DNA methylation plays a role in several biological functions, such as gene expression regulation, and several endogenous and exogenous factors affect these DNA methylation patterns in the cell. One such alteration of a cell line's DNA methylation pattern is caused by the insertion of a vector into the cell line. Using the cytosine–extension assay and realtime methylation–specific PCR, alterations of DNA methylation levels on both global and gene–specific levels were investigated. In some cell lines the cellular transformation led to an increase in DNA methylation levels, and in others a decrease in DNA methylation amounts was observed. The same phenomenon was seen in the promoter regions of specific genes, showing that vector–insertion into a cell line caused DNA methylation alterations in many regions of the genome. These alterations in DNA methylation are investigated in this reduced representation study using enrichment of the methylated fraction of fragmented DNA and subsequent GS FLX Titanium sequencing of these methylated fragments. The results of sequence data analysis showed that methylated fragments are distributed over the whole genome, but could be related to only a few specific genes. These results have implications for cell culture work, biotechnological applications and uses in gene therapy. / Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.

DNA methylation plays a role in several biological functions, such as gene expression regulation, and several endogenous and exogenous factors affect these DNA methylation patterns in the cell. One such alteration of a cell line's DNA methylation pattern is caused by the insertion of a vector into the cell line. Using the cytosine–extension assay and realtime methylation–specific PCR, alterations of DNA methylation levels on both global and gene–specific levels were investigated. In some cell lines the cellular transformation led to an increase in DNA methylation levels, and in others a decrease in DNA methylation amounts was observed. The same phenomenon was seen in the promoter regions of specific genes, showing that vector–insertion into a cell line caused DNA methylation alterations in many regions of the genome. These alterations in DNA methylation are investigated in this reduced representation study using enrichment of the methylated fraction of fragmented DNA and subsequent GS FLX Titanium sequencing of these methylated fragments. The results of sequence data analysis showed that methylated fragments are distributed over the whole genome, but could be related to only a few specific genes. These results have implications for cell culture work, biotechnological applications and uses in gene therapy. / Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.

"Dipeptidyl peptidase-IV Activity and/or Structure Homologues"(DASH) represent a newly defined group of multifunctional molecules, typically bearing dipeptidyl peptidase-IV- like hydrolytic activity. Dipeptidyl peptidase-IV (DPP-IV) cleaves out X-Pro dipeptides from the N-terminus of peptides. Other molecules carrying similar enzyme activity, such as Fibroblast activation protein (FAP), DPP-II, DPP8 and DPP9 or even DPP-IV structure-like but hydrolytically inactive molecules (DPP6 and DPP10) also belong to this group. Recent knowledge suggest a substantial role of DASH in cancer pathogenesis. The aim of this study is a preparation of a biological model and its use for understanding the mechanisms of interaction(s) between transformed glial cells and stroma in the processes of origin and development of tumors derived from neuroectoderm. Stable transfected human glioblastoma cell lines with inducible gene expression of DPP-IV, Fibroblast activation protein and their enzymatically inactive mutated forms, were prepared within the project. Prepared cell lines are used as a tool for studying not only the "autocrine" importance of DPP-IV and FAP for the expressing cells in in-vitro, but also for their potential "paracrine" effect(s) within the tumor microenvironment after homotopic implantation into the...

Introdução: O câncer de próstata (CaP) é o tumor mais comum do homem nos países ocidentais e a segunda causa de óbito por câncer em homens nos EUA, Europa e Brasil. O câncer localizado tem sobrevida câncer especifica elevada quando tratado adequadamente, porém a doença metastática ainda apresenta tratamentos pouco eficientes com sobrevida global de 28%. Os microRNAs (miRNAs) são um grupo de moléculas pequenas de RNA que contém entre 19 a 25 nucleotídeos não codificantes de proteína, com ação fundamental na regulação da expressão gênica. Eles estão envolvidos em processos essenciais nas células normais e neoplásicas como ciclo celular, proliferação, apoptose, metabolismo energético, invasão e metastatização. Objetivos: Realizar estudos in vitro e in vivo usando miRNA em um modelo de câncer de próstata metastático inédito no nosso meio com intuito de analisar o seu potencial como agente terapêutico dessa neoplasia. Métodos: Nos estudos in vitro, três linhagens celulares foram utilizadas (PC3, DU145 e LNCaP). Essas linhagens foram transfectadas com os miRNAs 100, 145 e 373 e seus respectivos antiMiRs utilizando-se lipofectamina. Analisamos a expressão dos genes alvo mTOR, SMARCA5, KRAS, CMYC, MMP9, CD44 por PCR quantitativo em tempo real (qRT-PCR). Foram realizados também estudos de apoptose, ciclo celular e ploidia utilizando o citômetro de fluxo. Alterações no potencial de invasão foram avaliadas pela técnica do matrigel. O modelo in vivo pré-clínico foi desenvolvido pela injeção intra-cardíaca da linhagem PC-3M-Luc-C6 em camundongos NUDE com 9 semanas. O crescimento tumoral foi avaliado com o sistema de bioluminescência in vivo. Após o pleno estabelecimento das metástases no dia 21, os animais foram tratados com três injeções na veia da cauda contendo o miRNA conjugado com o atelocolágeno. Os animais foram sacrificados e no dia 48 para análise dos tecidos. Resultados: miR-100 aumenta a apoptose na LNCaP, e reduz a apoptose na DU145. Na linhagem DU145 o miR 100 inibiu a proliferação. Na análise da expressão gênica o miR-100 inibe SMARCA5 na DU145 e PC3 e mTOR na LNCaP, o anti-miR 100 estimula mTOR e SMARCA5 na LNCaP. O miR-145 promoveu aumento da apoptose em 24% na DU145. Na linhagem PC3 o miR-145 age inibindo a proliferação, com uma diferença absoluta de 18% em relação ao seu controle. O miR-145 inibe KRAS e CMYC nas três linhagens e o anti-miR-145 estimula CMYC na DU145 e RAS nas três linhagens O miR-373 reduziu a apoptose em 29% na DU145 e diminui a proliferação com uma diferença absoluta de 13% em relação ao controle. O miR- 373 estimula a MMP9 na DU145 e na LNCaP e inibe o CD44 na PC3. O antimiR- 373 inibe MMP9 na DU145 e LNCaP. Nos estudos in vivo de CaP metastático o miR-100 apresenta tendência a redução no crescimento tumoral (p=0,23) e o miR-145 reduz o crescimento de forma significativa no dia 34 (p=0,02). Após esses dias o tumor volta a crescer de forma agressiva. Os animais tratados com anti-miR-373 não apresentaram alterações em relação aos controles. Conclusões: O miR-100 é um miRNA contexto dependente, com papel supressor tumoral em linhagens de tumor de próstata agressivo e o miR- 373 age in vitro como oncomiR. O miR-145 age como supressor tumoral in vitro e em modelo animal de CaP metastático apresentando resposta terapêutica consistente, podendo ser utilizado no arsenal terapêutico contra essa neoplasia. Estudos futuros devem avaliar o uso dos miRNAs isoladamente ou de forma adjuvante no tratamento do CaP metastático / Introduction: Prostate cancer (PCa) is the most common neoplasia of man in Western countries and the second cause of death by cancer in men in the US, Europe and Brazil. The localized cancer has high cancer-specific survival when treated properly, however metastatic disease still presents low effective treatments with 28% of global survival. microRNAs (miRNAs) are a group of small RNA molecules containing from 19 to 25 nucleotides of noncoding protein with fundamental action in the regulation of gene expression. They are involved in key processes in normal and neoplastic cells as cell cycle, proliferation, apoptosis, energy metabolism, invasion and metastasis. Objectives: To carry out studies in vitro and in vivo using miRNA in a novel model of metastatic prostate cancer in our country in order to evaluate its potential as a therapeutic agent of this neoplasia. Methods: In the in vitro studies, three cell lines were used (PC3, DU145 and LNCaP). These cell lines were transfected with miRNAs 100, 145 and 373 and their antiMiRs using lipofectamine. We analyzed the gene expression of mTOR, SMARCA5, KRAS, CMYC, MMP9, CD44 by real-time polymerase chain reaction (qRT-PCR). We also performed studies of apoptosis, cell cycle and ploidy using flow cytometer. Changes in the invasion potential were evaluated by the technique of matrigel. The pre-clinical model in vivo was developed by intracardiac injection of PC-3MLuc-C6 cell line in NUDE mice with 9 weeks. Tumor growth was evaluated with an in vivo image system (IVIS). After the full establishment of metastases on day 21, the animals were treated with three injections into the tail vein containing the miRNA plus atelocollagen. The animals were sacrificed on day 48 for tissues analysis. Results: MiR-100 increases apoptosis in LNCaP and reduces apoptosis in DU145. The anti-miR-100 increased apoptosis in 14% in PC3. In cell line DU145, miR-100 inhibited proliferation. In the analysis of gene expression, the miR-100 inhibits SMARCA5 in DU145 and PC3 and mTOR in LNCaP, anti-miR-100 stimulates mTOR and SMARCA5 in LNCaP. The miR-145 promoted an increased in apoptosis by 24% in DU145. In PC3 cell line miR-145 acts by inhibiting the proliferation, with an absolute difference of 18% compared to control. MiR-145 inhibits KRAS and CMYC in the three cell lines and anti-miR-145 stimulates CMYC in DU145 and KRAS in the three cell lines. The miR-373 reduced apoptosis by 29% in DU145 and reduces proliferation with an absolute difference of 13% relative to control. MiR-373 stimulates MMP9 in DU145 and LNCaP cells and inhibits CD44 in PC3. The anti -miR-373 inhibits MMP9 in DU145 and LNCaP. In the in vivo studies of metastatic PCa, miR-100 shows a tendency to decrease tumor growth (p=0.23) and miR-145 reduces tumor growth on day 34 (p=0.02). After those days, the tumor grows back aggressively. Animals treated with anti-miR-373 showed no changes relative to controls. Conclusion: The miR-100 is a context-dependent miRNA, with tumor suppressor role in aggressive tumor cell lines. The miR-373 acts in vitro as oncomiR and miR-145 acts as a tumor suppressor in vitro and in an animal model with consistent therapeutic response and can be used in the therapeutic arsenal against this neoplasia. Future studies should evaluate the use of miRNAs alone or adjuvant in the treatment of metastatic prostate cancer

The biggest hurdle in success of gene and drug therapy is designing and preparation of suitable bio-nanomaterials to carry the desired nucleic acid and drug to the targeted site. The work described in the present thesis encompasses two different approaches for the delivery of bioactive oligo/polynucleotides and drugs in vitro and in vivo using either cationic lipids or their nanocomposites with different carbon nanomaterials. The idea of using carriers for oligo/polynucleotides and drugs came into existence because of numerous physiological barriers in pathway of delivery of naked oligo/polynucleotides or drugs which reduces the overall activity of these bioactives in biological systems. These barriers trigger scientific research toward the preparation of appropriate biomaterials which can overcome the physiological barriers and improve the activity of bioactive oligo/polynucleotides and drugs in cellular systems. Toward this end, the design and synthesis of different cationic lipids and carbon nanomaterials were undertaken as described in seven chapters of the thesis. A series of novel cationic lipids with structural variability was prepared and used for gene delivery in vitro. They were further tuned chemically to sustain delivery efficiency in high serum percentage during in vitro transfection. These serum compatible lipids were used to perform transfection of reporter gene plasmid and found to be more efficient compared to the some well known commercial products for the same purpose. Another series of novel lipids were synthesized for the targeted gene delivery in vitro. These tryptophan based cholesteryl lipids were used to prepare mixed liposomes. These mixed liposomes were highly efficient in targeting sigma receptor rich HEK293T over sigma receptor negative HeLa cells. Mixed liposomes were also prepared for selective targeting of αvβ3 and αvβ5 integrins in gene transfection protocol using a palmitoyl-RAFT-RGD4 template. A mixed liposomal formulation was developed to carry out anti-sense siRNA mediated knockdown of Smad-2 protein with better efficiency compared to some of the best known commercial products for the same purpose. These mixed liposomes were also highly efficient for regression via induction of p53 mediated apoptosis in xenograft tumors developed in nude mice. Carbon nanomaterials have been extensively explored as nanoscale gene/drug carriers for potential applications. But the challenge is to solubilize these highly hydrophobic materials in aqueous medium for use in biological systems. Although there are reports for covalent modifications of such nanomaterials but it could be done only with the loss of some beneficial features of these materials. Herein a non-covalent technique has been efficiently used to suspend single walled carbon nanotubes in water using biocompatible cationic lipids. These nanosuspensions were used to complex plasmid DNA and transfect them in vitro. They proved to be highly serum compatible DNA carriers which did not drop the efficiency even in very high percentage of serum. Similarly exfoliated graphene was modified with cationic lipid and serum components to improve IC50 of Tamoxifen citrate and Methotrexate to a considerable extent in vitro. The improved Methotrexate formulations were highly efficient for regression in size of xenograft tumors developed in nude mice. Thus, the present thesis entails generation of cationic lipids and carbon nanomaterials based nanocomposites which were not only highly biocompatible themselves but their efficiency was found many fold better compare to some of the best commercial delivery agents. These were useful for the delivery of various bioactive oligo/polynucleotides and drugs in vitro and in vivo.

SMC1 and SMC3 form a high-affinity heterodimer, which provides an open backbone of the cohesin ring, to be closed by a kleisin protein. RNAi mediated knock-down of either one heterodimer partner, SMC1 or SMC3, is expected to cause very similar if not identical phenotypes. However, we observed highly distinct, protein-specific phenotypes. Upon knock-down of human SMC1, much of SMC3 remains stable, accumulates in the cytoplasm and does not associate with other cohesin proteins. Most of the excess nuclear SMC3 is highly mobile and not or only weakly chromosome-associated. In contrast, human SMC3 knock-down rendered SMC1 instable without cytoplasmic accumulation. As observed by differential protein extraction and in FRAP experiments the remaining SMC1 or SMC3 proteins in the respective SMC1 or SMC3 knock-down experiments constituted a cohesin pool, which is associated with chromatin with highest affinity, likely the least expendable. Expression of bovine EGFP-SMC1 or mouse EGFP-SMC3 in human cells under conditions of human SMC1 or SMC3 knock-down rescued the respective phenotypes, but in untreated cells over-expressed exogenous SMC proteins mis-localized. Paucity of either one of the SMC proteins causes RAD21 degradation. These results argue for great caution in interpreting SMC1 and SMC3 RNAi or over-expression experiments. Under challenged conditions these two proteins unexpectedly behave differently, which may have biological consequences for regulation of cohesin-associated functions and for human cohesin pathologies.

Nonviral gene delivery, though limited by inefficiency, has extensive utility in cell therapy, tissue engineering, and diagnostics. Substrate-mediated gene delivery (SMD) increases efficiency and allows transfection at a cell-biomaterial interface, by immobilizing and concentrating nucleic acid complexes on a surface. Efficient SMD generally requires substrates to be coated with serum or other protein coatings to mediate nucleic acid complex immobilization, as well as cell adhesion and growth; however, this strategy limits reproducibility and may be difficult to translate for clinical applications. As an alternative, we screened a chemically defined combinatorial library of 20 different extracellular matrix mimetic substrates containing combinations of (1) different sulfated polysaccharides that are essential extracellular matrix glycosaminoglycans (GAGs), with (2) mimetic peptides derived from adhesion proteins, growth factors, and cell-penetrating domains, for use as SMD coatings. We identified optimal substrates for DNA lipoplex and polyplex SMD transfection of fibroblasts and human mesenchymal stem cells. Optimal extracellular matrix mimetic substrates varied between cell type, donor source, and transfection reagent, but typically contained Heparin GAG and an adhesion peptide. Multiple substrates significantly increased transgene expression (i.e. 2- to 20-fold) over standard protein coatings. Considering previous research of similar ligands, we hypothesize extracellular matrix mimetic substrates modulate cell adhesion, proliferation, and survival, as well as plasmid internalization and trafficking. Our results demonstrate the utility of screening combinatorial extracellular matrix mimetic substrates for optimal SMD transfection towards application- and patient-specific technologies.

Foamy viruses (FVs) or heterologous retroviruses pseudotyped with FV glycoprotein enable transduction of a great variety of target tissues of disparate species. Specific cellular entry receptors responsible for this exceptionally broad tropism await their identification. Though, ubiquitously expressed heparan sulfate proteoglycan (HS-PG) is known to serve as an attachment factor of FV envelope (Env)-containing virus particles, greatly enhancing target cell permissiveness. Production of high-titer, FV Env-containing retroviral vectors is strongly dependent on the use of cationic polymer-based transfection reagents like polyethyleneimine (PEI). We identified packaging cell-surface HS-PG expression to be responsible for this requirement. Efficient release of FV Env-containing virus particles necessitates neutralization of HS-PG binding sites by PEI. Remarkably, remnants of PEI in FV Env-containing vector supernatants, which are not easily removable, negatively impact target cell transduction, in particular those of myeloid and lymphoid origin. To overcome this limitation for production of FV Env-containing retrovirus supernatants, we generated 293T-based packaging cell lines devoid of HS-PG by genome engineering. This enabled, for the first, time production of inhibitor-free, high-titer FV Env-containing virus supernatants by non-cationic polymer-mediated transfection. Depending on the type of virus, produced titers were 2- to 10-fold higher compared with those obtained by PEI transfection.

No / Phosphorylation or SUMOylation of the kainate receptor (KAR) subunit GluK2 have both individually been shown to regulate KAR surface expression. However, it is unknown whether phosphorylation and SUMOylation of GluK2 are important for activity-dependent KAR synaptic plasticity. We found that protein kinase C-mediated phosphorylation of GluK2 at serine 868 promotes GluK2 SUMOylation at lysine 886 and that both of these events are necessary for the internalization of GluK2-containing KARs that occurs during long-term depression of KAR-mediated synaptic transmission at rat hippocampal mossy fiber synapses. Conversely, phosphorylation of GluK2 at serine 868 in the absence of SUMOylation led to an increase in KAR surface expression by facilitating receptor recycling between endosomal compartments and the plasma membrane. Our results suggest a role for the dynamic control of synaptic SUMOylation in the regulation of KAR synaptic transmission and plasticity.

Wir nutzten in dieser Studie den apikomplexen Parasiten Eimeria falciformis als Modell. Unsere Ergebnisse zeigen, dass das in infizierten Wildtypmäusen dominierende Zytokin IFN-γ für Immunschutz und für die Entwicklung der Darmpathologie entbehrlich war. E. falciformis-infizierte IFN-γR-/- and IFN-γ-/- Mäuse zeigten extremen Körpergewichtsverlust und starke Pathologie im Darm. Die Entwicklung des Parasiten in diesen Mäusen war überraschenderweise reduziert. Diese Beobachtungen gingen mit einer drastisch erhöhten Produktion von parasiten-spezifischem IL-17A und IL-22 durch CD4+ T Zellen einher. Gleichzeitige Neutralisierung von IL-17A und IL-22 in E. falciformis-infizierten IFN-γR-/- Mäusen verringerte den Körpergewichtsverlust und die Darmpathologie, und führte zu einer erhöhten Ausscheidung von Parasiten. Die Behandlung einer E. falciformis-infizierten intestinalen Epithelzelllinie mit IL-17A oder IL-22 führte zu einer signifikant reduzierten Entwicklung von E. falciformis in vitro. Diese Daten demonstrieren erstmalig einen anti-parasitären Effekt von IL-22 im Darm und deuten auf redundante Rollen von IL-17A und IL-22 im Hinblick auf die Förderung von Darmpathologie in Abwesenheit von IFN-γ hin. Um E. falciformis als Modellsystem weiter zu entwickeln, haben wir die Transfektion von E. falciformis Sporozoiten mit verschiedenen Plasmiden die den Reporter YFP und den Resistenzmarker DHTS enthalten etabliert. Rektal in Mäuse injizierte Sporozoiten entwickelten sich erfolgreich zu Oocysten, wenn auch mit geringerer Effizienz im Vergleich zur oralen Infektion mit Oozysten. Wiederholte in vivo Selektion YFP-exprimierender Oozysten führte zu Populationen mit maximal 34 % YFP-exprimierenden Parasiten. Wir demonstrieren in dieser Arbeit zum ersten Mal die Transfektion von E. falciformis und zeigen Perspektiven im Hinblick auf die Etablierung einer stabil transgenen Parasitenlinie auf. / The roles of Th1 and Th17 responses as mediators of host protection and pathology in the intestine are the subjects of intense research. Here we investigated a model of intestinal inflammation driven by the intracellular apicomplexan parasite Eimeria falciformis. Although IFN-γ was the predominant cytokine during E. falciformis infection in wild type mice, it was found to be dispensable for host defence and the development of infection-driven intestinal inflammation. E. falciformis-infected IFN-γR-/- and IFN-γ-/- mice developed dramatically exacerbated body weight loss and intestinal pathology, but surprisingly harboured fewer parasites. This was associated with a striking increase in parasite-specific IL-17A and IL-22 production in the mesenteric lymph nodes and at the site of infection. Concurrent neutralisation of IL-17A and IL-22 in E. falciformis infected IFN-γR-/- mice resulted in a reduction in infection induced body weight loss and inflammation and significantly increased parasite shedding. Taken together these data demonstrate for the first time an anti-parasitic effect of IL-22 during an intestinal infection and suggest that IL-17A and IL-22 have redundant roles in driving intestinal pathology in the absence of IFN-γ signalling. To further develop E. falciformis as a model system, we established transfection of E. falciformis sporozoites using various plasmids that contain the fluorescent reporter YFP and the resistance marker DHTS. Sporozoites applied rectally to mice were shown to complete their life cycle, albeit with a lower efficiency in comparison to oral infection with oocysts. Repeated in vivo selection using pyrimethamine and/or FACS and manual sorting led to a maximum percentage of 34 % YFP-expressing oocysts. Taken together, we demonstrate for the first time transfection of E. falciformis and provide perspectives for further work on the establishment of a stable transgenic parasite line.