Bai Hsing Chen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 89-94). / Abstracts in English and Chinese. / Acknowledgments --- p.ii / Publication --- p.iii / List of Abbreviations --- p.iv / List of Tables --- p.v / List of Figures --- p.vi / Abstract --- p.vii / 摘要 --- p.x / Table of Contents --- p.xii / Chapter Chapter 1 --- INTRODUCTION / Chapter 1.1 --- Molecular Biology in Cancer Development --- p.2 / Chapter 1.1.1 --- Cell Cycle and Cancer --- p.2 / Chapter 1.1.2 --- Oncogenes and Tumor Suppressor Genes --- p.4 / Chapter 1.1.3 --- Epigenetic Alteration in Tumor Cells --- p.6 / Chapter 1.2 --- Colorectal Cancer Development --- p.9 / Chapter 1.2.1 --- Epidemiology of Colorectal Cancer --- p.9 / Chapter 1.2.2 --- Adenoma-Carcinoma Sequence --- p.11 / Chapter 1.2.2.1 --- Hyperplastic (metaplastic) Polyps --- p.11 / Chapter 1.2.2.2 --- Aberrant Crypt Foci (ACF) --- p.13 / Chapter 1.2.2.3 --- Adenomas --- p.13 / Chapter 1.2.2.4 --- Serrated adenomas --- p.15 / Chapter 1.2.2.5 --- Colorectal Carcinomas --- p.16 / Chapter 1.2.3 --- Genetic alterations in CRC --- p.18 / Chapter 1.2.4 --- Epigenetic alterations in CRC --- p.21 / Chapter 1.2.5 --- Staging of Colorectal Cancer --- p.23 / Chapter 1.3 --- Hypothesis --- p.25 / Chapter 1.4 --- Aim of Study --- p.26 / Chapter Chapter 2 --- MATERIALS and METHODES / Chapter 2.1 --- Patient Populations --- p.28 / Chapter 2.2 --- Microdissection and Immunohistochemistry --- p.29 / Chapter 2.3 --- DNA Isolation and Modification --- p.31 / Chapter 2.3.1 --- DNA Extraction from Microdissected Tissues --- p.31 / Chapter 2.3.2 --- DNA Extraction from Frozen Biopsy --- p.31 / Chapter 2.3.3 --- Bisulfite Modification of DNA --- p.32 / Chapter 2.4 --- Detection of K-ras Mutation --- p.33 / Chapter 2.5 --- Methylation-specific PCR (MSP) --- p.36 / Chapter 2.6 --- Bisulfite DNA Sequencing --- p.42 / Chapter 2.7 --- Statistical analysis --- p.44 / Chapter Chapter 3 --- RESULTS / Chapter 3.1 --- Promoter Hypermethylation of Tumor Related Genes in the Progression of Colorectal Neoplasia --- p.46 / Chapter 3.1.1 --- Clinico-Pathological parameters --- p.46 / Chapter 3.1.2 --- "Frequencies of Promoter Hypermethylation in Colorectal Cancers, Adenomas and Normal Colonic Tissues" --- p.47 / Chapter 3.1.3 --- Promoter Hypermethylation in Multiple Genes --- p.50 / Chapter 3.1.4 --- Promoter Hypermethylation in Advanced vs. Non-advanced Adenoma --- p.50 / Chapter 3.1.5 --- Methylation Patterns in Paired Adjacent Tissues from Cancer Patients --- p.53 / Chapter 3.1.6 --- Immunohistochemistry --- p.55 / Chapter 3.1.7 --- K-ras mutation --- p.61 / Chapter 3.1.8 --- Clinicopathological Correlations with Promoter Hypermethylation --- p.64 / Chapter 3.2 --- DNA Methylation Spread within HLTF CpG Island in Colorectal neoplasia --- p.67 / Chapter Chapter 4 --- DISCUSSION / Chapter 4.1 --- Methylation is an early event in Colorectal Carcinogenesis --- p.72 / Chapter 4.1.1 --- Methylation is frequently detected in both adenoma and carcinoma --- p.74 / Chapter 4.1.2 --- Concurrent methylation in multiple genes --- p.76 / Chapter 4.1.3 --- Methylation in advanced and non-advanced colorectal adenomas --- p.76 / Chapter 4.1.4 --- Relationship between K-ras mutation and methylation --- p.78 / Chapter 4.1.5 --- Methylation in adjacent tissues --- p.80 / Chapter 4.2 --- DNA Methylation Spread in HLTF gene --- p.81 / Chapter 4.2.1 --- HLTF is Frequently Methylated in Gastrointestinal Neoplasm --- p.82 / Chapter 4.2.2 --- Methylation Spread Patterns in Cancers and Adenomas --- p.83 / Chapter 4.2.3 --- Age Dependent Methylation Spread --- p.85 / Chapter Chapter 5 --- CONCLUSION --- p.87 / References --- p.89

In order to gain insights into the underlying mechanisms, several methods including, flow cytometric, western blot and quantitative real-time PCR analyses were employed. AITC-induced cell growth inhibition in SW620 cells was mainly caused by G2/M arrest, which was accompanied by regulatory proteins modifications. Results of western blot and quantitative real-time PCR analysis showed clear downregulation of pivotal phosphatases Cdc25B and Cdc25C at both transcriptional and post-translational levels in AITC-treated cells. Subsequently, accumulation of inhibitory phosphorylation of Cdc2 on Thr14 and Tyr15 were resulted. Furthermore, an AITC induced apoptosis after prolonged exposure was observed. It was a caspase-mediated apoptosis as evidenced by the activation of initiator caspases (-8 and -9), effector caspases (-3 and -7) and cleavage of Poly (ADP-ribose) polymerase (PARP). Besides in vitro studies, the antitumor activity of AITC was further illustrated by a nude mice xenografts experiment. Treatment with 10 micromol AITC could effectively suppress the growth of SW620 xenografts in vivo. Taken together, our results suggest that AITC is an attractive candidate for future research in chemotherapy and chemoprevention. / Many epidemiological studies indicate that a high intake of cruciferous vegetables, such as cabbage, broccoli and Brussels sprouts, may reduce the risk of certain types of cancer. Glucosinolates in cruciferous vegetables and their digested products are suggested to play an important role in such chemoprevention. When plant tissue is physically damaged, glucosidic bonds are cleaved by endogenous myrosinase to produce various products. Among these products, isothiocyanates (ITCs) draw most of the attention because of their potent antitumor activities. But the molecular mechanism leading to such effects has not yet been defined. / The objective of this study was to investigate the chemotherapeutic potential of allyl isothiocyanate (AITC) towards human colorectal adenocarcinoma cells. Another commonly founded ITC, phenylethyl isothiocyanate (PEITC) was employed as a reference sample. The growth inhibitory effects of ITCs on different colorectal adenocarcinoma cells were investigated using in vitro cell models. Both AITC and PEITC were found to inhibit the growth and proliferation of Caco-2, COLO 201 and SW620 cells in a time- and dose-dependent manner. Based on sensitivity, the most vulnerable SW620 cells were chosen for further studies. In the following BrdU assay, IC50 values for 24-h AITC and PEITC treatments were determined to be 30.2 and 9.21 microM, respectively. At the same time, the effects of ITCs on human normal skin fibroblast Hs68 cells were also investigated. It was found that the survival of Hs68 cells was not affected by the treatments of AITC. However, the survival of Hs68 cells was greatly affected by PEITC-treatments in a dose- and time-dependent manner. / Lau, Wing Sze. / Adviser: Wong Yum Shing. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 115-128). / 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.

Acute colitis was induced by exposing male SD rats to 4% DSS in drinking water for 8 days. Rats were divided into four groups as follows: DSS group---DSS-induced colitis; DSS + SRE group---SRE, 100 mg/kg/day in addition to DSS; Ctr + SRE group---SRE alone; and Ctr group---sham control group. The colon damage was elucidated by macroscopic, histological, electrophysiological and biochemical assessment. Orally administered SRE significantly reduced the colonic damage in all four aspects. However, baicalein did not show similar effect in the same experiment. / In summary, our finding indicated that both SRE and its major flavonoid, baicalein, could stimulate chloride secretion in human colonic T84 cells and mucosa freshly isolated from human colon. Although SRE was effective in treating acute DSS-induced ulcerative colitis, baicalein is unlikely the active anti-inflammatory component of SRE. Nevertheless, the results demonstrated that this TCM has a scientific basis for its effectiveness. Our data support further evaluation of the therapeutic potential of SRE for the treatment of IBD. / In TCM, Scutellariae radix and Coptidis Rhizoma (CR) derived compounds have been frequently used for gastroenteritis and secretory diarrhea. Our laboratory findings suggested that the major flavonoid component of SR, baicalein, stimulates chloride secretion in rat distal colon, probably via CFTR activation (Ko et al., 2002). In contrast, limited information about the cellular mechanism of chloride secretion induced by SR in human colonic epithelia is available. Therefore, the effect of Scutellariae radix extract (SRE) on electrolyte transport in a human colonic epithelial cell line, T84, was examined using the short-circuit current (ISC) technique. Results demonstrated that SRE stimulated a Cl--dependent secretion across T84 cells, probably via both Ca2+- and cAMP-mediated pathway. / On the other hand, the cellular mechanism of baicalein-induced Cl - secretion in T84 cells was further investigated. It was found that the secretory mechanisms involve protein kinase A (PKA)-, adenylate cyclase (AC)- and luminal cAMP-dependent Cl- channels, most likely cystic fibrosis transmembrane conductance regulator (CFTR) and serosal 293B-sensitive K + channels. However, the action of baicalein cannot be solely explained by its cAMP-elevating effect. In addition, the effect of baicalein could be potentiated by the inhibition of mitogen-activated protein kinase (MAPK) and phosphoinositide-3 kinase (PI3K). Furthermore, it was found that inhibition of protein kinase C (PKC) delta limited the baicalein-induced chloride secretion. / Our laboratory has found that baicalein (Ko et al., 2002 and Yue et al., 2003) stimulates chloride secretion in rat distal colon and human colonic T84 cells. As it is known that responses in the animal model or the cell line may not completely reflect the in vivo physiology, it is important to study the above responses in human colon. With scarce supply of freshly isolated human colonic mucosa, the results showed that the effect of SRE and baicalein on ion transport in human samples is similar to that obtained in T84 cell line and rat model. / Scutellariae radix (SR) is the dry root of Scutellariae baicalensis Georgi (Huangqin). SR has been employed for centuries as a traditional Chinese medicine (TCM) for various purposes. It contains a large amount of flavonoids such as baicalein, baicalin, and wogonin, which possess a number of beneficial bioactivities including anti-oxidant, anti-bacterial and anti-inflammatory, etc. / Ulcerative colitis (UC), an inflammatory bowel disease (IBD), has been known for more than half a century. Recent studies have shown that two flavonoids derived from SR, baicalein and wogonin, might alleviate the symptoms of IBD. Moreover, SR is the major component of Hange-shasshin-to (HST), one of the Chinese herbal formulas, which has been reported to suppress the pathogenesis of IBD. The above scientific background led us to examine the effect of SRE administration on DSS-induced colitis in rats in a way to evaluate new treatments potentially applicable to UC in humans. / Chung, Ho Lam. / "August 2007." / Adviser: W. H. Ko. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0925. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references. / 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.

Chan, Man Hung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 111-126). / Abstract also in Chinese. / Examination Committee List --- p.ii / Declaration --- p.iii / Acknowledgements --- p.iv / 摘要（Abstract in Chinese) --- p.vi / Abstract --- p.viii / List of Abbreviations --- p.x / List of Figures and Tables --- p.xii / Table of Content --- p.xiv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Background of photodynamic therapy (PDT) --- p.2 / Chapter 1.1.1 --- History of PDT --- p.2 / Chapter 1.1.2 --- Photochemistry --- p.3 / Chapter 1.1.3 --- Principal stages of PDT --- p.5 / Chapter 1.1.4 --- Light sources of PDT --- p.6 / Chapter 1.2 --- Anti-tumor effect of PDT --- p.8 / Chapter 1.2.1 --- Mode of cell death --- p.8 / Chapter 1.2.2 --- PDT-induced anti-tumor immunity --- p.9 / Chapter 1.3 --- Clinical applications of PDT --- p.11 / Chapter 1.3.1 --- Photofrin® --- p.11 / Chapter 1.3.2 --- Clinical applications of PDT --- p.13 / Chapter 1.3.3 --- Challenges of PDT for clinical applications --- p.15 / Chapter 1.4 --- The development of new photosensitizers --- p.16 / Chapter 1.4.1 --- Targeted PDT --- p.16 / Chapter 1.4.2 --- Phthalocyanine --- p.18 / Chapter 1.5 --- Objective of my study --- p.21 / Chapter Chapter 2 --- Materials and Methods --- p.23 / Chapter 2.1 --- Synthesis of glucosylated silicon(IV) phthalocyanine (SiPcGlu) --- p.24 / Chapter 2.2 --- In vitro studies --- p.24 / Chapter 2.2.1 --- Cell line and culture conditions --- p.24 / Chapter 2.2.2 --- Photodynamic treatment --- p.25 / Chapter 2.2.3 --- Cell viability assay --- p.27 / Chapter 2.2.4 --- Light dose effect on the photocytotoxicity of SiPcGlu-PDT --- p.27 / Chapter 2.2.5 --- Determination of reactive oxygen species (ROS) production by SiPcGlu-PDT --- p.29 / Chapter 2.2.6 --- Effect of antioxidants on the photocytotoxicity of SiPcGlu-PDT --- p.29 / Chapter 2.2.7 --- Determination of ROS production after SiPcGlu-PDT --- p.30 / Chapter 2.2.8 --- Glucose competitive assay --- p.30 / Chapter 2.2.9 --- Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay --- p.30 / Chapter 2.2.10 --- DNA fragmentation analysis by gel electrophoresis --- p.31 / Chapter 2.2.11 --- Annexin-V & propidium iodide staining assay --- p.32 / Chapter 2.2.12 --- Subcellular localization studies --- p.33 / Chapter 2.2.13 --- Detection of mitochondrial superoxide production --- p.34 / Chapter 2.2.14 --- Assessment of mitochondrial membrane potential --- p.34 / Chapter 2.2.15 --- Caspase-3 activity assay --- p.35 / Chapter 2.2.16 --- "Western blot analyses for cytochrome c, caspase-3, PARP and glucose-regulated protein 78 (GRP78)" --- p.36 / Chapter 2.2.17 --- Ca2+ release from endoplasmic reticulum (ER) --- p.37 / Chapter 2.3 --- In vivo studies --- p.37 / Chapter 2.3.1 --- HT29 tumor-bearing nude mice model --- p.37 / Chapter 2.3.2 --- In vivo photodynamic treatment --- p.39 / Chapter 2.3.3 --- Biodistribution of SiPcGlu --- p.39 / Chapter 2.3.4 --- Assay for plasma enzyme activities --- p.40 / Chapter 2.4 --- Statistical analysis --- p.41 / Chapter Chapter 3 --- Results --- p.42 / Chapter 3.1 --- In vitro studies --- p.43 / Chapter 3.1.1 --- SiPcGlu-PDT induced cytotoxicity on HT29 cells --- p.43 / Chapter 3.1.2 --- Light dose effect on cytotoxicity by SiPcGlu-PDT --- p.46 / Chapter 3.1.3 --- SiPcGlu-PDT induced ROS production --- p.48 / Chapter 3.1.4 --- SiPcGlu-PDT induced cell death through Type I and II photoreactions --- p.48 / Chapter 3.1.5 --- ROS production after SiPcGlu-PDT --- p.51 / Chapter 3.1.6 --- Glucose competitive Assay --- p.55 / Chapter 3.1.7 --- SiPcGlu-PDT induced apoptosis in HT29 cells --- p.57 / Chapter 3.1.8 --- Subcellular localization of SiPcGlu --- p.61 / Chapter 3.1.9 --- SiPcGlu-PDT induced mitochondrial changes --- p.66 / Chapter 3.1.10 --- SiPcGlu-PDT induced caspase activation --- p.68 / Chapter 3.1.11 --- SiPcGlu-PDT increased expression of ER chaperone GRP78 --- p.72 / Chapter 3.1.12 --- SiPcGlu-PDT induced release of Ca2+ from ER --- p.72 / Chapter 3.2 --- In vivo studies --- p.75 / Chapter 3.2.1 --- In vivo photodynamic activities --- p.75 / Chapter 3.2.2 --- Tissue distribution of SiPcGlu --- p.77 / Chapter 3.2.3 --- Analysis of intrinsic toxicity --- p.77 / Chapter Chapter 4 --- Discussion --- p.80 / Chapter 4.1 --- Physical Properties of SiPcGlu --- p.81 / Chapter 4.2 --- In vitro studies --- p.82 / Chapter 4.2.1 --- SiPcGlu-PDT exhibits a high potency in killing HT29 cells --- p.82 / Chapter 4.2.2 --- ROS production is responsible for the cytotoxic effect of SiPcGlu-PDT --- p.83 / Chapter 4.2.3 --- SiPcGlu-PDT induced apoptosis in HT29 cells --- p.85 / Chapter 4.2.4 --- SiPcGlu is localized in various membranous organelles --- p.87 / Chapter 4.2.5 --- SiPcGlu-PDT induced mitochondria-mediated apoptosis --- p.89 / Chapter 4.2.6 --- SiPcGlu-PDT induced ER stress --- p.93 / Chapter 4.3 --- In vivo studies --- p.96 / Chapter 4.3.1 --- SiPcGlu failed to target to tumor tissues --- p.96 / Chapter 4.3.2 --- SiPcGlu-PDT induced retardation in tumor growth --- p.99 / Chapter 4.3.3 --- SiPcGlu is a safe photosensitizer for PDT --- p.101 / Chapter Chapter 5 --- Conclusion and Future Perspectives --- p.103 / Chapter 5.1 --- Conclusion --- p.104 / Chapter 5.2 --- Future Perspectives --- p.106 / Chapter 5.2.1 --- In vitro studies --- p.106 / Chapter 5.2.1.1 --- Lysosomal pathway to cell death --- p.106 / Chapter 5.2.2 --- In vivo studies --- p.107 / Chapter 5.2.2.1 --- Pharmacokinetic studies --- p.107 / Chapter 5.2.2.2 --- Eradication of HT29 tumor by repeated dose of SiPcGlu --- p.108 / Chapter 5.2.2.3 --- SiPcGlu-PDT-induced anti-tumor immunity --- p.108 / Chapter 5.2.2.4 --- Enhancement of tumor selectivity by conjugating with biomolecules --- p.109 / References --- p.110

Colorectal cancer (CRC) is one of the most common malignancies worldwide. However, adjuvant chemotherapeutic agents exhibit poor accumulation in the tumor mass and frequently result in serious side effects due to nonspecific damage to normal organs. Therefore, the development of more selective anticancer drugs with targeted delivery to tumor sites is the current trend in cancer therapies. Among these sites, tumor neovasculature is an attractive target for anticancer agents. It is because tumor growth is largely limited by blood supply which is dependent on the extent of angiogenesis in the tumor. / Experimental analysis suggested that TCP-1 phage and synthetic TCP-1 peptide specifically homed to colorectal cancer tissues and co-localized with the tumor vasculature. Moreover, TCP-1 peptide also recognized the vasculature of human colorectal cancer specimens. Subsequently, the homing abilities of TCP-1 phage were extensively tested in other cancer models. Results showed that TCP-1 peptide could also target the vasculature of orthotopic gastric cancer induced by human colon cancer cell line (MKN45) in BALB/c nude mice. Meanwhile, TCP-1 phage exhibited binding activity to colorectal cancer cells such as colon 26 and SW1116. TCP-1 peptide could carry a pro-apoptotic peptide into these cells and markedly enhanced its pro-apoptotic action. / In summary, we have used the phage display technology to isolate two unique peptides TCP-1 and TCP-2, which targeted the vasculature of orthotopic colorectal cancer and also recognized the vasculature of human colorectal cancer. Moreover, they could deliver fluorescein or pro-apoptotic peptide only to the tumor vasculature but not to other normal tissues, for imaging detection and targeted therapy. In conclusion, both TCP-1 and TCP-2 may have significant clinical applications as carriers in diagnostic imaging and ligand-mediated targeted therapy for human colorectal cancer. / Similarly, TCP-2 phage or its peptide also targeted specifically the orthotopic colorectal cancer, and co-localized with the tumor vasculature in mice. Meanwhile, TCP-2 peptide recognized the vasculature of human colorectal cancer specimens. FITC-labeled TCP-2 peptide could also be used to detect cancer tissues in tumor-bearing mice. / To identify specific ligands targeting the tumor neovasculature, in vivo phage display technology has been extensively used. Several dozens of peptides homing to normal or diseased vasculature have been identified through this technology. However, these peptides target mainly the tumors growing at distant sites but not at the primary organ, thus limiting their clinical application. To obtain specific peptides targeting the neovasculature of colorectal cancer growing in situ, we established an orthotopic colorectal cancer model in normal BALB/c mice by using syngeneic colon cancer cells (colon 26). Subsequently, in vivo phage display technology was utilized to isolate peptides which specifically recognized the vasculature of the cancer. Four peptides (termed TCP-1, 2, 3, 4) were enriched more than once after four-round selections. Further investigation disclosed that TCP-1 and TCP-2 phages had relatively stronger binding abilities to cancer tissues among the four phage clones. They were chosen for further study. / We further demonstrated that TCP-1 could serve as a carrier for image detection and drug delivery. FITC-labeled TCP-1 could specifically produce a strong fluorescence signal in the tumors after intravenous injection into the orthotopic tumor-bearing mice. Moreover TCP-1, when conjugated with a pro-apoptotic peptide, could also specifically induce apoptosis of tumor vasculature in vivo. / Li, Zhijie. / Adviser: Cho Chiltin. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 194-221). / 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.

Source: Masters Abstracts International, Volume: 46-03, page: 1373. Advisers: Robert J. Hardy; Asha S. Kapadia. Includes bibliographical references.

An important problem in bioinformatics is the reconstruction of gene regulatory networks from expression data. The analysis of genomic data stemming from high- throughput technologies such as microarray experiments or RNA-sequencing faces several difficulties. The first major issue is the high variable to sample ratio which is due to a number of factors: a single experiment captures all genes while the number of experiments is restricted by the experiment’s cost, time and patient cohort size. The second problem is that these data sets typically exhibit high amounts of noise.<p><p>Another important problem in bioinformatics is the question of how the inferred networks’ quality can be evaluated. The current best practice is a two step procedure. In the first step, the highest scoring interactions are compared to known interactions stored in biological databases. The inferred networks passes this quality assessment if there is a large overlap with the known interactions. In this case, a second step is carried out in which unknown but high scoring and thus promising new interactions are validated ’by hand’ via laboratory experiments. Unfortunately when integrating prior knowledge in the inference procedure, this validation procedure would be biased by using the same information in both the inference and the validation. Therefore, it would no longer allow an independent validation of the resulting network.<p><p>The main contribution of this thesis is a complete computational framework that uses experimental knock down data in a cross-validation scheme to both infer and validate directed networks. Its components are i) a method that integrates genomic data and prior knowledge to infer directed networks, ii) its implementation in an R/Bioconductor package and iii) a web application to retrieve prior knowledge from PubMed abstracts and biological databases. To infer directed networks from genomic data and prior knowledge, we propose a two step procedure: First, we adapt the pairwise feature selection strategy mRMR to integrate prior knowledge in order to obtain the network’s skeleton. Then for the subsequent orientation phase of the algorithm, we extend a criterion based on interaction information to include prior knowledge. The implementation of this method is available both as part of the prior retrieval tool Predictive Networks and as a stand-alone R/Bioconductor package named predictionet.<p><p>Furthermore, we propose a fully data-driven quantitative validation of such directed networks using experimental knock-down data: We start by identifying the set of genes that was truly affected by the perturbation experiment. The rationale of our validation procedure is that these truly affected genes should also be part of the perturbed gene’s childhood in the inferred network. Consequently, we can compute a performance score / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Indiana University-Purdue University Indianapolis (IUPUI) / Carboxylesterases (CES) are enzymes that metabolize a wide variety of compounds including esters, thioesters, carbamates, and amides. In humans there are three known carboxylesterase genes CES1, CES2, and CES3. Irinotecan (CPT-11) and capecitabine are important chemotherapeutic prodrugs that are used for the treatment of colorectal cancer. Of the three CES isoenzymes, CES2 has the highest catalytic efficiency for irinotecan activation. There is large inter-individual variation in response to treatment with irinotecan. Life-threatening late-onset diarrhea has been reported in approximately 13% of patients receiving irinotecan. Several studies have reported single nucleotide polymorphisms (SNPs) for the CES2 gene. However, there has been no consensus on the effect of different CES2 SNPs and their relationship to CES2 RNA expression or irinotecan hydrolase activity. Three CES2 mRNA transcripts of approximately 2kb,3kb, and 4kb have been identified by multi-tissue northern analysis. The expressed sequence tag (EST) database indicates that CES2 undergoes several splicing events that could generate up to six potential proteins. Four of the proteins CES2, CES2458-473, CES2+64, CES21-93 were studied to characterize their expression and activity. Multi-tissue northern analysis revealed that CES2+64 corresponds to the 4kb and 3kb transcripts while CES21-93 is located only in the 4 kb transcript. CES2458-473 is an inactive splice variant that accounts for approximately 6% of the CES2 transcripts in normal and tumor colon tissue. There is large inter-individual variation in CES2 expression in both tumor and normal colon samples. Characterization of CES2+64 identified the protein as normal CES2 indicating that the signal peptide is recognized in spite of the additional 64 amino acids at the N-terminus. Sub-cellular localization studies revealed that CES2 and CES2+64 localize to the ER, and CES21-93 localizes to the cytoplasm. To date CES2 SNP data has not provided any explanation for the high inter-individual variability in response to irinotecan treatment. Multi-tissue northern blots indicate that CES2 is expressed in a tissue specific manner. We have identified the CES2 variants which correspond to each mRNA transcript. This information will be critical to defining the role of CES2 variants in the different tissues.

Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: Introduction: The ability of different polyunsaturated fatty acids (PUFAs), especially n-3 PUFAs, to prevent the development of cancer has been under intense investigation the past three decades. Numerous studies have shown that these fatty acids can kill cancer cells in vitro as well as in vivo whilst normal cells remain unaffected. Unfortunately, the cellular and molecular mechanisms responsible for this phenomenon are still poorly understood. This study investigated the signalling pathways modulated by docosahexaenoic acid (DHA) in an adenocarcinoma cell line, in order to shed some light on these unknown mechanisms. Materials & Methods: NCM460 (normal colon epithelial) and CaCo2 (colon adenocarcinoma) cells were cultured and treated with low doses of palmitic acid (PMA), oleic acid (OA), arachidonic acid (AA), and DHA. The effects of these fatty acids on the proliferation of the cells were measured with the MTT assay. The composition of membrane phospholipids of CaCo2 cells was determined after 48h supplementation with different fatty acids by gas chromatography. Also, CaCo2 cells were treated with DHA (10 μM) only and proteins were harvested at fixed time points ranging from 2 minutes to 48 hours. The protein inhibitors wortmannin (PI3 kinase inhibitor), PD 98059 (MEK inhibitor) and SB 203580 (p38 inhibitor) and also RNA interference (RNAi) of the p38 MAPK protein were used to investigate cross-talk between signalling pathways. ERK, p38 MAP kinase, Akt, and p53 were then analysed by Western blotting using phospho-specific and total antibodies. The cleavage of the apoptotic proteins, caspase-3 and PARP were also analysed. Results and discussion: MTT assays revealed that none of the fatty acids were toxic to normal cells. In addition, DHA was shown to be most effective to kill CaCo2 cells whilst protecting NCM460 cells and a subsequent dose response experiment revealed that lower concentrations are most suitable for this purpose. DHA was also shown to be readily incorporated into phospholipids, along with AA. This is associated with increased membrane fluidity, which could affect the localisation, and downstream effects, of various signalling proteins within the membrane. Western blot analysis revealed a rapid increase in activity in most proteins under investigation, especially ERK and Akt (Ser473). Long-term DHA supplementation suppressed the full activation of Akt. This down regulation of survival signalling could lead to cell death in CaCo2 cells. In addition, it was shown that after 48h, DHA induced the cleavage of caspase-3 and PARP, which is indicative of apoptosis. RNAi experiments suggested a possible role for p38 MAPK in the phosphorylation of p53 at Ser15, a site which is associated with DNA damage. Conclusion: DHA exerts its effects by means of cellular signal transduction pathways, particularly by suppression of the important survival-related kinase, Akt. This could have implications for future therapeutic interventions in cancer patients, as fatty acids are safe to use and do not interfere with the functionality of normal tissue. / AFRIKAANSE OPSOMMING: Inleiding: Die vermoë van verskillende poli-onversadigde vetsure (POVSe), veral n-3 POVSe, om die ontstaan van kanker te voorkom, is intens nagevors die afgelope drie dekades. Menigte studies het aangevoer dat hierdie vetsure kankerselle in vitro asook in vivo kan doodmaak, terwyl normale selle nie daardeur beïnvloed word nie. Ongelukkig word die sellulêre and molekulêre meganismes onderliggend tot hierdie verskynsel nie goed begryp nie. Hierdie studie het verskeie seintransduksie-paaie wat deur dokosaheksaenoësuur (DHS) in ‘n adenokarsinoom sellyn gemoduleer word, ondersoek. Materiale & Metodes: NCM460 (normale kolonepiteel) en CaCo2 (kolon adenokarsinoom) selle is onderhou in ‘n selkultuur-laboratorium en behandel met lae dosisse palmitiensuur (PMS), oleïensuur (OS), aragidoonsuur (AS), en DHS. Die invloed van hierdie vetsure op die proliferasie van die selle is d.m.v. die MTT toets bepaal. The samestelling van membraan-fosfolipiede van CaCo2 selle is na 48h behandeling met die verskillende vetsure bepaal deur middel van gaschromatografie. Die CaCo2 selle is ook met DHA (10 μM) alleenlik behandel en teen vaste tydpunte wat wissel van 2 minute tot 48h, waarna proteïene geëkstraeer is. Die proteïen-inhibitore wortmannin (PI3 kinase inhibitor), PD 98059 (MEK inhibitor), en SB 203580 (p38 inhibitor) asook RNAinterferensie (RNAi) teen die p38 MAPK proteïen is ingespan om oorvleueling tussen seintransduksie–weë te ondersoek. ERK, p38 MAPK, Akt, en p53 is geanaliseer deur middel van die Western–klad metode met fosfo–spesifieke en totale antiliggame. Die kliewing van die apoptotiese proteïene caspase-3 en PARP is ook bepaal. Resultate en bespreking: MTT toetse het ontul dat geen vetsure toksies was vir die normale selle nie. Daar is ook gevind dat DHS die mees effektiewe vetsuur was om CaCo2 selle te dood, terwyl NCM460 selle beskerm word. Gevolglik het ‘n dosis-respons eksperiment getoon dat laer konsentrasies die beste geskik is vir hierdie doel. Daar is ook gevind dat DHA maklik in fosfolipiede geïnkorporeer word, tesame met AS. Dit word geassosieer met verhoogde membraan-vloeibaarheid, wat die ligging, en ook stroom-af werking, van verskeie seintransduksie proteïene in die membraan, kan beïnvloed. Westernklad analises het ‘n vinnige verhoging in die aktiwiteite van die meeste proteïene onder die soeklig, getoon, veral ERK en Akt (Ser473). Langdurige DHS behandeling het die maksimale aktiwiteit van Akt onderdruk. Hierdie afname van oorlewing-gerigte seine kan lei tot seldood in CaCo2 selle. Daar is boonop geving dat DHS die kliewing van caspase-3 en PARP geïnduseer het na 48, wat dui op apoptose. Uit die RNAi eksperiment kon daar ook ‘n moontlike rol vir p38 MAPK in die fosforilering van p53 by Ser15, wat geassosieer word met DNS-skade, getoon word. Gevolgtrekking: DHS beoefen sy effekte deur middel van seintransduksie paaie, veral deur die oorlewing-geassosieerde kinase, Akt, te onderdruk. Dit kan implikasies hê vir toekomende terapeutiese ingrypings in kankerpasiënte, aangesien vetsure veilig is om te gebruik en nie skadelik is vir normale weefsel nie.

Colorectal cancer is the second leading cause of cancer-related mortality in Hong Kong and lack of selectivity has limited the success of conventional chemotherapy. Given the recent interest in the anti-cancer effects of traditional Chinese medicine (TCM), there are two approaches to studying its bioactivity: as a mixture of ingredients or as single compounds. The objective of the present study is to examine the anti-tumor effects of Angelicae Sinensis Radix (DG) and Garcinia hanburyi resin (TH) using both approaches, respectively, as they are traditionally used to treat inflammation. In the present study, their anti-cancer effects and the mechanisms of actions were examined for the development of potential novel chemotherapeutic drugs for colon cancer since inflammation is a predisposing factor for colon cancer. / DG extract and its three main bioactive phtbalides: n-butylidenephthalide, senkyunolide A and z-ligustilide (LGT), were found to be cytotoxic to HT-29 cells with IC50 values (24 h) of 20.70 +/- 0.85, 72.51 +/- 8.65, 18.74 +/- 1.14 and 41.98 +/- 3.64 mug/ml, respectively. The results evidenced that LGT induced G0/G 1 arrest and apoptosis, triggering cleavage of PARP, pro-caspases-3, -8 and -9 and nuclear fragmentation. LGT and cisplatin synergistically reduced the viability of HT-29 cells. More interestingly, DG extract was more potent than individual phthalides, suggesting that there are other bioactive components and/or synergistic interactions. / Individual compounds purified from TH were investigated because gambogic acid isolated from this herb has been used clinically to treat cancer, 30-Epicambogin (EPC) and guttiferone K (GUTK) showed the highest cytotoxic selectivity and potency on HT-29 cells among 15 isolated compounds. IC50 values (24 h) for EPC and GUTK in HT-29 cells were 5.36+/-0.25 and 5.39+/-0.22 muM, respectively, and both induced G0/G1 arrest by down-regulation of cyclins D1, D3, CDK4 and CDK6, while up-regulation of p21Waf1/CiP1 and p27KiP1. Both compounds triggered the activation of caspases-3, -8 and -9 in apoptosis. The in vivo anti-tumor effects of GUTK were further investigated by using a subcutaneous Colon-26 mouse tumor model. GUTK (10 mg/kg i.p.) reduced tumor volume by 33.6% and potentiated the anti-tumor effects of 5-fluorouracil when administered concurrently. / Our findings revealed that DG rather than individual phthalides, is worthy for further study as a potential anti-cancer drug, due to the synergistic interactions among multi-components in the herb. On the other hand, EPC and GUTK, isolated from TH have potential to be developed as novel anti-tumor candidates for combination use with 5-fluorouracil. The results strongly support the use of different approaches to study TCM for chemotherapy, according to its traditional and empirical use. / Subsequently, the anti-proliferative effects of DG and Chuanxiong Rhizoma (CX) extracts and mixtures containing three phthalides in the proportions similar to their presence in both extracts were examined, since CX also contains the same phthalides, but in different proportions. DG extract was significantly more potent than its corresponding phthalide mixture to inhibit cancer cell proliferation and synergistic interaction was observed among the phthalides and other bioactive components, while the phthalides in CX extract interacted antagonistically with other components. / Kan, Lai Ting Winnie. / Adviser: Ge Lin. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 267-311). / 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.