Hepatitis C virus (HCV) infects an estimated 200,000 people in Canada, and is the leading cause of liver transplants in North America. Viral infection usually leads to chronic infection, and complications include liver fibrosis, steatosis and hepatocellular carcinoma (HCC). The HCV non-structural proteins 3 and 4A (NS3/4A), is a multifunctional protein complex with roles in RNA replication and polyprotein processing. Additionally, the NS3 protease has been shown to induce advanced cellular transformation in vivo and tumour formation in nude mice. However, the mechanism by which transformation occurs remains unknown. The objective of this study was to determine if the naturally occurring NS3/4A protein complex, rather than the NS3 protease domain on its own, could also induce cellular transformation and to determine the changes that NS3/4A expression had on the host cell proteome.

In the last decade omics technologies enabled detailed and system-wide analysis of complex biological samples. Genomics, transcriptomics and metabolomics all benefited tremendously from technological advances in their respective fields. Proteomics was revolutionised by mass spectrometry, which allowed simultaneous identification of thousands of proteins in cells, tissues and organisms. And this mainly qualitative revolution, quickly turned quantitative. This work had two main objectives. Firstly, to apply the state of the art instrumentation, data analysis and bioinformatics methods to better our understanding of basic cell biology in a model organism Saccharomyces cerevisiae. Specifically, to quantitatively describe the effects of perturbations, such as adverse environmental conditions or chaperone gene deletions, on protein abundances in the cell. Additionally, it was aimed to demonstrate and evaluate the ability of a new timeof-flight mass spectrometer to perform large-scale absolute quantification. First, it was found that yeast cells are remarkably robust to deletions of major chaperone hub proteins (Ssa1p or Ssb1p deletions). This ability was attributed to network structure and redistribution of folding workload among other related chaperones rather than simple functional redundancy. Second, to build on the first set of results, a detailed time resolved description of yeast proteome dynamics in response to heat stress was provided for the wild type and Ssb1p chaperone mutant strains. In this study, for the first time in the literature, temporal expression patterns of many hallmark heat shock proteins were elucidated. Globally, a slow and sustained proteome remodelling or 'buffering' was revealed in both strains. However, it was also shown that the cells knocked out for the Ssb1p chaperone respond to heat in a distinctly different manner to the wild type strain. Finally, consistent and reproducible absolute quantification of multiple yeast proteomes was demonstrated using a new commercial time-of-flight mass spectrometer with ion mobility separation capabilities. The data obtained revealed global differences in cellular protein content between various chaperone prefoldin mutants as well as differential expression of a set of proteins promising to be interesting targets for further investigations.

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No. of bitstreams: 1 Dissertação - Aline Castro Rodrigues Lucena (final).pdf: 3260035 bytes, checksum: d0b775f25026c251662a16fbc7b5d26d (MD5) Previous issue date: 2015 / Instituto Carlos Chagas / Durante a metaciclogênese in vitro, a forma epimastigota de Trypanosoma cruzi, agente etiológico da doença de Chagas, se diferencia em tripomastigota metacíclica após ser submetido a estresse nutricional em meio TAU, com isso, adquire a capacidade de infectar o hospedeiro vertebrado. Durante a diferenciação, os parasitas sofrem diversas adaptações que incluem a modulação de modificações pós-traducionais. Em um trabalho recente, nosso grupo delineou, sem quantificar, o perfil de fosforilação em T. cruzi durante a metaciclogênese. Neste trabalho, visando realizar a quantificação dos sítios de fosforilação, foi utilizada a metodologia SILAC, que marca proteínas durante o cultivo celular, através da incorporação de aminoácidos contendo isótopos pesados. Visando compreender a sinalização através de fosforilação que ocorre nos momentos iniciais de metaciclogênese, ou seja, durante o estresse nutricional, foram selecionados os pontos epimastigotas em crescimento exponencial (epimastigotas 3 dias, EPI-3D) e na fase estacionária (epimastigotas 5 dias – EPI-5D), bem como alguns pontos ao longo do estresse nutricional (5 e 15 minutos, 1 e 2 horas). Para cada ponto experimental, os peptídeos foram digeridos, fracionados por FR básica, então os fosfopeptídeos foram enriquecidos utilizando beads de TiO2, e analisados por LC-MS/MS. Foram identificados 5.405 grupos de proteínas, 1.679 grupos de fosfoproteínas, 3.893 grupos de sítios de fosforilação sendo 3049 em Serina, 786 em Treonina vii e, 58 em Tirosina, entre os quais cerca de 99% foram quantificados. As análises foram realizadas de duas formas: inicialmente comparando as diferentes fases de cultivo celular (exponencial e estacionária), e os diferentes pontos ao longo do estresse nutricional. Foram observadas diversas alterações no perfil de expressão das proteínas e modulação dos sítios de fosforilação, envolvidos em diversos processos como síntese de ácidos graxos, sinalização celular, locomoção, estresse oxidativo, processamento de RNA, entre outros. Projetos “ômicos”, assim como este, são importante para gerar listas com um número limitado de alvos para posterior caracterização. Nesse sentido, nós objetivamos caracterizar alguns dos elementos apontados visando elucidar o “gatilho” da metaciclogênese. / During metacyclogenesis in vitro, the epimastigote form of Trypanosoma cruzi, etiologic agent of Chagas disease, differentiates into metacyclic trypomastigote, after nutritional stress in TAU medium, and acquires capability to infect the vertebrate host. During differentiation, the parasites suffer several adaptations that include modulation of post-translational modulations. In a recent work, our group outlined, without quantifying, the protein phosphorylation profile of T. cruzi during metacyclogenesis. Here, in order to accomplish the quantification the phosphorylation sites, we applied the SILAC methodology, which labels proteins by incorporation of amino acids containing heavy isotopes, in culture. Aiming to understand the signaling that occurs through phosphorylation in the initial moments of metacyclogenesis, that is, during the nutritional stress, epimastigotes in exponential growth (Epimastigote 3 days, EPI-3D) and in the late log phase (Epimastigote 5 days, EPI-5D), as well as several points during the nutritional stress (5 and 15 minutes, 1 and 2 hours) were selected. For each experimental point, peptides were digested, fractionated by basic RP, then phosphopeptides were enriched with TiO2 beads, and analyzed by LC-MS/MS. In total, 5,405 proteins groups were identified, including 1,679 groups of phosphoproteins and 3,893 phosphorylation sites, being 3,049 in Serine, 786 in Threonine and, 58 in Tyrosine residues, among which around 99% were quantified. The analyzes were performed in two ways: first comparing the ix different stages of cell growth (exponential and stationary), and the different points along the nutritional stress. Several changes were observed in the expression profile of the proteins and modulation of the phosphorylation sites, involved in various processes such as fatty acid synthesis, cell signaling, mobility, oxidative stress, RNA processing, among others. Omics projects like this one are important to generate lists that have limited number of targets for further characterization. In this sense we aim to characterize some of the elements pinpointed to elucidate the trigger of metacyclogenesis.

Staphylococcus aureus (S. aureus) is the etiological agent of food-borne diseases, skin infections in humans and mastitis in bovines. S. aureus is also known to exist as a commensal on skin, nose and other mucosal surfaces of the host. This symbiotic association is a result of immune dampening or tolerance induced in the host by this pathogen. We proposed the variation in protein expression by commensal and pathogenic strain as an important factor behind the difference in pathogenicity. The identification of differentially expressed proteins was carried out using a quantitative mass spectrometry (MS)-based proteomic approach, known as stable isotope labeling of amino acids in cell culture (SILAC). Four commensal and pathogenic strains each were grown in the SILAC minimal media (RPMI 1640), containing light (12C) and heavy (13C) form of lysine, respectively, until early stationary growth phase. Various protein fractions, including cell wall, membrane and secreted, were extracted from the bacterial cultures and mixed in a 1:1 ratio. The relative abundance of proteins present in light and heavy labeled samples was determined using MS analysis. From a total of 151 differentially expressed proteins, 58 were found to be upregulated in the pathogenic strains. These proteins are involved in a variety of cellular functions, including immune modulation, iron-binding, cellular transport, redox reactions, and metabolic enzymes. The differentially expressed proteins can serve as putative candidates to improve current approach towards development of a vaccine against S. aureus. / Master of Science

<p>Protein biomarkers can facilitate the diagnosis of many diseases such as cancer and they can be important for the development of effective therapeutic interventions. Current large-scale biomarker discovery and disease state characterization studies have largely focused on the global analysis of gene and protein expression levels, which are not directly tied to function. Moreover, functionally significant proteins with similar expression levels go undetected in the current paradigm of using gene and protein expression level analyses for protein biomarker discovery. Protein-ligand interactions play an important role in biological processes. A number of diseases such as cancer are reported to have altered protein interaction networks. Current understanding of biophysical properties and consequences of altered protein interaction network in disease state is limited due to the lack of reproducible and high-throughput methods to make such measurements. Thermodynamic stability measurements can report on a wide range of biologically significant phenomena (e.g., point mutations, post-translational modifications, and new or altered binding interactions with cellular ligands) associated with proteins in different disease states. Investigated here is the use of thermodynamic stability measurements to probe the altered interaction networks and functions of proteins in disease states. This thesis outlines the development and application of mass spectrometry based methods for making proteome-wide thermodynamic measurements of protein stability in multifactorial complex diseases such as cancer. Initial work involved the development of SILAC-SPROX and SILAC-PP approaches for thermodynamic stability measurements in proof-of-concept studies with two test ligands, CsA and a non-hydrolyzable adenosine triphosphate (ATP) analogue, adenylyl imidodiphosphate (AMP-PNP). In these proof-of-principle studies, known direct binding target of CsA, cyclophilin A, was successfully identified and quantified. Similarly a number of known and previously unknown ATP binding proteins were also detected and quantified using these SILAC-based energetics approaches. </p><p>Subsequent studies in this thesis involved thermodynamic stability measurements of proteins in the breast cancer cell line models to differentiate disease states. Using the SILAC-SPROX, ~800 proteins were assayed for changes in their protein folding behavior in three different cell line models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. Approximately, 10-12% of the assayed proteins in the comparative analyses performed here exhibited differential stability in cell lysates prepared from the different cell lines. Thermodynamic profiling differences of 28 proteins identified with SILAC-SPROX strategy in MCF-10A versus MCF-7 cell line comparison were also confirmed with SILAC-PP technique. The thermodynamic analyses performed here enabled the non-tumorigenic MCF-10A breast cell line to be differentiated from the MCF-7 and MDA-MB-231 breast cancer cell lines. Differentiation of the less invasive MCF-7 breast cancer cell line from the more highly invasive MDA-MB-231 breast cancer cell line was also possible using thermodynamic stability measurements. The differentially stabilized protein hits in these studies encompassed those with a wide range of functions and protein expression levels, and they included a significant fraction (~45%) with similar expression levels in the cell line comparisons. These proteins created novel molecular signatures to differentiate the cancer cell lines studied here. Our results suggest that protein folding and stability measurements complement the current paradigm of expression level analyses for biomarker discovery and help elucidate the molecular basis of disease.</p> / Dissertation

Cyanobacteria is perhaps the phylum that profit the most from the escalating hypereutrophication of continental waters. The resulting cyanobacterial blooms may accumulate a variety of potent toxins. Cylindrospermopsin (CYN) is a cyanotoxin known for inhibiting protein synthesis, and producing oxidative stress as well as DNA damage in eukaryotic cells. Since the toxin\'s molecular mechanisms and targets are still unclear, we purified the cyanotoxin from our lab strains and employed a shotgun proteomics approach to reveal the major changes in HepG2 cells at sublethal doses of CYN (1 &#181;M for 6, 12 and 24h). Metabolically labeled cells were stimulated and lysed after each treatment, their tryptic digests were separated by nano HPLC and analyzed by high-resolution tandem mass spectrometry (HRMS) on data dependent acquisition mode. We scanned an average of 4000 proteins in every sample throughout the three timepoints. Cholesterol biosynthesis and transport was mostly downregulated throughout the timepooints of the experiment. Downregulation of proteins related to ubiquitination (e.g. UBE2L3) and proteolysis pathways (e.g. PSMA2) was observed in the proteomics dataset, and these results were validated by western blot. Transcription, translation and cell cycle processes showed convoluted regulation dynamics involving known cell cycle regulators like PCNA. Downregulation of mitochondrial enzymes, oxidative stress and damage to the mithochondrial inner membrane was early evidenced after a 6 hrs treatment and validated using a JC-1, a mitochondrial membrane potential probe. The resulting dataset gives us a first glimpse of the protein groups affected at the early stage of CYN cell intoxication. / Cianobactéria é o filo que mais se beneficia da crescente hipereutrofização das águas continentais. As florações de cianobactérias resultantes podem acumular potentes toxinas. A Cilindrospermopsina (CYN) é uma cianotoxina conhecida por inibir a síntese protéica e produzir estresse oxidativo, além de danos ao DNA em células eucarióticas. Os mecanismos moleculares e alvos de toxicidade aguda desta toxina ainda não são claros. Por esse motivo adoptamos uma abordagem de proteômica quantitativa baseada em descoberta para revelar as principais alterações nas células HepG2 em doses subletais de CYN (1 &#181;M para 6, 12 e 24h). As proteinas dos hepatócitos foram marcadas metabolicamente, foram estimuladas com a toxina e os digestos trípticos foram analisados por espectrometria de massa em tandem de alta resolução (HRMS) no modo de aquisição dependente de dados. Escaneamos uma média de 4000 proteínas ao longo dos intervalos de tempo. A biosintese e transporte do colesterol foi inibida durante a maior parte do tratamento com a toxina. Proteínas e enzimas relacionadas com o processo de ubiquitinação (ex. UBE2L3) e proteólise (ex. PSMA2) foram inibidas, e alterações nas proteínas envolvidas nesses processos foram validadas por meio de Western Blot. Os processos de transcrição, tradução e ciclo celular mostraram uma dinâmica de regulação complexa, envolvendo reguladores e disruptores do ciclo celular como por exemplo PCNA. Danos à membrana mitocondrial e evidência de estresse oxidativo foram detectados após 6 horas de tratamento, e essas mudanças no proteoma foram validados por meio do corante JC-1 (test que detecta mudanças no potencial da membrana mitocondrial). O banco de dados resultante nos dá um primeiro vislumbre das proteinas afetados no estágio inicial da intoxicação celular pela CYN.

Cyanobacteria is perhaps the phylum that profit the most from the escalating hypereutrophication of continental waters. The resulting cyanobacterial blooms may accumulate a variety of potent toxins. Cylindrospermopsin (CYN) is a cyanotoxin known for inhibiting protein synthesis, and producing oxidative stress as well as DNA damage in eukaryotic cells. Since the toxin\'s molecular mechanisms and targets are still unclear, we purified the cyanotoxin from our lab strains and employed a shotgun proteomics approach to reveal the major changes in HepG2 cells at sublethal doses of CYN (1 &#181;M for 6, 12 and 24h). Metabolically labeled cells were stimulated and lysed after each treatment, their tryptic digests were separated by nano HPLC and analyzed by high-resolution tandem mass spectrometry (HRMS) on data dependent acquisition mode. We scanned an average of 4000 proteins in every sample throughout the three timepoints. Cholesterol biosynthesis and transport was mostly downregulated throughout the timepooints of the experiment. Downregulation of proteins related to ubiquitination (e.g. UBE2L3) and proteolysis pathways (e.g. PSMA2) was observed in the proteomics dataset, and these results were validated by western blot. Transcription, translation and cell cycle processes showed convoluted regulation dynamics involving known cell cycle regulators like PCNA. Downregulation of mitochondrial enzymes, oxidative stress and damage to the mithochondrial inner membrane was early evidenced after a 6 hrs treatment and validated using a JC-1, a mitochondrial membrane potential probe. The resulting dataset gives us a first glimpse of the protein groups affected at the early stage of CYN cell intoxication. / Cianobactéria é o filo que mais se beneficia da crescente hipereutrofização das águas continentais. As florações de cianobactérias resultantes podem acumular potentes toxinas. A Cilindrospermopsina (CYN) é uma cianotoxina conhecida por inibir a síntese protéica e produzir estresse oxidativo, além de danos ao DNA em células eucarióticas. Os mecanismos moleculares e alvos de toxicidade aguda desta toxina ainda não são claros. Por esse motivo adoptamos uma abordagem de proteômica quantitativa baseada em descoberta para revelar as principais alterações nas células HepG2 em doses subletais de CYN (1 &#181;M para 6, 12 e 24h). As proteinas dos hepatócitos foram marcadas metabolicamente, foram estimuladas com a toxina e os digestos trípticos foram analisados por espectrometria de massa em tandem de alta resolução (HRMS) no modo de aquisição dependente de dados. Escaneamos uma média de 4000 proteínas ao longo dos intervalos de tempo. A biosintese e transporte do colesterol foi inibida durante a maior parte do tratamento com a toxina. Proteínas e enzimas relacionadas com o processo de ubiquitinação (ex. UBE2L3) e proteólise (ex. PSMA2) foram inibidas, e alterações nas proteínas envolvidas nesses processos foram validadas por meio de Western Blot. Os processos de transcrição, tradução e ciclo celular mostraram uma dinâmica de regulação complexa, envolvendo reguladores e disruptores do ciclo celular como por exemplo PCNA. Danos à membrana mitocondrial e evidência de estresse oxidativo foram detectados após 6 horas de tratamento, e essas mudanças no proteoma foram validados por meio do corante JC-1 (test que detecta mudanças no potencial da membrana mitocondrial). O banco de dados resultante nos dá um primeiro vislumbre das proteinas afetados no estágio inicial da intoxicação celular pela CYN.

Acetylation was previously thought to occur exclusively on histones, but recent high-throughput screens have identified thousands of non-histone substrates. Despite the identification of these sites, little is known about how these acetyltransferase enzymes target their substrates. Gcn5 is the catalytic acetyltransferase found within the highly conserved SAGA complex. Recently, a member of this complex, Ada2, was found to impact Gcn5 substrate selection. In the yeast model organism Saccharomyces cerevisiae, a synthetic substrate developed from a proposed Gcn5-specific consensus sequence is used to identify regulators of Gcn5 substrate selection. This work is the first to demonstrate that addition of a consensus sequence is enough to confer acetylation of a non-substrate. With this method, Ada3 was identified as a key regulator, and acetylome profiling identified novel targets for Gcn5 dependent acetylation specifically regulated by Ada3. This system could be adapted for other acetyltransferases to identify regulators of substrate selection.

O câncer de pâncreas é considerado um dos adenocarcinomas mais agressivos, ocupando o quarto lugar de mortes devidas a câncer, isto é dado principalmente a seu desenvolvimento silencioso e a sua complexidade genética, tornando-o de difícil detecção. Consequentemente, o diagnóstico desta doença ocorre apenas em fase tardia, quando o tratamento é apenas para fins paliativos. As anomalias genéticas mais frequentes no câncer de pâncreas invasivo estão relacionadas à ativação por mutações do gene KRAS e à inativação dos genes supressores de tumor CDKN2A, TP53, SMAD4 e BRCA2. Além destas conhecidas vias de sinalização, fatores de crescimento como o TGF-? e EGF também apresentam papel fundamental na progressão e metástase do câncer de pâncreas. Interessantemente, TGF-? e EGF são também indutores do processo denominado transição epitelial-mesenquimal (EMT), onde células epiteliais normais, durante a embriogênese, ou células cancerosas durante a progressão tumoral e metástase, perdem seus contatos intracelulares e adquirem caráter migratório. Desta forma a EMT, induzida por altos níveis de TGF-? e/ou EGF, é considerada como um dos mecanismos de progressão tumoral em adenocarcinomas. No presente estudo, foram estudados os proteomas e o fosfoproteoma da EMT do PanCa. Assim, células de câncer de pâncreas PANC- 1 foram induzidas à EMT em cultura com os fatores de crescimento TGF-?1 ou TGF-?2 e EGF, e após a indução, marcadores moleculares e propriedades funcionais de migração e invasão foram confirmados. Duas condições de indução da EMT foram estabelecidas, para as quais foram desenvolvidas as análises proteômicas quantitativas. A abordagem foi baseada em marcação isotópica de células em cultura (SILAC), em conjunto com fracionamento celular e de proteínas intactas, e cromatografia líquida acoplada à espectrometria de massas para identificação de proteínas em larga escala. No total, aproximadamente 5.000 proteínas foram identificadas, e a maioria delas quantificadas com precisão nas duplicatas experimentais. Foram selecionadas 37 proteínas com expressão diferencial estatisticamente significativa nos experimentos proteômicos, as quais participam principalmente em processos de biogênese, adesão e apoptóticos. A análise de redes de interação revelou que as proteínas alteradas estavam principalmente localizadas em vias de sinalização que controlam processos de organização da matriz extracelular, splicing alternativo e regulação da apoptose. A análise do fosfoproteoma foi feita usando TGF-?1 como agente indutor da EMT nas células PANC-1, usando a estratégia ERLIC para o enriquecimento de fosfopeptídeos. No total, foram identificados 5.965 fosfopeptídeos não redundantes, correspondendo a um total de 2.250 fosfoproteínas analisadas, sendo quantificadas 2.053 ao menos em duas replicatas, e destas foram identificados 61 fosfopeptídeos regulados pertencentes a 55 fosfoproteínas, relacionados com processos de regulação do mRNA e vias de sinalização ligadas à adesão celular. Em conclusão, nosso estudo elucida potenciais novos alvos para inibição da EMT, controle da metástase, ou para auxiliar no diagnóstico da doença, quando devidamente validada. / Pancreatic cancer kills more than 200 thousand people worldwide every year. Also, pancreatic cancer is considered one of the most aggressive adenocarcinomas and difficult to diagnose since it develops silently and presents a high genetic complexity. Consequently, the diagnostic is often late, when the pancreatic cancer has already metastasized and the treatment has only palliative purposes. The most frequent genetic alterations observed in pancreatic cancer are related to mutations in KRAS oncogene and CDKN2A, TP53, SMAD4 and BRCA2 tumor suppressor genes. In addition to these known frequent mutations, growth factors such as TGB- ? and EGF play important roles in pancreatic cancer progression and metastasis. Interestingly, TGB- ? and EGF are also inducers of the Epithelial to Mesenchymal Transition (EMT), in which epithelial cells lose their intracellular contacts and acquire migratory capacities. Therefore, EMT is considered one of the mechanisms responsible for tumor progression and metastasis in adenocarcinomas in addition of being correlated to the process of generating cancer stem cells. In our present study, pancreatic cancer cell line PANC-1 was induced to EMT by using growth factors TGF-?1 or TGF-?2 and EGF. Both molecular and functional properties, such as invasion and migration, were evaluated in PANC-1 cells undergoing EMT and confirm the induction. Two conditions of EMT induction were properly established and in-depth quantitative proteomic analysis based on stable isotope labeling in cell culture (SILAC) followed by cellular and protein fractionation were assessed. In total, 5.000 proteins were identified and most of them were accurately quantified in duplicate experiments. Thirty-seven proteins were selected as differentially expressed with statistical significance, and were related mainly with biogenesis, adhesion and apoptosis processes. Interaction network analysis showed that regulated proteins were predominantly participating in signaling pathways linked to extracellular matrix organization, alternative splicing and apoptosis regulation. Phosphoproteome analysis was done using TGF-?1 as EMT-inductor agent on PANC-1 cells and ERLIC strategy for phosphopeptides enrichment. In total, were identified 5.965 non-redundant phosphopeptides corresponding to approximately 2.250 analyzed phosphoproteins, thereof 2.053 were quantified in at least two replicates. At comparison, were identified 61 regulated phosphopeptides belonging to 55 phosphoproteins, which were related with mRNA regulation processes and signialing pathways linked to cellular adhesion. In conclusion, our study highlighted potential new targets for EMT inhibition, metastasis control or to help in pancreatic cancer diagnosis, when careful validated.

No description available.