P-glycoprotein (Pgp, ABCB1) is a polyspecific efflux transporter implicated in multidrug resistance in human cancers. In this study, tetramethylrhodamine-5-carbonyl azide (AzTMR) was covalently crosslinked to the Pgp drug binding pocket with a stoichiometry of 1. The Pgp-AzTMR adduct was functionally equivalent to unlabelled Pgp and retained its ability to transport Hoechst 33342. The binding site of AzTMR in Pgp was nonpolar, with a similar environment to that of propanol. Pgp-AzTMR could bind a second drug molecule, with a higher affinity for H-site drugs and lower affinity for other R-site drugs. Unlabelled Pgp interacted with dimeric versions of known Pgp modulators, binding them with higher affinity than the monomer. These compounds were also found to either stimulate or inhibit Pgp ATPase activity depending on the concentration. Pgp-AzTMR was able to bind dimeric drugs, indicating that 3 substrate moieties can fit into the binding pocket. / The Canadian Cancer Society

This thesis is an investigation of diagnostic staging and palliative radiation therapy (RT) for appendicular osteosarcoma (OSA) in dogs. Osteosarcoma is a common, highly metastatic primary bone tumour of dogs. The purpose of the first study was to assess the utility of whole body computed tomography (CT) in evaluation of metastasis in dogs with primary appendicular OSA. The objectives were to determine the utility of whole body CT as a staging tool for dogs with appendicular OSA, compare the lesion detection rate of bone scintigraphy, long bone survey radiography and whole body CT in dogs with appendicular OSA and determine the prevalence of CT-detected lung metastasis in dogs with appendicular OSA that have normal thoracic radiographs. This was a prospective cross-sectional observational study involving fifteen dogs. Test modalities were assessed against a construct reference standard for detection of bone metastasis and thoracic radiographs negative for metastatic lesions were compared against thoracic CT. Bone scintigraphy identified 5 bone lesions in 4 dogs with 2 false positive and 2 false negative results. No lesions were identified on survey radiographs or CT during blinded assessment. CT was useful for further characterizing lesions identified by bone scintigraphy. Thoracic CT identified both definitive and equivocal lesions not visible radiographically. Four dogs had equivocal ground glass pulmonary lesions on CT; 3 of these lesions progressed to radiographically discrete nodules. Overall, bone scintigraphy was the only modality that identified metastatic bone lesions. Whole body CT did not appear to be useful as alternative to bone scintigraphy; however, it may have some utility as an adjunctive diagnostic modality. Thoracic CT identified pulmonary lesions that were not visible radiographically. Ground glass pulmonary lesions in dogs should be considered suspicious for metastasis and serially monitored. The purpose of the second study was to retrospectively assess factors affecting survival time in dogs undergoing palliative RT for appendicular OSA. Fifty dogs undergoing a palliative RT protocol for spontaneous primary appendicular bone tumours were included and divided into treatment groups based on treatments administered in addition to RT. Median survival times (MST) were longest for dogs receiving RT and chemotherapy (307 days; 95%CI= 279-831) and shortest in dogs receiving RT and pamidronate (69 days; 95%CI=47-112 days). The difference in MST between dogs who received pamidronate and those who did not in this population was statistically significant on univariate (p=0.039) and multivariate analysis (p=0.0015). The addition of chemotherapy into any protocol improved survival (p<0.001). Based on the findings in this study, chemotherapy should be recommended in addition to a palliative RT protocol to improve survival of dogs with primary appendicular bone tumours. When combined with RT +/- chemotherapy, pamidronate decreased MST. / Ontario Veterinary College Pet Trust Fund

Osteosarcoma is the most common bone malignancy in children and adolescents with poorly understood aetiology. Recently, disease susceptibility and aetiology in several cancers have been associated with genomic copy-number (CN) change. We therefore studied the contribution of CN change in osteosarcoma. We report that individuals with osteosarcoma have increased germline structural variation compared to controls. These CN variants (CNVs) preferentially localize to genes implicated in control of osteoblast differentiation, bone mineralization and ossification. We propose that germline CNVs contribute to osteosarcoma susceptibility through deregulation of developmental processes controlled by genes contained within CNVs. Further supporting the notion that germline CNVs in individuals with osteosarcoma are pathogenic, we demonstrate that CNVs are associated with poor patient survival. Finally, we characterize two germline CNVs, at chromosome 1q43 and 2p11.2, which are overrepresented in osteosarcoma patients and propose that they contribute to osteosarcoma susceptibility through effect on neighbouring genes, which could be involved in control of microtubule dynamics and tumour suppression. We further characterize two regions in the tumour genome of osteosarcoma patients that harbour recurrent CN alterations (CNAs). These include deletions at chromosome 3q13.31 and vi ii amplifications at chromosome 7p14.1, which are the most altered regions in osteosarcoma and contest the view that CNAs in osteosarcoma are non-recurrent. Both chromosome 3q13.31 and 7p14.1 CNAs involve genes implicated in carcinogenesis, including LASMP at 3q13.31 and TARP at 7p14.1, while 3q13.31 CNAs also involve two non-coding RNAs. We further show that expression of 3q13.31 genes correlates with the presence of 3q13.31 CNAs. We report that chromosome 3q13.31 and 7p14.1 CNAs are also common in other cancers, identifying these loci as candidates with a global role in carcinogenesis. Supporting the notion that 3q13.31 deletions play a role in osteosarcomagenesis, we find that depletion of 3q13.31 genes promotes proliferation of osteoblasts by regulation of apoptotic and cell-cycle transcripts and also VEGF receptor 1 and that genetic deletions of 3q13.31 are associated with poor survival of osteosarcoma patients. In summary, our study implicates germline and somatic CN changes in osteosarcoma and represents a model approach for elucidation of elements contributing to disease susceptibility and aetiology in human cancer.

The Caenorhabditis elegans Eph RTK, VAB-1, has known roles in neuronal and epidermal morphogenesis as well as oocyte maturation through interaction with its ephrin ligands. In humans, Eph receptors are involved in nervous and vascular system development and have been implicated in cancer formation and progression. DAF-18, a C. elegans ortholog of the human tumour suppressor gene, PTEN, has been identified as an interacting partner with the Eph RTK, VAB-1. Mutations in human PTEN have been associated with numerous cancers and in the worm, DAF-18 is a well studied member of the DAF-2/Insulin receptor-like signaling pathway which has roles in dauer formation, thermotolerance and adult longevity. Our lab has previously shown that VAB-1/EphR binds DAF-18. To further investigate the significance of this interaction as well as offer additional function to the proteins involved, I have shown that VAB-1/EphR is a negative regulator of DAF-18/PTEN at the protein level. Western blotting reveals that endogenous expression of DAF-18/PTEN is low in wild-type animals and expression is increased in a vab-1/ephR mutant. Additionally, VAB-1/EphR and DAF-18/PTEN are expressed in head neurons, oocytes and the germline precursor cells, Z2/Z3. vab-1/ephR mutants show increases longevity and sensitivity to dauer conditions which is consistent with increased DAF-18/PTEN activity. Lastly, daf-18(ok480) is able to suppress the oocyte maturation phenotype and increased MAPK expression displayed by vab-1(dx31) animals, providing genetic evidence of an interaction. By identifying the tissues where these proteins are co-expressed and substantiating the interaction with multiple analyses, novel roles may be proposed for each: VAB-1/EphR in DAF-2/Insulin signaling and DAF-18/PTEN in oocyte maturation downstream of VAB-1/EphR signaling. This work provides further understanding of how an organism coordinates complex developmental processes and reiterates the notion that cellular signaling is a complex network of interacting players. As many signaling pathways are evolutionarily conserved, my research in C. elegans may provide a mechanism on how Eph RTKs and PTEN are regulated in more complex organisms, including humans. / Thesis (Master, Biology) -- Queen's University, 2009-02-27 17:09:10.582

No description available.

Osteosarcoma is the most common bone malignancy in children and adolescents with poorly understood aetiology. Recently, disease susceptibility and aetiology in several cancers have been associated with genomic copy-number (CN) change. We therefore studied the contribution of CN change in osteosarcoma. We report that individuals with osteosarcoma have increased germline structural variation compared to controls. These CN variants (CNVs) preferentially localize to genes implicated in control of osteoblast differentiation, bone mineralization and ossification. We propose that germline CNVs contribute to osteosarcoma susceptibility through deregulation of developmental processes controlled by genes contained within CNVs. Further supporting the notion that germline CNVs in individuals with osteosarcoma are pathogenic, we demonstrate that CNVs are associated with poor patient survival. Finally, we characterize two germline CNVs, at chromosome 1q43 and 2p11.2, which are overrepresented in osteosarcoma patients and propose that they contribute to osteosarcoma susceptibility through effect on neighbouring genes, which could be involved in control of microtubule dynamics and tumour suppression. We further characterize two regions in the tumour genome of osteosarcoma patients that harbour recurrent CN alterations (CNAs). These include deletions at chromosome 3q13.31 and vi ii amplifications at chromosome 7p14.1, which are the most altered regions in osteosarcoma and contest the view that CNAs in osteosarcoma are non-recurrent. Both chromosome 3q13.31 and 7p14.1 CNAs involve genes implicated in carcinogenesis, including LASMP at 3q13.31 and TARP at 7p14.1, while 3q13.31 CNAs also involve two non-coding RNAs. We further show that expression of 3q13.31 genes correlates with the presence of 3q13.31 CNAs. We report that chromosome 3q13.31 and 7p14.1 CNAs are also common in other cancers, identifying these loci as candidates with a global role in carcinogenesis. Supporting the notion that 3q13.31 deletions play a role in osteosarcomagenesis, we find that depletion of 3q13.31 genes promotes proliferation of osteoblasts by regulation of apoptotic and cell-cycle transcripts and also VEGF receptor 1 and that genetic deletions of 3q13.31 are associated with poor survival of osteosarcoma patients. In summary, our study implicates germline and somatic CN changes in osteosarcoma and represents a model approach for elucidation of elements contributing to disease susceptibility and aetiology in human cancer.

Intensity modulated arc therapy is a novel treatment technique that has shown great potential to be superior to conventional intensity modulated radiotherapy, both in terms of treatment plan quality as well as treatment delivery. Based on previous literature, a simplified technique called two-step intensity modulated arc therapy (2-step IMAT) was implemented into a treatment planning system. In order to automatically generate treatment plans for this technique, a beam portal shaping method was developed to generate beam segments. A sensitivity analysis was carried out on a geometric phantom to determine optimal parameters for the 2-step IMAT implementation for that particular phantom. The segment weights were optimized using the dose-based and dose-volume-based objective functions. The optimal solution search was based on the gradient-descend algorithm. The dose-based objective function was implemented using a so-called lambda-value-dose-based objective function developed in this work in order to increase both speed and flexibility of the optimization. The successful implementation demonstrated the feasibility of automatic 2-step IMAT treatment planning. A comparison of conventional arc therapy and 2-step IMAT showed improvements in the target dose uniformity by about 50% for both geometric phantom and clinical paraspinal tumor case, whilst also improving the organ sparing. The comparisons between the lambda-value-dose-based and dose-volume-based optimizations showed a speed advantage of the former by a factor of over five in the phantom study. The current beam portal shaping approach can be improved by optimizing the segment width and including multiple organs-at-risk in the segment generation algorithm. Future work will also include the implementation of a stochastic optimization to minimize the chance of getting trapped in local minima during the segment weight optimization. In summary, the work of this research showed that the automatic 2-step IMAT planning is a viable technique that can result in highly conformal plans while keeping the treatment planning and delivery simple and straightforward.

Primary esophageal (E) and gastro-esophageal junction (GEJ) cancer xenografts have the potential to become useful pre-clinical models of disease. In this study, we determined that p16 negative tumors that have not been exposed to neo-adjuvant chemo-radiation have higher engraftment chances. Morphological features and expression of certain molecular markers (p53, p16, Ki-67, EGFR, Her-2/neu) suggest that no major changes occur between primary tumors and xenografts or between early passage and late passage xenografts. Global gene expression data supported these results but revealed that approximately 2000 genes differed significantly between passage one xenografts and human tumors. Most of these genes, however, might coincide with stromal signals present in patient tumors but absent in xenografts. Primary E/GEJ cancer xenografts also showed a wide range of chemosensitivities to cisplatin-paclitaxel treatment, confirming the usefulness of these models in drug testing. These models also revealed potential ways to interrogate tumor initiating cell (TIC) dynamics after chemotherapy.

Primary esophageal (E) and gastro-esophageal junction (GEJ) cancer xenografts have the potential to become useful pre-clinical models of disease. In this study, we determined that p16 negative tumors that have not been exposed to neo-adjuvant chemo-radiation have higher engraftment chances. Morphological features and expression of certain molecular markers (p53, p16, Ki-67, EGFR, Her-2/neu) suggest that no major changes occur between primary tumors and xenografts or between early passage and late passage xenografts. Global gene expression data supported these results but revealed that approximately 2000 genes differed significantly between passage one xenografts and human tumors. Most of these genes, however, might coincide with stromal signals present in patient tumors but absent in xenografts. Primary E/GEJ cancer xenografts also showed a wide range of chemosensitivities to cisplatin-paclitaxel treatment, confirming the usefulness of these models in drug testing. These models also revealed potential ways to interrogate tumor initiating cell (TIC) dynamics after chemotherapy.

This work is a revision of the article "Die Kalkulation kalkulierbarer Mutationen” by the same author. In some chapters errors have been corrected in the mathematical representation. Chapters 6 and 7 have been re-edited. In this work, corrected excerpts from "Tumour Physics" and from "Evolution and mutation Physics" are used. To the agencies concerned should be noted.