Whether certain Epstein-Barr virus (EBV) strains are associated with pathogenesis of nasopharyngeal carcinoma (NPC) is still an unresolved question. In the present study, we aimed to sequence the complete EBV genomes harbored in NPC tumor biopsies and compare against the non-NPC EBV strains to identify NPC-specific EBV variations. In the first part of the study, EBV genome contained in one primary NPC tumor biopsy was PCR-amplified and sequenced using next-generation and dideoxy-DNA sequencing. The EBV genome, designated HKNPC1 (Accession number JQ009376), was generated by reference mapping and it appears to be a uniform strain in general despite minor heterogeneity. Phylogenetic analysis with the four published EBV strains, B95-8, AG876, GD1, and GD2, indicated HKNPC1 was more closely related to the Chinese NPC strains. HKNPC1 contains 1,589 single nucleotide variations (SNVs) and 132 insertions or deletions (indels). We found 76 non-synonymous SNVs shared amongst the Chinese GD1, GD2 and HKNPC1 isolates, while another 88 nonsynonymous SNVs were shared only by the two NPC tumor-derived strains HKNPC1 and GD2. In the second part of the study, SureSelect target enrichment technology was used instead of PCR to capture EBV DNA from total DNA. The study was scaled-up to sequence EBV strains in cell lines, saliva and NPC tumor, using the MiSeq Personal Sequencer and the Genome Analyzer IIx platforms. The reads were de novo assembled to generate 17 complete EBV genomes, out of which 9 were NPC-EBV strains. Phylogenetic analysis of all available EBV strains has demonstrated that all NPC strains were type 1 EBV. Phylogeny predicted by LMP-1 gene showed clear geographical pattern of where the EBV strains were isolated. A total of 5,011 variations were identified by comparing every EBV strain against the reference. MicroRNAs and EBERs are generally well conserved across all genomes. Comparative analysis of variations between NPC and non-NPC EBV strains discovered 904 NPC-specific variations, out of which 112 appeared in more than one NPC strains. Among these recurrent variations, 39 non-synonymous substitutions and seven deletions in coding region were found. About half of these recurrent variations were located in EBNA-3A, -3B and -3C, while the rest was found in latent, tegument, capsid and packaging-related proteins and transcription factors. There were two NPC EBV strains isolated from the primary tumors which later diagnosed to have distant metastasis. Unique variations were shared in these two EBV strains in regions between IR2 and IR3, where genes such as BPLF1, BOLF1 and EBNA-3A, -3B and -3C were located, and leftward of IR3, where BBLF2/3 and BBRF1 were found. In conclusion, we have demonstrated the feasibility of target capture and next-generation sequencing in whole genome sequencing of EBV. Comparison of reference mapping and de novo assembly of EBV sequences illustrated that both are feasible approaches, though de novo assembly is preferred since the method is less dependent on the reference genome. Large-scale sequencing of NPC and non-NPC EBV strains may facilitate the discovery of previously unknown variations of biological significance and reveal the diverse role of EBV in NPC pathogenesis. words) / published_or_final_version / Paediatrics and Adolescent Medicine / Doctoral / Doctor of Philosophy

Hong Kong, situated in the Southern part of China, is an endemic area where the incidence of nasopharyngeal carcinoma (NPC) is among the highest in the world. The cancer, which is located at the deepest part of the human skull, represents one of the most difficult tumours to treat in the head and neck region. The management of tumour recurrence after radiotherapy is even more challenging. Epstein-Barr virus (EBV) is a human herpes virus and it is the first virus that is discovered to be associated with human malignancy. Over the past few decades, the role of EBV serology in the management of NPC has been extensively investigated. More recently, a series of EBV encoded microRNAs, which are short, non-coding RNAs, are found to be commonly expressed in NPC. In our studies, we have investigated the role of EBV DNA and EBV miRNA BART7 in the management of recurrent NPC. Plasma EBV DNA is accepted as a tumour marker for NPC. We found that in patients with recurrent NPC, the pre-operative level of plasma EBV DNA reflects the tumour load and correlates with the T-stage of the tumour. It also predicts the chance of resection margins that are histologically positive for malignancy. When measured serially after surgery, it is useful to detect tumour recurrence. However, we found that up to 15.5% of our patients, who had tumour recurrence in the nasopharynx, were seronegative for EBV DNA. In such circumstances, plasma EBV miRNA BART7, which is expressed independently of EBV DNA, may be used for such purpose. Moreover, using the in-vitro model, we demonstrated that the expression of EBV miRNA BART7 in the HONE1 cell line increases the rate of proliferation, migration and invasion of tumour cells. By using the same in-vitro model, we found that the EBV miRNA BART7 increases the sensitivity of the HONE1 cells to ionizing radiation in a dose-dependent manner. This is confirmed with the in-vivo experiments using the zebra fish model. In our previous study on the multivariate analysis of prognostic factors in salvage nasopharyngectomy for recurrent NPC, we found that the resection margin status is one of the most important independent factors influencing the local tumour control and overall survival. In order to improve the chance of obtaining clear margins after surgery, we have to depend on the intra-operative frozen section analysis and the post-operative histological examination of the resection margin specimen. In our current study, we showed that contrast MRI is accurate in assessing the local extent of recurrent nasopharyngeal carcinoma. During nasopharyngectomy, a radial resection margin of 15mm should be taken with the underlying medial pterygoid muscle. For tumours with parapharyngeal extension, the pharyngobasilar fascia should be resected enbloc with the specimen. The chance of local recurrence after salvage nasopharyngectomy in patients with histologically uninvolved margins was 20.0%. Tissue EBV miRNA BART7 is useful to identify a subgroup of patients with histologically close margins who are at increased risk of subsequent local tumour recurrence. Post-operative adjuvant treatment is warranted for these patients. / published_or_final_version / Surgery / Doctoral / Doctor of Philosophy

published_or_final_version / Medicine / Master / Doctor of Medicine

The Best PhD Thesis in the Faculties of Dentistry, Engineering, Medicine and Science (University of Hong Kong), Li Ka Shing Prize,1997-1999 / published_or_final_version / abstract / Pathology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / toc / Paediatrics and Adolescent Medicine / Master / Master of Philosophy

published_or_final_version / Microbiology / Master / Master of Philosophy

published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

Proefschrift Universiteit van Amsterdam. / Met bibliogr., lit. opg. - Met samenvatting in het Nederlands.

Erlangen, Nürnberg, Universiẗat, Diss., 2006. / Enth. 1 Sonderabdr. aus: Journal of pathology ; 203. 2004 und 1 weiteren Sonderabdr. - Beitr. teilw. dt., teilw. engl.

Diss. (sammanfattning) Göteborg : Univ., 2008. / Härtill 4 uppsatser.