Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Cancer, the second most common cause of death in the United States, is a collection of diseases caused by uncontrolled cell growth and metastasis. The main treatment for cancer is chemotherapy, which generally kills fast growing cells nonspecifically and has many side effects. A different type of cancer treatment, called targeted therapy, aims to avoid general toxicity by using drugs that block the activity of specific gene products, usually encoded by oncogenes, which have been shown to drive tumor growth. To date, targeted therapies, alone or in combination with chemotherapies, have mainly been successful in rare subsets of patients with tumors addicted to single oncogenes. This has created a rationale to mainly treat patients with an oncogene-addiction (such as those carrying mutated or overexpressed kinases) with targeted therapies like erlotinib and trastuzumab, which inhibit human epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2/ErbB2), respectively. Here, evidence is provided that targeted therapies are also effective in tumors that are dependent on multiple growth factors - a phenomenon that is called combinatorial ligand addiction. Specifically, it is shown that ligands that bind the EGFR family and the hepatocyte growth factor receptor (HGFR/MET) can activate protein kinase B (PKB/ AKT) across a broad set of cancer cell lines, suggesting that ligand signaling is redundant and widespread. It is also shown that ErbB ligands have distinct signaling dynamics and strengths, which provides a rationale for investigating each component of the ErbB signaling network. Using a systematic approach, we found that ErbB3 is an imp01tant therapeutic target even though it is not overexpressed and lacks kinase activity. Furthermore, it is shown that cell lines with and without known oncogene-addiction express autocrine ligands and have improved growth inhibition with drug combinations that include autocrine ligand-blocking antibodies. This research demonstrates that combinatorial ligand addiction creates a new rationale for therapeutic combinations to improve efficacy and prevent resistance in cancer cells that are treated with current targeted drugs. / 2031-01-01

With all the improvements in cancer treatments, multidrug resistance is still the major challenge in treating cancer. Cells can develop multidrug resistance (MDR) during or after treatment, which will render the cancer cells resistant not only to the chemotherapy drug being used but also to many other structurally- and mechanically-different chemotherapeutics. In the first project, the main focus was on development of drug resistant cell lines by selection with taxol. Gene changes in the L1T2 cell line after treatment with Taxol was studied. Treatment of L1T2 cells with taxol leads to changes in the expression of ABC transporter proteins, whereas the combination of Taxol with protease inhibitors leads to increased efficacy via inhibition of P-glycoprotein (P-gp). In the second project, we showed that our innovatively-designed Au-loaded poly(lactide-co-glycolic acid) nanoparticles (GPLGA NPs) are able to cross biological barriers and deliver inside the cells without being recognized by the ABC protein transporter. (We focus specifically on P-gp-mediated drug efflux in a model of HEK cell lines.) The concentration of gold was measured using inductively-coupled plasma/mass spectrometry (ICP-MS) after 6- and 24-hour treatment of GPLGA NPs, which did not show significant increase of gold inside the cells in presence of the P-gp inhibitor valspodar. Cancer cells were treated with the GPLGA NPs for 24 hours and then irradiated 5 minutes at 1Wcm-2 using laser settings at 680 or 808 nm. Heat generation in cancer cells, after internalizing GPLGA NPs and laser irradiation, was significant irrespective of laser wavelength. The plasmomic heating response in this in vitro model can be a step closer to overcome MDR. Finally, for the third and last project represented in this dissertation, the focus was on the design and synthesis of innovative, biodegradable PLGA NPs, encapsulated with the platinum(II)-based non-organometallic/non-cyclometalated phosphorescent complex PTA = [Pt(ptp)2], a brightly phosphorescent complex (ptp = square-planar bis[3,5-bis(2-pyridyl)-1,2,4-triazolato]). Size-tunable, emission-polarized phosphorescent PTA-loaded PLGA NPs were synthesized using a single-emulsion, solvent evaporation technique. Photoluminescence characterization shows that PTA-loaded PLGA NPs exhibit strong and stable orange emission with peak maximum ~ 580 nm. The photoluminescence quantum yield (QY) of the synthesized PTA-PLGA NPs was evaluated at ~55%, which allows recording of images with a much better contrast than that with PTA in organic solvents without the PLGA (QY ~0.5% and ~0 emission polarization) or even that with typical fluorescent organic dyes like rhodamines.

Thesis (M.A.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Autologous Bone Marrow Transplantation (ABMT) provides a way to rescue the hematopoietic system in patients receiving high dose chemotherapy. Solid tumors like lung and breast cancer are the targets for new therapies that involve high dose chemotherapy with AMBT due to their growth and pathologic characteristics. Reinfusion of bone marrow with metastatic neoplastic cells could also seed viable tumor cells, and thus be a reason for treatment failure, restricting high-dose chemotherapy with bone marrow support to patients whose marrow is morphologically free of tumor cells. The use magnetic beads for physical separation of tumor from normal cells and the use of a toxin delivered by a monoclonal antibody are examined as two purging methods for treatment. The use of magnetic beads conjugated with specific antibodies (SM1, LAM2 and LS1) against tumor antigens to purge 2-3 logs of Small Cell Lung Cancer (SCLC) contamination from bone marrow is demonstrated. Optimal performance calls for short double exposure to anti-tumor cell-antigen monoclonal antibodies, followed by exposure to magnetic beads coated with antibodies specific for the monoclonal anti-SCLC antibodies, maintaining a bead-to-cell ratio of 10:1 to 100:1. Specific toxin delivery to three breast cancer cell lines (ZR-75, BT20 and MCF7) expressing the DF3 antigen was demonstrated by the use of DF3 immunotoxin (DF3-IT). The optimal concentration of the DF3-IT immunotoxin for highest tumor kill was shown to be 1x1Q-9 M, but this caused a loss of bone marrow progenitor cell colonies of about 30%. Both methods are limited chiefly by the level of antigen expression in the target tumor cells. The purging efficiency could be improved by targeting a wider range of antigens or by inducing higher levels of antigen expression. From the clinical perspective, the advantages and need for purging involved bone marrow to bring about substantially improved curative strategies remains a question still unanswered. / 2031-01-01

We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.

We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.

abstract: Cancer diseases are among the leading cause of death in the United States. Advanced cancer diseases are characterized by genetic defects resulting in uncontrollable cell growth. Currently, chemotherapeutics are one of the mainstream treatments administered to cancer patients but are less effective if administered in the later stages of metastasis, and can result in unwanted side effects and broad toxicities. Therefore, current efforts have explored gene therapy as an alternative strategy to correct the genetic defects associated with cancer diseases, by administering genes which encode for proteins that result in cell death. While the use of viral vectors shows high level expression of the delivered transgene, the potential for insertion mutagenesis and activation of immune responses raise concern in clinical applications. Non-viral vectors, including cationic lipids and polymers, have been explored as potentially safer alternatives to viral delivery systems. These systems are advantageous for transgene delivery due to ease of synthesis, scale up, versatility, and in some cases due to their biodegradability and biocompatibility. However, low efficacies for transgene expression and high cytotoxicities limit the practical use of these polymers. In this work, a small library of twenty-one cationic polymers was synthesized following a ring opening polymerization of diglycidyl ethers (epoxides) by polyamines. The polymers were screened in parallel and transfection efficacies of individual polymers were compared to those of polyethylenimine (PEI), a current standard for polymer-mediated transgene delivery. Seven lead polymers that demonstrated higher transgene expression efficacies than PEI in pancreatic and prostate cancer cells lines were identified from the screening. A second related effort involved the generation of polymer-antibody conjugates in order to facilitate targeting of delivered plasmid DNA selectively to cancer cells. Future work with the novel lead polymers and polymer-antibody conjugates developed in this research will involve an investigation into the delivery of transgenes encoding for apoptosis-inducing proteins both in vitro and in vivo. / Dissertation/Thesis / M.S. Chemical Engineering 2011

Developing personalized cancer therapies based on cancer genomics methodologies forms the basis for future cancer therapeutics. A genomics platform was developed based on canine cancer to produce a proof-of-concept for personalized genomics led therapeutic choices but also developing personalized therapeutics for canine cancer patients themselves. The platform identified the genetic state of a canine cancer patient within two drugable pathways; p53 and HSP90/IRF1. The former gene was wild-type p53 thus directing the use of p53 activating molecules. The latter mutations in both HSP90 and IRF1 suggested an investigation into HSP90 and interferon signalling molecules as drug leads. Drugs that target both of these pathways were subsequently used to measure drug effects in cell line models but also to identify novel biomarkers of drug responses. My study focused on the effect of the HSP90-inhibitor Ganetespib had on its client proteins, particularly IRF-1. Briefly my results indicated the following:(i) Ganetespib downregulated IRF-1 protein levels in A375 cell lines and this attenuation was not mediated by either MDM2 or CHIP (E3 ligase). IFNγ- induced IRF-1 was also observed to be downregulated when Ganetespib was used in combination therapy.(ii) Insitu proximity ligation assay showed induced HSC70 upregulation upon HSP90 inhibition by Ganetespib and HSC70/MDM2 complexes were seen to be stabilized compared to the usage of MDM2/p53 inhibitor-nutlin. I hypothesize that MDM2/HSC70 complex might chaperon IRF-1 into lysosome for degradation via chaperon mediated autophagy pathway. (iii) My results also indicate that Ganetespib can downregulate IFN γ- induced PDL-1 expression in melanoma cell lines. Pre-sensitizing the cells with Ganetespib prior to the addition of IFNγ could attenuate PDL-1 to basal levels. (iv) My results also showed that the downregulation of PDL-1 by Ganetespib is an IRF-1 dependent mechanism. Therefore, my results suggest that HSP90 represents an important emerging target for cancer therapy because its inactivation results in the simultaneous blockade of multiple signalling pathways and can also sensitize tumor cells to other anticancer agents. Targeting HSP90 could also help to disrupt PD1/PDL- 1 interaction and activate immune system to recognise tumor cells. I conclude that HSP90 and IRF-1 play a critical role in types II interferon pathways and these findings establish a novel basis for the design of future Ganetespib-based combinatorial approaches to improve patient outcomes in this disease. These approaches finally demonstrate that cancer genomics can stratify choice of cancer drugs used on patients but also provide evidence that cancer patient samples can be used for the specific stratification of cancer drug choice based on cancer genomics data.

Oncolytic viruses (OVs) are emerging as a potent therapeutic platform for the treatment of malignant disease. The tumor cells inability to induce antiviral defences in response to a small cytokine known as interferon (IFN) is a common defect exploited by OVs. Heterogeneity in IFN signalling across tumors is therefore a pillar element of resistance to these therapies. I have generated a mathematical model and simulation platform to study the impact of IFN on OV dynamics in normal and cancerous tissues. In the first part of my thesis, I used this model to identify novel OV engineering strategies which could be implemented to overcome IFN based resistance in tumor tissues. From these simulations, it appears that a positive feedback loop, established by virus-mediated expression of an interferon-binding decoy receptor, could increase tumor cytotoxicity without compromising normal cells. The predictions set forth by this model have been validated both qualitatively and quantitatively in in-vitro and in-vivo models using two independent OV strains. This model has subsequently been used to investigate OV attenuation mechanisms, the impact of tumor cell heterogeneity, as well as drug-OV interactions. Following these results, it became apparent that selectivity should equally be observed when overwhelming the cell with a non replicating virus. While normal tissues will clear this pseudo-infection rapidly, owing to their high baseline in antiviral products at the onset of infection, tumor cells with defective anti-viral pathways should not have readily available biomachinery required to degrade this pro-apoptotic signal. Recapitulated by the mathematical model, non-replicating virus-derived particles generated by means of UV irradiation selectively kill tumor cells in cultured cell lines and patient samples, leading to long term cures in murine models. Taken together, this thesis uses a novel mathematical model and simulation platform to understand, design & improve oncolytic virus-based therapeutics.

Les thérapies anticancéreuses nécessitent aujourd’hui une approche plus ciblée. L’approche immunologique est devenue dans cette optique un enjeu d’importance notamment grâce à sa capacité d’atteindre de manière plus spécifique des cibles tumorales. Récemment, mon équipe a identifié des peptides antigéniques issus de la préprocalcitonine (ppCT), qui étaient capables d’induire une réponse T cytotoxique spontanée chez un patient atteint de cancer bronchique non à petites cellules bénéficiant d’une longue survie et correspondent donc à des candidats potentiels dans des approches vaccinales. Dans ma thèse, je fournis une preuve de concept préclinique pour un vaccin fondé sur la ppCT à usage thérapeutique contre le cancer du poumon. Cette approche est optimisée en la combinant avec un anticorps monoclonal anti-PD- 1. En plus, j'ai identifiée de nouveaux épitopes issus de cet antigène et j'ai construit un lentivirus codant la ppCT pour des perspectives thérapeutiques. / Cancer therapies today require a more targeted approach to optimize the anti-tumor response. In this context, the immunological approach has become an important issue, mostly through the identification of specific tumor-associated antigens (TAA). Recently, my team identified new tumor antigens derived from the preprocalcitonin (ppCT) which were able to induce a spontaneous cytotoxic T-cell response with long term survival in patients with non-small cell lung cancer and therefore correspond to be potential candidates for vaccine approaches. In my thesis, I provide a preclinical proof of concept for the ppCT peptide vaccine for the therapeutic use against lung cancer which is optimized by combining the treatment with the monoclonal antibody anti-PD-1, nivolumab. In addition, I identified new epitopes from this Ag and constructed a lentivirus encoding ppCT for further therapeutic perspectives.

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