Esquizofrenia é um transtorno psiquiátrico complexo que afeta cerca de 1% da população mundial. Apesar de progressos consideráveis nos últimos anos, a etiologia da doença ainda não foi elucidada principalmente pela heterogeneidade tanto do início quanto da progressão da doença. Frequentemente os sintomas dos pacientes são comuns a outras desordens neuropsiquiátricas, dificultando a diferenciação por meio de métodos essencialmente clínicos. Por isso, pesquisadores têm tentado identificar medidas baseadas em características moleculares que justifiquem e expliquem a etiologia da esquizofrenia. Já há alguns estudos com marcadores no cérebro, mas por esse ser um material com disponibilidade limitada, os esforços tem se concentrado em encontrar biomarcadores periféricos. Este estudo visou traçar um perfil proteico, em plaquetas, de pacientes drug-naïve com diagnóstico de esquizofrenia. Para tanto, comparamos este grupo com controles saudáveis e com controles psiquiátricos. Utilizamos duas abordagens proteômicas complementares para análise: a primeira, uma ferramenta clássica utilizando eletroforese bidimensional com posterior identificação dos spots por espectrometria de massas; e a segunda, uma abordagem de identificação em larga escala por shotgun label-free. Foram analisadas amostras de 16 controles saudáveis, de 11 pacientes com esquizofrenia e de 8 pacientes com transtornos do humor (controle psiquiátrico). Com a eletroforese bidimensional foram identificados 110 spots comuns nos géis de controles saudáveis, 83 spots comuns aos géis de pacientes com esquizofrenia e 80 spots comuns aos géis de pacientes com diagnóstico de transtornos do humor. Foram encontrados 27 spots exclusivos do grupo controle, não sendo detectados em nenhum dos dois grupos de pacientes. Esses spots foram recortados e analisados por espectrometria de massas revelando proteínas relacionadas com: neurotransmissão, sinapse, neurodesenvolvimento, homeostase celular, sinalização de cálcio, apoptose, resposta imune, e estresse oxidativo. Para verificação dos resultados, escolhemos proteínas de acordo com sua função já descrita na literatura e ineditismo na matriz e na casuística estudadas. Por meio da técnica de western blotting, encontramos diminuições significantes nos níveis de anexina A3 e peroxirredoxina 6 nos dois grupos de pacientes. Ambas proteínas diferentemente expressas nos pacientes já foram relacionadas à fosfolipase A2, que é a principal enzima responsável pelo metabolismo de fosfolípides de membrana e tem sido associada à desordens neuropsiquiátricas, inclusive à esquizofrenia. Ainda há algumas abordagens analíticas e bioinformáticas a serem realizadas na busca por candidatos a biomarcadores de esquizofrenia em plaquetas. Os resultados obtidos por shotgun necessitam de uma análise mais aprofundada além da verificação e validação em coortes maiores. A casuística utilizada para este trabalho é bastante valiosa já que permitirá a elucidação de alterações proteômicas já no primeiro episódio psicótico / Schizophrenia is a mulfatorial psychiatric disorder that affects about 1% of the world\'s population. Despite considerable progress in recent years, the etiology of the disease has not yet been elucidated mainly because the heterogeneity of disease onset and progression. Often the symptoms overlap to other neuropsychiatric disorders, which turns difficult to differentiate through essentially clinical methods. The researchers have focused in identify mesureable molecular characteristics that can help to elucidate schizophrenia etiology. There are already important findings regarding markers in the brain, but recent efforts have focused on finding peripheral biomarkers. This study aimed to find a protein profile in platelets of schizophrenia drug-naïve patients. For comparision we recruited two more groups: healthy controls and psychiatric control. We used two complementary proteomic approaches for analysis: a classic tool using two-dimensional electrophoresis with subsequent identification of the spots by mass spectrometry; and a large-scale label-free shotgun identification approach. The sample comprised 11 schizophrenic patients, 8 patients with mood disorders (psychiatric control and 16 healthy controls. 2-DE profiles of each sample were generated in triplicate. 110 proteins spots were identified in most gels of control group, 83 in most gels of schizophrenia group, and 80 proteins spots in most gels of bipolar disorder patients. Among these proteins spots, 76 were common to all three groups; 5 to controls and schizophrenia group; 2 common to controls and bipolar disorders groups; 2 exclusive of bipolar disorder patients and 27 proteins spots were identified exclusively in the control group. The 27 exclusive protein spots of control group were identified by LC-MS/MS. Proteins related to neurotransmission, synapse, neurodevelopment, cellular homeostasis, calcium signaling, apoptosis, immune response, and oxidative stress were identified. To verify the results, we chose proteins according to their function already described in the literature and novelty in platelets and first onset psychosis patients research. By western blotting we verified the difference in levels of annexin A3 and peroxiredoxin 6 between groups, but not of glutathione S-transferase pi 1 or 78-kDa glucose-regulated protein. Both proteins differentially expressed have already been related to phospholipase A2, which is the main enzyme responsible for the membrane phospholipids metabolism and has been associated with neuropsychiatric disorders, including schizophrenia. Despite the good and promising results presented and published, there are still some analytical and bioinformatic approaches to be performed in search for candidates for platelet schizophrenia biomarkers. The data from shotgun approach require further analysis, as well as verification and validation in larger cohorts. The sample enrroled in this study is greatly important and certainly informed us much about the proteomic alterations still in the first onset psychosis

A cana-de-açúcar é uma das principais culturas em países tropicais. O Brasil, além de ser o maior produtor mundial, é também líder em produção de açúcar e álcool. Atualmente, a maior parte da cana-de-açúcar cultivada no Brasil encontra-se em condições , como resultado, a cultura é sujeita ao déficit hídrico em alguns estágios. Portanto, é essencial entender as respostas fisiológicas e moleculares da planta à disponibilidade de água. Nesse contexto, as análises de metabolômica e proteômica objetivam identificar diferentes vias metabólicas e proteínas relacionadas ao mecanismo de defesa e de recuperação. Plantas de Saccharum spp com sete meses de idade foram submetidas a diferentes condições hídricas, déficit e reidratação, e amostras controle foram mantidas irrigadas. A identificação do perfil metabólico primário foi realizada através da cromatografia gasosa combinada com espectrometria de massas (GC-MS). Para identificação das proteínas nucleares, as amostras complexas foram digeridas, e posteriormente, sequenciadas por (LC-MS). As análises estatísticas entre os tratamentos (PLS-DA) mostraram diferenças significativas tanto para metabólitos quanto para as proteínas. Um total de 86 metabólitos foram identificados, onde 8 compostos foram preferencialmente abundantes no estresse, e 10 na recuperação e, portanto, podem ser utilizados como marcadores. Alguns desses compostos participam de vias metabólicas comuns, como biossíntese de alcaloides derivados da ornithine, lysine e nicotinate e de biossíntese de fenilpropanoides. Metabólitos que não participam dessas vias mas foram, pelo menos, duas vezes mais abundantes nos tratamentos quando comparados ao controle também foram discutidos, para o déficit destacam-se galacturonic acid-1-phosphate, pyroglutamic acid e creatinine e para recuperação methyl dihydrogen phosphate, phosphoric acid e 2-hydroxypyridine. Um total de 761 proteínas foram identificadas, sendo 21 nucleares e responsivas ao déficit hídrico, e 32 nucleares e relacionadas ao processo de recuperação. As classes funcionais das proteínas relacionadas ao déficit são de tradução e processo de oxidação-redução, e das proteínas da recuperação são de tradução e proteólise envolvida no processo catabólico proteico. A combinação de diferentes técnicas nesse estudo revela uma dinâmica regulatória complexa no mecanismo de tolerância da cana-de-açúcar ao déficit hídrico. / Sugarcane is one of the main crops in tropical countries. Brazil, besides being the world\'s largest producer of this crop, is also a leader in sugar and ethanol production. Nowadays, most of the sugarcane growing in Brazil is under rain-fed conditions, as a result, the culture is subject to water deficit at certain stages. Thus, it is essential to understand the physiological and molecular plant responses to water availability. In this context, the metabolomic and proteomic analyses aims to identify different metabolic pathways and proteins related to the mechanisms of tolerance and recovery. Samples of seven month old plants of Saccharum spp were subjected to different water conditions, deficit and rehydratation, whereas control samples were kept irrigated. The identification of primary metabolite profile was performed by Gas-Chromatography combined with Mass- Spectrometry (GC-MS). To identify nuclear proteins, the complex samples were digested and then sequenced by LC-MSE. Statistical analyses among treatments PLS-DA showed significant differences in both metabolites and proteins of Saccharum spp in different conditions. A total of 86 metabolites were identified, where 8 are preferably abundant in water stress and 10 in recovery, thus, they can be used as markers. Some of these compounds are present in common pathways like biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid and biosynthesis of phenylpropanoids. Metabolites that do not participate in these pathways, but that were at least two times more abundant in treatments when compared to control, were also discussed. They were galacturonic acid-1-phosphate, pyroglutamic acid and creatinine that were related to deficit condition and methyl dihydrogen phosphate, phosphoric acid and 2-hydroxypyridine to recovery. A total of 761 proteins were identified, of which 21 were nuclear and drought responsive and 32 were nuclear and recovery responsive. The functional classes of water stress proteins are translation and oxidation-reduction process and of recovery proteins are translation and proteolysis involved in cellular protein catabolic process. The combination of different techniques in this study revealed a complex regulatory dynamics in the mechanism of sugarcane water stress tolerance that have not been discussed in the literature.

O desenvolvimento tumoral é um processo que compreende diversas etapas e consiste no desenvolvimento progressivo de células normais para um estado neoplásico através de diversas mudanças bioquímicas e fenotípicas. Entre as principais marcas do câncer estão a capacidade de invasão tecidual e metástase. A metástase é responsável por, aproximadamente, 90% das mortes causadas por câncer. Assim, os métodos mais efetivos para a melhoria dos índices de morbidade e mortalidade relacionados ao câncer são a detecção precoce, a prevenção e o tratamento da metástase. O processo de EMT, que ocorre naturalmente durante a embriogênese e reparo tecidual, está envolvido também na progressão e metástase do câncer. A EMT induz alterações celulares e microambientais complexas que resultam na aquisição de um fenótipo mesenquimal pelas células epiteliais, juntamente com um aumento das capacidades migratórias e invasivas celulares. A EMT pode ser induzida por diversos fatores extracelulares, como os fatores de crescimento TGF?, EGF, HGF e PDGF. Além disso, a superexpressão de fatores de transcrição como SNAIL, SLUG, ZEB1 e TWIST1 também é capaz de induzir a EMT in vitro. A fim de ampliar o conhecimento dos mecanismos envolvidos no processo de EMT a nível de proteínas, foram realizadas neste trabalho análises de alterações proteômicas em diferentes modelos de indução da EMT na linhagem de adenocarcinoma de mama MCF7, sendo eles a superexpressão do FT SNAIL, o tratamento com o inibidor de histonas deacetilases SAHA e o tratamento com o fator de crescimento EGF. A análise proteômica detalhada por LC-MS/MS das frações subcelulares de núcleo, citoplasma e membrana das células superexpressando SNAIL gerou uma lista de proteínas reguladas relacionadas com o processo de EMT e que foram avaliadas nos demais modelos de indução. Entre essas, a proteína HDAC1, que teve seus níveis diminuídos pela superexpressão de SNAIL. O tratamento da linhagem MCF7 com o inibidor de histonas deacetilases SAHA demonstrou uma correlação positiva com o aumento dos níveis de SNAIL nas células MCF7, sugerindo um cross-talk entre ambas as proteínas. Além disso, otratamento com SAHA induziu alterações celulares e proteicas que também sugerem a indução do processo de EMT nas células MCF7. Por fim, o tratamento com o fator de crescimento EGF também foi capaz de induzir a EMT nas células MCF7 e apresentou envolvimento na regulação do ciclo celular, alterações de proteínas em comum com os demais tratamentos e regulação diferencial de proteínas entre os subcompartimentos, indicando similaridades entre os processos e potenciais mecanismos de translocação subcelular. Em conclusão, este estudo relevou proteínas alvo relacionadas à EMT, abrindo possibilidades para tentar alterar processos relacionados à progressão tumoral e ao processo metastático. / Tumor development is a process comprising several steps and consists in the progressive development of normal cells into a neoplastic state through various biochemical and phenotypic changes. Among the major marks of cancer are the capacity for tissue invasion and metastasis. Metastasis accounts for approximately 90% of cancer deaths. Thus, the most effective methods for improving cancer-related morbidity and mortality rates are early detection, prevention and treatment of metastasis. The EMT process, which occurs naturally during embryogenesis and tissue repair, is also involved in cancer progression and metastasis. EMT induces complex cellular and microenvironmental changes that result in the acquisition of a mesenchymal phenotype by epithelial cells, together with an increase in migratory and invasive cellular capacities. EMT can be induced by various extracellular factors, such as TGF?, EGF, HGF and PDGF. In addition, overexpression of some transcription factors such as SNAIL, SLUG, ZEB1 and TWIST1 is also capable of inducing EMT in vitro. In order to increase the knowledge of the mechanisms involved in the EMT process, we performed proteomic analysis in different models of EMT induction in the MCF7 breast adenocarcinoma cell line, which were the overexpression of SNAIL, treatment with the histone deacetylase inhibitor SAHA and treatment with the growth factor EGF. The detailed proteomic analysis by LC-MS/MS of the subcellular fractions of nucleus, cytoplasm and membrane of the overexpressing SNAIL cells generated a list of regulated proteins related to the EMT process and that were evaluated in the other models of induction. Among these, the HDAC1 protein, which had its levels decreased by SNAIL overexpression. Treatment of the MCF7 cell line with the histone deacetylase inhibitor SAHA showed a positive correlation with the increase of SNAIL levels, suggesting a cross-talk between both proteins. In addition, SAHA treatment induced cellular and protein alterations that also suggest the induction of the EMT process in MCF7 cells. Finally, the treatment with the growth factor EGF was also able to induce the EMT in MCF7 cells and showed involvement in the regulation of the cell cycle, changes in proteins in common with the other treatments and differential regulation of proteins among thesubcompartiments, indicating similarities between the processes and potential mechanisms of subcellular translocation. In conclusion, this study revealed target proteins related to EMT, opening possibilities to try to alter processes related to tumor progression and metastatic process.

O câncer de ovário (OvCa) se destaca dentre as neoplasias ginecológicas por ser um dos mais letais e de difícil diagnóstico. O OvCa ocorre devido ao acúmulo de alterações celulares progressivas promovidas por mutações no genoma de uma célula que, consequentemente, alteram as complexas vias de regulação celular que respondem a fatores internos, como reprogramação genética, ou externos, como a resposta a fatores de crescimento, que juntamente com outras alterações moleculares favorecem a progressão e a metástase. Uma importante etapa da cascata metastática é a transição epitélio-mesenquimal (EMT), um processo bem orquestrado que resulta na perda do fenótipo epitelial e aquisição do fenótipo mesenquimal pelas células tumorais, que adquirem um caráter mais invasivo e migratório, além de se tornarem mais resistentes às drogas. A desregulação de fatores de transcrição como ZEB1, TWIST e SNAI1, vias de sinalização, microRNAs e fatores de crescimento incluindo EGF, TGF? e HGF podem desencadear a EMT. Após a eficiente indução da EMT com EGF na linhagem epitelial de adenocarcinoma de ovário humano Caov-3, foi realizada a análise proteômica quantitativa detalhada, baseada na análise de frações subcelulares enriquecidas em proteínas de membrana, citosol e núcleo, obtidas por centrifugação diferencial e subsequente fracionamento de proteínas por SDS-PAGE, a fim de compreender mais profundamente os mecanismos moleculares modulados pela EMT no OvCa. A partir da análise dos dados coletados em um sistema de espectrometria de massas de alta resolução acoplados a cromatografia líquida (LCMS/MS) e com o auxílio da bioinformática foram identificadas redes de interação proteína-proteína diferencialmente expressas, relacionadas principalmente com a regulação do ciclo celular e do metabolismo. A indução da EMT por EGF resultou na ativação de importantes vias de sinalização, tais como PI3K/Akt/mTOR e Ras/MAPK Erk, além da parada do ciclo celular na fase G1 regulada pelo aumento dos níveis de p21Waf1/Cip1, independentemente de p53, e diminuição de proteínas checkpoint. Através da proteômica dirigida, o monitoramento de reações múltiplas (MRM) revelou que, após a indução da EMT por EGF, o metabolismo das células Caov-3 foi alterado de uma maneira bastante peculiar. O estudo proteômico descrito permitiu a correlação entre processo da EMT induzido por EGF com o controle translacional, a regulação do ciclo celular e a alteração do metabolismo energético. / Ovarian cancer (OvCa) stands out among gynecological malignancies for being one of the most lethal and difficult to diagnose. OvCa occurs due to the accumulation of progressive cell changes promoted by mutations in the cell genome which, consequently, alter the complex cellular regulation pathways that respond to internal factors, such as genetic reprogramming, or external, such as response to growth factors, which together with other molecular changes favor the progression and metastasis. An important step of the metastatic cascade is the epithelial-mesenchymal transition (EMT), a well-orchestrated process that results in the loss of epithelial phenotype and acquisition of mesenchymal phenotype by tumor cells that acquire a more invasive and migratory character, and become more resistant to drugs. Deregulation of transcription factors such as ZEB1, TWIST and SNAI1, signaling pathways, microRNAs and growth factors including EGF, TGF? and HGF can trigger EMT. After an efficient EMT induction by EGF in the epithelial cell line of human adenocarcinoma ovarian Caov-3, detailed quantitative proteomic analysis was performed based on analysis of subcellular fractions enriched in proteins from membrane, cytosol and nucleus, obtained by differential centrifugation and subsequent fractionation of proteins by SDS-PAGE, in order to understand deeply the molecular mechanisms modulated by EMT in OvCa. From the analysis of data collected in a highresolution mass spectrometry system coupled to liquid chromatography (LC-MS/MS) and with the aid of bioinformatics were identified protein-protein interaction networks differentially expressed, mainly related to regulation cell cycle and metabolism. EGF induced-EMT resulted in the activation of major signaling pathways such as PI3K/Akt/mTOR and Ras/MAPK Erk, in addition to G1 phase cell cycle arrest regulated by increased levels of p21Waf1/Cip1, regardless of p53, and reduction of checkpoint proteins. Through the targeted proteomics, multiple reaction monitoring (MRM) showed that after EGF induced-EMT, Caov-3 cells metabolism was changed in a very particular way. The proteomic study described allowed the correlation between EMT process induced by EGF with translational control, regulation of cell cycle and the change in the energy metabolism.

Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-08-20T17:17:13Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Rejected by Ana Paula Lisboa Monteiro (monteiro@univates.br), reason: Inserir o Lattes do autor. on 2018-09-11T18:28:07Z (GMT) / Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-09-17T17:18:08Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Approved for entry into archive by Ana Paula Lisboa Monteiro (monteiro@univates.br) on 2018-10-03T16:31:01Z (GMT) No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Made available in DSpace on 2018-10-03T16:31:01Z (GMT). No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) Previous issue date: 2018-08-20 / High levels of Schizotetranychus oryzae phytophagous mite infestation on rice leaves can severely affect pro- ductivity. Physiological characterization showed that S. oryzae promotes a decrease in chlorophyll concentration and the establishment of a senescence process in rice leaves. Late-infested leaves also present high levels of superoxide radical and hydrogen peroxide accumulation, along with high levels of membrane integrity loss, which is indicative of cell death. To better understand the rice molecular responses to high levels of mite in-festation, we employed the Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We identified 83 and 88 proteins uniquely present in control and late-infested leaves, respectively, along with 11 and one proteins more abundant in control and late-infested leaves, re-spectively. S. oryzae infestation induces a decreased abundance of proteins related to translation, protease in-hibition, and photosynthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation. Our results also suggest that S. oryzae infestation interferes with in-tracellular transport, DNA structure maintenance, and amino acid and lipid metabolism in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of late-infested rice leaves and suggest several targets which could be tested in future bio-technological approaches aiming to avoid the population increase of phytophagous mite in rice plants.

Vesicle trafficking provides the solution to the 'sorting problem' - how the eukaryotic cell maintains the distinct identities, and thus functional properties, of its membrane-bound organelles. During vesicle trafficking, proteins are selectively sorted into membrane bound transport intermediates by vesicle adaptors, which include those of the highly conserved adaptor protein (AP) complex family. Each AP complex has a distinct subcellular localisation and functions in the sorting of a specific subset of transmembrane cargo proteins. Adaptor protein complex 4 (AP-4) is one of the more recently identified AP complexes, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder, suggesting an important role in neuronal development and homeostasis. However, the pathomechanisms that underly the neuronal pathology in AP-4 deficiency are currently unknown. AP-4 is proposed to function in protein sorting at the trans-Golgi network (TGN), so AP-4 deficiency can be thought of as a disease of missorting. The aim of this study was to apply unbiased global proteomic approaches to define the composition of AP-4 vesicles and to identify physiological cargo proteins of the AP-4 pathway. Using 'Dynamic Organellar Maps' and comparative analysis of vesicle-enriched fractions from wild-type and AP-4-depleted cells, three ubiquitously expressed transmembrane cargo proteins, ATG9A, SERINC1 and SERINC3, were found to be mislocalised in AP-4-deficient cells. Two novel cytosolic AP-4 accessory proteins, RUSC1 and RUSC2, were also identified. Further proteomic analyses confirmed the interactions between these proteins. AP-4 deficiency was found to cause missorting of ATG9A in diverse cell types, including patient derived cells, as well as dysregulation of autophagy. RUSC2 facilitates the transport of AP-4-derived, ATG9A and SERINC-positive vesicles from the TGN to the cell periphery. These vesicles cluster in close association with autophagosomes, suggesting they are the 'ATG9 reservoir' required for autophagosome biogenesis. This study uncovers ATG9A trafficking as a ubiquitous function of the AP-4 pathway. Furthermore, it provides a potential molecular pathomechanism of AP-4 deficiency, through dysregulated spatial control of autophagy.

Critical illness is an aetiologically and clinically heterogeneous syndrome that is characterised by organ failure and immune dysfunction. Mortality in critically ill patients is driven by inflammation-associated organ damage and a profound vulnerability to nosocomial infection. Both factors are influenced by the complement protein C5a, released by unbridled activation of the complement system during critical illness. C5a suppresses antimicrobial functions of key immune cells, in particular the neutrophil, and this suppression has been shown to be associated with poorer outcomes amongst critically ill adults. The intracellular signalling pathways which mediate C5a-induced neutrophil dysfunction are incompletely understood, and scalable tools with which to assess immune cell dysfunction in patients are lacking. This thesis aimed to develop tools with which to assess neutrophil function and delineate intracellular signalling pathways driving C5a-induced impairment. Neutrophils were isolated from healthy volunteer blood and functions (priming, phagocytosis and reactive oxygen species production) were assessed using light microscopy, confocal microscopy and flow cytometry. A new assay was developed using an Attune Nxt™ acoustic focusing cytometer (Life Technologies) which allowed the rapid assessment of multiple neutrophil functions in small samples of unlysed, minimally-manipulated human whole blood. Complete proteomes and phosphoproteomes of phagocytosing neutrophils were obtained from four healthy donors pre-treated with C5a or vehicle control. Several key insights were gained from this work and are summarised here. Firstly, C5a was found to induce a prolonged (greater than seven hours) impairment of neutrophil phagocytosis. This defect was found to be preventable by previous or concurrent phagocytosis, indicating common signalling mechanisms. Secondly, a novel assay was developed which allows the rapid assessment of multiple neutrophil functions in less than 2 mL of whole blood, and this assay can feasibly be applied in clinical settings. Thirdly, cell-surface expression of the C5a receptor was found to be markedly decreased during phagocytosis, and this decrease was not mediated by protease activity. Finally, unbiased proteomics quantified 4859 proteins and 2712 phosphoproteins respectively. This quantification is the deepest profile of the human neutrophil proteome published to date, and has revealed novel insights into the mechanisms of C5a-induced neutrophil dysfunction and phagocytosis.

La polarité cellulaire est une caractéristique commune à tous les organismes. Jusqu’à récemment, il était assumé que la sécrétion de protéines vers des domaines polaires de la cellule végétale se faisait de façon non polarisée, mais ce point de vue a été re-étudié, la sécrétion est polarisée mais la dynamique, les voies de traficempruntées et les mécanismes sont toujours inconnus. Précédemment, mon laboratoire d’accueil a caractérisé un enrichissement en sphingolipides contenant des acides gras à très longues chaines (VLCFAs) au niveau d’un sous-domaine du trans-Golgi Network (TGN) appelé Vésicules de Sécrétions (SVs). Plus précisément, il a été montré que la longueur des acides gras des sphingolipides jouait un rôle critique dans la sécrétion du transporteur d’auxine PIN2 des SVs vers des domaines polaires de la membrane plasmique. Pendant ma thèse, je me suis intéressé à la question suivante : comment les sphingolipides agissent-t-ils au TGN? En identifiant le protéome des SVs, ainsi qu'en utilisant des outils génétiques et pharmacologiques en combinaison avec la visualisation de marqueurs lipidiques, j'ai pu identifier que les sphingolipides agissent sur l’homéostasie des phosphoinositides en mettant en avant un lien fonctionnel entre ces deux classes de lipides au sein de la cellule végétale. En utilisant un set de marqueurs des phosphoinositides (PIPs), j’ai pu montrer que les sphingolipides ciblent principalement le phosphatidyl-inositol-3-phosphate, PI(3)P et le phosphatidylinositol- 4-phosphate, PI(4)P. De plus, mon analyse protéomique a montré que la localisation d'un ensemble de protéines liées aux PIPs était diminuée dans les SVs/TGN immunopurifiées quand la composition des sphingolipides est altérée. Mes résultats nous forcent à revoir notre vision de la dynamique des lipides au niveau des membranes, et suggère l’idée que la dynamique de remodelage de la composition d’une classe de lipide, les phosphoinositides, peut être modulée par une autre classe de lipide, les sphingolipides. / Cell polarity is a defining feature of all organisms. Until very recently, it was thought that delivery of proteins to polar domains of root epidermal cells plasma membrane was non-polar, but this view has been re-examined, the delivery is polar but the dynamics, the paths taken, and the mechanisms are unknown. My host team previously characterised an enrichment of Very-Long-Chain-Fatty-Acids (VLCFAs)-containing sphingolipids at the site of secretory vesicles (SVs) sub-domain of the trans-Golgi Network (TGN). Moreover, the length of sphingolipids acyl-chain was found to play a critical role in secretory sorting of the auxin carrier PIN2 from SVsassociated TGN to apical polar domain of the plasma membrane (PM). During my PhD, I addressed the following question: how sphingolipids act at SVs/TGN? Using proteomics of SVs, genetics and pharmacological tools in combination with visualisation of lipid probes we could identify that sphingolipids act on phosphoinositides (PIPs) homeostasis establishing a new functional link between these two lipids in plant cells. Using a set of multi-affinity fluorescent PIPs probes I could show that sphingolipids target phosphatidylinositol-3-phosphate (PI3P) and phosphatidylinositol-4-phosphate (PI4P). Moreover, my proteomic analyses show that several PIPs-related proteins are downregulated in immuno-purified TGN-associated SVs when the sphingolipid composition is altered pharmacologically. My results force the reassessment of our view of lipid membranes dynamics and highlight the idea that dynamic remodelling of the composition of one lipid class, the phosphoinositides, can be modulated by another lipid class, the sphingolipids.

Infants born prematurely are a vulnerable population with diverse nutritional needs to battle their increased risk of gastrointestinal (GI) diseases. Human milk is considered the 'gold standard' of infant nutrition. Human milk not only provides nutrition for newborn growth, but contains bioactive components which contribute to GI maturation, immune protection and neurological development. Among these bioactive components are extracellular vesicles known as exosomes. Exosomes are double-lipid membrane vesicles containing mRNA, microRNA and proteins, secreted by cells as a form of cell-to-cell communication. Human milk exosomes contain immune-related microRNA and proteins that withstand in vitro simulated human digestion, suggesting that signals are being delivered to the cells residing in the GI tract of a newborn. In premature birth, disruption of GI tract maturation predisposes the infant to increased susceptibility of GI inflammatory diseases. To prevent inflammation, immune tolerance in the GI tract of premature infants should be promoted and I hypothesized that exosomes differ between preterm and term milk, and may contribute to the anti-inflammatory effects of human milk. Human milk exosomes from mothers who gave birth to term or preterm infants were characterized based on size, surface protein markers and total protein. Preterm milk exosomes contained a more diverse protein profile. The effects of milk exosomes on intestinal epithelial cells were observed in an in vitro model using Caco-2/15 cells. Milk exosomes were able to attenuate the inflammatory response induced by heat-killed bacteria as measured by the transcription of pro-inflammatory cytokines.

Análise proteômica da matriz do esmalte nos estágios de secreção e maturação em camundongos susceptíveis ou resistentes à fluorose dentária, expostos cronicamente ao fluoreto através da água de beber. Os mecanismos pelos quais a ingestão excessiva de fluoreto (F) durante a amelogênese levam à fluorose dentária ainda não são precisamente conhecidos. Tem sido demonstrado que determinadas linhagens de camundongos são mais susceptíveis que outras à fluorose dentária, o que faz destas linhagens o modelo ideal para se estudarem os fenômenos moleculares envolvidos nesta patologia. No presente estudo, foi empregada uma abordagem proteômica para avaliar alterações na expressão de proteínas da matriz do esmalte dentário nos estágios de secreção e maturação, em duas linhagens de camundongos com diferentes susceptibilidades à fluorose (A/J, susceptível e 129P3/J, resistente). Camundongos de ambos os gêneros, representantes das linhagens 129P3/J (n=200) e A/J (n=200) foram distribuídos em dois grupos para cada linhagem, que receberam ração com baixa concentração de F e água de beber contendo 0 (controle) ou 50 mg/L F por 6 semanas. A concentração de F foi analisada no plasma e no esmalte dos incisivos. Para a análise proteômica, foi realizada a raspagem da matriz do esmalte dos incisivos, nos estágios de secreção e maturação. Para a extração das proteínas do esmalte, foram pesados 15 mg de pó da matriz do esmalte, aos quais foi adicionado 1 mL de tampão de lise contendo uréia 7 M, tiouréia 2 M, CHAPS 4 %, DTT 1 %, anfólitos carreadores 0,5 % pH 3-10 e um coquetel de inibidores de proteases. As proteínas do esmalte extraídas para cada grupo foram separadas pela técnica de eletroforese bidimensional e posteriormente submetidas a LC-ESI-MS/MS. A concentração média (±DP) de F encontrada no plasma dos camundongos foi de 0,023±0,010 e 0,019±0,007 mg/L para os animais do grupo controle, das linhagens A/J e 129P3/J, respectivamente, e de 0,151±0,043 e de 0,252±0,060 mg/L de F para os animais das linhagens A/J e 129P3/J, respectivamente, tratados com água contendo 50 mg/L de F. A ANOVA a 2 critérios revelou que houve diferença significativa entre os tratamentos (F= 658,0, p<0,0001), mas não entre as linhagens (F=3,3 p=0,075), tendo havido interação significativa entre estes critérios (F=16,50, p=0,0002). Já a concentração média (±DP) de F incorporado no esmalte dos incisivos dos camundongos foi 471,4±215,8 mg/kg e 151,7±58,8 mg/kg para os animais do grupo controle das linhagens 129P3/J e A/J, respectivamente, e 2711,2±1019,2 mg/kg, 1756,9±921,6 mg/kg para os animais das linhagens 129P3/J e A/J, respectivamente, tratados com água contendo 50 mg/L de F. A ANOVA a 2 critérios encontrou diferença significativa entre as linhagens (F=11,36, p=0,0016) e entre os tratamentos (F=103,50, p<0,0001), sem interação significativa entre ambos (F=2,82, p=0,1004). Os resultados proteômicos mostraram redução na abundância de proteínas no estágio de maturação, quando comparado com o de secreção. Foi observado que o tratamento com F aumentou consideravelmente o número de spots proteicos detectados em ambos os estágios, sendo que este aumento foi maior para os animais da linhagem A/J, indicando uma tentativa de se combater os efeitos deletérios do F e reforçando a maior susceptibilidade aos seus efeitos desta linhagem. A identificação das proteínas com expressão diferencial revelou que tanto a linhagem quanto o tratamento com F levaram à expressão diferencial de proteínas pertencentes a todas as categorias funcionais. / The mechanisms by which excessive ingestion of fluoride (F) during amelogenesis leads to fluorosis are still not precisely known. It has been shown that certain strains of mice are more susceptible to dental fluorosis than others, which turns these strains the ideal model for studying the molecular phenomena involved in this pathology. In the present study, we employed a proteomic approach to identify and evaluate changes in protein expression of secretory and maturation-stage enamel matrix in two strains of mice with different susceptibilities to dental fluorosis (A/J, susceptible and 129P3/J, resistant). Mice of both genders, from 129P3/J (n=200) and A/J (n=200) strains were divided into two groups for each strain. They received a low-F diet and drinking water containing 0 (control) or 50 mg/L F for 6 weeks. The F concentration was analyzed in plasma and enamel incisors. For proteomic analysis, the enamel matrix of secretory and maturation stages (incisors) was scrapped. For the extraction of enamel proteins, 1 ml of lysis buffer containing 7 M urea, 2 M thiourea, 4% CHAPS, 1% DTT, 0.5% ampholytes carriers pH 3-10 and a cocktail of protease inhibitors was added to 15 mg of enamel matrix powder. The enamel proteins extracted for each group were separated by two-dimensional electrophoresis and subsequently subjected to LC-ESIMS/ MS. The mean (± SD) F concentrations found in plasma were 0.023 ± 0.010 and 0.019 ±0.007 mg/L for the control group, A/J and 129P3/J strains, respectively; and 0.151 ± 0.043 and 0.252 ± 0.060 mg/L F for A/J and 129P3/J mice, respectively, treated with water containing 50 mg/L F. Two-way ANOVA revealed significant differences between treatments (F = 658.0, p <0.0001), but not between strains (F = 3.3 p = 0.075), with was significant interaction between these criteria (F = 16.50, p = 0.0002). The mean (± SD) F concentrations in the enamel of the incisors were 471.4 ± 215.8 mg/kg and 151.7 ± 58.8 mg/kg for the control group of 129P3/J and A/J strains, respectively; and 2711.2 ± 1019.2 mg/kg and 1756.9 ± 921.6 mg/kg for 129P3/J and A/J mice, respectively, treated with water containing 50 mg/L F. Two-way ANOVA detected significant differences between the strains (F=11.36, p=0.0016) and between treatments (F=103.50, p <0.0001), without significant interaction between these criteria (F=2.82, p=0.1004). The proteomic results revealed a reduction in the abundance of proteins in the maturation stage, as compared with the secretory stage. Treatment with F greatly increased the number of protein spots detected in both stages. This increase was greater for A/J mice, indicating an attempt to fight the deleterious effects of F and, thus, reinforcing the susceptibility of this strain to the effects of F. The identification of differentially expressed proteins revealed that both the strain and the treatment with F led to differential expression of proteins belonging to all functional categories.