published_or_final_version / Clinical Oncology / Doctoral / Doctor of Philosophy

published_or_final_version / Clinical Oncology / Doctoral / Doctor of Philosophy

published_or_final_version / Clinical Oncology / Doctoral / Doctor of Philosophy

Sirtuins (Silent Information Regulator Two (SIR2) protein) are NAD-dependent protein deacetylases, originally discovered in yeast. Sirtuins play a critical role in the regulation of different cellular processes involving aging, chromatin silencing and cellular differentiation. SIRT6 is a member of Sirtuins and plays a role in regulation of DNA repair and suppression of genomic instability. Many studies have shown SIRT6 to be associated with diseases of aging, including cancer. The finding by our collaborator that SIRT6 expression was found in chemotherapy-resistant breast cancer cell lines stimulated this study which aims to explore the role of SIRT6 expression as a prognostic marker in breast cancer. One hundred and eighteen breast cancer samples in tissue microarray blocks were examined for SIRT6 expression by immunohistochemistry. As SIRT6 expression is predominantly located in the nucleus but with a small fraction in cytoplasm, the calculation of nuclear or cytoplasmic localization scores were divided by total localization scores to increase accuracy. The nuclear localization scores represent the SIRT6 expression in breast cancer. Statistical analysis was performed using SPSS software. SIRT6 overexpression in the nucleus was significantly associated with poorer overall survivals (p=0.018) while low cytoplasmic expression of SIRT6 was also associated with poorer overall survivals (p=0.014). There was no relationship between SIRT6 expression and disease-specific survivals. By multivariate analysis, SIRT6 expression was an independent predicator of poorer overall survivals. These results suggest that SIRT6 overexpression induces apoptosis in cancer cells through deacetylation of transcription factor p65. SIRT6 interacts with and deacetylates p65 to activate nuclear factor kappa B gene linked to cancer. Also high levels of SIRT6 were associated with resistance to paclitaxel and epirubicin inMCF-7 breast cancer cell lines. This provides evidence that Sirt6 is an important prognostic marker and therapeutic target for breast cancer. / published_or_final_version / Pathology / Master / Master of Medical Sciences

Cancer is a fearful, deadly disease. Currently there is almost no cure. The reason is that the disease mechanisms are hardly understood to humans. This in turn is because of the complex molecular activities that underlie cancer processes. Some variables of these processes, such as gene expressions, copy number profiles and point mutations, recently became measurable in high-throughput. However, these data are massive and non-readable even to experts. A lot of efforts are being made to develop engineering tools for the analysis and interpretation of these data, for various purposes. In this thesis, we focus on addressing the problem of individuality in cancer. More specifically, we are interested in knowing the subgroups of processes in a cancer, called subtypes. This problem has both theoretical and practical implications. Theoretically, classification of cancer patients represents an understanding of the disease, and may help speed up drug development. Practically, subgroups of patients can be treated with different protocols for optimal outcomes. Towards this end, we propose an approach with two specific aims: performing subtypes for a given set of high-throughput data, and identifying candidate genes (called drivers) that drive the subtype-specific processes. First, we assume that a subtype has a distinctive process, compared not just with normal controls, but also with other cases of the same cancer. The process is characterized with a set of differentially expressed genes uniquely found in the corresponding subtype. Based on this assumption, we develop a signature based subtyping algorithm, which on the one hand divides a set of cases into as many subtypes as possible, while on the other hand merges subtypes that have too small a signature set. We applied this algorithm to datasets of the pediatric brain tumor of medulloblastoma, and found no more than three subtypes can meet the above criteria. Second, we explore subtype patterns of the copy number profiles. By regarding all events on a chromosome arm as a single event, we quantize the copy number profiles into event profiles. An unsupervised decision tree training algorithm is specifically designed for detecting subtypes on these profiles. The trained decision tree is intuitive, predictive, easy to implement and deterministic. Its application to datasets of medulloblastoma reveals interesting subtype patterns characterized with co-occurrence of CNA events. / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

Esophageal squamous cell carcinoma (ESCC) is a common cancer worldwide with a high mortality rate. High occurrence of ESCC is observed in Southeast Asia. Identification and characterization of ESCC important tumor suppressor genes will be highly beneficial to the understanding of the disease and for the early diagnosis and improvement of therapy for the cancer. In our previous microcell-mediated chromosome transfer (MMCT) studies, the transfer of an intact chromosome 13 into the recipient ESCC cell line revealed the tumor suppressive ability and putative tumor suppressive function of chromosome 13 in ESCC. One candidate gene, Plant-Homeodomain Finger Protein 11(PHF11), was identified from the study and selected for further functional studies in this current study. PHF11, located on chromosomal region 13q14, contains two plant homeodomain fingers and is a member of the PHD finger protein family. PHF11was reported to be associated with asthma and atopic diseases, yet no studies of PHF11havebeen reported in cancer to date. This study is the first to report the functional role of PHF11in tumor suppression. In this current study, two isoforms of PHF11, PHF11aand b, were reintroduced into ESCC cell lines by methods of transient tranfection and lentiviral-infection. In vitro studies showed both isoforms have cell proliferation and colony-formation inhibition abilities. In the nude mouse tumorigenicity assay, however, it was revealed that only thePHF11aisoform was tumor suppressive in vivo. No differences in angiogenesis-related factors and apoptosis-related factors were observed in PHF11a-and b-expressing cells. Further studies by Western blotting analysis and flow cytometry analysis showed that PHF11amay play a role in delaying cell cycle progression by the down-regulation of cyclin expression, while the PHF11bmay be functionally inactive, The results of this current study further confirm the tumor suppressive role of PHF11ain ESCC, whereas the PHF11b isoform was unable to suppress tumor formation in vivo. Further study of the PHF11 isoforms to identify their differential functions and interacting partners will provide a better understanding of the mechanism by which PHF11a suppressestumor growth. / published_or_final_version / Clinical Oncology / Master / Master of Philosophy

Hepatocellular carcinoma (HCC), which constitutes 75%-80% of primary liver cancer, is one of the most common malignancies worldwide. Hepatocarcinogenesis is a complicated and slow process accumulating multiple genetic and epigenetic alterations. In spite of its prolonged pre-malignant stage, HCC is usually diagnosed late and of high aggressiveness. A better understanding of the genetic and epigenetic changes during HCC development and progression is of great importance to early diagnosis and treatment of HCC. Gain of chromosome 1q21 is one of most frequent genetic alteration in HCC and chromodomain helicase DNA binding protein 1-like (CHD1L) was recently identified to be responsible for this amplification. As a family member of SNF-2 like transcription factors, CHD1L plays an important role in HCC development via regulation of various downstream targets. In this study, a novel oncogene, sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1 (SPOCK1), was identified as a CHD1L target. CHD1L protein directly bound to the promoter region (nt -1662 to +34) of SPOCK1 and activated its transcription. Clinically, overexpression of SPOCK1 was detected in 60% of human HCC samples and was significantly associated with advanced clinical stage (P=0.020), shorter overall survival (P=0.011) and poorer disease-free survival of patients (P=0.039). Functionally, the ectopic expression of SPOCK1 in HCC cells conferred strong tumorigenic ability, while shRNA-mediated SPOCK1 silencing abolished this effect. Further study showed that the SPOCK1-enhanced cell survival could be attributed to its anti-apoptotic effects. SPOCK1 could suppress HCC cell apoptosis through the activation of AKT and subsequent inhibition of the (cytochrome c)-(caspase-9)-(caspase-3) pathway. In addition to its tumorigenic roles, the overexpression of SPOCK1 in HCC cells conferred strong metastatic ability via MMP9-mediated extracellular matrix remodeling. In addition to genetic alterations, epigenetic changes also get increasing attentions due to their profound effects on gene activity and expression. A-to-I RNA editing is a post-transcriptional epigenetic modification which converts a site-selective adenosine nucleotide into inosine. The importance of RNA editing has long been underestimated because most of RNA editing modifications occur in a subtle way. The next-generation sequencing provides enough depth to unravel this mystery. The transcriptome sequencing data obtained from this study identified an A-to-I RNA editing at codon 367 (Ser→Gly) of antizyme inhibitor 1 (AZIN1). A high modification rate of AZIN1 was found to be prevalent in HCC specimens and closely associated with HCC pathogenesis. Adenosine deaminase acting on RNA-1 (ADAR1), but not ADAR2 or ADAR3, was responsible for AZIN1 RNA editing. This recoding editing event conferred “gain-of-function” phenotypes as manifested by augmented tumorigenic capabilities and higher aggressive potentials. Compared with wild-type AZIN1 protein, the edited form possessed stronger affinity to antizyme. As a result, edited AZIN1 demonstrated higher protein stability and ensuing neutralization of the antizyme-mediated degradation of ODC and CCND1 oncoproteins. The rescued ODC and CCND1 robustly accelerated cell proliferation thereby promoting HCC development. In conclusion, two novel molecular mechanisms, (CHD1L)-(SPOCK1)-(AKT) and (ADAR1)-(edited AZIN1)-(ODC/CCND1), were delineated during HCC initiation and progression. Also, a causal link between RNA hyper-editing activity and cancer development was established for the first time in this study. / published_or_final_version / Clinical Oncology / Doctoral / Doctor of Philosophy

Breast cancer is the most frequent malignancy in women. Recent studies have proposed that sirtuin 1 (SIRT1) may play a certain role in the tumorgenesis and disease progression of cancer. Therefore, in this study, we demonstrate the localization of SIRT1 in the breast cancer cells by immunohistochemistry method and try to correlate the expression level of SIRT1 with various clinical-pathological parameters as well as the survival time of breast cancer patients. One hundred and eighteen breast cancer cases, arrayed as dual‐cores, were studied in the tissue microarray blocks for their SIRT1 nuclear and cytoplasmic stain. The expression of SIRT1 is found in over 95% of the tumor samples. Although the active functioning site of SIRT1 is known to be mainly the nucleus, both nuclear and cytoplasmic localization score are assessed separately for SIRT1 expression for more accurate statistically analysis. By bi‐variate Pearson correlation analysis, high nuclear localization of SIRT1 is significantly correlated with low tumor grade (p=0.006) and ER (p=0.001) and PR positive status (p=0.044). Moreover, the cytoplasmic localization score of SIRT1 shows positive correlation with tumor grade (p=0.010). The relationship of SIRT1 expression and survival time of breast cancer patient was studied by Kaplan‐Meier analysis. Despite a marginal fail in obtaining a statistically significant result, the trend in survival curve clearly indicated that nuclear localization of SIRT1 is associated with a poorer overall survival (p=0.052). Although the pathway of how SIRT1 affects the survival of breast cancer patient is still unknown, many studies suggested that it is largely due to the deacetylated inactivation of p53 tumor suppressor protein by SIRT1. In conclusion, we propose that nuclear localization of SIRT1 can be a potential prognostic factor of breast cancer patients. / published_or_final_version / Pathology / Master / Master of Medical Sciences

Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. The development and progression of HCC is a multistep process which attributed to the accumulation of genetic alterations. Recently, mounting evidence has suggested the role of non-coding RNAs (ncRNAs) as the master driver of carcinogenesis, through their regulation on different oncogenes and tumor suppressive genes. Deregulation of ncRNAs was frequently observed in multiple types of cancers, including HCC. Herein, we demonstrated the aberrant expression pattern of miRNAs and lncRNAs in human HCC and investigated their functional roles in promoting hepatocarcinogenesis. Deregulation of miRNAs was previously demonstrated as a common event in human HCC, and miR-142-3p and miR-142-5pwereidentified as one of the significantly down-regulated miRNAs in HCC. Down-regulation of miR-142-3p and miR-142-5p was frequently observed in HCC patients and their expressions were progressively decreased along the multi-steps HCC development and progression. Functionally, overexpression of miR-142 has significantly inhibited HCC cell migration and invasion. Ectopic expression of miR-142 also markedly attenuated stress fiber formation and disrupted the cytoskeleton organization of HCC cells. Mature miR-142-3p and miR-142-5p, which derived from the same miRNA precursor were shown to collaboratively inhibited HCC cell migration through targeting different components of the key pathways regulating cell motility. On the other hand, we demonstrated the aberrant expression of lncRNAs in HCC by profiling of 88 well-annotated lncRNAs in 20 pairs of primary HCC and their corresponding non-tumorous liver. HOXA distal transcript antisense RNA (HOTTIP)was identified as the most frequently up-regulated lncRNA in HCC. Functionally, knock down of HOTTIP significantly attenuated cell proliferation in HCC cells and markedly abrogated tumorigenicity in nude mice. Knockdown of HOTTIP had lead to a global reduction in the HOXA genes expression, which are highly expressed in human HCC. Our data suggested that HOTTIP may regulate the expression of its neighboring protein-coding genes and contribute to the development of HCC. We also investigated the up-stream regulation of HOTTIP and identified miR-125b and miR-29a as regulators of HOTTIP in HCC. Clinically, miR-125b and miR-29a exhibited a reverse expression pattern to HOTTIP in HCC. Ectopic expression of miR-125b and miR-29a abolished HOTTIP-coupled luciferase activity and suppressed the endogenous level of HOTTIP. Intriguingly, we also identified a negative feedback relationship between HOTTIP and miR-125b. Taken together, our findings suggested the up-regulation of HOTTIP may be attributed to the down-regulation of miR-125b and miR-29a in HCC, and the sophisticated regulatory network between HOTTIP and miR-125b has further increased the complexity of gene regulation in HCC. In conclusion, we demonstrated the dysregulated expression pattern of miRNAs and lncRNAs in HCC and well illustrated their functional roles in promoting hepatocarcinogenesis. From the studies of miR-142 and lncRNA HOTTIP we appreciated the complex interactions and regulations between different ncRNAs. Taken together, our study has enriched the current knowledge on ncRNAs and their involvements in HCC development. / published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

abstract / Clinical Oncology / Doctoral / Doctor of Philosophy