Identification of a candidate tumor suppressor gene on 1p36.32 in oligodendrogliomas.

Abstract

Ng Yeung Lam.Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.Includes bibliographical references (leaves 180-209).Abstracts in English and Chinese.acknowledgements --- p.iabstract --- p.iiabstract in chinese --- p.vitable of contents --- p.ixlist of tables --- p.xiiilist of figures --- p.xi vlist of abbreviations --- p.xviChapter 1 --- chapter1 introduction and literature review --- p.1Chapter 1.1 --- Introduction of brain tumors --- p.1Chapter 1.2 --- Oligodendroglial tumors (OTs) --- p.3Chapter 1.2.1 --- Oligodendroglioma (OD) and anaplastic oligodendroglioma (AOD) --- p.3Chapter 1.2.1.1 --- WHO's definition and grading --- p.3Chapter 1.2.1.2 --- "Incidence, age, sex distribution, tumor location and survival rate" --- p.3Chapter 1.2.1.3 --- Clinical presentation --- p.4Chapter 1.2.1.4 --- Macroscopy and histopathology --- p.4Chapter 1.2.1.5 --- Immunohistochemistry --- p.5Chapter 1.2.1.6 --- Treatment --- p.6Chapter 1.2.2 --- Oligoastrocytoma (OA) and anaplastic oligoastrocytoma (AOA) --- p.11Chapter 1.2.2.1 --- WHO's definition and grading --- p.11Chapter 1.2.2.2 --- "Incidence, age, sex distribution, tumor location and survival rate" --- p.12Chapter 1.2.2.3 --- Clinical features --- p.12Chapter 1.2.2.4 --- Macroscopy and histopathology --- p.12Chapter 1.3 --- Overview of Genetic and Epigenetic Aberrations of OTs --- p.14Chapter 1.3.1 --- Chromosomal and genetic aberrations in OTs --- p.14Chapter 1.3.2 --- Candidate regions and genes on 1 p --- p.15Chapter 1.3.3 --- Candidate regions and genes on 19q --- p.20Chapter 1.3.4 --- Other aberrations in WHO grade II OTs --- p.24Chapter 1.3.5 --- Progression-associated aberrations in ODs --- p.25Chapter 1.3.6 --- Chromosomal and genetic aberrations in OAs --- p.29Chapter 1.4 --- Correlation of genetic alterations with response to therapy and survival --- p.31Chapter 1.4.1 --- Response to PCV chemotherapy correlates with lp and combined lp/19q status in patients with AODs --- p.31Chapter 1.4.2 --- Survival of patients with AODs correlates with lp/19q status --- p.32Chapter 1.4.3 --- WHO grade II ODs behavior and lp/19q status --- p.32Chapter 1.4.4 --- Response to other therapies (temozolomide and radiotherapy) and lp/19q status in patients with ODs --- p.33Chapter 1.4.5 --- lp and 19q loss in OAs and diffuse astrocytomas --- p.34Chapter 1.5 --- Microarray-based expression profiling of OTs --- p.35Chapter 1.6 --- Description of p73 protein --- p.37Chapter 1.6.1 --- Introduction of p73 --- p.37Chapter 1.6.2 --- p73: gene structure and splicing variants --- p.37Chapter 1.6.3 --- Signaling in p73 --- p.40Chapter 1.6.4 --- Regulation ofp73 protein stability and transcriptional activity --- p.43Chapter 1.6.4.1 --- Regulation by DNA damage --- p.43Chapter 1.6.4.2 --- Regulation by oncogenes --- p.44Chapter 1.6.4.3 --- Interaction with viral proteins --- p.44Chapter 1.6.5 --- Role of p73 in the nervous system --- p.45Chapter 1.6.6 --- p73 in cancer --- p.45Chapter 1.6.6.1 --- p73 knockout mice --- p.45Chapter 1.6.6.2 --- Alteration of p73 expression in human cancers --- p.46Chapter 1.6.7 --- p73 and chemosensitivity --- p.50Chapter CHAPTER2 --- AIMS OF STUDY --- p.51Chapter CHAPTER3 --- MATERIALS AND METHODS --- p.53Chapter 3.1 --- Tumor and blood samples --- p.53Chapter 3.2 --- Cell culture --- p.53Chapter 3.3 --- DNA extraction from frozen tissues and blood samples --- p.54Chapter 3.4 --- Detection of allelic loss of chromosome lp --- p.58Chapter 3.4.1 --- LOH analysis --- p.58Chapter 3.4.2 --- Fluorescence in situ Hybridization (FISH) analysis on Paraffin and Frozen Sections --- p.60Chapter 3.6 --- DNA sequencing analysis --- p.62Chapter 3.7 --- Analysis of Methylation --- p.63Chapter 3.7.1 --- Bisulfite sequencing --- p.63Chapter 3.7.2 --- Methylation-specific polymerase chain reaction (MSP) --- p.66Chapter 3.8 --- Northern Blot analysis --- p.68Chapter 3.9 --- RNA isolation and cDNA preparation --- p.70Chapter 3.10 --- Laser microdissection and RNA extraction from microdissected tumor cells --- p.71Chapter 3.10.1 --- Conventional RT-PCR --- p.71Chapter 3.11 --- Primer design for TP73 and its isoforms --- p.74Chapter 3.12 --- Real-time RT-PCR --- p.77Chapter 3.12.1 --- Real-time RT-PCR for TP73 and its isoforms --- p.78Chapter 3.12.2 --- Real-time RT-PCR for KIAA0495 --- p.79Chapter 3.13 --- Statistical analyses --- p.81Chapter CHAPTER4 --- RESULTS --- p.82Chapter 4.1 --- Genes annotated in the minimally deleted regions --- p.82Chapter 4.2 --- Expression analyses of TP73 and its isoforms in ODs by quantitative real-time RT-PCR --- p.85Chapter 4.3 --- Methylation analysis of TP73 in ODs by methylation sensitive PCR (MSP) --- p.97Chapter 4.4 --- A rapid screen of candidate genes for aberrant expression in microdissected tumors --- p.100Chapter 4.5 --- Quantitative real-time RT-PCR of KIAA0495 gene --- p.103Chapter 4.6 --- Mutation analysis of KIAA0495 gene --- p.110Chapter 4.7 --- Methylation analysis of KIAA0495 in ODs by bisulfite sequencing…… --- p.112Chapter 4.8 --- Detection of allelic loss of lp by LOH analysis and interphase FISH --- p.121Chapter 4.9 --- Two-hit inactivation of KIAA0495 gene in ODs --- p.126Chapter 4.10 --- Tissue distribution of KIAA0495 gene --- p.130Chapter 4.11 --- Bioinformatics of KIAA0495 --- p.133Chapter CHAPTER5 --- DISCUSSION --- p.146Chapter 5.1 --- Expression analysis of TP73 and its isoforms in ODs by isoform-specific RT-PCR --- p.148Chapter 5.2 --- Methylation status ofTP73 in ODs --- p.153Chapter 5.3 --- A rapid screening of candidate genes for aberrant expressionin microdissected tumors --- p.156Chapter 5.4 --- Expression pattern of KIAA0495 mRNA in a large cohort of ODs --- p.157Chapter 5.5 --- No somatic mutation in coding region of KIAA0495 --- p.158Chapter 5.6 --- Methylation status of putative promoter region of KIAA0495 in ODs --- p.159Chapter 5.7 --- Status of chromosome lp in ODs --- p.161Chapter 5.8 --- Two-hit inactivation of KIAA0495 gene in ODs by promoter hypermethylation and allelic loss of lp --- p.162Chapter 5.9 --- Evaluation of expression of KIAA0495 gene as a marker for the response to chemotherapy and prognostic marker in patients with OTs --- p.164Chapter 5.10 --- Tissue distribution of KIAA0495 --- p.166Chapter 5.11 --- "KIAA0495 cDNA sequence, protein sequence and potential functional features" --- p.167Chapter 5.12 --- Candidate tumor suppressor genes on lp in other type of tumors with loss of lp --- p.171Chapter CHAPTER6 --- CONCLUSIONS --- p.174Chapter CHAPTER7 --- FUTURE STUDIES --- p.177Chapter CHAPTER8 --- REFERENCES --- p.18