The potential application of a hydrogel-based strong anion-exchange (Q) membrane to purify plasmid DNAs was evaluated. The maximum binding capacity of plasmid DNA was estimated to be 12.4 mg/ml of membrane volume with a plasmid DNA recovery of ~ 90%, which is superior to other commercially available anion-exchange resins and membranes. The membrane was able to retain its structural integrity and performance after multiple cycles of usage (> 30 cycles). The inherent properties of plasmid DNA, membrane adsorbent, and the ionic environment on membrane performance were identified as the factors affecting membrane performance and their effects were systematically investigated. Plasmid DNAs with smaller tertiary structure have shorter dynamic radius and/or lowersurface charge densities, which tended to have a better adsorption and recovery than those with larger tertiary structure. Environmental Scanning Electron Microscopy (ESEM) revealed that the hydrogel structure is more porous on one side of membrane than the other, and higher plasmid DNA adsorption and recovery capacities were observed if the more porous side of the membrane was installed upward of flow in the chromatographic unit. ESEM also revealed improved pore distribution and increased membrane porosity if membrane was pre-equilibrated in the buffer solution for 16 hours. The development of better flow through channel in the hydrogel membrane upon extensive soaking further improved plasmid DNA adsorption and recovery capacities. The ionic environment affects the tertiary size of plasmid DNA; and the optimal operating pH of membrane chromatography was different for the plasmid DNAs investigated in this study. The relative contribution of these factors to improve membrane chromatography of plasmid DNAs was analyzed using statistical modeling. It was found that the adsorption of plasmid DNA was mainly affected by the available adsorptive area associated with membrane porosity, whereas the recovery of plasmid DNAs was mainly affected by the environmental pH. A novel, RNase-free, and potentially scalable bioprocess was synthesized using the hydrogel membrane as the technology platform for the manufacturing of pharmaceutical-grade plasmid DNA. High bioprocess recovery and product quality were primarily associated with the optimal integration of impurity removal by calcium chloride precipitation and anion-exchange membrane chromatography and the implementation of isopropanol precipitation as a coupling step between the two impurity-removing steps. Complete removal of total cellular RNA impurity was demonstrated without the use of animal-derived RNase. High-molecular-weight (HMW) RNA and genomic DNA (gDNA) were removed by selective precipitation using calcium chloride at an optimal concentration. Complete removal of the remaining low-molecular-weight (LMW) RNA was achieved by membrane chromatography using the high-capacity and high-productive hydrogel membrane. The simultaneous achievement of desalting, concentrating and buffer exchange by the coupling step of isopropanol precipitation and the high efficiency and resolution of DNA-RNA separation by anion-exchange membrane chromatography significantly reduced the operating complexity of the overall bioprocess, increased the overall recovery of plasmid DNA, and enhanced product quality by removing trace amounts of impurities of major concern for biomedical applications, such as gDNA, proteins, and endotoxin.

Nosso grupo demonstrou que a captura de baixas doses de DNA plasmideal pode inibir a apresentação de antígeno e induzir um padrão de resposta anti-inflamatória, e que após a captação do DNA plasmideal por macrófagos, estas moléculas podiam prevenir a acidificação de vesículas endossomais, um passo essencial para a apresentação de antígenos para células T CD4+. Além disso, em modelos in vivo, a baixa dose de DNA foi suficiente para amenizar o quadro inflamatório e diminuir a produção de citocinas inflamatórias. Estes resultados estão em contraste com os modelos de vacinas gênicas comumente utilizadas. A baixa dose de DNA plasmideal, no contexto da indução da resposta imune, pode levar à modificação na apresentação do antígeno e ativação celular levando ao controle da resposta imune exacerbada desencadeada por outro antígeno, tornando o tratamento por DNA um importante foco de estudo para o combate de doenças autoimunes e inflamações. O objetivo deste trabalho foi identificar os microRNAs expressos em macrófagos tratados com alta ou baixa dose de DNA plasmideal e avaliar o papel destas moléculas na modulação da cascata de sinalização intracelular visando esclarecer o mecanismo imunomodulador observado. Macrófagos da linhagem J774 foram estimulados por 2 horas com o vetor plasmideal pcDNA3, nas concentrações de 10 g ou 100 g de pcDNA3/mL de RPMI. O RNA total foi extraído e o ensaio de microarray para microRNAs foi realizado. Os miRNAs diferencialmente expressos foram confirmados pela RT-qPCR, e o programa de bioinformática miRDB foi utilizado para predição de genes alvos. Os miRNAs e genes selecionados também foram dosados em macrófagos estimulados com LPS e tratados com pcDNA3. Foram detectados 6 miRNAs (miR-494-3p, miR-21-3p, miR-1897-5p, miR-1894-3p, miR-294-3p e miR-483-5p) diferencialmente expressos em macrófagos estimulados somente com pcDNA3. A expressão do miR-494-3p foi aumentado somente em células tratadas com DNA em baixa concentração tanto na ausência quanto presença de LPS. O gene IBk (IKK-) foi identificado como alvo do miR-494-3p, dosado e teve sua função detectada por western blot, mostrando que seu papel biológico foi alterado na presença deste miRNA. Além disso, os dados do tratamento com pcDNA3 em camundongos knockout para o receptor TLR9, sugerem que a expressão do miR-494-3p é independente deste tipo de receptor, porém é inibida na presença do mesmo quando no tratamento com alta dose de DNA. Os dados sugerem que quando macrófagos são tratados com baixa dose de DNA plasmideal (10 g/mL), o miR-494-3p age como regulador negativo do fator de transcrição NF-B, por meio da inibição da expressão e função da proteína IKK-. / Our group demonstrated that the capture of low doses of plasmid DNA can inhibit antigen presentation and induce an anti-inflammatory response pattern together with the decrease of pro-inflammatory cytokines expression, as observed in in vivo experimental models. Moreover, we observed that after the uptake of plasmid DNA by macrophages, these molecules could prevent endosomal vesicles acidification, an essential step for antigen presentation to CD4+ T cell. These results are in contrast with the usual DNA vaccines models commonly used. The low dose of plasmid DNA, in the context of immune response induction, can take to a modification in antigen presentation leading to the control of the response already established, what can be a potential treatment in auto-immune diseases and inflammation. The objective of this work is to identify expressed microRNAs on J774 macrophages triggered by different concentrations of plasmid DNA stimuli in order to evaluate the observed immunomodulatory mechanism. J774 macrophages were treated with low (10 µg/mL) and high (100 µg/mL) doses of pcDNA3 for 2 hours. Total RNA was extracted and microarray (Agilent plataform) was performed for detection of differentially expressed microRNAs. All obtained data was normalized in Genespring GX11.5 software. The microRNAs expression was confirmed by RT-qPCR and their mRNA targets were predicted by miRDB software. The miRNAs and their respective targets were also evaluated on DNA and LPS-treated macrophages. We detected 6 differentially expressed microRNAs (miR-494-3p, miR-21-3p, miR-1897-5p, miR-1894-3p, miR-294-3p e miR-483-5p) between the two conditions (fold change 2, p-value 0,05). The miR-494-3p expression increased only in cells treated with low dose of pcDNA3, on either previously LPS-stimulated cells or not. IBk (IKK-) was one of the predicted targets for miR-494-3p. RT-qPCR was performed to calculate its expression and its biological function was assessed by western blot. Besides, results from pcDNA3-treated cells from TLR9 knockout mice suggest that miR-494-3p expression is TLR9 independent although the receptor presence impaired miR-494-3p expression on high dose of pcDNA3-treated cells. Together, the data indicate that when macrophages are treated with low dose of plasmid DNA, miR-494-3p expression is increased, acting as negative regulator of the transcription factor NF-B, through IKK- inhibition.

京都大学 / 0048 / 新制・課程博士 / 博士(薬学) / 甲第18551号 / 薬博第813号 / 新制||薬||238(附属図書館) / 31451 / 京都大学大学院薬学研究科医療薬科学専攻 / (主査)教授 橋田 充, 教授 髙倉 喜信, 教授 佐治 英郎 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(薬学) / 甲第18552号 / 薬博第814号 / 新制||薬||238(附属図書館) / 31452 / 京都大学大学院薬学研究科医療薬科学専攻 / (主査)教授 髙倉 喜信, 教授 橋田 充, 教授 佐治 英郎 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

Due to the safety concerns surrounding viral vectors, non-viral alternatives are desirable for fulfilling the aim of gene therapy. In this project gel mobility shift assays demonstrated how cross-linked PVA nanoparticles successfully form complexes with plasmid DNA and are of a size and charge that should, theoretically, permit endocytosis by eukaryotic cells. However, during in vitro transfection studies no reporter (GFP) gene expression was noted. The collective evidence from electroporation, fluorescent-DNA-tagging, Lipofectin® or calcium phosphate chimeric and chloroquine experiments suggest that a lack of cell uptake is responsible. Nevertheless, the same cross-linked PVA nanoparticles have been shown to exhibit much promise in the field of drug delivery during in vitro experiments, even when used to target the same cell types as those used during transfection studies. Nanagel®, a cross-linked PVA nanoparticle containing budesonide, achieved higher levels of drug delivery than a commercially available form of the same drug (Pulmicort®) after 1 or 24 hours drug exposure. Furthermore, by measuring superoxide production during a stimulated respiratory burst, the budesonide delivered to cells appears fully functional and significantly more effective than Pulmicort® in preventing the formation of reactive oxygen species, following a 24-hour pre-treatment period with the formulation. These findings have exciting possibilities for the use of hard-to-dissolve corticosteroids in the treatment of respiratory disease. / AGT Sciences Ltd

Non-viral gene delivery agents, such as cationic polyelectrolytes, are attractive replacements to viruses due to the absence of potential immunogenic risk and the ability to tune their macromolecular structure. Although non-viral vectors possess numerous design advantages, several investigators have shown that transfer efficiencies are considerably lower when compared to viral vectors. The work reported in this dissertation aims to fundamentally understand the underlying structure-transfection relationships involved in polycation-mediated gene delivery. Efforts focused on the influence of molecular weight, macromolecular topology, carbohydrate modifications, and charge density on the overall transfection activity in vitro. Several families of polycations were synthesized in order to correlate chemo-physical characterization with transfection results. Results revealed that seemingly small changes in the structure of cationic polyelectrolytes can have profound consequences on their transfection activity. / Ph. D.

BACKGROUND: DNA damage occurs as a consequence of both direct and indirect effects of ionizing radiation. The severity of DNA damage depends on the physical characteristics of the radiation quality, e.g., the linear energy transfer (LET). There are still contrary findings regarding direct or indirect interactions of high-LET emitters with DNA. Our aim is to determine DNA damage and the effect on cellular survival induced by (223)Ra compared to (188)Re and (99m)Tc modulated by the radical scavenger dimethyl sulfoxide (DMSO). METHODS: Radioactive solutions of (223)Ra, (188)Re, or (99m)Tc were added to either plasmid DNA or to PC Cl3 cells in the absence or presence of DMSO. Following irradiation, single strand breaks (SSB) and double strand breaks (DSB) in plasmid DNA were analyzed by gel electrophoresis. To determine the radiosensitivity of the rat thyroid cell line (PC Cl3), survival curves were performed using the colony formation assay. RESULTS: Exposure to 120 Gy of (223)Ra, (188)Re, or (99m)Tc leads to maximal yields of SSB (80 %) in plasmid DNA. Irradiation with 540 Gy (223)Ra and 500 Gy (188)Re or (99m)Tc induced 40, 28, and 64 % linear plasmid conformations, respectively. DMSO prevented the SSB and DSB in a similar way for all radionuclides. However, with the α-emitter (223)Ra, a low level of DSB could not be prevented by DMSO. Irradiation of PC Cl3 cells with (223)Ra, (188)Re, and (99m)Tc pre-incubated with DMSO revealed enhanced survival fractions (SF) in comparison to treatment without DMSO. Protection factors (PF) were calculated using the fitted survival curves. These factors are 1.23 ± 0.04, 1.20 ± 0.19, and 1.34 ± 0.05 for (223)Ra, (188)Re, and (99m)Tc, respectively. CONCLUSIONS: For (223)Ra, as well as for (188)Re and (99m)Tc, dose-dependent radiation effects were found applicable for plasmid DNA and PC Cl3 cells. The radioprotection by DMSO was in the same range for high- and low-LET emitter. Overall, the results indicate the contribution of mainly indirect radiation effects for each of the radionuclides regarding DNA damage and cell survival. In summary, our findings may contribute to fundamental knowledge about the α-particle induced DNA damage.

Um problema recorrente no desenvolvimento de vacinas de DNA e terapia gênica utilizando vetores não virais é a baixa eficiência de transfecção gênica. Isso ocorre devido às diversas barreiras físicas, enzimáticas e difusionais que o DNA precisa superar para chegar ao núcleo das células. Neste trabalho tem-se por objetivo o desenvolvimento de novos vetores não virais de entrega gênica, formados por DNA plasmidial (pDNA), proteínas (protamina ou T-Rp3) e nanopartículas de ouro (NPAu) na forma de complexos ternários. Para tal, NPAu\'s foram sintetizadas por redução com citrato de sódio, apresentando diâmetros entre 20,3 e 57,3 nm e potencial zeta entre -69,0 e +43,3 mV, dependendo das condições de síntese, a saber, das quantidades de citrato de sódio adicionadas e da ordem de adição dos reagentes. Em seguida, vetores compostos por pDNA-protamina/T-Rp3-NPAu foram formados, transfectados em células HeLa cultivadas in vitro, e a atividade da enzima repórter luciferase foi medida. Deste modo, a partir de variações em proporção mássica e tamanho de nanopartículas, foi possível obter complexos utilizando protamina e ouro com uma eficiência de transfecção 33 vezes melhor do que transfecções utilizando apenas protamina. Por outro lado, complexos contendo T-Rp3 e ouro se mostraram ainda mais eficazes na entrega, apresentando níveis de transfecção próximos ao do reagente comercial Lipofectamina. Ensaios de transfecção utilizando a droga nocodazol indicaram a importância dos microtúbulos no mecanismo de entrega gênica, e ensaios com a droga cloroquina evidenciaram que as nanopartículas de ouro atuam de maneira diferenciada no escape endossomal dos vetores não virais utilizados. Visando relacionar características físico-químicas com a eficiência de transfecção, alguns destes complexos foram caracterizados por espalhamento dinâmico de luz, em que complexos com protamina apresentaram tamanhos entre 116 e 363 nm e complexos com T-Rp3 apresentaram entre 135 e 307 nm e potenciais zeta entre +7,3 e +22,5 mV e +10,6 e +27,2 mV, respectivamente, dependendo das características das NPAu\'s. / A recurrent problem in the development of DNA vaccines and gene therapy using non-viral vectors is the low efficiency of transfection. That is due to the many physical, enzymatic and diffusional barriers that DNA must overcome to reach the cell nucleus. This work aims to develop novel non-viral vectors based on plasmid DNA (pDNA), proteins (protamine or recombinant T-Rp3) and gold nanoparticles (AuNP) as ternary complexes. For such, AuNP\'s were first synthesized via sodium citrate reduction, with diameters varying from 20,3 to 57,3 nm and zeta potentials between -69,0 and +43,3 mV, depending on synthesis conditions, changing the quantities of sodium citrate added and the order of addition of reagents. Vectors formed by pDNA-protamine/T-Rp3-AuNP were then formed, transfected and luciferase activity was measured. Thus, from variations on mass ratios and gold nanoparticle sizes, it was possible to obtain complexes with protamine and gold with a transfection efficiency 33 times higher than analog complexes using only protamine. Also, complexes containing T-Rp3 and gold showed an even higher delivery efficiency, with transfection efficiency close to Lipofectamine. Assays using nocodazole indicated the importance of microtubule in the gene delivery process and, whereas assays with chloroquine showed that gold nanoparticles act in a different way over endossomal escape of used non-viral vectors. Finally, some of these complexes were characterized with dynamic light scattering. Complexes with protamine were within the size ragne of 116 to 363 nm and complexes with T-Rp3 were within the size range of 135 to 307 nm. The zeta potential varied from +7,3 to +22,5 mV and from +10,6 to +27,2 mV, respectively, depending on the gold nanoparticles used.

Um dos principais limitantes ao desenvolvimento e aprovação para utilização em humanos das vacinas de DNA é a falta de um vetor ideal de entrega gênica, que seja ao mesmo tempo eficiente e seguro. Embora mais seguros, os vetores não virais enfrentam uma série de barreiras físicas, enzimáticas e difusionais que limitam a chegada do transgene ao núcleo das células alvo. Dando continuidade ao trabalho desenvolvido em nosso grupo de pesquisa, o principal objetivo desta dissertação de mestrado foi avaliar o desempenho do vetor não viral comercial Lipofectamina e da proteína multifuncional T-Rp3 na entrega do gene da glicoproteína do vírus da raiva (RVGP) a células BHK-21. Primeiramente, o gene RVGP foi inserido no plasmídeo modelo pVAX1. Foram então realizados estudos de transfecção em células BHK-21 (Baby Hamster Kidney), utilizando-se Lipofectamina como agente de transfecção, no sentido de constatar a correta expressão do gene RVGP contido no novo plasmídeo. Como controle positivo, foi utilizado o plasmídeo pCMV-RVGP. Os estudos de PCR quantitativo da transcrição reversa (qRT-PCR) e imunofluorescência indicaram a expressão da glicoproteína pelo pVAX1RVGP, ainda que em valores de expressão menores se comparados com o plasmídeo controle pCMV-RVGP. Foi também desenvolvido com sucesso um método quantitativo de determinação da expressão da RVGP em células utilizando-se citometria de fluxo, que confirmou os resultados anteriores. Devido ao plasmídeo pVAX1RVGP ter apresentado baixa eficiência de expressão da RVGP, buscou-se a elevação da eficiência a partir da adição da sequência de KOZAK no plasmídeo pVAX1RVGP. Nesse caso, ainda que os resultados indiquem um aumento na expressão, não houve confirmação estatística (p<0,05). Os estudos de entrega com a proteína T-Rp3 foram realizados com um lote da T-Rp3 armazenada em ultrafreezer. A proteína demonstrou-se não ser estável após o congelamento em nitrogênio líquido e armazenamento em ultrafreezer pelo tempo de 10 meses. Apesar de ser capaz de complexar o pDNA após esse tempo, não foi eficiente em ensaios de transfecção, tendendo a agregar em relações molares altas e ausência de soro fetal bovino. / One of the major bottlenecks on the development and approval of DNA vaccines in humans is the lack of an ideal gene delivery vector, which must be safe and efficient at the same time. Although safer, the non-viral vectors face a series of physical, enzymatic and diffusion barriers that limits the arrival of the endogenous gene in the nuclei of the target cells. The main goal of this work was the evaluation of the performances of the commercial non-viral vector Lipofectamine, and the recombinant protein T-Rp3, a multifunctional protein, on the delivery of the rabies virus glycoprotein (RVGP) gene to BHK-21 cells. First, the RVGP gene was inserted into the pVAX1 plasmid, and transfections using BHK-21 (Baby Hamster Kidney) cells were performed using the Lipofectamine reagent to verify the correct expression of the RVGP gene present in the new plasmid. As a positive control, the plasmid pCMV-RVGP was used. The quantitative reverse transcription (qRT-PCR) and immunofluorescence studies indicated the expression of RVGP from pVAX1RVGP, although in lower expression values in comparison to the control plasmid. In addition, a flow cytometry quantitative method to quantify and compare the expression of the RVGP in the membrane of the transfected cells was developed, confirming the previous results. With the purpose of increase, the expression of RVGP, the KOZAK consensus sequence was added to the new pVAX1RVGP plasmid, and despite of the apparent increase of RVGP expression, this could not be confirmed statistically. The experiments of gene delivery using the T-Rp3 protein were performed using a protein batch storaged in ultrafreezer for 10 months. However, the protein has shown not being stable after storage for this long period. Moreover, despite of being capable to complex pDNA after this time, T-Rp3 was not efficient in the transfection assays and tended to aggregate in high molar ratios.

O uso de DNA plasmidial (pDNA) visando a aplicações terapêuticas tem aumentado nos últimos anos. A cromatografia aparece como a técnica de purificação mais comum para obtenção de amostras de pDNA com o elevado grau de pureza exigido. Porém, as resinas cromatográficas disponíveis apresentam ainda uma série de desafios, nomeadamente no desenvolvimento de ligantes específicos e matrizes capazes de acomodar este tipo de molécula. Relativamente à apuração de novos ligantes, alguns estudos têm mostrado o potencial do aminoácido arginina para estabelecer interações específicas e preferenciais com o pDNA. Por outro lado, resinas monolíticas surgem como suportes interessantes devido às suas excelentes propriedades de transferência de massa e altas capacidades de adsorção. Neste estudo, diferentes ligantes baseados em arginina (arginina, di-arginina e tri-arginina) foram imobilizados em resinas de agarose previamente ativadas. Um primeiro estudo de adsorção em batelada foi realizado a fim de avaliar e compreender os mecanismos envolvidos no processo de adsorção dos ácidos nucleicos pDNA e RNA em resina com o aminoácido arginina. Na sequência, apresentamos uma proposta inovadora para o uso de ligantes de arginina em resinas de agarose, em um único passo de purificação em modo negativo a seguir ao passo de concentração por isopropanol. A capacidade da resina para o pDNA foi substancialmente maior do que a obtida para o mesmo tipo de resina no modo positivo, com notória vantagem de capacidade no uso de di-arginina face a arginina com rendimentos próximos de 100% do plasmídeo carregado. Os ligantes di-arginina e tri-arginina foram também imobilizados em resinas monolíticas. Em comparação com o aminoácido arginina, a imobilização dos homopeptídeos nas resinas monolíticas levou ao aumento da capacidade de adsorção (cerca de 2,5 vezes superior) e especicificidade de interações, mostrando-se como uma estratégia promissora para processos de purificação de pDNA. / The use of plasmid DNA (pDNA) for therapeutic applications has increased in recent years. Chromatography appears as the most common purification technique to obtain samples of pDNA with the high degree of purity required. However, the available chromatographic resins still present a series of challenges, namely in the development of specific ligands and matrices capable of accommodating this type of molecule. Regarding the determination of new ligands, several studies have shown the potential of the arginine amino acid to establish specific and preferential interactions with the pDNA. On the other hand, monolithic resins appear as interesting approaches due to their excellent mass transfer properties and high adsorption capacities. In this study, different arginine based ligands (arginine and di-arginine) were firstly immobilized on activated agarose resins. The first part of the work describes the adsorption equilibrium of plasmid DNA adsorption process, as well as the interaction with its main impurity (RNA) on arginine supports in a batch format, in order to compare and gather crucial information about adsorption mechanisms involved in this type of affinity system. Then, a new use for chromatographic bead matrixes based on arginine ligands was proposed, working as an adsorption matrix pDNA purification in negative mode after isopropanol concentration of the sample. The arginine based supports capacity for pDNA under negative mode for pDNA was substantially higher than that obtained with the same type of resin in the conventional positive mode, with a notable advantage of using di-arginine with recovery yields near 100%. The homopeptides (di-arginine and tri-arginine) were also immobilized on functionalized monolithic resins (BIA Separations, Slovenia). Effectively, the immobilization of the arginine homopeptides made the monolithic resins more functional compared to the (mono)arginine based resin, exhibiting greater binding capacities (around 2,5 times higher) and interaction intensities, proving to be a promising strategy for purification processes of pDNA.