Lee Tin Lap. / "January 2001." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (p. 161-185). / 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. / Abstracts in English and Chinese.

Lam, Man Ting. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 128-138). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Wang, Shiyan. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 123-139). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Gastric cancer is the second leading cause of cancer death worldwide and in China. The mechanism of gastric carcinogenesis is not fully understood. Epigenetic studies indicated that inactivation of tumor suppressor genes by DNA hypermethylation plays a crucial role in the progression of gastric cancer. Epigenetic inactivation of secreted frizzled-related protein (SFRP 1) by methylation plays a pivotal role on the development of various cancers. However, the role of SFRP family genes in gastric cancer remains largely unknown. We aimed to characterize the epigenetic abnormalities and discover novel biomarkers for early detection of gastric cancer. We investigated the epigenetic alterations in gastric adenocarcinoma by microarray based analysis and gene promoter hypermethylation. Based of the microarray data, we determined the functional significance and frequency of SFRP family genes hypermethylation in human gastric cancer. We screened the mRNA expression and methylation status of the SFRP family members in human gastric cancer cell lines and primary gastric cancer samples. Demethylation study of SFRP family genes were done by treating gastric cancer cell lines with 5'Aza. The biological effects of SFRP were analyzed by flow cytometry, cell viability assay and tumor growth in nude mice. SFRP1, 2, 4 and 5 were undetectable in 100% (7/7), 100% (7/7), 42.8% (3/7) and 85.7% (6/7) of gastric cancer cell lines, respectively. However, only SFRP2 showed significant down-regulation in gastric cancer compared with adjacent non-cancer samples (P<0.01). Treatment with demethylation agent, 5'-Aza, restored the expression of SFRP2 in all 7 cancer cell lines. Promoter hypermethylation of SFRP2 was detected in 73.3% of primary gastric cancer samples and 20% of adjacent non-cancer tissue (P<0.01). Bisulfite sequencing confirmed the density of promoter methylation in cell line, primary gastric cancer tissue and their adjacent non-cancer tissue. Transfection of SFRP2 induced cell apoptosis, inhibited proliferation in vitro and suppressed tumor growth in vivo. Furthermore, SFRP2 methylation was detected in 37.5% of samples showing intestinal metaplasia. Methylated SFRP2 was also detected in 66.7% of serum samples from cancer patients but not in normal controls. Epigenetic inactivation of SFRP2, but not SFRP1, SFRP4 and SFRP5 is a common and early event of carcinogenesis. Hence, detection of SFRP2 methylation in serum may have diagnostic value in gastric cancer patients. / by Cheng, Yuen Yee. / Adviser: FKL Chan. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0803. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 165-179). / 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 also in Chinese. / School code: 1307.

Array comparative genomic hybridization (array-CGH) was used in this study to analyze the chromosomal aberrations in 9 gastric cancer cell lines. Our results showed good concordance with those of conventional CGH. We correlated the results from array-CGH with expression profiling and found some novel and independent target genes which deserved further confirmation. / Gastric cancer is one of the most common malignancies worldwide and is the second most frequent cause of cancer related death. A variety of genetic and epigenetic aberrations underlie development abnormality of gastric cancer. / Taken together, our findings supported YAP1 is a functional oncogene in gastric cancer. We provided the first evidence that YAP1 exerted the oncogenic function by enhancing the capacity to activate the early response gene pathway. YAP1 could be a prognostic biomarker and potential therapeutic target for gastric cancer. / The study was focused on the putative oncogene Yes-associated Protein 1 (YAP1) located in 11q22.1. Up-regulation of YAP1 was observed in 92.3% of gastric cancer by immunohistochemistry (IHe) on gastric cancer tissue microarrays. YAP1 nuclear accumulation correlated with cancer specific survival. In addition, multivariate Cox regression showed that YAP1 was an independent predictor of short disease specific survival time for patients with early stage gastric cancer (P=0.042) in addition to T stage ( P=O.038). Knockdown YAP1 in gastric cancer cell lines MKN1 and AGS resulted in a significant reduction in proliferation, anchorage-dependent colony formation, cell invasion and cell motility. Ectopic YAP1 expression in MKN45 cells promoted anchorage-independent colony formation, induced a more invasive phenotype and accelerated cell growth both in vitro and in vivo. Microarray analysis highlighted the alteration of MAPK pathway by YAP1. We confirmed a constitutive activation of RAF/MEKJERK in YAP1-expressing MKN45 cells and further demonstrated that YAP1 enhanced serum/EGF induced c-Fos expression in gastric cancer cells. Furthermore, we demonstrated that ectopic MST1 promoted phosphorylation and cytoplasmic translocation of YAP1 and subsequently quenched the oncogenic function of YAP1 in the nucleus. / Kang, Wei. / "December 2010." / Adviser: To Kai-fai. / Source: Dissertation Abstracts International, Volume: 73-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 175-185). / 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, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

研究背景及目的：EB病毒(EBV)相關性胃癌的發病率約占胃癌的10%。近年來，越來越多的研究表明， EBV相關性胃癌的腫瘤抑制基因發生異常甲基化。然而，EBV的感染對全基因組DNA甲基化的影響尚不清楚。本研究通過分析EBV感染的細胞中全基因組DNA甲基化的情況，篩選出因EBV感染而發生甲基化的基因，並闡明靶基因在胃癌發生過程的作用。 / 方法：本研究應用穩定轉染EBV的胃癌細胞AGS (AGS-EBV)和無EBV轉染的AGS細胞為模型。採用高解析度的甲基化DNA免疫共沉澱晶片技術(MeDIP-chip)比較AGS-EBV 和AGS全基因組DNA甲基化的變化，並根據基因本體論(GO)，對EBV誘導的甲基化基因進行分類。採用RT-PCR，去甲基化處理及亞硫酸氫鈉測序(BGS)等方法驗證EBV誘導的甲基化基因。同時，採用基因敲除和過表達方法體外研究靶基因的生物學功能：通過細胞活力實驗和集落形成實驗判斷靶基因對細胞增殖的影響；通过流式细胞技术、伤口愈合实验及侵袭实验研究筛选到的靶基因生长抑素受体1（SSTR1）的功能；此外，还通過腫瘤通路基因PCR晶片分析靶基因調控的下游腫瘤相關基因。 / 结果：EBV編碼的小RNA(EBER)原位雜交方法和EBV潛伏期膜蛋白(LMP2A)的表達均證實AGS-EBV細胞中確實存在EBV的感染。和AGS細胞相比，發現AGS-EBV細胞中DNA甲基轉移酶3b(DNMT3b)的表達和活性顯著增加。AGS細胞中， LMP2A過表達後，DNMT3b的表達和活性也顯著增加。通過MeDIP-chip篩選出AGS-EBV中1,065甲基化有差異的基因，其中886基因為高甲基化。GO分析結果表明這些高甲基化基因參與KEGG信號通路。其中，六個新的高甲基化基因(MDGA2, IL15RA, SCARF2, EPHB6, SSTR1 和 REC8)在AGS-EBV細胞中的表達低於AGS；經過去甲基化處理之後，這些基因的表達水準有顯著增加。 / 通過深入研究生長抑素受體1(SSTR1)的生物學功能，發現：敲除SSTR1 能促進胃癌細胞的增殖和集落形成；通過调节G1/S期的調節因子，加快細胞進入S期，顯著增加S期的細胞數目。此外，胰腺癌細胞PANC1細胞中，SSTR1的過表達，也進一步證實SSTR1確實是一種腫瘤抑制基因。腫瘤通路基因PCR晶片結果顯示SSTR1通過促進細胞週期抑制因數(包括p15，p16，p21和p27)的表達，同時抑制CDC25A 和Myc的表達，發揮抑制增殖作用，導致細胞週期停滯在G1期，減少細胞增殖。SSTR1也通過減少凋亡相關基因的表達參與細胞凋亡的過程。此外，SSTR1還能顯著下調遷移相關基因的表達。這些結果表明，在EB病毒相關胃癌的發生過程中，SSTR1通過調節細胞週期、凋亡及遷移的有關基因，進而抑制細胞增殖，減少細胞的遷移和轉移。 / 结论：AGS感染EBV後，通過LMP2A促進DNMT3b的表達，激活DNMT3b的活性，導致886個腫瘤相關基因发生甲基化。SSTR1是一種EBV誘導的新的甲基化基因，在胃癌中具有抑制腫瘤的特性。研究表明， 由EBV誘導的SSTR1所具有的表觀遺傳學抑制作用參與EB病毒相關性胃癌的發病機制。 / Background and Aims: Epstein-Barr virus (EBV)-associated gastric cancer (GC) accounts for about 10% of all GCs. Accumulating evidences revealed aberrant rmethylation of tumor suppressor genes in EBV-associated GCs. However, the effect of EBV infection on the genome-wide aberrant DNA methylation remains unclear. We aim to profile the genome-wide EBV-associated hypermethylation in EBV-infected cells, to identify EBV-associated methylated genes and to elucidate their function in gastric carcinogenesis. / Methods: The cell model of gastric cancer AGS cells with or without stable EBV infection was used in this study. Genome-wide DNA methylation profiles were compared between AGS-EBV and AGS cells by high resolution Methyl-DNA immunoprecipitation microarry (MeDIP-chip) assay. EBV-associated methylated genes were classified according to gene ontology (GO). The novel EBV-associated methylated candidates were validated using bisulfite genomic sequencing (BGS), RT-PCR, and demethylation treatment. Biological function of one of the candidate genes (Somatostatin Receptor 1, SSTR1) was studied in vitro using gene knockdown and over-expression approaches simultaneously. Effects of SSTR1 expression on gastric cancer cell was measured by cell viability assay, colony formation assay, flow cytometry, wound-healing assay and invasion assay. Gene modulation by SSTR1 in human cancer pathways was assessed by cancer pathway PCR array. / Results: EBV infection was confirmed by EBER in situ hybridization. LMP2A expression was detected in AGS-EBV cells but not in EBV negative AGS cells. Expression and activity of DNMT3b was found to be significantly increased in AGS-EBV cells compared to AGS cells. Ectopic expression of LMP2A in AGS enhanced the expression and activity of DNMT3b. MeDIP-chip profiling identified a total of 1,065 genes differentially methylated by EBV infection (fold changes ≥2, P < 0.05) (fold-changes 2.4365.2). Gene ontology analysis indicated the enrichment of hypermethylated genes involving in important KEGG pathways. Notably, in addition to higher methylation levels confirmed by BGS, six novel hypermethylated genes (MDGA2, IL15RA, SCARF2, EPHB6, SSTR1 and REC8) were down-regulated in AGS-EBV cells as compared with AGS cells. Furthermore, demethylation treatment increased transcription levels of the six genes in AGS-EBV cells. / The biological function of SSTR1 gene was further investigated. Knockdown of SSTR1 in GC cells increased cell proliferation (P < 0.05) and colony formation ability (P < 0.01), and markedly increased cells in S phase through regulating G1/S phase mediators. Overexpression of SSTR1 in PANC1 cell line further confirmed that SSTR1 indeed was a tumor suppressor gene. Analysis of SSTR1 regulation of cancer pathway demonstrated that SSTR1 exerted antiproliferative effect by inducing cyclin-dependent inhibitors (p15, p16, p21 and p27) and inhibiting cell divison cycle 25 homolog A (CDC25A) and Myc, resulting in cell cycle arrest in G1 phase and reduction of cell proliferation. SSTR1 also took part in proliferation by decreasing expression of apoptosis regulators. Moreover, SSTR1 significantly downregulated the expression of migration-related genes, including ITGA1, ITGA2, ITGA3, ITGB5, IL8, MMP1 and PLAUR. These findings suggest that SSTR1 inhibits proliferation and reduces cell migration/invasion in gastric cancer by deregulating genes invloved in the regulation of cell cycle, survival/apoptosis and migration. / Conclusions: EBV infection in AGS cells induces genome-wide aberrant hypermethylation of 886 genes which involved in important cancer-related pathways. EBV-associated methylation is mediated by activation of DNMT3b through LMP2A. We identified and functionally characterized a novel EBV-associated methylated gene SSTR1 which exerted anti-tumor properties in GC. Epigenetic silencing of SSTR1 associated with EBV infection contributes to the pathogenesis of EBV-associated GC. / 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. / Zhao, Junhong. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 129-141). / Abstract also in Chinese. / ABSTRACT --- p.i / 摘 要 --- p.iv / Acknowledgements --- p.vi / Publications --- p.vii / Research articles --- p.vii / Conference abstracts --- p.viii / Table of contents --- p.x / list of tables --- p.xiii / list of figures --- p.xiv / list of abbreviations --- p.xvi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- General introduction --- p.1 / Chapter 1.2 --- Gastric Cancer --- p.3 / Chapter 1.2.1 --- Eipdemiology of Gastric Cancer --- p.4 / Chapter 1.2.2 --- Pathology of Gastric Cancer --- p.8 / Chapter 1.2.3 --- Risk Factors for Gastric Cancers --- p.11 / Chapter 1.3 --- Epstein-Barr Virus-associated Gastric Cancer (EBVaGC) --- p.15 / Chapter 1.3.1 --- Historical Discovery and Harm of EBV --- p.15 / Chapter 1.3.2 --- Molecular Biology of EBV --- p.16 / Chapter 1.3.3 --- Latent and Lytic Infection of EBV --- p.18 / Chapter 1.3.4 --- EBV Products --- p.18 / Chapter 1.3.5 --- EBV-associated gastric cancer (EBVaGC) --- p.28 / Chapter 1.4 --- EBV-induced Epigenetic Alteration in Gastric Carcinogenesis --- p.36 / Chapter 1.4.1 --- Cytosine Methylation and CpG Island --- p.36 / Chapter 1.4.2 --- DNA Methylation in Gastric Cancer --- p.39 / Chapter 1.5 --- How to identify EBV-induced promoter methylation in gastric cancer --- p.45 / Chapter 1.5.1 --- Methylated DNA Immunoprecipitation (MeDIP) --- p.48 / Chapter 1.5.2 --- Combined Bisulfite Restriction Analysis (COBRA) --- p.49 / Chapter 1.5.3 --- Bisulfite Genomic Sequencing --- p.49 / Chapter 1.5.4 --- Pyrosequencing --- p.49 / Chapter Chapter 2 --- Materials and Methods --- p.51 / Chapter 2.1 --- Materials --- p.51 / Chapter 2.1.1 --- Cancer Cell Lines and Culture Condition --- p.51 / Chapter 2.1.2 --- Primary GC Samples --- p.52 / Chapter 2.2 --- EBV Encoded Nuclear RNA (EBER) in situ Hybridization (EBER-ISH) --- p.52 / Chapter 2.3 --- Western Blot Analysis --- p.53 / Chapter 2.4 --- Plasmid and Transfection --- p.56 / Chapter 2.4.1 --- Plasmid Construction and Extraction --- p.56 / Chapter 2.4.2 --- Plasmid Transfection --- p.59 / Chapter 2.5 --- Gene Expression Analysis --- p.59 / Chapter 2.5.1 --- Purification of Total RNA (RNeasy Kit, Qiagen) --- p.59 / Chapter 2.5.2 --- cDNA Reverse Transcription --- p.60 / Chapter 2.5.3 --- Semi-Quantitative PCR --- p.62 / Chapter 2.5.4 --- Quantitative Real-Time PCR (qRT-PCR) --- p.64 / Chapter 2.6 --- DNMT1 and 3b Activity Assay --- p.64 / Chapter 2.7 --- DNA Methylation Analysis --- p.64 / Chapter 2.7.1 --- Genomic DNA Extraction --- p.64 / Chapter 2.7.2 --- Genome-wide Profiling of EBV-associated DNA Methylation by MeDIP-chip --- p.65 / Chapter 2.7.3 --- Bioinformatics Analysis --- p.66 / Chapter 2.7.4 --- CpG Island Prediction and Analysis of the Targets’ Promoter Region --- p.66 / Chapter 2.7.5 --- DNA Sodium Bisulfite Modification --- p.67 / Chapter 2.7.6 --- Target Gene Methylation in GC Cell Lines --- p.67 / Chapter 2.7.7 --- Bisulfite Pyrosequencing Analysis in GC Tissue Samples --- p.70 / Chapter 2.8 --- Biological Function Analysis of SSTR1 --- p.72 / Chapter 2.8.1 --- Cell Proliferation Assay for Stable Transfection --- p.72 / Chapter 2.8.2 --- Colony Formation Assay --- p.72 / Chapter 2.8.3 --- Cell Cycle Analysis Assay --- p.72 / Chapter 2.8.4 --- Cell Migration Analysis --- p.73 / Chapter 2.8.5 --- Invasion Analysis --- p.73 / Chapter 2.8.6 --- Human Cancer Pathway Finder RT2 Profiler PCR Array Analysis --- p.74 / Chapter 2.9 --- Statistical Analysis --- p.76 / Chapter Charpter 3 --- results --- p.77 / Chapter 3.1 --- EBV Infection in AGS-EBV Cell Model --- p.77 / Chapter 3.2 --- Activation of DNMT3b in AGS-EBV Cells --- p.80 / Chapter 3.3 --- LMP2A Induced DNMT3b Activity in AGS Cells --- p.82 / Chapter 3.4 --- Genome-wide Profiling of DNA Methylation Associated with EBV Infection Using MeDIP-chip --- p.84 / Chapter 3.5 --- EBV-associated Cancer Pathways Defined by EBV-associated Promoter Methylated Genes --- p.86 / Chapter 3.6 --- CpG Hypermethylation and Transcriptional Silencing of EBV-associated Methylated Genes in AGS-EBV Cells --- p.88 / Chapter 3.7 --- Bioinformatics Analysis of SSTR1 Using University of California Santa Cruz Genome Bioinformatics (UCSC) Database and CpG Island Searcher --- p.93 / Chapter 3.8 --- COBRA Analysis of SSTR1 Promoter Methylation in GC Cell Lines --- p.93 / Chapter 3.9 --- Frequent SSTR1 Hypermethylation was Associated with EBV Positive Primary Gastric Cancer --- p.96 / Chapter 3.10 --- SSTR1 was Down-regulated in GC Cell Lines through RNA Interference --- p.103 / Chapter 3.11 --- SSTR1 Knockdown Induced Cell Proliferation in GC Cell Lines --- p.105 / Chapter 3.12 --- SSTR1 Knock-down Promoted Cells to Enter into S Phase --- p.108 / Chapter 3.13 --- SSTR1 Knock-down Increased the Migration Ability of GC --- p.110 / Chapter 3.14 --- SSTR1 Knock-down Promoted Cell Invasion --- p.112 / Chapter 3.15 --- Ectopic Expression of SSTR1 Inhibited Proliferation and Clonogenicity in PANC1 Cancer Cells --- p.114 / Chapter 3.16 --- Identification of Genes Modulated by SSTR1 --- p.116 / Chapter Chapter 4 --- Discussion --- p.119 / Chapter Chapter 5 --- Limitation of the study --- p.127 / ConclusionS --- p.128 / Reference --- p.129

Array-CGH analysis of the gastric cancer cell lines suggested that TXNIP loci were intact, suggesting that allelic loss might not be the major mechanism responsible for the downregulation of TXNIP in these cells. Furthermore, our data suggested that promoter hypermethylation of TXNIP may not be an important epigenetic mechanism that regulate the silencing of this gene. Chromatin immunoprecipitation (ChIP) assay revealed that SAHA induced hyperacetylation of histone H3 and H4 at the 5' flanking region of TXNIP gene, suggesting SAHA could promote TXNIP gene transcription via modification of histones located at the promoter region. Our data revealed that the loss or reduced expression of TXNIP in gastric cancer cells is associated with epigenetic histone acetylation mechanism. / Gastric cancer is a common cancer especially in Asian countries and is associated with high morbidity and mortality. Epigenetic inactivation of tumor suppressor is a common mechanism involved in carcinogenesis of a variety of human cancers and recent evidence suggested that targeting epigenetic modifications may be an approach to combat cancer. Our group and others have demonstrated frequent promoter methylation of cancer related genes in gastric cancer. In this study, we aim to identify cancer associated genes regulated by another important epigenetic mechanism, namely histone acetylation. / In addition, we demonstrated that over-expression of TXNIP significantly reduced cell migration ability and inhibited cell invasiveness in gastric cancer cells. Furthermore, absence or reduced expression of TXNIP in gastric cancer was associated with diffuse-type gastric cancer, advanced stage disease and predicted a poor disease specific survival. The findings supported that TXNIP is a functional tumor suppressor gene and may be a potential biomarker in gastric cancer. / We analyzed 25 paired gastric cancer and non-cancer gastric mucosa and found that expression of TXNIP mRNA level was reduced in 84% of gastric cancer and was significantly downregulated as compared to the paired non-cancer gastric tissues (p=0.002). Expression of TXNIP protein by western blot was down-regulated in 3 out of 5 cases. Furthermore, by immunohistochemical staining of TXNIP in tissue array containing 150 cases of gastric cancer also showed frequent down-regulation of TXNIP expression and &sim;26% with complete lack of TXNIP expression. / We first showed that suberoylanilide hydroxamic acid (SAHA), a well known histone deacetylase inhibitor, has anti-proliferative effect in a panel of gastric cancer cell lines (MKN1, MKN7, MKN28, MKN45, SNU1, SNU16, AGS, N87 and KatoIII cells). We compared gene expression profiles of SAHA treated vs control AGS cells to identify a set of genes that were differentially upregulated by SAHA treatment. Based on our microarray analysis in nine gastric cancer cell lines (MKN1, MKN7, MKN28, MKN45, SNU1, SNU16, AGS, N87 and KatoIII) and normal gastric tissues, a set of commonly downregulated genes in gastric cancer cells was elucidated. Analysis of these data sets with subsequent confirmation using real-time PCR analysis, genes that were downregulated in gastric cancer cells but upregulated upon SAHA treatment were identified. Among these selected genes, Thioredoxin Interacting Protein (also known as VDUP-1/TBP2/TXNIP ) was down-regulated in all cancer cell lines tested, and its protein expression was significantly induced by SAHA treatment in a numbers of gastric cancer cell lines including AGS, MKN1, MKN45, N87 and KatoIII. Thus, we focused on the TXNIP in the subsequent studies. / Tang, Angie. / Adviser: To Ka Fai. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 180-202). / 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 Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Liu, Xin. / "December 2009." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 119-126). / Abstracts in English and Chinese. / Abstract in English --- p.i / Abstract in Chinese --- p.iv / Acknowledgements --- p.vi / List of abbreviations --- p.vii / List of Tables List of Figures --- p.X xii / List of Publications --- p.xiv / Chapter Chapter 1 --- Literature Review --- p.1 / Chapter 1.1 --- Gastric cancer epidemiology and etiology --- p.1 / Chapter 1.2 --- Molecular carcinogenesis --- p.4 / Chapter 1.3 --- Tumor suppressor gene and the modes of tumor suppressor gene inactivation --- p.4 / Chapter 1.4 --- DNA methylation and carcinogenesis --- p.8 / Chapter 1.5 --- Identification of tumor suppressor genes --- p.15 / Chapter 1.6 --- "Vitamins, vitamin B complex, thiamine transporters and diseases" --- p.18 / Chapter 1.7 --- "Glucose metabolism, glycolysis and carcinogenesis" --- p.22 / Chapter 1.8 --- Clinical implications of DNA methylation --- p.28 / Chapter Chapter 2 --- Research Aim and Procedure --- p.31 / Chapter Chapter 3 --- Materials and Methods --- p.35 / Chapter 3.1 --- Cell lines and human tissue samples --- p.35 / Chapter 3.2 --- Cell culture --- p.35 / Chapter 3.3 --- Total RNA extraction --- p.36 / Chapter 3.4 --- Genomic DNA extraction --- p.37 / Chapter 3.5 --- Reverse transcription PCR (RT-PCR) --- p.38 / Chapter 3.5.1 --- Reverse transcription (RT) --- p.38 / Chapter 3.5.2 --- Semi-quantitative RT-PCR --- p.40 / Chapter 3.5.3 --- Real time RT-PCR --- p.42 / Chapter 3.6 --- General techniques --- p.44 / Chapter 3.6.1 --- DNA and RNA quantification --- p.44 / Chapter 3.6.2 --- Gel electrophoresis --- p.44 / Chapter 3.6.3 --- LB medium and LB plate preparation --- p.44 / Chapter 3.6.4 --- Plasmid DNA extraction --- p.45 / Chapter 3.6.4a --- Plasmid DNA mini extraction --- p.45 / Chapter 3.6.4b --- Plasmid DNA midi extraction --- p.46 / Chapter 3.6.5 --- DNA sequencing --- p.46 / Chapter 3.7 --- Methylation status analysis --- p.49 / Chapter 3.7.1 --- CpG island analysis --- p.49 / Chapter 3.7.2 --- Sodium bisulfite modification of DNA --- p.49 / Chapter 3.7.3 --- Methylation-specific PCR (MSP) --- p.50 / Chapter 3.7.4 --- Bisulfite genomic sequencing (BGS) --- p.53 / Chapter 3.8 --- Construction of expression plasmid DNA --- p.55 / Chapter 3.8.1 --- Construction of the SLC19A3-expressing vector --- p.55 / Chapter 3.8.2 --- Construction of the FBP1-expressing vector --- p.57 / Chapter 3.9 --- Functional analyses --- p.58 / Chapter 3.9.1 --- Monolayer colony formation assay --- p.58 / Chapter 3.9.2 --- Cancer cell growth curve analysis --- p.59 / Chapter 3.9.3 --- Lactate assay --- p.60 / Chapter 3.10 --- Statistical analysis --- p.61 / Chapter Chapter 4 --- Results --- p.62 / Chapter 4.1 --- Identification of novel candidate tumor suppressor genes downregulated by DNA methylation --- p.62 / Chapter 4.2 --- Selection of genes for further study --- p.62 / Chapter 4.3 --- Identification of SLC19A3 as a novel candidate tumor suppressor gene in gastric cancer --- p.64 / Chapter 4.3.1 --- Pharmacological restoration of SLC 19A3 downregulation in gastric cancer --- p.64 / Chapter 4.3.2 --- Methylation analysis of SLC 19A3 promoter region --- p.66 / Chapter 4.3.3 --- Functional analysis of SLC 19A3 in gastric cancer --- p.72 / Chapter 4.3.4 --- Clinicopathologic characteristics of SLC 19A3 promoter methylation in gastric cancer --- p.75 / Chapter 4.3.5 --- Discussion --- p.78 / Chapter 4.4 --- Identification of FBP1 as a novel candidate tumor suppressor gene regulated by NF-kB in gastric cancer --- p.85 / Chapter 4.4.1 --- Pharmacological restoration of FBP1 downregulation in gastric cancer --- p.85 / Chapter 4.4.2 --- Methylation analysis of FBP 1 promoter region --- p.87 / Chapter 4.4.3 --- Functional analysis of FBP 1 in gastric cancer --- p.93 / Chapter 4.4.4 --- Reduction of lactate generation under FBP1 expression --- p.95 / Chapter 4.4.5 --- Clinicopathologic characteristics of FBP 1 promoter methylation in gastric cancer --- p.98 / Chapter 4.4.6 --- NF-kB mediated FBP1 promoter hypermethylation in gastric cancer --- p.104 / Chapter 4.4.7 --- Discussion --- p.106 / Chapter Chapter 5 --- General discussion --- p.112 / Chapter Chapter 6 --- Summary --- p.117 / Reference list --- p.119

Background & aims. DNA methylation induced tumor suppressor gene silencing plays an important role in carcinogenesis. By using methylation-sensitive representational difference analysis, we identified paired box gene 5 (PAX5) being methylated in human cancer. PAX5 locates at human chromosome 9p13.2 and encodes a 391 amino acids transcription factor. However, the role of PAX5 in gastric cancer is still unclear. Hence, we analyzed its epigenetic inactivation, biological functions, and clinical implications in gastric cancer. / Conclusions. Our results demonstrated that PAX5 promoter methylation directly mediates its transcriptional silence and commonly occurs in gastric cancer. PAX5 gene can act as a functional tumor suppressor in gastric carcinogenesis by playing an important role in suppression of cell proliferation, migration, invasion, and induction of cell apoptosis. Detection of methylated PAX5 may be utilized as a biomarker for the prognosis of gastric cancer patients. / Methods. Methylation status of PAX5 promoter in gastric cancer cell lines and clinical samples was evaluated by methylation specific polymerase chain reaction (MSP) and bisulfite genomic sequencing (BGS). The effects of PAX5 re-expression in cancer cell lines were determined in proliferation, cell cycle, apoptosis, migration and invasion assays. Its in vivo tumorigenicity was investigated by injecting cancer cells with PAX5 expression vector subcutaneously into the dorsal flank of nude mice. Chromosome Immunoprecipitation (ChIP) and cDNA expression array were performed to reveal the molecular mechanism of the biological function of PAX5. / Results. PAX5 was silenced or down-regulated in seven out of eight of gastric cancer cell lines examined. A significant down-regulation was also detected in paired gastric tumors compared with their adjacent non-cancer tissues (n = 18, P = 0.0196). In contrast, PAX5 is broadly expressed in all kinds of normal adult and fetal tissues. The gene expression of PAX5 in the gastric cancer cell line is closely linked to the promoter hypermethylation status. In addition, the expression levels could be restored by exposure to demethylating agents 5-aza-21-deoxycytidine. Re-expression of PAX5 in AGS, BGC823 and HCT116 cancer cells reduced colony formation (P &lt; 0.01) and cell viability (P &lt; 0.05), arrested cell cycle in G0/G1 phase (P = 0.0055), induced cell apoptosis (P &lt; 0.05), repressed cell migration and invasion (P = 0.0218) in vitro. It also inhibited tumor growth in nude mice (P &lt; 0.05). The molecular basis of its function were investigated by cDNA expression array and demonstrated that ectopic expression of PAX5 up-regulated tumor suppressor gene P53, anti-proliferation gene P21, pro-apoptosis gene BAX, anti-invasion gene MTSS1 and TIMP1; and down-regulated anti-apoptosis gene BCL2, cell cycle regulator cyclinD1, migration related gene MET and MMP1. ChIP assay indicated that P53 and MET are direct transcriptional target of PAX5. Moreover, PAX5 hypermethylation was detected in 90% (145 of 161) of primary gastric cancers compared with 16% (3 of 19) of non-cancer tissues (P &lt; 0.0001). After a median follow-up period of 15.4 months, multivariate analysis revealed that gastric cancer patients with PAX5 methylation had a significant poor overall survival compared with the unmethylated cases (P = 0.0201). / Li, Xiaoxing. / Advisers: Hsiang Fu Kung; Jun Yu. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 134-159). / 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 Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.