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Cancer therapy traditionally seeks to achieve complete tumor eradication via induction of cancer cell death by chemotherapeutic agents or radiation. An alternative strategy is to induce cytostasis, i.e. to arrest proliferation of cancer cells, perhaps in parallel with conventional chemotherapy. Such an alternative strategy could provide prolonged survival with less severe consequences of cytotoxic agents. To be truly effective, a chemotherapeutic drug should exert its action on biochemical targets specific for neoplastic cells while leaving the normal cells unaffected. Therefore, the knowledge of tumor cell-specific biochemical and signaling pathways is a pre-requisite for development of new, prospective anticancer drugs. In this study, we concentrated on the energy metabolism which is remarkably different in tumor and healthy cells. Cancer cells generate ATP mainly through the glycolytic pathway, and depend far less on oxidative phosphorylation (the Warburg effect). The way cancer cells generate energy reflects their need for energy as well as building blocks required for fast biosynthesis. Glycolysis, in contrast to oxidative phosphorylation, enhances biosynthetic pathways thus accelerating progression of tumor cells through the cell cycle. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) occupies a central position in the glycolytic pathway thus playing a critical role in the energy metabolism of cancer cells. Along with its enzymatic activity, GAPDH is a multifunctional protein which acts as a signaling and regulatory molecule in several cellular mechanisms. Based on the fact that glycolysis plays a pivotal role in survival of cancer cells, we hypothesized that down-regulation of GAPDH protein would alter the cancer cell proliferation, and cellular sensitivity of cancer cells to chemotherapy. The goal of this study was to evaluate GAPDH as a potential molecular target for treatment of cancer. In this project, our aims were: 1) To determine the effect of GAPDH level on cell proliferation and cell cycle progression of human carcinoma cells; 2) To elucidate the molecular mechanism(s) causing proliferation arrest in GAPDH-depleted cells; 3) To identify the chemotherapeutic agents exhibiting cytotoxic effect against non-dividing, senescent cells; 4) To analyze molecular dynamics of nuclear GAPDH and its mutant variants in the context of chemotherapy-induced stress. Towards these aims, we developed an experimental model where the level of GAPDH in human carcinoma cells was modulated by RNA interference (RNAi) technology. In vitro experiments were performed in this model system to evaluate the energy status, and signaling pathways in cancer cells after GAPDH depletion. Human carcinoma isogenic cell lines with different levels of GAPDH protein were analyzed for the sensitivity to various chemotherapeutic agents. Using site-mutagenesis, we prepared mutated variants of GAPDH and estimated their enzymatic activity. We also prepared constructs where GAPDH cDNA was fused with green fluorescent protein (EGFP) cDNA, and transiently expressed them in human cancer cells, to assess GAPDH localization and biological effects. We analyzed intranuclear localization and dynamic characteristics of GAPDH and its variants in the live cells using image confocal technologies (e.g. FRAP). In our study, we demonstrated that GAPDH is a molecular target with clinical potential for senescence-based tumor suppression. Our experiments revealed that depletion of GAPDH induces energy crisis and proliferation arrest in human carcinoma cells. We elucidated the molecular mechanisms initiated by GAPDH depletion, and demonstrated that GAPDH-depleted cells acquire the accelerated senescence phenotype. Moreover, we found chemotherapeutic agents cytotoxic to the senescent cells, a finding that opens a way to combination chemotherapy with therapy-induced senescence agents. Our results on dynamic characteristics of intranuclear GAPDH and its mutant forms indicate that in the nucleus, GAPDH interacts with biomolecules yet to be identified. The results of this study suggest a novel, prospective molecular target for pharmacotherapeutic intervention in cancer management. / Pharmaceutical Sciences

Aedes aegypti is an important vector of human pathogens including the viruses yellow fever, dengue and chikungunya. The small interfering RNA (siRNA) pathway is a critical immune response for controlling viral replication in Aedes aegypti. The goal of this research is to identify components of the Aedes aegypti genome that influence this pathway. A transgenic mosquito strain that reports the status of the siRNA pathway via enhanced green fluorescent protein (EGFP) intensity was employed to differentiate silencing abilities among individuals. Extreme EGFP expression phenotypes, representing efficient and poor silencing abilities, were enriched over five generations. Transcriptome sequencing and analyses were performed from pools of individuals from each enriched phenotype, revealing potential RNAi contributors. 1,120 transcripts were significantly different (FDR<0.0001) among the extreme phenotypes. Four genes were chosen, amplified, sequenced for SNP analysis. These analyses were performed on samples obtained by crossing enriched, extreme phenotype F0 individuals, intercrossing their progeny, then selecting individuals representing the extreme phenotypes from the F2 population. Though further verification is needed, findings from these analyses imply the regions of Aedes aegypti, Liverpool strain (AAEL) gene identifiers AAEL005026, AAEL013438 and AAEL011704 amplified do not contribute to the two extreme, opposite RNAi silencing in the sensor strain used here. SNP analyses of AAEL000817 indicate this gene either influences extreme RNAi phenotypes or is closely linked to a gene(s) that contributes to RNAi in Aedes aegypti. The 1,120 genes identified can be validated or eliminated as potential targets in the quest to mitigate the impact of Aedes aegypti. / Master of Science in Life Sciences

Stem cells have the ability to self-renew and to differentiate into a variety of cell types. Stem cells can be found naturally in the body, can be derived from the inner cell mass of blastocysts, or can be made by dedifferentiation of adult cells. Regenerative medicine aims to utilize the potential of stem cells to treat disease and injury. The ability to create stem cell lines from a patient's own tissues allows for transplantation without immunosuppressive therapy as well as patient-specific disease modeling and drug testing. The objective of this study was to use cellular dedifferentiation to create in vitro cell lines with which to study regenerative medicine. First, we used siRNA targeted against myogenin to induce the dedifferentiation of murine C2C12 myotubes into myoblasts. Timelapse photography, immunofluorescence, and western blot analysis support successful dedifferentiation into myoblasts. However, the inability to separate the myotubes and myoblasts prior to siRNA treatment confounded the results. This system has the potential to be used to study mechanisms behind muscle cell regeneration and wound healing, but a better method for separating out the myoblasts needs to be developed before this will be achievable. Second, we used a doxycycline-inducible lentiviral vector encoding the transcription factors Oct4, Sox2, cMyc, and Klf4 to create a line of naive-like porcine induced pluripotent stem cells (iPSCs). This reprogramming vector was verified first in murine cells, the system in which it was developed. Successful production of both murine and porcine iPSC lines was achieved. Both showed alkaline phosphatase activity, immunofluorescence for pluripotency marker (Oct4, Sox2, and Nanog) expression, PCR for upregulation of endogenous pluripotency factors (Oct4, Sox2, cMyc, Klf4, and Nanog), and the ability to form embryoid bodies that expressed markers of all three germ layers. Additionally, we were able to create secondary porcine iPSC lines by exposing cellular outgrowths from embryoid bodies to doxycycline to initiate more efficient production of porcine iPSCs. The secondary porcine iPSCs were similar to the primary porcine iPSCs in their morphology, behavior, alkaline phosphatase expression, and Nanog expression with immunofluorescence. The porcine iPSCs were dependent on doxycycline to maintain pluripotency, indicating that they are not fully reprogrammed. Despite this dependence on doxycyline, this system can be used in the future to study the process of reprogramming, to develop directed differentiation protocols, and to model diseases. / Master of Science / Stem cells have the ability to self-renew and to differentiate into a variety of cell types. Stem cells can be found naturally in the body, can be derived from the inner cell mass of blastocysts (the stage of development just prior to implantation), or can be made by dedifferentiating, or reprogramming, adult cells into stem cells. Regenerative medicine aims to utilize the potential of stem cells to treat disease and injury. The ability to create stem cell lines from a patient’s own tissues allows for transplantation without immunosuppressive therapy as well as patient-specific disease modeling and drug testing. The objective of this study was to use cellular dedifferentiation to create cell lines in the laboratory with which to study regenerative medicine. First, we knocked down the expression of myogenin, a key factor in muscle cell development, to induce the dedifferentiation of mouse myotubes (adult muscle cells) into myoblasts (progenitor cells). Various methods of analysis supported successful dedifferentiation into myoblasts, but the inability to completely separate myotubes and myoblasts prior to myogenin knockdown confounded the results. With better separation of the cells, this system has the potential to be used to study mechanisms behind muscle cell regeneration and wound healing. Second, we used a viral vector encoding reprogramming factors to create both mouse and pig induced pluripotent stem cells (iPSCs) from skin cells. Pluripotent cells have the ability to differentiate into any cell type in the body, except for the placenta. Multiple pluripotency assays indicated that both the mouse and pig iPSCs were truly pluripotent. Additionally, we were able to differentiate the iPSCs into adult cells, then reprogram those back into “secondary” iPSCs. The production of secondary iPSCs is much more efficient compared to the initial creation of the primary iPSCs, which increases the usefulness of these cells for future experiments. Unfortunately, the porcine iPSCs were dependent on the reprogramming vector to maintain pluripotency. This indicates that these cells are not fully reprogrammed. Despite this, the system can still be used in the future to study the process of reprogramming, to develop cellular differentiation protocols, and to model diseases.

2 Abstract Eukaryotic initiation factor 3 (eIF3) is a critical player involved in many steps of translation initiation, which ultimately result in the formation of the elongation competent 80S ribosome. With its 13 subunits (eIF3a - eIF3m) it is the largest and the most complex translation initiation factor composed of three mutually interconnected modules (i - iii), however, the role of individual subunits involved in its structural integrity and proper function is not fully explored. The eIF3e subunit was shown to be a part of the human eIF3 structural core and to help in the mRNA recruitment to the 43S pre-initiation complex by forming a molecular bridge between the 40S ribosomal subunit and the mRNA cap-binding complex. In this study, we employed siRNA-directed downregulation of eIF3e in HeLa cells and analysed its impact on the overall eIF3 integrity and function in vivo. The eIF3e knock-down (eIF3eK.D. ) led to the severe reduction of protein amounts of other three subunits (eIF3d, k and l), which together with the subunit eIF3c and e form module ii of the eIF3 complex. Remaining module i (composed of a, b, g and i) and iii (containing f, h and m) stayed partially bound perhaps thanks to a bridging effect of eIF3c, and showed reduced binding efficiency towards the 40S subunit compared to control...

A comprovação de que siRNA pode ser usado para supressão de genes em diferentes células de mamíferos atraiu grande atenção como nova possibilidade de tratamento para diversas doenças. No entanto, para aplicação terapêutica de siRNA é necessário o desenvolvimento de um sistema de liberação efetivo e não tóxico, que permita a captação celular do siRNA e também que evite a sua degradação por enzimas. A capacidade de supressão de genes promovido pelo siRNA depende tanto do número de moléculas de siRNA transfectadas quanto da taxa de duplicação da célula. Uma das formas farmacêuticas que vem sendo amplamente utilizadas na literatura com o objetivo de prolongar e proteger a liberação de fármacos são as formulações com capacidade de formação de gel in situ. Desta forma, a presente pesquisa teve por objetivo o desenvolvimento farmacotécnico de formulações líquido cristalinas com formação de gel in situ após administração por via subcutânea para veiculação sustentada de siRNA. Misturas adequadas de monoleína, propilenoglicol, tampão Tris e polietilenoimina ou oleilamina (polímero e lipídeo catiônico, respectivamente) formaram sistemas precursores capazes de se geleificar in situ com excesso de água e, como demonstrado pelo estudo de absorção de água, a formação do gel é um processo rápido. As formulações desenvolvidas também foram eficientes para complexar o siRNA comprovando a importância da incorporação dos aditivos catiônicos aos sistemas. A liberação in vitro dos sistemas líquido cristalinos mostraram que a liberação é dependente da taxa de absorção de água e os estudos in vivo em modelo animal para avaliação da formação do gel in situ e toxicidade demonstraram que o gel se forma in vivo com a absorção de água dos fluidos corporais, sendo biodegradável e biocompatível. Os sistemas desenvolvidos mostraram-se promissores para o tratamento de doenças onde a administração localizada e sustentada de siRNA é necessária. / The evidence that siRNA can be used for suppression of genes in different mammalian cells attracted wide attention as a new possibility of treatment for various diseases. However, for siRNA therapeutic application is necessary to develop an effective non-toxic delivery system, which facilitate the siRNA cell uptake and avoid its degradation by enzymes. The genes suppression promoted by siRNA depends on the number of siRNA molecules transfected as the cell replication rate. One of the dosage forms that have been widely used in literature in order to prolong and protect the drug release is the in situ gelling formulations. Thus, the present study aimed the development and characterization of the in situ gelling liquid crystal-based systems for subcutaneous application of siRNA in gene therapy. Appropriate mixtures of monoolein, propylene glycol, Tris buffer and polyethyleneimine or oleylamine (cationic polymer and lipid, respectively) was able to form precursor formulation that gelling in water excess and, as demonstrated by the swelling studies, the gel formation is a fast process. The developed formulations were also effective for complexing the siRNA, indicating the importance of the incorporation of cationic additives in the systems. The in vitro release study showed that the release is dependent on the water absorption rate. In vivo studies in animal models have shown the gel is formed in vivo after water uptake of body fluids, and it is biodegradable and biocompatible. The systems developed are promising for the treatment of diseases where the local and sustained administration of siRNA is necessary.

A terapia gênica por RNA de interferência (RNAi) trata-se de um processo de silenciamento pós-transcricional capaz de suprimir a expressão de um determinado gene. No entanto, para se tornar eficaz, a terapia gênica utilizando siRNA (small interfering RNA - siRNA) é dependente de uma eficiente liberação e expressão do acido nucléico nas células-alvo dentro dos tecidos ou órgãos. A literatura atual mostra algumas propostas de sistemas de liberação tópica de siRNA, entretanto, o uso de nanopartículas híbridas polimérico-lipídicas para complexação e liberação de siRNA na pele para o tratamento tópico de doenças cutâneas, ainda é pouco explorado, o que configura a inovação deste trabalho. Neste contexto, o presente trabalho tem como objetivo o desenvolvimento de uma nanopartícula hibrida lipídica associada a um polímero catiônico (NLS-PEI) como sistema de liberação tópica para siRNA, visando a terapia gênica como nova abordagem no tratamento de patologias cutâneas. Primeiramente a composição e o método de produção das NLS-PEI foram otimizados. Como polímero catiônico, utilizou-se a polietilenoimina (PEI). As NLS-PEIs otimizadas, compostas pelo lipídeo Compritol® 888 ATO (2,0%), Poloxamer 188 (1,5%) e PEI (0,15 e 0,25%), apresentaram-se esféricas com superfície lisa e um tamanho médio de 165 nm, potencial zeta médio de +20 mV, concentração de partículas de 1013/mL e com alta estabilidade (90 dias a 4°C). Foi demonstrado, por DSC, que a PEI interage tanto com o tensoativo na superficie das nanoparticulas como também com o lipídeo. A avaliação de comportamento e ação in vitro das NLS-PEIs foi estudada em queratinócitos e fibroblastos, evidenciando que o tratamento não diminuiu a viabilidade celular e houve alta captação verificada por citometria de fluxo (acima de 80% de células transfectadas) e por microscopia confocal. No estudo in vitro de penetração das NLS-PEI complexado com siRNA-FAM em pele de orelha de porco, foi demonstrado a penetração cutânea aumentada de siRNA-FAM a partir das NLS-PEIs. Ensaio in vivo em modelo de inflamação cutânea aguda e crônica mostrou a eficácia das NLS-PEIs contendo siTNF-?, reduzindo a espessura da epiderme em comparação ao grupo controle, reduzindo o rubor, a descamação e os níveis da citocina pró-inflamatória TNF-? e seu RNAm correspondente. A NLS-PEI também promoveu a penetração cutânea das moléculas de siRNA nas camadas mais profunda da pele, in vivo. Diante dos resultados obtidos, podese concluir que as formulações desenvolvidas são sistemas de liberação promissores para administração tópica de siRNA para o tratamento de patologias cutâneas na terapia gênica. / Small-interfering RNA (siRNA) has a high application potential for therapeutic silencing of pathologic or drug-resistance genes. Nonetheless, free siRNA molecules are known to have poor transfection efficiency and biological stability, so a carrier use is necessary. Lipid-polymeric nanocarriers are the new generation of nanoparticulate that have been used as siRNA carrier system and are attracting attention as novel colloidal drug carrier for topical use. In this context, the aim of this study was to develop of hybrid lipidpolyethylenimine nanocarriers (SLN-PEI) as topical delivery systems for siRNA. First, the SLN-PEI composition and production method were optimized. Polyethyleneimine (PEI) was used as cationic polymer. The optimized SLN-PEIs, composed of the lipid Compritol® 888 ATO (2.0%), Poloxamer 188 (1.5%) and PEI (0.15 and 0.25%), were spherical with a smooth surface and average size of 200 nm, mean zeta potential of +20 mV, mean number of particles per mL in the 1013 frame and remained stable for 90 days at 4 °C. It has been demonstrated by DSC that PEI interacts with both the surface surfactant of the nanoparticles and with the lipid. The evaluation SLN-PEI\'s behavior and in vitro action was studied in keratinocytes and fibroblasts, evidencing that the nanoparticles did not decrease cell viability and there was high cellular uptake evidenced by flow cytometry (above 80% of transfected cells) and by confocal microscopy. In the permeation in vitro study, it was demonstrated that SLN-PEI increased cutaneous penetration of siRNA-FAM. In vivo assay, in model of acute and chronic skin inflammation, demonstrated the efficacy of SLN-PEIs carrying siTNF-?, reducing epidermal thickness compared to control group, reducing redness, desquamation and levels of the pro-inflammatory cytokine TNF- ? and its corresponding mRNA. SLN-PEI also promoted penetration of the siRNA molecules in the deeper layers of the skin, in vivo. In view of the results obtained, we can conclude that the formulations developed are promising delivery systems for topical administration of siRNA for the treatment of cutaneous pathologies in gene therapy.