Cheung Shiu-fai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 131-139). / Abstracts in English and Chinese. / ACKNOWLEDGEMENTS --- p.i / ABSTRACT --- p.iii / 摘要 --- p.vi / TABLE OF CONTENTS --- p.ix / LIST OF FIGURES --- p.xvi / LIST OF TABLES --- p.xviii / ABBREVIATIONS --- p.xix / PUBLICATION --- p.xxi / AWARD --- p.xix / Chapter SECTION 1. --- INTRODUCTION OF HEPATOCELLULAR CARCINOMA --- p.1 / Chapter 1.1 --- Epidemiology of Hepatocellular Carcinoma --- p.1 / Chapter 1.2 --- Etiologies of HCC --- p.1 / Chapter 1.2.1 --- Hepatitis B Virus and Hepatitis C Virus --- p.2 / Chapter 1.2.2 --- Aflatoxins and Alcohol --- p.3 / Chapter 1.3 --- Major Diagnostic and Prognostic Markers of HCC --- p.4 / Chapter 1.3.1 --- Biochemical Tumor Markers --- p.5 / Chapter 1.3.2 --- Clinico-pathological Features of HCC --- p.6 / Chapter SECTION 2. --- THE MITOCHONDRION --- p.7 / Chapter 2.1 --- Structure of the Mitochondrial Genome --- p.9 / Chapter 2.1.1 --- Nicotinamide Adenine Dinucleotide Dehydrogenase --- p.10 / Chapter 2.1.2 --- Cytochrome b --- p.10 / Chapter 2.1.3 --- Cytochrome c Oxidase --- p.11 / Chapter 2.1.4 --- ATP Synthase --- p.11 / Chapter 2.1.5 --- Ribosomal RNA --- p.11 / Chapter 2.1.6 --- Transfer RNA --- p.12 / Chapter 2.1.7 --- Displacement Loop --- p.12 / Chapter 2.2 --- Replication of Mitochondrial DNA --- p.17 / Chapter 2.3 --- Transcription of Mitochondrial DNA --- p.17 / Chapter SECTION 3. --- PHYSIOLOGY OF MITOCHONDRIA --- p.19 / Chapter 3.1 --- Energy Production by Oxidative Phosphorylation (OXPHOS) --- p.19 / Chapter 3.2 --- Programmed Cell Death: Apoptosis --- p.22 / Chapter 3.3 --- Morphology of Mitochondria in Hepatocytes --- p.25 / Chapter SECTION 4. --- MUTATIONS OF MITOCHONDRIAL DNA --- p.26 / Chapter 4.1 --- Special Terms Used in This Study --- p.26 / Chapter 4.1.1 --- Somatic Mutations and Polymorphisms --- p.26 / Chapter 4.1.2 --- Homoplasmic and Heteroplasmic Mutations --- p.26 / Chapter 4.2 --- Factors Causing High Mutation Frequency in mtDNA --- p.27 / Chapter 4.2.1 --- Presence of Reactive Oxygen Species --- p.27 / Chapter 4.2.2 --- Lack of Protective Histories --- p.28 / Chapter 4.2.3 --- Limited DNA Repair Mechanism --- p.29 / Chapter 4.3 --- Theories of Homoplasmic Mutations --- p.31 / Chapter 4.3.1 --- Replicative Advantage on Mutated mtDNA Sequence Selection --- p.31 / Chapter 4.3.2 --- Random Mutagenesis and Segregation --- p.32 / Chapter 4.4 --- MtDNA Mutations in Mitochondrial Disease and Aging --- p.33 / Chapter 4.5 --- MtDNA Deletions in Cancer --- p.34 / Chapter 4.6 --- Somatic Mutations of MtDNA in Various Cancers --- p.35 / Chapter 4.6.1 --- Frequencies of Somatic Mutations --- p.35 / Chapter 4.6.2 --- Distribution of Somatic Mutations in mtDNA --- p.36 / Chapter 4.7 --- Somatic Mutations of Mitochondrial DNA in HCC --- p.37 / Chapter SECTION 5. --- OBJECTIVES OF THIS STUDY --- p.44 / Chapter SECTION 6. --- MATERIALS AND METHODS --- p.46 / Chapter 6.1 --- Patients and Samples Collection --- p.46 / Chapter 6.2 --- DNA Extraction from Liver Tissues --- p.46 / Chapter 6.3 --- Amplification of Mitochondrial DNA by Polymerase Chain Reaction --- p.51 / Chapter 6.3.1 --- Design of Primers --- p.51 / Chapter 6.3.2 --- PCR Conditions and Contents --- p.54 / Chapter 6.3.3 --- Assessment of PCR Products by Agarose Gel Electrophoresis --- p.54 / Chapter 6.4 --- Purification of PCR Products --- p.54 / Chapter 6.5 --- Cyclesequencing of Mitochondrial DNA --- p.55 / Chapter 6.5.1 --- Design of Primers --- p.55 / Chapter 6.5.2 --- PCR Contents and Cycle Sequencing Procedures --- p.56 / Chapter 6.6 --- Purification of Sequencing Products --- p.56 / Chapter 6.7 --- Sequence Analysis by Automated Sequencer --- p.57 / Chapter 6.7.1 --- Preparation of Polyacrylamide Gel --- p.57 / Chapter 6.7.2 --- Sequence Analysis by Automated Sequencer --- p.58 / Chapter 6.7.3 --- "Search for Sequence Variants, Polymorphisms and Somatic Mutations" --- p.58 / Chapter 6.8 --- Further Studies on mtDNA Mutations --- p.59 / Chapter 6.8.1 --- Sequence Analysis in Buffy Coat --- p.59 / Chapter 6.8.2 --- Detection of the Presence of Somatic mtDNA Mutations in Plasma --- p.59 / Chapter 6.8.3 --- Frequency of Mutations in Two Nucleotide Repeat Sequences --- p.60 / Chapter 6.9 --- Clinical Data and Statistical Analysis --- p.61 / Chapter 6.9.1 --- Clinical and Pathological Data --- p.61 / Chapter 6.9.2 --- Statistical Analysis --- p.61 / Chapter SECTION 7. --- RESULTS --- p.63 / Chapter 7.1 --- Sequence Analysis of the Entire Mitochondrial Genome --- p.63 / Chapter 7.1.1 --- Sequence Variants and Polymorphisms --- p.63 / Chapter 7.1.2 --- Somatic Mutations --- p.71 / Chapter 7.2 --- Study of Mitochondrial Sequence in Lymphocytes --- p.78 / Chapter 7.3 --- Detection of Tumor DNA in Serum --- p.78 / Chapter 7.4 --- Analysis of Nucleotide Repeat Sequences --- p.79 / Chapter 7.4.1 --- General Results --- p.79 / Chapter 7.4.2 --- Statistical Analysis --- p.84 / Chapter SECTION 8. --- DISCUSSION --- p.89 / Chapter 8.1 --- Comparative Analysis of mtDNA Mutations with Two Previous HCC Studies --- p.89 / Chapter 8.1.1 --- Number of Cases and Region Studied --- p.89 / Chapter 8.1.2 --- Number and Distribution of Mutations in Normal Controls --- p.89 / Chapter 8.1.3 --- Number of Somatic Mutations --- p.90 / Chapter 8.1.4 --- Distribution of Somatic Mutations --- p.91 / Chapter 8.2 --- Similarities of Somatic mtDNA Mutations in This Study with Other Cancer Types --- p.93 / Chapter 8.2.1 --- Frequency and Distribution of Somatic Mutations --- p.93 / Chapter 8.2.2 --- Number of Homoplasmic Mutations --- p.93 / Chapter 8.3 --- Evaluation of Somatic Mutations of mtDNA in This Study --- p.96 / Chapter 8.3.1 --- Specificity of Somatic Mutations in Tumor Proved by Sequence Analysis in Lymphocytes --- p.96 / Chapter 8.3.2 --- Importance of Conserved Amino Acid Sequences with Other Species to the Presence of Somatic Mutations in Tumor --- p.96 / Chapter 8.3.3 --- Four Somatic Mutation Sites Are Detected in More than One Cancer Type --- p.101 / Chapter 8.3.4 --- Presence of Homoplasmic and Heteroplasmic Mutations --- p.101 / Chapter 8.3.5 --- Absence of Large-scale Deletions in Tumor Tissues --- p.102 / Chapter 8.4 --- Mutation Hotspots Region: Hypervariable Displacement-loop --- p.103 / Chapter 8.5 --- D310 Mononucleotide Repeats --- p.106 / Chapter 8.5.1 --- Description of D310 Mononucleotide Repeats --- p.106 / Chapter 8.5.2 --- Possible Causes of Varied Sequences at D310 --- p.106 / Chapter 8.5.3 --- Appearance of Nucleotide Repeats at D310 in Tumors --- p.107 / Chapter 8.5.4 --- Possible Outcomes of D310 Aberrations in mtDNA Replication and Transcription --- p.108 / Chapter 8.5.5 --- Comparison of D310 Alternations in HCC with Other Cancers --- p.109 / Chapter 8.6 --- Other Nucleotide Repeat Sequences --- p.112 / Chapter 8.6.1 --- The CA Dinucleotide Repeats --- p.112 / Chapter 8.6.2 --- Other Nucleotide Repeat Sequences Showing Genome Instability --- p.112 / Chapter 8.7 --- Evaluation of Somatic mtDNA Mutations as a Cancer Diagnostic Marker --- p.114 / Chapter 8.7.1 --- Coding Region --- p.114 / Chapter 8.7.2 --- D-loop Region --- p.114 / Chapter 8.7.3 --- D310 Nucleotide Repeats --- p.115 / Chapter 8.7.4 --- Possibility of Detecting Somatic Mutations in Serum --- p.116 / Chapter 8.8 --- Somatic mtDNA Mutations May Be a Prognostic Marker in HCC --- p.117 / Chapter 8.8.1 --- Possible Problems in Current Prognostic Factors --- p.117 / Chapter 8.8.2 --- Interpretation of Results --- p.117 / Chapter 8.8.3 --- Prognostic Values of Somatic Mutations at D310 --- p.118 / Chapter 8.9 --- Hypothesis of Somatic MtDNA Mutations on Tumorigenesis and Tumor Progression --- p.119 / Chapter 8.9.1 --- Somatic mtDNA Mutations Decline OXPHOS and May Inactivate Apoptotic Pathways --- p.119 / Chapter 8.9.2 --- Moderate Reactive Oxygen Species Production May Promote Mitosis --- p.120 / Chapter 8.10 --- Possible Appearance of Somatic Mutations in HCC with Chronic HBV Infection --- p.123 / Chapter 8.11 --- Possibility of HBx Protein Integration to MtDNA Mutations --- p.123 / Chapter 8.12 --- Conclusions --- p.125 / Chapter SECTION 9. --- LIMITATIONS AND FURTHER STUDIES --- p.127 / Chapter 9.1 --- Limitations and Improvements of Study --- p.127 / Chapter 9.1.1 --- Small Sample Size --- p.127 / Chapter 9.1.2 --- Sequence Analysis Method --- p.127 / Chapter 9.1.3 --- Fidelity of PCR Reactions and Long-range PCR Fragments --- p.128 / Chapter 9.2 --- Further Studies --- p.129 / Chapter SECTION 10. --- REFERENCES --- p.131

Guang Fu Chen. / "May 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 194-221). / 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.

We have previously shown that chronic Hepatitis C virus (HCV) infection can induce DNA damage and immune dysfunctions with excessive oxidative stress in T cells. Furthermore, evidence suggests that HCV contributes to increased susceptibility to metabolic disorders. However, the underlying mechanisms by which HCV infection impairs cellular metabolism in CD4 T cells remain unclear. In this study, we evaluated mitochondrial mass and intracellular and mitochondrial reactive oxygen species (ROS) production by flow cytometry, mitochondrial DNA (mtDNA) content by real-time qPCR, cellular respiration by seahorse analyzer, and dysregulated mitochondrial-localized proteins by Liquid Chromatography-Mass Spectrometry (LC-MS) in CD4 T cells from chronic HCV-infected individuals and health subjects. Mitochondrial mass was decreased while intracellular and mitochondrial ROS were increased, expressions of master mitochondrial regulators peroxisome proliferator-activated receptor 1 alpha (PGC-1α) and mitochondrial transcription factor A (mtTFA) were down-regulated, and oxidative stress was increased while mitochondrial DNA copy numbers were reduced. Importantly, CRISPR/Cas9-mediated knockdown of mtTFA impaired cellular respiration and reduced mtDNA copy number. Furthermore, proteins responsible for mediating oxidative stress, apoptosis, and mtDNA maintenance were significantly altered in HCV-CD4 T cells. These results indicate that mitochondrial functions are compromised in HCV-CD4 T cells, likely the deregulation of several mitochondrial regulatory proteins.