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Activation of innate immune surveillance mechanisms during the development of cancer is well-documented. However, knowledge of how these innate immune proteins, when added exogenously, independent of tumour microenvironment, affect tumour cells is limited. In Chapter 3, the effects of human C1q and its individual globular domains (ghA, ghB and ghC) on an ovarian cancer cell line, SKOV3, have been examined. C1q and globular head modules induced apoptosis in approximately 55% of cells, which involved upregulation of TNF-α and Fas and activation of the caspase cascade. This occurred in parallel to the downregulation of mTOR, RICTOR and RAPTOR survival pathways, which are often over-expressed in the majority of the cancers. Thus, this study provided evidence for another complement-independent role of C1q. The second part of this thesis was to investigate the effect of Human Surfactant Protein-D (SP-D), which is known to modulate secretion of a range of cytokines and chemokines by effector immune cells, such as TNF-a and TGF-β, at mucosal surfaces during infection and inflammation. Our hypothesis was that SP-D can influence these soluble factors as a part of its putative role in the immune surveillance against pancreatic cancer, where the inflammatory tumour microenvironment contributes to the epithelial-to-mesenchymal transition (EMT) invasion and metastases. In this study, a recombinant fragment of human SP-D (rfhSP-D) inhibited TGF-β expression in a range of pancreatic cancer cell lines, thereby reducing their invasive potential by downregulating Smad2/3 expression that may have interrupted signal transduction negatively, which affected the transcription of key mesenchymal genes such as Vimentin, Zeb1 and Snail. Furthermore, prolonged treatment with rfhSP-D induced apoptosis in the pancreatic cancer cell lines via activation of the caspase cascade. Thus, this study added another layer to the well-known protective role of SP-D.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2005. / Härtill 3 uppsatser.

Diss. (sammanfattning) Umeå : Umeå universitet, 2006. / Härtill 5 uppsatser.

Orientador: Nilson Ivo Tonin Zanchin / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T18:49:26Z (GMT). No. of bitstreams: 1 Alves_BeatrizSantosCapela_D.pdf: 5512305 bytes, checksum: 707ea6299bc24ddc6fb459520d79aeee (MD5) Previous issue date: 2008 / Resumo: O combate à dengue atualmente está limitado praticamente aos esforços de eliminação do mosquito transmissor, o Aedes aegypti, porém esta estratégia não tem se mostrado eficiente. O desenvolvimento de novos instrumentos de combate à dengue requer, portanto, maior conhecimento sobre a biologia do vírus com relação à sua interação com seus hospedeiros. O genoma do vírus é constituído por um RNA simples-fita de polaridade positiva e possui duas regiões não traduzidas (5¿ e 3¿ UTR). A região 5¿UTR viral possui organização similar à dos mRNAs eucarióticos, diferentemente da região 3¿UTR que é longa e não possui cauda de poli(A). Em vez disso, na região 3¿UTR encontram-se estruturas conservadas entre os diferentes Flavivirus, dentre elas a estrutura 3¿ stem-loop (3¿SL) que é indispensável para a replicação do RNA viral. O objetivo do nosso estudo foi identificar novas proteínas humanas capazes de interagir com a estrutura 3¿SL do RNA do vírus da dengue. Dados da literatura descrevem que a proteína Mov34 de camundongo interage com 3¿SL do vírus da encefalite japonesa. Devido à alta similaridade entre as proteínas ortólogas humana e de camundongo, bem como das respectivas estruturas 3¿SL dos vírus da dengue e da encefalite japonesa, foi testada a interação entre a Mov34 humana com o 3¿SL do vírus da dengue. Porém, em nenhuma das condições testadas foi possível obter evidência de interação da Mov34 humana com 3¿SL dos vírus da dengue e da encefalite japonesa. Para a identificação de novas proteínas que são capazes de interagir com a estrutura 3¿SL do RNA do vírus da dengue foi utilizado o ensaio de triplo-híbrido de levedura. A proteína humana PACT, conhecida como proteína celular ativadora de PKR, foi isolada neste ensaio utilizando 3¿SL como isca. PKR é uma quinase ativada por PACT ou RNA dupla-fita. A ativação de PKR leva a um estado antiviral adquirido pela fosforilação do fator de iniciação da tradução eIF2a e conseqüente inibição da tradução. Além disso, PKR está envolvida em outras vias de transdução de sinal e na resposta celular à proteínas desenoveladas. A ação antiviral de PACT é evidenciada pela ação de proteínas dos vírus influenza A e herpes simplex tipo 1 que inibem a ativação de PKR por PACT e por RNA dupla-fita. A interação direta de PACT com 3¿SL do RNA do vírus da dengue foi confirmada por ensaio de UVcrosslinking PACT possui três domínios de interação com RNA dupla-fita, sendo que os dois domínios N-terminais são responsáveis pela sua interação com o 3¿SL. Foi identificada uma região específica do 3¿SL, o stem-loop superior, onde PACT interage com maior afinidade. Além disso, foi mostrado que PACT endógena de células HEK293 é capaz de interagir com o 3¿SL biotinilado. Para caracterizar a função desta interação durante a infecção viral, foi desenvolvida uma linhagem celular com inibição da expressão de PACT através da técnica de RNA de interferência. Com esta linhagem poderemos analisar a importância da interação entre PACT e o RNA do vírus da dengue quanto à ativação e/ou inibição de PKR durante a infecção viral / Abstract: The combat to the dengue virus is basically limited to the efforts in eliminating the transmitter mosquito, the Aedes aegypti. But this strategy is not very efficient. The development of new instruments of combat to dengue virus requires improved knowledge about the virus biology and its relation to hosts. The dengue virus genome is a single-stranded RNA of positive polarity flanked by a 5¿ untranslated region (UTR) of ~100 bases and a highly structured 3¿ UTR of ~450 bases. As many other viruses, dengue encodes the enzymes required for its genome replication, but relies completely on the host translational machinery to synthesize its proteins. The essential difference between host cellular mRNAs and dengue virus genome RNA involves the 3¿UTR, which instead of a polyadenylate tail contains highly conserved structural elements, including the 3' stem-loop (3¿SL), located at the 3' terminus of the 3'UTR of many flaviviruses that is essential for their replication. The aim of this study is to identify new human proteins capable of interacting with dengue virus RNA 3¿SL structure. Literature data describe that the murine Mov34 protein interacts with Japanese encephalitis virus 3¿SL. Giving the high similarity between the human and murine ortholog proteins, as well as the conservation of the Flavivivirus RNA 3¿SL structure, we tested the interaction between the human Mov34 and the dengue virus 3¿SL. However, no interaction was detected under the conditions used in this work. In addition, the yeast three-hybrid system was used to screen for novel proteins that interact with the dengue virus 3¿SL. Human PACT, known as the cellular protein activator of PKR, was identified as a putative 3¿SL-interacting protein. PKR is an interferon-inducible, PACT or double-stranded RNA activated protein kinase. Activated PKR phosphorylates the translation initiation factor eIF2a, inhibiting translation of cellular and viral RNAs, leading to a cellular antiviral state. PACT and doublestranded RNA activation of PKR is inhibited by influenza A and herpes simplex type 1 virus proteins during viral infection, indicating that PACT plays a role in the cellular antiviral state. Direct interaction between PACT and 3¿SL was confirmed by UV-crosslinking assays. PACT contains three doublestranded RNA interaction motifs, but only the two N-terminal motifs are responsible for 3¿SL interaction. A 3¿SL specific region, the top stem-loop, was identified to interact with PACT with higher affinity. Furthermore, HEK293 cells endogenous PACT interacts with biotin-labeled 3¿SL. To further characterize PACT-3¿SL interaction during dengue virus infection, a cell line with low expression of PACT was developed using the RNA interference technique. This cell line will be used to determine the propagation rate of dengue virus which is expected to reveal the importance of PACT either for the cell antiviral state or for dengue virus proliferation / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 111-140).

Developmental disorders including: autism, intellectual disability, and congenital abnormalities are present in 3-8% of live births and display a huge amount of phenotypic and genetic heterogeneity. Traditionally, geneticists have identified individual monogenic diseases among these patients but a majority of patients fail to receive a clinical diagnosis. However, the genomes of these patients frequently harbour large copynumber variants (CNVs) but their interpretation remains challenging. Using pathway analysis I found significant functional associations for 329 individual phenotypes and show that 39% of these could explain the patients’ multiple co-morbid phenotypes; and multiple associated genes clustered within individual CNVs. I showed there was significantly more such clustering than expected by chance. In addition, the presence of a multiple functionally-related genes is a significant predictor of CNV pathogenicity beyond the presence of known disease genes and size of the CNV. This clustering of functionally-related genes was part of a broader pattern of functional clusters across the human genome. These genome-wide functional clusters showed tissuespecific expression and some evidence of chromatin-domain level regulation. Furthermore, many genome-wide functional clusters were enriched in segmental duplications making them prone to CNV-causing mutations and were frequently seen disrupted in healthy individuals. However, the majority of the time a pathogenic CNV affected the entire functional cluster, where as benign CNVs tended to affect only one or two genes. I also showed that patients with CNVs affecting the same functional cluster are significantly more phenotypically similar to each other than expected even if their CNVs do not affect any of the same genes. Lastly, I considered one of the major limitations in pathway analysis, namely ascertainment biases in functional information due to the prioritization of genes linked to human disease, and show how the modular nature of gene-networks can be used to identify and prioritize understudied genes.

Effective management of acute pancreatitis has for centuries eluded mankind. The disease has a wide spectrum of presentation; the milder form is usually a self limiting condition, whereas the severe form presents as a highly morbid and frequently lethal attack. The ability to predict disease progression on admission would aid in the comprehensive and multidisciplinary management of patients. The perfect predictor of disease progression has been an elusive factor hindering the management of the disease. On systematically reviewing literature and identifying appropriate biochemical markers in predicting progression of acute pancreatitis, the ideal predictor would be a combination of biochemical, clinical and contemporary organ dysfunction scoring systems. Early prediction of disease progression however, is important in the better management of the disease. The pathophysiological changes of acinar cell injury and death are the earliest events that occur in acute pancreatitis. Identification of potential pharmacological interventions offered through valuable insight in to experimental and clinical acute pancreatitis may lead on to the development of various natural and synthetic potential disease modifiers. Green Tea Extracts (GTE) consumed in many parts of the world has been examined as a potential therapeutic medication. Experimental results have demonstrated the effect of GTE on the oxidative pathway significantly ameliorating the effects of pancreatic injury. The various green tea catechins especially Epigallocatechin-3- gallate (EGCG) can perhaps be useful lead compounds for new drug discovery. With no specific targeted therapy for severe acute pancreatitis at present, various medications have been tested. The possibility of targeting initial acinar cell injury may not be a feasible option as patient presentation and management would usually be after this phase. As the disease progresses, severe acute pancreatitis is characterised by inflammation and necrosis. The hypothesis of preserving pancreatic parenchymal microvascular patency and thus ameliorating pancreatic injury through the early administration of recombinant human Activated Protein C (rhAPC) has identified a potential treatment for acute pancreatitis. rhAPC converted from its inactive precursor, protein C, by thrombin acts through fibrinolysis and inhibition of thrombosis. Studies on rhAPC in experimental acute pancreatitis examined the modulation of rhAPC on inflammatory markers, morphology, microvascular thrombosis and apoptosis. The encouraging results from initial experimental work helped set up the Phase 2 clinical trial of administering rhAPC early on in severe acute pancreatitis. Prior to taking this significant step from bench to bed side, the variation in functional protein C levels with the severity of the disease was examined as a precursor to the Phase 2 trial.

Human RPA (replication protein A), a single-stranded DNA-binding protein, is required for many cellular pathways including DNA repair, recombination and replication. However, the role of RPA in nucleotide excision repair remains elusive. In the present study, we have systematically examined the binding of RPA to a battery of well-defined ssDNA (single-stranded DNA) substrates using fluorescence spectroscopy. These substrates contain adducts of (6-4) photoproducts, N-acetyl-2-aminofluorene-, 1-amino-pyrene-, BPDE (benzo[a]pyrene diol epoxide)- and fluorescein that are different in many aspects such as molecular structure and size, DNA disruption mode (e.g. base stacking or non-stacking), as well as chemical properties. Our results showed that RPA has a lower binding affinity for damaged ssDNA than for non-damaged ssDNA and that the affinity of RPA for damaged ssDNA depends on the type of adduct. Interestingly, the bulkier lesions have a greater effect. With a fluorescent base-stacking bulky adduct, (+)-cis-anti-BPDE-dG, we demonstrated that, on binding of RPA. the fluorescence of BPDE-ssDNA was significantly enhanced by up to 8-9-fold. This indicated that the stacking between the BPDE adduct and its neighbouring ssDNA bases had been disrupted and there was a lack of substantial direct contacts between the protein residues and the lesion itself. For RPA interaction with short damaged ssDNA, we propose that, on RPA binding, the modified base of ssDNA is looped out from the surface of the protein, permitting proper contacts of RPA with the remaining unmodified bases.

The need to close wounds and prevent air/liquid leakage is commonly faced in surgical operations. It is a necessary step required for proper post-operative tissue function and healing. In the past, sutures and staples have been used to carry out this function; however, these different methods each come with limitations based on material and application. Recent studies have shown sealant glues to be a new method with much promise in connecting tissues. Several commercially available products have shown biocompatibility, along with ease of application and strong adherence; however, these come with their own set of limitations. In this project I present a novel tissue adhering substance made from human protein elastin. This protein sealant will allow us to address several issues in tissue-engineered materials such as biocompatibility, cytotoxicity, adhesion strength, binding in wet environment and elasticity. Using recombinant technology, we have been able to purify this protein monomer and form glue-like hydrogels using a cross-linker and UV light activator. This sealant was tested in in vitro models and porcine ex vivo lung model. The results indicate an increased adherence to the tissue as well as a high elasticity allowing the sealant to move more naturally with the tissue. Further testing in large animal in vivo studies will be performed to show safety and efficacy before being implemented into clinical practice.