Thesis (M. Phil.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Thesis (Ph. D.)--University of Chicago, Dept. of Pathology, December 2001. / Includes bibliographical references. Also available on the Internet.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Clinical Oncology / Master / Master of Philosophy

published_or_final_version / Clinical Oncology / Doctoral / Doctor of Philosophy

Multiple myeloma (MM) is an incurable haematological malignancy. It is characterized clinically by an asymptomatic precursor stage, known as monoclonal gammopathy of undetermined significance (MGUS), which will transform into symptomatic MM at a rate of 1% per year. Gene promoter hypermethylation by catalytic conversion of cytosine into 5?methylcytosine at promoter?associated CpG island is an alternative mechanism of gene inactivation. MicroRNA (miRNA) is a class of short, single?stranded, non?coding RNA molecules, which will repress the expression of target protein by sequence?specific binding to the three prime untranslated region of the corresponding messenger RNA. In carcinogenesis, miRNA can be either oncogenic when tumour suppressor genes are targeted, or tumour suppressive when oncogenes are targeted. Despite reports of hypermethylation of multiple protein?coding tumour suppressor genes, little is known about DNA methylation of non?coding tumour suppressor miRNA genes in MM. This thesis aimed to investigate the role of promoter hypermethylation of tumour suppressor miRNA genes in MM using a candidate miRNA approach. Moreover, the prognostic significance of tumour suppressor miRNA hypermethylation was studied in a uniformly?treated cohort of MM patients. The role of DNA methylation at the promoter of miR?203, miR?34a, miR?34b/c, miR?124?1, miR?129?2 and miR?224 were studied in MM. The tumour suppressor role of miR?34b/c, miR?124?1, miR?203 and miR?224 were demonstrated in human myeloma cell lines (HMCLs). In particular, restoration of miR?203 in MM cells was shown to inhibit cellular proliferation via targeting and hence direct downregulation of a proto?oncogene, cyclic AMP responsive element binding protein. There are several observations in primary MM samples. First, there was frequent methylation of miR?129?2, miR?203 and miR?224 but infrequent methylation of miR?34a, miR?34b/c and miR?124?1 in MM at diagnosis. Second, tumour?specific hypermethylation of each of the miR?203 and miR?224 promoters was detected at comparable frequencies in MGUS, diagnostic and relapsed/progressed MM, and hence implicated as an early event in myelomagenesis. Thirdly, miR?129?2 methylation was more frequent in diagnostic MM than MGUS, and hence implicated in MGUS progression to MM. On the other hand, despite rare miR?34b/c methylation at diagnosis, miR?34b/c methylation was frequent at relapse/progression, thereby implicating miR?34b/c methylation in MM relapse/progression. Fourthly, despite frequent miR?124?1 methylation in HMCLs, miR?124?1 methylation was rare in both diagnostic and relapsed MM marrow samples, suggesting that miR?124?1 methylation was acquired during in vitro cell culture. Finally, the prognostic significance of methylation of a panel of tumour suppressor miRNAs was studied in a uniformly?treated cohort of MM patients, which revealed that miR?224 hypermethylation as an independent favourable prognostic factor for survival. In conclusion, hypermethylation of tumour suppressor miRNAs is implicated in the pathogenesis (miR?203, miR?129?2, miR?224), progression (miR?34b/c), and prognostification (miR?224) of MM. / published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Thesis (Ph.D.) -- McMaster University, 1998. / Includes bibliographical references (leaves 167-182). Also available via World Wide Web.

Thesis (PH.D.)--Michigan State University. Cell and Molecular Biology, 2008. / Title from PDF t.p. (viewed on Aug. 11, 2009) Includes bibliographical references. Also issued in print.

Thesis (M. Med. Sc.)--University of Hong Kong, 2005.

Transcription factors (TFs) are key regulators of gene expression whose failure has been implicated in many diseases, including cancer. They bind at various sites at different specificity depending on the prevailing cellular conditions, disease, development stage or environmental conditions of the cell. TF binding specificity is how well a TF distinguishes functional sites from potential non-functional sites to form a useful regulatory network. Owing to its role in diseases, various techniques have been used to determine TF binding specificity in vitro and in vivo, including chromatin immuno-precipitation followed by massively parallel sequencing (ChIP-seq). ChIP-seq is an in vivo technique that considers how the chromatin landscape affects TF binding. Motif enrichment analysis (MEA) tools are used to identify motifs that are over-represented in ChIP-seq peak regions. One such tool, CentriMo, finds over-represented motifs at the center since peak calling software are biased to declaring binding regions centered at the TF binding site. In this study, we investigate the use of CentriMo and other MEA tools to determine the difference in motif enrichment attributed presence of Chronic Myeloid leukemia (CML)), treatment with Interferon (IFN) and Dexamethasone (DEX) compared to control based on Fisher’s exact test; using uniform peaks ChIP-seq data generated by the ENCODE consortium. CentriMo proved to be capable. We observed differential motif enrichment of TFs with tumor promoter activity: YY1, CEBPA, Egr1, Cmyc family, Gata1 and JunD in K562 while Stat1, Irf1, and Runx1 in Gm12878. Enrichment of CTCF in Gm12878 with YY1 as the immuno-precipitated (ChIP-ed) factor and the presence of significant spacing (SpaMo analysis) of CTCF and YY1 in Gm12878 but not in K562 could show that CTCF, as a repressor, helps in maintaining the required YY1 level in a normal cell line. IFN might reduce Cmyc and the Jun family of TFs binding via the repressive action of CTCF and E2f2. We also show that the concentration of DEX treatment affects motif enrichment with 50nm being an optimum concentration for Gr binding by maintaining open chromatin via AP1 TF. This study has demonstrated the usefulness of CentriMo for TF binding specificity analysis.