Relevant Thesis-Based Degree Programs
Graduate Student Supervision
Doctoral Student Supervision
Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.
Oral cancer metastasis to cervical lymph nodes (LN+) has been one of the major indicators of poor prognosis, which has not been improved over the past five decades. There remains a need for improved biomarkers for risk assessment. Pathology of primary tumours has been commonly used to indicate risk of tumour spread; however, a biomarker with greater clinical utility, especially for clinically early-stage cancer, would need to come with increased accuracy. Objective and quantifiable genetic or phenotypic characteristics may add complementary information in the decision of neck management for early-stage oral cancer. With the aims of identifying putative biomarkers that are clinically applicable, I analyzed the genetic, by microRNA sequencing and immune gene expression using NanoString technology, and phenotypic, by image analysis of nuclear phenotype, from surgical primary tumours of oral squamous cell carcinoma (OSCC). The analysis provided predictive marker panels modeled through training and test sets of surgical tissues. Of note, I identified miRNAs and immune genes that were overexpressed in tumours with nodal disease and further suggested a possible inverse relationship between the markers. In addition, I characterized the cancer nuclear phenotype of OSCC and developed a machine-leaning-based cell classification algorithm that can be applied to characterize any area of interests on both nuclear and spatial resolution. I presented predictive biomarker panels that outperforms conventional pathological criteria for neck management of clinically early-stage OSCC. By integrating the results from each aim, I also proposed a patient triage algorithm for elective neck dissection. Overall, the research presented in this thesis is a major step forward in our understanding of the biological alterations that can differentiate high-risk OSCC of nodal disease. Due to its detrimental impact on patient outcomes, the need for objective biomarkers for nodal disease is urgent. The findings generated from robust technologies on routine clinical samples demonstrate great promise in developing new strategies for risk stratification with biomarkers that could be clinically applicable in guiding elective neck dissection. Through early intervention and avoidance of unnecessary procedures, the outcomes of OSCC can be improved.
Master's Student Supervision
Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Early detection and intervention of oral premalignant lesions (OPLs) are at the forefront of clinical endeavors for oral cancer control. Quantitative cytology (QC) and loss of heterozygosity (LOH) have shown to be promising prognostic biomarkers for identifying high-risk OPLs. The objectives of this thesis are to optimize the screening utility of the QC algorithm by assessing nuclear morphology and explore if QC or LOH may serve as predictive biomarkers in treatment management of OPLs. In this thesis, we first used 169 brushing samples from 156 patients to examine the comparability between the MoticEasyScan and ClearCyte and 105 samples from 100 patients to construct a morphometric-based QC-model for screening. Random Forest Models and Receiver Operating Characteristic curves were used to determine the cut-offs to identify abnormalities at cellular and case levels. To evaluate LOH and QC as biomarkers for predicting topical treatment response, a set of 28 OPLs from 28 patients were included for analysis. The Fisher’s exact test was used to assess the predictive value of LOH and QC. The results from the MoticEasyScan system are comparable to those from the ClearCyte for QC analysis. We have identified problems in the previous system with staining batch variations and normalization and both have significant impacts on photometric features used for previous software development. To overcome these problems, we developed a new QC model using morphometric only features. To develop a screening test, using 94 morphometric features with 65.7% of abnormal votes for abnormal cells and 2.7% abnormal cells for abnormal cases, the new model (RF94) yielded a 100% sensitivity in the Test set. To triage OPLs for treatment, the model (mRF10), using 10 morphometric features with 67.3% of abnormal votes for abnormal cells and 6.7% abnormal cells for abnormal cases, yielded in 87.5% specificity in the Test set. Using mRF10 model, no significant differences in proportions of the persistent and resolved groups in QC or LOH were identified at the pre-treatment timepoints. LOH may not be sensitive predictive markers for topical treatment of OPLs. In conclusion, QC models using morphometric-based features can potentially be a useful screening test.
With 1 “aneuploid” cell or ≥1.7% combined “hyperdiploid” with “tetraploid” group frequency) identified high-grade samples with the sensitivity, specificity, PPV and NPV of 100.0%, 86.7%, 89.7%, and 100.0%, respectively. In conclusion, iClearCyte test has potential to serve as robust non-invasive oral cancer screening tool, bridging geographic gap between communities and oral specialists, promoting early oral cancer detection, decreasing the number of unnecessary invasive biopsies, and guiding lesion management.
Oropharyngeal squamous cell carcinoma (OpSCC) patients have improved survival when tested positive for high-risk human papillomavirus (HR-HPV). However, tissue assessment of HPV status is currently not standardized and additional factors may influence survival among HPV-positive patients. The main objectives were to evaluate HPV detection methods and to identify possible factors that impact survival of OpSCC patients in British Columbia.We retrospectively analyzed 972 primary OpSCC patients diagnosed between 2000-2008 and referred to the BC Cancer Agency for treatment with curative intents of radiotherapy with or without concurrent chemotherapy. Patient charts were reviewed and collected information for demographics, smoking history, clinical assessments, treatment received, and outcomes. We analyzed two cohorts of Study Cohort, 244 cases with enough formalin-fixed, paraffin-embedded (FFPE) tissues for experiment, and General Cohort, 728 cases without tissues available. Experimental procedures included in situ hybridization (ISH) to detect DNA and RNA HPV and immunohistochemistry (IHC) to detect p16, p53, the retinoblastoma protein (pRB), cyclin D1, and Ki67. We used polymerase chain reaction (PCR) to detect type-specific HPV from cases with enough FFPE tissues for DNA extraction (n=41). Cox proportional hazard (Cox-PH) and Kaplan-Meier (KM) survival analysis were conducted to identify potential clinical and biological factors impacting on 5-year overall survival (OS), disease-specific survival (DSS), and development of loco-regional recurrence (LRR). The incidence rates of males increased from 3.2 to 7.6 per 100,000 whereas females declined from 1.1 to 0.8 per 100,000. The Study Cohort was relatively representative of the General Cohort. The Study Cohort of patients classified as ever-smokers, had tumours staged at T3/4, and received radiotherapy only had poorer 5-year OS, DSS, and LRR (p
For patients of oral squamous cell carcinoma (OSCC), tumour spread to regional lymph nodes reduces survival by half. On the account of this widely demonstrated fact, prophylactic neck treatment has been advocated for clinically node negative (cN0) necks of which the risk of nodal disease is considerably high. However, there is a lack of sensitive and specific marker to determine such risk and benefits of prophylactic treatment await confirmation. The first part of this thesis presents a population-based retrospective review on OSCC in British Columbia. The incidence of regional failure (RF) in early-stage, cN0 patients was 28%, with median time of only 10 months after local excision. This group of patients needed to be identified and treated at earliest time possible. Tumour depth of invasion (DOI) was significantly associated with RF (P=0.01). However, it has low accuracy in predicting nodal disease with AUC of 63%. Moreover, assessment of performance for 4mm cut-off of DOI showed 55% sensitivity and 68% specificity. Furthermore, we demonstrated that using DOI as an indicator of neck treatment resulted in 25% under-treated occult metastasis and 55% over-treated necks. Thus, we concluded that, at least for BC population, conventional histological attributes of tumour cannot predict RF and we need a new marker for risk assessment. The second part presents a pilot study exploring a novel approach of risk assessment by utilizing Quantitative Tissue Pathology (QTP) on tumour nests. We were able to quantitate and evaluate 120 features describing nuclear phenotypes of tumour cell nuclei and tissue architectures of tumour nests. Compared to node-negative (N0) group, cell nuclei of the node positive (N+) group had higher fractions of heterochromatin regions. Also, the combination of two features, which describe chromatin condensation, from the outermost two layers of tumour nests had performance of AUC 94%, sensitivity of 100% and specificity of 75% in discriminating N0 and N+ group. QTP may be a potential proxy for predicting the metastatic risk of OSCC. Further investigation on potential biomarkers in risk assessment for nodal disease of early-stage OSCC patients is warranted to provide precision management to improve mortality and reduce morbidity.
Low-income residents from the Vancouver’s Downtown Eastside (DTES) are known to be medically underserved, but little is known about their oral health (OH) status. The objectives of this study are to: 1) determine OH characteristics (clinical and subjective) of low-income adults in this community; 2) identify explanatory factors for their OH status.Material and Methods: Screening clinics were set up in the DTES. Eligibility criteria were adults 19 years of age or over and residence in the DTES for the preceding 3 months. Data were collected through questionnaires and clinical examinations.Results: Among the 356 screened participants, most were males, middle-aged, less educated, and living with low-income (≤$20,000/year). Alcohol and tobacco consumption was common. About 80% had dental coverage, mostly publicly funded benefits (94%). Fifty (14%) participants were edentulous. Dentate participants (n=306), on average, had 3.8 decayed (Dt), 8.6 missing (Mt), 4.9 filled (Ft), 17.2 DMF teeth, and a care index (CI) of 41.5%. Many (86%) perceived a dental need. Although more participants with dental insurance had a dental visit within the past 12 months, there were no differences in OH indices between those with or without dental insurance. After adjusting gender and recruitment site, social (barriers to care & length of DTES residence), behavioural (brush/floss), and personal (HCV/methadone) factors were identifiable explanatory factors for the CI level. Conclusion: DTES low-income have poor oral health status and many perceive a need for dental care. We identified several factors that may affect their levels of dental care; however, this community may inherited more complicated social issues. Further investigations to truly understand their challenges and needs are required for a better oral health promotion in this community.
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