Background: Periodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets. Methods: Two periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis. Results: We produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three “master” immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways. Conclusion: This study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.

Huntington disease (HD) is a devastating and fatal neurodegenerative disease. At the moment, no disease modifying therapies are available, with only symptomatic treatment offered to alleviate psychiatric and some types of motor deficits. As a result, many people will continue to suffer and die from this disease. Small molecule therapies have failed to provide benefit in HD, necessitating more complex gene therapy approaches and the identification of less traditional therapeutic targets. A previous study demonstrated that preventing cleavage of the huntingtin (HTT) protein, the protein that when mutated causes HD, by caspase 6 (C6) at amino acid 586 prevents the onset of disease in transgenic HD model mice. This suggests that inhibiting the toxicity initiated by N586 cleavage could be a promising therapeutic strategy, but a safe and specific way to do this in humans has not been identified. General C6 inhibition is not a feasible strategy due to the vital functions it plays throughout life. Thus, the purpose of this study was to investigate whether the C6 cleavage fragment of HTT, N586, is itself a toxic species of HTT or if it initiates a toxic proteolytic pathway in order to identify more viable therapeutic strategies for HD. To accomplish this, we are using novel and highly sensitive immunoprecipitation and flow cytometry (IP-FCM) protein detection assays, specific for the N586 neoepitope of HTT, to evaluate the in vivo persistence of N586 in HD model mice. If N586 is detected, it is likely that it is itself toxic and promoting its degradation may be beneficial. Conversely, if it is not detected, N586 cleavage likely initiates a toxic degradation pathway and promoting its stability may be beneficial. The results of these studies have the potential to define new therapeutic strategies for HD that can be addressed more specifically than generalized C6 inhibition for the prevention of N586-mediated toxicity. The selective targeting of N586 toxicity, either to promote or prevent its degradation depending on our results, would ensure that therapeutic activity is restricted to HTT and reduce the potential for deleterious off-target effects

No description available.

On note un taux élevé de résistance aux traitements dans la leucémie myéloïde aiguë (LMA). Cette résistance peut être associée aux altérations de TP53. Les « ubiquitin specific peptidases » (USP) sont impliquées dans plusieurs cancers mais leurs rôles ne sont pas élucidés dans les LMA. L’analyse de l’expression génique par RT-PCR quantitative de 21 USP et des gènes de l’axe USP7-MDM2-TP53-CDKN1A dans 111 échantillons de LMA a montré une dérégulation de USP44, USP1, USP28 et CDKN1A dans respectivement 72%, 44%, 25% et 42% des cas. CDKN1A, une cible importante de TP53, pourrait avoir un rôle dans la résistance au traitement. Nous avons développé un modèle expérimental pour évaluer la réponse des cellules leucémiques à la doxorubicine et au nutlin 3, un modulateur non génotoxique de TP53, selon l’expression initiale de CDKN1A. Ce travail préliminaire suggère que certains membres de la famille des USP et CDKN1A pourraient représenter de nouvelles cibles thérapeutiques dans les LMA. / There is a high rate of drug resistance in acute myeloid leukemia (AML) which may be associated with TP53 alterations. The « Ubiquitin specific peptidases » (USP) are involved in several cancers but their roles in AML are not elucidated. Gene expression analysis of 21 USP and genes of the USP7-MDM2-TP53-CDKN1A axis by quantitative RT-PCR in 111 AML samples, showed a deregulation of USP44, USP1, USP28 and CDKN1A in respectively 72%, 44%, 25% and 42% of cases. CDKN1A, an important TP53 target, may have a role in treatment resistance. We have developed an experimental model to assess the response of leukemic cells to doxorubicin and nutlin 3, a non genotoxic TP53 modulator, in relation to the CDKN1A expression level. This preliminary work suggests that some members of the USP family and CDKN1A could represent novel therapeutic targets in AML.

L'avancée technologique dans les nanosciences a permis le développement d'une large gamme de matériaux nanostructurés aux applications biomédicales. Ces outils, constitués de matériaux différents, ont été développés à des fins de diagnostic et de thérapie pour réaliser notamment le ciblage, le marquage cellulaire, l'imagerie médicale et pour concevoir des systèmes de délivrance de médicaments pour le traitement de cancers ou de maladies infectieuses. La création de nano-objets regroupant l'ensemble de ces propriétés de type théranostique constitue une étape essentielle vers un traitement personnalisé et non invasif des cancers solides de petite taille. Dans cette thèse, une première partie est consacrée à la mise au point et à l'utilisation de nanoparticules de silice mésoporeuse pour le traitement des rétinoblastomes. Ce travail visait à améliorer la thérapie photodynamique en augmentant la biodisponibilité de molécules actives dans les cellules cancéreuses par deux stratégies : leur vectorisation par un nano-objet et le ciblage spécifique des cellules cancéreuses. Pour cela, les profils d'expression des récepteurs du mannose ont été analysés et les récepteurs MRC2 et CD209 se sont révélés être de bons candidats pour une thérapie ciblée du rétinoblastome. La deuxième partie des recherches réalisées s'oriente vers l'élaboration de différents nanosystèmes pour le traitement des cancers et l'imagerie médicale. Premièrement, des nanotransporteurs de principe actif à relargage pH-sensible, structurés à partir de nanoparticule de silice mésoporeuse, ont été étudiés. Ces systèmes de délivrance, sous l'effet de stimuli internes, se sont révélés être très efficaces in vitro et ex vivo pour le traitement du cancer du côlon. Deuxièmement, le potentiel de délivrance contrôlée de molécules anticancéreuses renfermées dans des nanomachines soumises à une activation externe biphotonique, a été démontré sur des cellules de cancer du sein. Enfin, les propriétés de nanoparticules magnétiques de polymères de coordination cyano-pontés se sont révélées très prometteuses pour une utilisation en tant que nouvel agent de contraste intravasculaire pour l'imagerie par résonance magnétique in vivo. / The technological advance in nanoscience has allowed the development of a wide range of nanostructured materials for biomedical applications. These tools, composed of different materials, have been developed for diagnosis and therapy, in particular to achieve targeting, cellular labeling, medical imaging and to design drug delivery systems for the treatment of cancer or infectious diseases. The elaboration of nano-tools possessing these theranostic properties would be a major step towards personalized and non-invasive treatments of small solid cancers.In this thesis, the first part is devoted to the development and the application of mesoporous silica nanoparticles for the treatment of retinoblastoma. The aim of this work was to improve photodynamic therapy by increasing the bioavailability of active molecules in cancer cells following two strategies: their vectorization through nanodevice and the specific targeting of cancer cells. For this, expression profiles of mannose receptors were analyzed and both MRC2 and CD209 receptors were found to be interesting candidates for targeted therapy of retinoblastoma.The second part corresponds to a multidisciplinary approach focused on the research of different nanosystems designed for cancer treatment and medical imaging. We first studied pH-operated hybrid silica nanocarriers designed for drug release. Under internal stimuli, these delivery systems have shown to be very efficient in vitro and ex vivo against colon cancer. Then, we demonstrated the potential of nanoimpellers designed for anticancer drug delivery mediated by external two-photon activation on breast cancer cells. Finally, we report the promising use in vivo of new magnetic cyano-bridged coordination polymer nanoparticles as an efficient intravascular magnetic resonance imaging contrast agent.

No description available.

No description available.

Submitted by SARA DE SOUZA COSTA null (sarah_sc_0705@hotmail.com) on 2017-03-30T13:36:06Z No. of bitstreams: 1 Dissertação Sara de Souza Costa.pdf: 2766240 bytes, checksum: 20b447fe5bf3c49e40aa0b5fdf4dff1f (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2017-04-06T13:29:26Z (GMT) No. of bitstreams: 1 costa_ss_me_sjrp.pdf: 2766240 bytes, checksum: 20b447fe5bf3c49e40aa0b5fdf4dff1f (MD5) / Made available in DSpace on 2017-04-06T13:29:26Z (GMT). No. of bitstreams: 1 costa_ss_me_sjrp.pdf: 2766240 bytes, checksum: 20b447fe5bf3c49e40aa0b5fdf4dff1f (MD5) Previous issue date: 2017-03-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / As lesões uterinas são causas importantes de desconforto, infertilidade e óbito entre as mulheres no Brasil e no mundo. O câncer de endométrio é um tumor maligno frequente e sua incidência vem aumentando nas últimas décadas. Enquanto, o tumor uterino benigno mais comum, o leiomioma, acomete cerca de 40% das mulheres na idade reprodutiva, sendo relacionado à menorragia, dismenorreia e infertilidade. Investigações indicam que o microambiente tumoral é crucial para o avanço do câncer, sendo caracterizado, principalmente, pela composição alterada da matriz extracelular, alta densidade de microvasos e abundância de células inflamatórias, como mastócitos (MCs). MCs desgranulados liberam fatores quimiotáticos e proteases, como triptase e quimase, para o meio extracelular, contribuindo na degradação da matriz extracelular, promoção da angiogênese, propiciando ambiente favorável para invasão tumoral e remodelação tecidual por meio de proteólises seletivas na matriz e ativação de metaloproteinases. Outro aspecto importante no crescimento tumoral é a proteína anti-inflamatória Anexina A1 (ANXA1), relacionada à regulação dos processos de crescimento e migração/invasão celular, sendo seus efeitos mediados por receptores para peptídeos formilados (FPRs), especialmente FPR1 e FPR2. Diante da importância dos MCs e da ANXA1/FPR no desenvolvimento tumoral, o objetivo desta investigação foi analisar a heterogeneidade dos MCs e a expressão das proteínas ANXA1, FPR1 e FPR2 em biópsias humanas das variáveis clínico-patológicas de útero normal: hiperplasia endometrial simples (HES), adenomiose, leiomiomas e adenocarcinoma (ADC) endometrial de graus I e II. Os MCs foram quantificados de acordo com seu estado de ativação e expressão das proteases triptase e quimase. A expressão da ANXA1 e seus receptores FPR1 e FPR2 nos MCs e tecidos uterinos foram analisadas nas diferentes biópsias estudadas. Nossos resultados mostraram MCs intactos e desgranulados, no endométrio e miométrio normais e aumentados na HES, margens tumorais nos leiomiomas, adenomiose e ADC endometrial de graus I e II, e diminuídos significantemente na região tumoral do leiomioma. Com relação à heterogeneidade, os MCs triptase-positivos foram observados em maior quantidade. As expressões endógenas da ANXA1 e do FPR1 foram observadas nos tecidos uterinos e MCs, com ausência para o FPR2. As modulações dos MCs, da proteína ANXA1 e de modo específico do receptor FPR1, nas variáveis clínico-patológicas das lesões uterinas investigadas indicam o envolvimento dessas células e a interação ANXA1/FPR1 no desenvolvimento de inflamação e neoplasia uterina. / Uterine lesions are important causes of discomfort, infertility and death among women in Brazil and in the world. Endometrial cancer is a frequent malignant tumor and its incidence has been increasing in the last decades. Besides, the most common benign uterine tumor, leiomyoma, affects about 40% of women at reproductive age, being related to menorrhagia, dysmenorrhea and infertility. Investigations indicate that the tumor microenvironment is crucial for the advancement of cancer, being characterized mainly by the altered composition of the extracellular matrix, high microvessel density and abundance of inflammatory cells, such as mast cells (MCs). Degranulated MCs release chemotactic and protease factors, such as tryptase and chymase, to the extracellular medium, contributing to the degradation of the extracellular matrix, promoting angiogenesis, providing a favorable environment for tumor invasion and tissue remodeling through selective proteolysis in the matrix and activation of metalloproteinases. Another important aspect of tumor growth is the anti-inflammatory protein Annexin A1 (ANXA1), related to the regulation of growth and migration / invasion processes, and its effects mediated by receptors for formylated peptides (FPRs), especially FPR1 and FPR2. The objective of this investigation was to analyze the heterogeneity of the MCs and the expression of the ANXA1, FPR1 and FPR2 proteins in human biopsies of clinical-pathological variables of normal uterus: simple endometrial hyperplasia (HES), adenomyosis, leiomyomas and endometrial adenocarcinoma (ADC) of grades I and II. MCs were quantified according to their state of activation and expression of tryptase and chymase proteases. Expression of ANXA1 and its FPR1 and FPR2 receptors in the MCs and uterine tissues were analyzed in the different biopsies studied. Our results showed intact and degranulated MCs in the normal endometrium and myometrium and increased MCs in HES, tumor margins in leiomyomas, adenomyosis and endometrial ADC of grades I and II, but significantly decreased in the leiomyoma tumor region. In relation to the heterogeneity, it was observed that the tryptase-positive MCs were observed in greater quantity. Endogenous expressions of ANXA1 and FPR1 were observed in uterine tissues and MCs, but absent for FPR2. Modulations of MCs and ANXA1 protein expression and the specificity of FPR1 receptor immunolabeling in the clinical-pathological variables of the investigated uterine lesions indicate the involvement of these cells and the interaction ANXA1/FPR1 in the development of inflammation and uterine neoplasia.

The pre-symptomatic stage of neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) occurs several decades before the clinical onset. Changes in the lysosomal network, i.e. the autophagosomal, endosomal and lysosomal vesicular system, are among the first alterations observed. There are currently no treatments to slow or cure neurodegenerative diseases, and there is a great need for discovery of treatment targets in cellular pathways where pathology pre-dates the neuronal death. It is also crucial to be able to diagnose neurodegenerative diseases earlier, both to enable early intervention treatment and aid in selecting clinical trial populations before the patient has widespread pathology. This thesis aims at investigating the potential of lysosomal network proteins as biomarkers and therapeutic targets in neurodegenerative disease. A targeted search for lysosomal network proteins was performed in cerebrospinal fluid (CSF) from AD patients, and seven proteins: early endosomal antigen 1 (EEA1), lysosomal-associated membrane proteins 1 and 2 (LAMP-1, LAMP-2), lysozyme, microtubule-associated protein 1 light chain 3 (LC3), Rab3 and Rab7, were elevated. The levels of EEA1, LAMP-1, LAMP-2, LC3, lysozyme and Rab3 were also measured in CSF from parkinsonian syndrome patients: PD, clinically diagnosed 4-repeat tauopathy, pathologically confirmed corticobasal degeneration (CBD) and pathologically confirmed progressive supranuclear palsy (PSP) patients. LAMP-1 and LAMP-2 were decreased in PD. LC3 and lysozyme levels were increased in 4-repeat tauopathy patients. EEA1 was decreased and lysozyme increased in PSP, and LAMP-1, LAMP-2, LC3 and lysozyme were increased in CBD. The lysosomal network proteins had different CSF protein profiles in all the parkinsonian syndromes, as well as in AD. It should be emphasized that only a select few of the lysosomal network proteins were observed to be changed, rather than a general change in lysosomal network proteins, which implicates the involvement of these seven proteins in specific pathological processes. The most interesting candidates, LAMP-2 and lysozyme, were selected for further study for their involvement in the pathology of AD. Lysozyme was found to co-localise with Aβ plaques in AD patients and overexpression prolonged survival and improved the activity in a Drosophila model of AD. Lysozyme was found to alter the aggregation pathway of Aβ1-42, to counteract the formation of toxic Aβ species and to protect from Aβ1-42 induced cell toxicity. Aβ1-42 in turn was found to increase the expression of lysozyme in both neuronal and glial cells. These data suggest that lysozyme levels rise in AD as a compensatory response which is protective against Aβ associated toxicity. LAMP-2 mRNA and protein were found increased in brain areas relevant for AD pathology and various cellular models showed complex involvement of LAMP-2 in Aβ related pathology, with extensive crosstalk between LAMP-2 and Aβ. Exposure to oligomeric Aβ1-42 caused an upregulation of LAMP-2 and in turn, overexpression of LAMP-2 caused a reduction in secreted levels of Aβ1-42, as well as changing the generation pattern of Aβ and affecting clearance and secretion of Aβ1-42. These data indicate that the increased levels of LAMP-2 in AD could be an attempt to regulate Aβ generation and secretion. In summary, this thesis reports that utilising lysosomal network proteins as biomarkers and novel therapeutic targets for neurodegenerative diseases holds great promise.

Les cardiolipines (CL) sont des phospholipides possédant de nombreux rôles dans la structure et le fonctionnement des mitochondries. Elles sont, par exemple, impliquées dans la stabilisation des complexes des oxydations phosphorylantes, la fusion/fission des membranes mitochondriales, l’import de protéines mitochondriales, la biogénèse des centres fer-soufre (Fe-S), l’apoptose, la protection des mitochondries contre le stress oxydatif…L’ensemble de ces fonctions nécessitent que les chaînes d’acides gras de la CL soient majoritairement insaturées. Le maintien de cette composition en chaînes insaturées requiert une activité acyltransférase portée par la protéine tafazzine, qui est codée par le gène nucléaire TAZ. Des mutations dans ce gène sont la cause du syndrome de Barth (BTHS), qui se caractérise notamment par des myopathies cardiaques et squelettiques, une neutropénie (responsable de nombreuses infections) et des défauts de la chaîne respiratoire. Malgré des progrès considérables dans la compréhension des mécanismes conduisant à la pathogénicité, il n’existe toujours aucune thérapie pour traiter cette maladie. Nous avons donc utilisé la levure Saccharomyces cerevisiae, chez qui la voie de remodelage des CL par la tafazzine est bien conservée, pour modéliser le BTHS et, ainsi non seulement étudier les mécanismes moléculaires sous-jacents de cette maladie, mais aussi identifier différentes voies thérapeutiques potentielles (suppresseurs génétiques et molécules pharmacologiques). Nous avons tout d’abord construit une levure délétée pour le gène orthologue TAZ (TAZ1 chez la levure), la souche Δtaz1. En accord avec des études précédentes, la souche Δtaz1 présente une diminution quantitative de la CL accompagnée d’un changement qualitatif des chaînes d’acides gras1,2 (plus d’acides gras saturés et moins d’insaturés). Nous montrons aussi que cette levure mutante a un défaut de croissance en milieu respiratoire à température élevée (36°C) ainsi que des défauts dans plusieurs composants impliqués dans les oxydations phosphorylantes2. De façon intéressante, alors que le défaut primaire (diminution des CL et changement qualitatif des chaines d’acide gras) est toujours présent, nous montrons que les oxydations phosphorylantes sont restaurées dans la souche Δtaz1 surexprimant Odc1p2, un transporteur mitochondrial d’intermédiaires du cycle de Krebs, ou par plusieurs composés chimiques. Plusieurs de ces drogues sauvant le mutant, dont la cycloheximide, sont des inhibiteurs partiels de la synthèse protéique cytosolique. Cet effet a été confirmé génétiquement par des mutations affectant les ribosomes cytosoliques. L’ensemble des résultats suggère qu’un défaut au niveau des CL provoquerait un stress protéostatique probablement impliqué dans le processus pathologique. / The phospholipid cardiolipin (CL) has many roles in mitochondrial structure and function, ranging from assembly/stability and functioning of the oxidative phosphorylation (OXPHOS) system, fusion and fission of mitochondrial membranes, mitochondrial protein import, iron-sulfur (Fe-S) biogenesis, apoptosis, and protection of mitochondria against oxidative damage. The maintenance of a proper unsaturated acyl chain composition of CL involves the acyltransferase tafazzin in which mutations cause Barth syndrome (BTHS), resulting in cardiac and skeletal myopathy, cyclic neutropenia and respiratory chain defects. Despite considerable progress in the understanding of the underlying pathogenic mechanisms, there are still no effective therapies to treat this disease. We are using the yeast Saccharomyces cerevisiae, in which the tafazzin-based cardiolipin remodeling pathway is conserved, as a model system for the exploration of potential therapeutic pathways against BTHS, by way of genetic suppressors and chemical screening. We first constructed a yeast strain lacking the orthologous taffazin gene (Δtaz1). Consistent with previous studies, our Δtaz1 yeast failed to grow on non-fermentable carbon sources at elevated temperatures (36°C) and exhibited defects in several components of the mitochondrial respiratory system. Interestingly, we found that oxidative phosphorylation was fully restored in Δtaz1 yeast by overexpressing Odc1p [1]-a mitochondrial carrier that transports Krebs cycle intermediates- and by a number of chemical compounds. Some of the rescuing drugs, especially cycloheximide, act by partially inhibiting cytosolic protein synthesis leading to a full recovery of oxidative phosphorylations. Our findings identify potential cellular components and pathways for the pharmacological treatment of BTHS patients.