Cancer is a group of diseases caused by aberrant continuously proliferating cells capable of metastasis. Despite significant advances in preventive, diagnostic and treatment measures, cancer is one of the major causes of death in the United States, second only to heart diseases. Main treatment approaches are surgery, radiotherapy, chemotherapy, and the recently expanding immunotherapeutic approaches. The main challenge in treating cancer is the ability of cancer cells to mutate and develop resistance to drug treatments therefore lowering the efficacy of chemotherapy in preventing metastatic tumors. Cancer vaccines are a treatment modality that employs the potential of the immune system to recognize and eliminate tumor cells by unmasking tumor cell antigens and generating an effective anti-tumor immune response with an immune memory capable of preventing metastases formation. This dissertation describes and evaluates an innovative cell-particle hybrid cancer vaccine construct involving irradiated tumor cell surface-engineered with polymeric particles using streptavidin-biotin cross-linking. The tumor cells were biotinylated indirectly using biotin-linked antibodies targeting a surface integrin and the particles were loaded with an immune adjuvant and coated with streptavidin. The tumor cells served as the source of tumor antigens and the anchored particles served to confine loaded immune adjuvant to the tumor cells. The vaccine construct was designed to co-deliver tumor antigens and the immune adjuvant to the same antigen presenting cell, a criteria that has been suggested recently to be important for optimal cancer vaccine potency. The first report on this cell-particle construct was published in my master’s thesis defended in May 2013. In that report, the feasibility of assembling the cell-particle hybrid was demonstrated. However, loading of the immune adjuvant, CpG ODN (cytosine phosphate guanine oligonucleotide), into streptavidin-coated particles was not optimal. In the current studies, this problem was addressed and the cancer vaccine potential of the cell-particle construct was assessed. We first evaluated a new TLR4 (toll like receptor 4) agonist, PET lipid A (pentaeryhtritol lipid A), for its potential use in cancer vaccines with the intention to incorporate it in the cell-particle hybrid. PET lipid A is a fully synthetic lipid A analog that has been demonstrated to have immunostimulatory properties. We evaluated the potential use of PET lipid A in cancer vaccine applications and the effect of particulate formulations on its adjuvant properties. Results showed improved in vitro immunostimulatory properties for particle based formulations. Upon testing the immunostimulatory properties of PET lipid A in vivo, moderate enhancement in antigen specific cytotoxic T cells stimulation was observed when PET lipid A was delivered in particles, which then translated into a corresponding trend toward increased survival in a prophylactic tumor study. PET lipid A was concluded to be a weak potential cancer vaccine adjuvant and was not chosen as the immune adjuvant to use in the cell-particle hybrid assembly. Instead, CpG ODN (TLR9 agonist) was chosen due to its strong record of efficacy as a cancer vaccine adjuvant. The second part of this research project aimed at addressing the challenges we encountered previously in achieving acceptable CpG ODN loading of the final streptavidin-coated PLGA (Polylactic-co-glycolic acid) particles. The approach taken was to modify the method used earlier to make the particles in order to circumvent CpG ODN loss. In the modified method the number of steps required to make streptavidin-coated CpG ODN-loaded PLGA particles was reduced and the fabrication media was altered to allow simultaneous particle fabrication and activation of surface carboxyl groups. The modified method resulted in 5-fold higher loading in the final streptavidin-coated particles compared to the original method. Subsequent to establishing the feasibility of constructing the cell-particle hybrid and characterizing the assembled hybrid in vitro, the in vivo cancer vaccine potential of the designed construct was examined. Two independent murine tumor models were chosen for this purpose, namely prostate cancer and melanoma. The proposed cell-particle hybrid vaccine construct had significant therapeutic outcomes in the prostate cancer tumor model where mice vaccinated with cell-particle hybrids were the only group to show significant improvement in survival compared to untreated controls whereas no other vaccine formulation had such an effect. Unfortunately, no prophylactic benefit was observed from any of the vaccine formulations used in the melanoma tumor model involving irradiated GM-CSF (granulocyte macrophage colony stimulating factor)-secreting B16.F10 cells. In vitro examination of the immunostimulatory properties of all cell lines used in these studies revealed that transfected and parent B16.F10 cells (representing murine melanoma) were possibly immunoinhibitory whereas RM11 (representing murine prostate cancer) cells lacked such immunosuppressive effect in vitro. Our objective was to design and evaluate a new cancer vaccine construct that improved the immunostimulatory properties of irradiated tumor cell based vaccines. The approach taken was to surface engineer tumor cells with immune adjuvant loaded polymeric particles. We reported a simple method for fabricating streptavidin-coated PLGA particles and a versatile method of tumor cell surface engineering. We found that the efficacy of tumor cell-based vaccines can be inconsistent across tumor models and the in vitro immunosuppressive effect of tumor cells might be a contributing factor.

Vaccines have become an important approach for the treatment of cancer. Cancer vaccines help the immune system to detect and eradicate tumor cells. Also, cancer vaccines are designed to stimulate an effective immune response that can create long-term immune memory to prevent tumor recurrence. This treatment approach involves the administration of a vaccine comprising or encoding an antigen and can often be combined with an adjuvant to further promote the immune response. The goal of this research was to study the effect of the polyanhydride composition of prophylactic cancer vaccine formulations on the tumor-specific immune response. To achieve this goal, three different amphiphilic polyanhydride copolymers were generated comprising different ratios of 1,6-bis-(p-carboxyphenoxy)-hexane (CPH) and 1,8-bis-(p-carboxyphenoxy)-3,6-dioxaoctane (CPTEG) or sebacic anhydride (SA) monomers. These copolymers were used to fabricate particles encapsulating a model antigen, ovalbumin (OVA), using a double emulsion solvent evaporation technique. The ability of the three different compositions of amphiphilic polyanhydride copolymers (50:50 CPTEG:CPH, 20:80 CPTEG:CPH, and 20:80 CPH:SA) encapsulating OVA to elicit immune responses was investigated. Further, the impact of soluble unmethylated oligodeoxynucleotides containing deoxycytidyl-deoxyguanosine dinucleotides (CpG ODN), an immunologic adjuvant, on the immune response to the three formulations was also studied. The immune response to cancer vaccines was measured after treatment of C57BL/6J mice with two subcutaneous injections, seven days apart, of 50 μg OVA encapsulated in particles composed of different polyanhydride copolymers with or without 25 μg CpG ODN. In vivo studies showed that 20:80 CPTEG:CPH particles encapsulating OVA significantly stimulated the highest level of CD8+ T lymphocytes, generated the highest serum titers of OVA-specific IgG antibodies, and produced longer survival in comparison to formulations involving the other polyanhydride copolymers. The results also revealed that supplementing the vaccine formulations with CpG ODN did not enhance the immunogenicity of OVA. These results accentuate the crucial role of the copolymer composition of polyanhydrides in stimulating the immune response and improving cancer vaccine efficacy.

Cancer immunotherapy has proven to be challenging as it depends on overcoming multiple mechanisms that mediate immune tolerance to self-antigens. In situ immunization is based on the concept that it is possible to break immune tolerance by inducing tumor cell death in situ in a manner that provides antigen presenting cells such as dendritic cells (DCs) with a wide selection of tumor antigens that can then be presented to the immune system and result in a therapeutic anticancer immune response. Based on recent advances in the understanding of antitumor immunity, we designed a three-step approach to in situ immunization to lymphoma: (1) Inducing immunogenic tumor cell death with the chemotherapeutic drug Doxorubicin (Dox). Dox enhances the expression of "eat-me" signals by dying tumor cells, facilitating their phagocytosis by dendritic cells (DCs). Due to the vesicant activity of Dox, microparticles (MPs) made of PLGA (a biodegradable polymer) can safely deliver Dox intratumorally and are effective vaccine adjuvants; (2) Enhancing antigen presentation and T cell activation using anti-OX40; (3) Sustaining T cell responses by checkpoint blockade using anti-CTLA-4. In vitro, Dox MPs were less cytotoxic to DCs than to B lymphoma cells, did not require internalization by the lymphoma cells, and significantly enhanced phagocytosis of tumor cells by DCs as compared to soluble Dox. In mice, this three-step therapy induced CD4- and CD8-dependent systemic immune responses that enhanced T cell infiltration into distant lymphoma tumors leading to their eradication and significantly improving survival. Our findings demonstrate that systemic antitumor immune responses can be generated locally by three-step therapy and merit further investigation of three-step therapy for immunotherapy of lymphoma patients. Furthermore, we designed another in situ immunization approach using PLGA MPs loaded with both Dox and CpG oligodeoxynucleotides (CpG). The addition of CpG was to further enhance the Dox MP design by including an agent that addresses Step Two in situ, by enhancing tumor antigen presentation by DCs. In vitro, we show that Dox/CpG MPs can kill B and T lymphoma cells and are less toxic to DCs than soluble Dox. In vivo, Dox/CpG MPs combined with anti-CTLA-4 and anti-OX40 generated systemic immune responses that suppressed injected and distant tumors in a murine B lymphoma model, leading to tumor-free mice. The combination regimen was also effective at reducing T cell lymphoma and melanoma tumor burdens. In conclusion, Dox/CpG MPs represent a versatile, efficient and safe tool for in situ immunization that could provide a promising component of immunotherapy for patients with a variety of types of cancer.

Master of Engineering / This thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.

L'environnement et la santé des populations sont devenus des préoccupations majeures aussi bien au niveau national qu'au niveau européen. REACH (Registration, Evaluation and Authorization of CHemicals) est un système adopté par l'Union Européenne qui regroupe plus de quarante directives afin d'éliminer et de remplacer les substances chimiques les plus toxiques. Dans ce contexte, la mise en place d'un tel système requiert des méthodes d'analyse robuste, fiables et reproductibles dans le but d'évaluer et de détecter à l'état d'ultra-traces les molécules prioritaires persistantes dans les eaux et les sols.<br />Après avoir ciblé plusieurs substances listées sur l'annexe XVII de REACH, nous avons complété cette sélection par des polluants prioritaires de l'environnement Rhône Alpin tels les pesticides. Ainsi, la méthode d'analyse proposée permet de détecter et de quantifier par CPG-SM et CPL-SM/SM 33 substances (10 alkylphénols, 5 fongicides triazole, 1 fongicide morpholine, <br />1 acaricide pyridazinone, 2 phtalates, bisphénol A, 2 insecticides carbamates, un résidu des pesticides dithiocarbamates, 2 pesticides organophosphorés et 8 organochlorés) dans des matrices environnementales aussi complexes que des effluents et des boues de station épuration. <br />L'extraction des analytes est menée par Extraction sur Phase Solide (SPE) pour les échantillons aqueux et par Extraction par Solvant Accélérée (ASE) qui a été entièrement optimisée par étude statistique des paramètres. Les extraits sont ensuite purifiés de la même manière par SPE. La préparation à la validation de ma méthode nous a permis de confirmer des limites de détection basses comprises entre 7,2 ppt et 1,27 ppb dans les eaux et entre 5 ppb et 1,7 ppm dans les boues/sols

Le but de ce travail de thèse a été d'analyser l'implication du tronc dans la locomotion, notamment sa commande rythmique, afin d'en comprendre les mécanismes de contrôle et les différentes activités segmentaires qui amènent ses mouvements. Ces m´ecanismes peuvent alors être modélisés pour reproduire les différentes synchronisations observées au niveau des activités de chaque segment vertébral considéré. Enfin, cette modélisation permet de spécifier les activités du tronc à observer pour suivre en continu le cycle de marche d'un individu se déplacant. Dans un premier temps nous rappellerons les données de la littérature sur la locomotion, et notamment l'activité du tronc, qui nous ont permis de définir les axes principaux dans lesquels nous allons orienter notre travail. Cet état de l'art nous a notamment amenés à étudier les structures de type ”générateurs de rythme centraux” (Central pattern generator, CPG, en anglais). Dans un second temps nous avons réalisé une série de mesures expérimentales pour analyser de facon systématique et précise l'activité musculaire et cinématique du tronc lors de diverses situations locomotrices (marche, course, bond, pédalage). Ces mesures nous ont permis de mieux comprendre la manière dont le tronc se mettait en mouvement et comment ses activités musculaires et cinématiques, notamment les synchronisations intersegmentaires, évoluaient afin de tirer le meilleur parti des mouvements du haut du corps lors de la locomotion proprement dite. Dans un troisième temps, les résultats obtenus par les mesures d'activités du tronc ayant mis en évidence l'utilité du tronc et les mécanismes de contrôle dans une locomotion efficace, nous avons exploré la modélisation de l'activité du tronc au moyen d'un réseau d'oscillateurs mimant un CPG. Le choix d'un modèle de CPG pour représenter l'activité du tronc fait suite à des considérations phylogénétiques qui semblent indiquer qu'une telle structure pourrait exister chez l'homme. Une des propriétés de ce type de réseaux est leur capacité à exprimer différentes synchronisations sans changer de structure, c'est ce que nous avons appliqué aux observations faites lors de la marche, la course... Une autre propriété de ces réseaux est leur aptitude à se synchroniser avec un signal externe, nous avons donc explor´e diff´erents moyens de commander ce réseau d'oscillateur en phase avec la locomotion, encore une fois à partir de l'activité du tronc, de son accélération pour être plus précis.

<p>Bacillus Calmette Guérin (BCG), or attenuated Mycobacterium bovis, is the gold standard of immunotherapy in the clinic to treat superficial bladder cancer. However, setbacks remain due to a high recurrence rate, side effects, and BCG-refractory disease. In this thesis, we explored the use of novel immunotherapeutic agents such as CpG oligodeoxynucleotides (CpG ODNs) or synthetic ODNs containing unmethylated CpG dinucleotides. Since unmethylated CpG motifs are predominant in bacterial but not vertebrate DNA, they function as a “danger signal” leading to a potent immune response.</p><p>To be able to test various immunotherapeutic agents, we optimized subcutaneous (s.c.), metastatic, and orthotopic models using the murine bladder-49 (MB49) cancer cell line. In the orthotopic model, we show that poly-L-lysine promotes MB49 attachment to the bladder leading to 100% tumor take. In addition, Clorpactin (sodium oxychlorosene) potently enhances adenoviral transduction in the bladder.</p><p>Utilizing the MB49 model, we compare CpG ODNs with BCG and demonstrate the increased efficacy of CpG ODNs which could cure both s.c. and aggressive orthotopic bladder cancer. In our model, type B ODNs were most optimal and the antitumor response required T cells in order to induce regression and tumor-specific immunity. We also combined CpG ODNs with adenoviral vectors (Ad) expressing the immunostimulatory molecules CD40L, TRANCE, lymphotactin, IL2 or IL15. However, we show that CpG ODNs are effective as a monotherapy and adenoviral vectors did not enhance the effect.</p><p>AdCD40L was also used to genetically modify human dendritic cells (DCs). AdCD40L-transduced DCs not only had a higher and prolonged expression of the Th1 cytokine IL12 compared to TNFα-matured DCs, but CD40L-activated DCs could also resist the suppressive effects of IL10 and TGFβ. Since TNFα is commonly used in clinical DC vaccination protocols and because tumors often secrete immunosuppressive cytokines, these data have important implications for optimizing cancer immunotherapy.</p>

Bacillus Calmette Guérin (BCG), or attenuated Mycobacterium bovis, is the gold standard of immunotherapy in the clinic to treat superficial bladder cancer. However, setbacks remain due to a high recurrence rate, side effects, and BCG-refractory disease. In this thesis, we explored the use of novel immunotherapeutic agents such as CpG oligodeoxynucleotides (CpG ODNs) or synthetic ODNs containing unmethylated CpG dinucleotides. Since unmethylated CpG motifs are predominant in bacterial but not vertebrate DNA, they function as a “danger signal” leading to a potent immune response. To be able to test various immunotherapeutic agents, we optimized subcutaneous (s.c.), metastatic, and orthotopic models using the murine bladder-49 (MB49) cancer cell line. In the orthotopic model, we show that poly-L-lysine promotes MB49 attachment to the bladder leading to 100% tumor take. In addition, Clorpactin (sodium oxychlorosene) potently enhances adenoviral transduction in the bladder. Utilizing the MB49 model, we compare CpG ODNs with BCG and demonstrate the increased efficacy of CpG ODNs which could cure both s.c. and aggressive orthotopic bladder cancer. In our model, type B ODNs were most optimal and the antitumor response required T cells in order to induce regression and tumor-specific immunity. We also combined CpG ODNs with adenoviral vectors (Ad) expressing the immunostimulatory molecules CD40L, TRANCE, lymphotactin, IL2 or IL15. However, we show that CpG ODNs are effective as a monotherapy and adenoviral vectors did not enhance the effect. AdCD40L was also used to genetically modify human dendritic cells (DCs). AdCD40L-transduced DCs not only had a higher and prolonged expression of the Th1 cytokine IL12 compared to TNFα-matured DCs, but CD40L-activated DCs could also resist the suppressive effects of IL10 and TGFβ. Since TNFα is commonly used in clinical DC vaccination protocols and because tumors often secrete immunosuppressive cytokines, these data have important implications for optimizing cancer immunotherapy.

Synthetic CpG containing oligodeoxynucleotides (ODNs) are recognized by Toll like Receptor 9 (TLR9) and induce a strong pro-inflamatory immune response. To date, four different CpG ODN classes have been described. K-Class ODNs (also known as B-ODN) are potent B cell activators and stimulate TNF

Methylation of CpG islands located at the promoter regions is a mechanism which controls gene silencing and expression. Hyper or hypo methylation of these sites on promoter sequences have been associated with many diseases, like cancer. Even though promoter CpG islands and their methylation profiles are important regulators of gene expression, the exact mechanism of gene silencing through methylation is not known. Here, we have investigated the status of promoter CpG methylation under various evolutionary pressures by calculating the differences in promoter CpG content and methylation profiles at different pass points. In order to determine the list of genes under each category we have analyzed and compared the orthologs among 58 genomes available through ENSEMBL. The total number of CpG dinucleotides at the promoter regions of all groups of genes have been calculated and compared. Additionally, we have compared the experimentally determined methylation profiles of these CpG&#039 / s between human blood cells and fibroblast cells. While the promoter CpG content changed through common to newer genes, the number of the CpG units methylated found to be consistent. Here, we present the functional level analysis of common gene lists at different pass points and report the differences of the promoter CpG content and the methylation profiles among these groups with distinct evolutionary conservation status. We have also observed the conservation status of individual methylated CpG units on the low and high methylated genes. Our analysis revealed that the surrounding methylation content had a positive effect on the conservation of individual CpG&rsquo / s.