Lee, Kwan Yeung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 103-113). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.v / Table of Content --- p.vi / List of Figures --- p.xi / List of Tables --- p.xiii / List of Abbreviations --- p.xiv / List of papers published during the study --- p.xvi / Chapter Chapter 1 --- Introduction and Aim of Study --- p.1 / Chapter 1.1 --- General Introduction --- p.1 / Chapter 1.2 --- Project objective and potential significances --- p.5 / Chapter Chapter 2 --- Literatures Review --- p.6 / Chapter 2.1 --- Cancer genetics and Tumor suppressor genes --- p.6 / Chapter 2.2 --- Epigenetic --- p.7 / Chapter 2.2.1 --- DNA methylation and promoter CpG island --- p.8 / Chapter 2.2.2 --- Establishment and maintenance of DNA methylation --- p.9 / Chapter 2.2.3 --- Transcriptional silencing by DNA hypermethylation --- p.9 / Chapter 2.3 --- Cancer epigenetic --- p.11 / Chapter 2.3.1 --- Hypomethylation of the cancer genome --- p.12 / Chapter 2.3.2 --- Hypermethylation in cancers --- p.12 / Chapter 2.3.3 --- Clinical relevance of cancer epigenetic --- p.13 / Chapter 2.4 --- Nasopharyngeal carcinoma --- p.14 / Chapter 2.4.1 --- NPC genetic and epigenetic --- p.15 / Chapter 2.5 --- 12p as a putative tumor suppressor locus --- p.16 / Chapter 2.5.1 --- Hematological malignancies associated with 12p loss --- p.17 / Chapter 2.5.2 --- Prostate cancer associated with 12p loss --- p.20 / Chapter 2.5.3 --- Lung cancer associated with 12p loss --- p.22 / Chapter 2.5.4 --- 12p deletion in other cancers --- p.23 / Chapter 2.6 --- 16q as a tumor suppressor locus --- p.24 / Chapter 2.6.1 --- Breast cancer and 16q --- p.25 / Chapter 2.6.2 --- Loss of 16q and prostate cancer --- p.26 / Chapter 2.6.3 --- Loss of 16q and hepatocellular carcinoma --- p.28 / Chapter 2.6.4 --- 16q deletion associated with other cancers --- p.29 / Chapter Chapter 3 --- Materials and Methods --- p.30 / Chapter 3.1 --- Cell lines and tissue samples --- p.30 / Chapter 3.1.1 --- Cell lines --- p.30 / Chapter 3.1.2 --- Maintenance of cell lines --- p.31 / Chapter 3.1.3 --- Drugs treatment of cell lines --- p.31 / Chapter 3.1.4 --- Normal tissues --- p.32 / Chapter 3.1.5 --- Total RNA extraction --- p.32 / Chapter 3.1.6 --- Genomic DNA extraction --- p.32 / Chapter 3.2 --- General techniques --- p.33 / Chapter 3.2.2 --- TA cloning and blunt end cloning of PCR product --- p.33 / Chapter 3.2.3 --- Transformation of cloning products to E. coli competent cells --- p.34 / Chapter 3.2.4 --- Preparation of plasmid DNA --- p.34 / Chapter 3.2.4.1 --- Mini-prep plasmid DNA extraction --- p.34 / Chapter 3.2.4.2 --- Midi-prep of plasmid DNA --- p.35 / Chapter 3.2.5 --- Measurement of DNA or RNA concentrations --- p.36 / Chapter 3.2.6 --- DNA sequencing of plasmid DNA and PCR products --- p.36 / Chapter 3.3 --- Preparation of reagents and medium --- p.37 / Chapter 3.4 --- Semi-quantitative Reverse-Transcription (RT) PCR expression analysis --- p.38 / Chapter 3.4.1 --- Reverse transcription reaction --- p.38 / Chapter 3.4.2 --- Semi-quantitative RT-PCR --- p.39 / Chapter 3.4.2.1 --- Primers design --- p.39 / Chapter 3.4.2.2 --- PCR reaction --- p.39 / Chapter 3.5 --- Methylation analysis of candidate genes --- p.40 / Chapter 3.5.1 --- Bisulfite treatment of genomic DNA --- p.41 / Chapter 3.5.2 --- Methylation-specific PCR (MSP) --- p.42 / Chapter 3.5.2.1 --- Bioinformatics prediction of CpG island --- p.42 / Chapter 3.5.2.2 --- Primers design --- p.42 / Chapter 3.5.2.3 --- PCR reaction --- p.42 / Chapter 3.5.3 --- Bisulfite Genomic Sequencing (BGS) --- p.43 / Chapter 3.5.3.1 --- Primers design --- p.43 / Chapter 3.5.3.2 --- PCR reaction --- p.44 / Chapter 3.6 --- Construction of expression vectors of candidate genes --- p.44 / Chapter 3.6.1 --- Construction of IRF8 expression vector --- p.44 / Chapter 3.6.2 --- Construction of PTPRO expression vector --- p.44 / Chapter 3.6.2.1 --- Experimental design --- p.44 / Chapter 3.6.2.2 --- PCR and cloning of PCR products --- p.46 / Chapter 3.6.2.3 --- Restriction digestion of cloning vectors and expression vector --- p.48 / Chapter 3.6.2.4 --- Ligation of cloning fragments --- p.48 / Chapter 3.7 --- Colony formation assay on monolayer culture --- p.48 / Chapter 3.8 --- Statistical analysis --- p.49 / Chapter Chapter 4 --- Identification of candidate TSGs in deleted regions --- p.50 / Chapter 4.1 --- Research plan --- p.50 / Chapter 4.2 --- Results --- p.50 / Chapter 4.2.1 --- Mapping of the deleted B AC clones on their chromosomal locations --- p.50 / Chapter 4.2.2 --- Identification of down-regulated genes in NPC by semi-quantitative RT-PCR analysis --- p.51 / Chapter 4.3 --- Discussion --- p.55 / Chapter Chapter 5 --- Tumor suppressor function studies of candidate TSGs --- p.60 / Chapter 5.1 --- Research plan --- p.60 / Chapter 5.2. --- IRF8 is the 16q candidate TSG --- p.60 / Chapter 5.2.1 --- Frequent silencing of IRF8 mRNA expression in multiple carcinomas --- p.60 / Chapter 5.2.2 --- Methylation status of IRF8 promoter region correlated with its transcriptional silencing --- p.62 / Chapter 5.2.3 --- Restoration of IRF8 expression by pharmacological and genetic demethylation --- p.65 / Chapter 5.2.4 --- IRF8 inhibited the anchorage dependent growth of tumor cells on monolayer culture --- p.67 / Chapter 5.2.5 --- Discussion --- p.68 / Chapter 5.3 --- PTPRO is the down-regulated target at 12pl3.2-12.3 tumor suppressor locus --- p.73 / Chapter 5.3.1 --- Frequent silencing of PTPRO in multiple carcinoma cell lines --- p.73 / Chapter 5.3.2 --- Frequent methylation of PTPRO promoter CpG island in multiple carcinoma cell lines correlated with its reduced expression --- p.74 / Chapter 5.3.3 --- Re-expression of PTPRO by pharmacological and genetic demethylation --- p.77 / Chapter 5.3.4 --- PTPRO inhibited the growth of tumor cells in vitro --- p.79 / Chapter 5.3.5 --- Discussion --- p.81 / Chapter 5.4 --- RERG is another candidate TSG in 12pl3.2 - 12.3 region --- p.87 / Chapter 5.4.1 --- Down-regulation of RERG mRNA expression in carcinoma cell line --- p.87 / Chapter 5.4.2 --- Hypermethylation of RERG promoter is a frequent event in multiple carcinomas --- p.88 / Chapter 5.4.3 --- Re-expression of RERG mRNA following pharmacological and genetic demethylation --- p.90 / Chapter 5.4.4 --- Discussion --- p.92 / Chapter Chapter 6 --- General discussion --- p.96 / Chapter Chapter 7 --- Summary --- p.101 / Reference --- p.103

Ng, Ka Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 103-113). / Abstracts in English and Chinese. / Acknowledgements --- p.i / List of abbreviations --- p.ii / List of Tables --- p.iv / List of Figures --- p.v / List of Publications --- p.viii / Abstract in English --- p.ix / Abstract in Chinese --- p.xi / Table of Contents --- p.xiii / Chapter Chapter 1 --- Literature Review --- p.1 / Chapter 1.1 --- Tumor suppressor genes (TSGs) and the modes of TSG inactivation during carcinogenesis --- p.1 / Chapter 1.2 --- Epigenetic modifications --- p.3 / Chapter 1.2.1 --- DNA methylation --- p.4 / Chapter 1.2.1a --- Establishment of DNA methylation patterns and DNA methyltransferases --- p.5 / Chapter 1.2.1b --- DNA hypermethylation and carcinogenesis --- p.6 / Chapter 1.2.1c --- Mechanism for gene silencing by CpG methylation --- p.6 / Chapter 1.2.1d --- DNA hypomethylation and carcinogenesis --- p.10 / Chapter 1.2.1e --- Loss of imprinting and carcinogenesis --- p.11 / Chapter 1.2.1f --- Potential factors leading to aberrant methylation patterns in cancers --- p.12 / Chapter 1.2.2 --- Deregulation of histone modifications and carcinogenesis --- p.14 / Chapter 1.2.3 --- Interplay between chromatin modifications and DNA methylation --- p.15 / Chapter 1.3 --- Identification of tumor suppressor genes (TSGs) --- p.17 / Chapter 1.4 --- Nasopharyngeal carcinoma as a cancer model of the current project --- p.18 / Chapter 1.5 --- Genetic and epigenetic changes in NPC --- p.19 / Chapter 1.6 --- Involvement of 5qll-ql2 and 14q32 in carcinogenesis --- p.22 / Chapter 1.6.1 --- Chromosome 5ql l-ql2 and carcinogenesis --- p.22 / Chapter 1.6.2 --- Chromosome 14q32 and carcinogenesis --- p.24 / Chapter 1.7 --- Clinical implications of epigenetics in cancers --- p.27 / Chapter Chapter 2 --- Aims of study and Research plan --- p.31 / Chapter Chapter 3 --- Materials and Methods --- p.34 / Chapter 3.1 --- Cell lines and Normal Tissues --- p.35 / Chapter 3.2 --- Routine cell line maintenance --- p.35 / Chapter 3.3 --- Drug treatments --- p.35 / Chapter 3.4 --- Total RNA extraction --- p.35 / Chapter 3.5 --- Genomic DNA extraction --- p.36 / Chapter 3.6 --- General techniques --- p.37 / Chapter 3.6.1 --- Gel electrophoresis --- p.37 / Chapter 3.6.2 --- DNA and RNA quantification --- p.37 / Chapter 3.6.3 --- LB medium and LB plate preparation --- p.38 / Chapter 3.6.4 --- Plasmid extraction --- p.38 / Chapter 3.6.4a --- Mini-scale preparation of plasmid DNA --- p.38 / Chapter 3.6.4b --- Large-scale preparation of endotoxin-free plasmid DNA --- p.39 / Chapter 3.6.5 --- DNA sequencing --- p.39 / Chapter 3.7 --- Reverse transcription-PCR (RT-PCR) --- p.40 / Chapter 3.7.1 --- Reverse transcription (RT) --- p.40 / Chapter 3.7.2 --- Semi-quantitative RT-PCR --- p.41 / Chapter 3.8 --- Methylation analysis --- p.42 / Chapter 3.8.1 --- Sodium bisulfite modification of DNA --- p.42 / Chapter 3.8.2 --- CpG island analysis --- p.42 / Chapter 3.8.3 --- Methylation-specific PCR (MSP) --- p.43 / Chapter 3.8.4 --- Bisulfite genomic sequencing (BGS) --- p.44 / Chapter 3.9 --- Construction of expression plasmids --- p.45 / Chapter 3.9.1 --- Construction of the MGC80-expressing vector --- p.45 / Chapter 3.9.2 --- Construction of the TUSC14-expressing vector --- p.46 / Chapter 3.10 --- Functional analyses --- p.47 / Chapter 3.10.1 --- Monolayer colony formation assay --- p.47 / Chapter 3.10.2 --- Soft agar assay --- p.48 / Chapter 3.11 --- Statistical analysis --- p.49 / Chapter Chapter 4 --- Results --- p.50 / Chapter 4.1 --- Identification of 5qll-ql2 and 14q32.2-q32.32 as frequently deleted regions in NPC by aCGH --- p.50 / Chapter 4.2 --- Identification of novel candidate TSGs at chromosome 5qll-ql2 through integrative genomics and epigenetics --- p.51 / Chapter 4.2.1 --- Expression profiling of the candidate genes at 5ql l-ql2 in NPC cell lines --- p.51 / Chapter 4.2.2 --- MGC80 as a target of study at 5ql2 --- p.54 / Chapter 4.2.2a --- Ubiquitous expression in normal human tissues and frequent down-regulation of MGC80 in multiple tumor cell lines --- p.54 / Chapter 4.2.2b --- Methylation analysis of MGC80 --- p.56 / Chapter 4.2.2c --- Restoration of MGC80 expression after pharmacologic and genetic demethylation --- p.59 / Chapter 4.2.2d --- Functional study of MGC80 in multiple carcinomas --- p.61 / Chapter 4.2.2e --- Discussion --- p.63 / Chapter 4.2.3 --- TUSC14 as a target of study at 5ql2 --- p.67 / Chapter 4.2.3a --- TUSC14 was broadly expressed in normal human tissues and frequently down-regulated in multiple tumor cell lines --- p.67 / Chapter 4.2.3b --- Methylation analysis of TUSCI4 --- p.69 / Chapter 4.2.3c --- Pharmacologic and genetic demethylation reactivated TUSC14 expression --- p.72 / Chapter 4.2.3d --- Functional study ofTUSC14 in multiple carcinomas --- p.74 / Chapter 4.2.3e --- Discussion --- p.76 / Chapter 4.3 --- Identification of candidate TSGs at chromosome 14q32 through integrative genomics and epigenetics --- p.80 / Chapter 4.3.1 --- Expression profiling of the candidate genes at 14q32 in NPC cell lines --- p.80 / Chapter 4.3.2 --- DLK1 as a target of study at 14q32 --- p.82 / Chapter 4.3.2a --- Expression analysis of DLK1 in normal tissues and NPC cell lines --- p.82 / Chapter 4.3.2b --- Methylation analysis ofDLKl in NPC --- p.83 / Chapter 4.3.2c --- Restoration of DLK1 expression after pharmacologic demethylation --- p.84 / Chapter 4.3.2d --- Functional study ofDLKl in NPC --- p.85 / Chapter 4.3.2e --- Discussion --- p.87 / Chapter Chapter 5 --- General discussion --- p.92 / Chapter Chapter 6 --- Summary --- p.99 / Chapter Chapter 7 --- Future study --- p.101 / Reference list --- p.103

Insects have evolved various physiological responses to cope with stressors such as pathogens, toxins and environmental factors. It is known that the responses resulting from infection or DNA damage share some of the same pathways. Exposure of Drosophila melanogaster and the dung beetle Euoniticellus intermedius to stress led to changes in the expression of proteins involved in metabolism, development, protein degradation, mRNA processing and stress responses. Stress responses in D. melanogaster are well characterised. However, the role played by Drosophila p53 (Dmp53) and a member of the retinoblastoma binding protein 6 (RBBP6) family, Snama, are unknown. Snama has been proposed to play a role in Dmp53 regulation. Following DNA damage we investigated the role of Dmp53 and Snama. Flies recovering from camptothecin treatment display a glycolytic flux, involving a metabolic shift, different to that observed in cancer cells. Camptothecin treatment leads to an increase in the mortality of both sexes. Furthermore, females show a specific decrease in fecundity which is due to an increase in Dmp53 dependent apoptosis in the ovaries and is accompanied by a depletion of Snama and an increase in Dmp53 transcripts. Expression data indicated that Dmp53 activity may be largely regulated at the protein level. Bypassing glycolysis through methyl pyruvate supplementation led to differential expression of Dmp53 and Snama and improved reproduction and embryonic development. These results highlight differences between the metabolic strategies used by cancerous and non-cancerous cells which may be exploited in future chemotherapies. While immune responses amongst insect orders are evolutionarily conserved, many remain uncharacterised. To investigate the immune system of an organism that lives in a microbe rich environment, E. intermedius was infected with the fungal pathogen Beauveria bassiana. This resulted in decreased lifespan and fecundity. Homologs of proteins involved in the immune response of insects were identified in E. intermedius, including a member of the Toll family of proteins, an insect defensin (present in the hemolymph) as well as a homolog of the serine protease Persephone. These results show that immune signalling pathways are conserved in this dung beetle.

A regulatory element involved in the transcriptional activation of the major capsid protein (VP5) of herpes simplex virus type 1 was identified and characterized in this research project. Gel mobility shift assay with nuclear extracts from both uninfected and HSV-1 infected HeLa cells identified two major protein-DNA complexes involving the VP5 promoter. No viral specific complex found. DNase I and orthophenanthroline-cu+ footprint analyses in the same laboratory revealed that the two complexes involve a single binding site, GGCCATCTTGAA, located between -64 and -75 bp relative to the VP5 cap site. To determine the function of this leaky-late binding site (LBS) in VP5 gene activation, mutated VP5 promoters with deletion and insertion around LBS were constructed and linked to a reporter gene, bacterial chloramphenicol acetyltransferase gene. The effect of mutations were tested in transient expression assay. Deletion of LBS resulted in seven to eight-fold reduction in the level of transactivation of the chloramphenicol acetyltransferase gene by superinfection with HSV-1 or by cotransfection of HSV immediate-early genes. These results indicated LBS is involved in the maximal transactivation of the VPS gene. A search of published gene sequences found the homologs of LBS exist in a number of HSV-1 By promoters, and other viral promoters, as well as cellar promoters. Some of these homologs have found involved in the transcription regulation.

The herpes simplex virus 1 (HSVl) VP5 gene codes for the major viral capsid protein. Understanding of the mechanism of how the VP5 gene is regulated in host cells will help us to understand the molecular action of the HSV 1 life cycle and its interplay with the host cell gene expression machinery (transcription and translation). This may ultimately provide scientific bases for both better prevention and cure of HSV 1 caused diseases. Previous work from Dr. Robert L. Millette' s laboratory has indicated that a 164 base pair region of the VP5 promoter gene could activate the transcription of an attached reporter gene (bacteria CAT gene). Furthermore, a 12 bp (GGCCATCTTGAA) cis-acting element situated within the 164 bp promoter region was required for the promoter activity. To understand the function of this cis-element in the regulation of VP5 transcription and to identify the trans-acting factors interacting with this element, gel mobility shift assays were first carried out using the fragment containing the 12 bp site as the probe. A cellular factor, YY 1, was found to bind to this site in a sequence specific manner. Based on the oligonucleotide competition assays, partial protease digestions, and antibody supershift assays, it became clear that two cellular factors bound to the VP5 promoter. These were related, if not identical, to the previously identified Yin-Yang- 1 factor (YY 1), and transcription factor the SPl. Site-directed mutagenesis studies indicated that these two factors bind to distinct sites on the 164 bp fragment. Point mutations studies on the 12 bp YYl binding site demonstrated that seven of the 12 bp were required for YY 1-DNA complex formation and the first four bp in the 12 bp were very important for VP5 gene regulation. Also, it was found that YY 1 performs both positive and negative regulator function in VP5 gene regulation. In conclusion, two cellular transcription factors, YY 1 and SPl, play a major role in VP5 gene expression.

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Bibliography: leaves [129]-146

"May 2002." Addendum inside back cover. Bibliography: p. 139-157. Aims to isolate ephrin ligands from Drosophila melanogaster and analyse their involvement in Drosophila deveopment. Also investigates the potential of ephrin B-1 as a causative gene in the human condition Aicardi's syndrome.

EDD (E3 isolated by differential display), located at chromosome 8q22.3, is the human homologue of the Drosophila melanogaster tumour suppressor gene 'hyperplastic discs'. Edd null mice and hyd mutants display embryonic lethality. EDD is also a multifunctional HECT family E3 ubiquitin protein-ligase, with reported roles in both progesterone action and the DNA damage response. To investigate the possible involvement of EDD in human cancer, several cancer types were analysed for allelic gain or loss (allelic imbalance, AI) at the EDD locus. AI of the EDD locus was most frequent in the serous subtype of ovarian cancer (16/22, 73%) and common in other cancers, including breast cancer (31%). AI is likely to represent amplification of the EDD gene locus rather than loss of heterozygosity, as quantitative RT-PCR and immunohistochemistry showed that EDD mRNA and protein are frequently overexpressed in breast and ovarian cancers. These data imply a potential role for EDD in cancer progression. However, depletion of EDD from cells in culture by RNA interference had very little effect on proliferation and cell survival. To identify EDD-regulated pathways, transcript analysis was performed on EDD-depleted cells. The results suggested that EDD modulates cell-cell communication and the actin cytoskeleton. Consistent with transcript analysis, depletion of EDD from two normal breast cell lines (HMEC-184 and MCF-10A) resulted in altered cell morphology, with decreased cell-cell contacts. This was concurrent with altered beta-catenin (an integral component of adherens junctions) at cell-cell contacts, which was also observed in the developing blood vessels of Edd null mice. Interestingly, total cellular beta-catenin levels were not affected. Furthermore, EDD depletion resulted in a decrease in expression of the cytoskeletal regulators twinfilin and R-RAS, with a simultaneous decrease in MAPK (ERK1 and ERK2) activity. Consistent with disruption of adherens junctions, EDD-depleted mammary acini lost tissue coordination and polarity. These data provide a significant advance in our knowledge of EDD, both in its role in regulating the organisation of cells into higher structures and its potential role in the development of cancer. This has relevance to an understanding of embryonic development and the role of tissue homeostasis in cancer progression.