter 2.10.2 --- Mini-preparation of plasmid DNA / Chapter 2.10.3 --- Transient transfection of plasmids in different cell lines / Chapter 2.10.4 --- Microscope observation of GFP transfected cells / Chapter Chapter 3 --- Results --- p.49 / Chapter 3.1 --- PCR selection of subtracted clones for sequencing analysis / Chapter 3.2 --- Partial sequencing of selected subtracted clones / Chapter 3.3 --- DNA homology searching using program - BLASTN / Chapter 3.4 --- Catalogue of the 467 ESTs from the subtracted normal-counterpart library / Chapter 3.5 --- Classification and frequency of the subtracted normal-counterpart cDNA clones / Chapter 3.6 --- Identification of putative differentially expressed genes in HCC surrounding normal liver / Chapter 3.7 --- Categorization of ESTs exclusively appeared in the subtracted normal- counterpart library / Chapter 3.8 --- In silico structural and functional analysis of zinc finger protein313 (Z313) / Chapter 3.9 --- Molecular cloning of zinc finger protein 313 (Z313) / Chapter 3.10 --- Northern analysis of zinc finger protein 313 (Z313) / Chapter 3.11 --- RT-PCR analysis of zinc finger protein 313 (Z313) / Chapter 3.12 --- Subcellular localization study of zinc finger protein 313 (Z313) / Chapter Chapter 4 --- Discussion --- p.104 / Chapter 4.1 --- EST analysis on the subtracted normal-counterpart cDNA clones / Chapter 4.1.1 --- Characterization of ESTs generated from the subtracted normal-counterpart library / Chapter 4.1.2 --- Putative differentially expressed genes in HCC surrounding normal liver related to hepatocellular carcinoma / Chapter 4.2 --- Molecular cloning and characterization of zinc finger protein313 (Z313) / Chapter 4.3 --- Future aspects / References --- p.121