AG to A transition at position -76 in the promoter region of the apoAI gene was previously identified, and the A-76 has been shown to be associated with high apoAI levels. The functional significance of the point mutation was assessed by analysing the DNA-protein binding and promoter activities of the different alleles. This data would suggest that the point mutation alters the function of the apoAI promoter as gel retention assays revealed that the G fragment (-140 to +10) formed an extra DNA-protein complex compared to the A fragment (-140 to +10). Concurrent with the altered DNA-protein interaction between the G and the A fragments, the transcriptional activities of the apoAI gene were found to also be altered. CAT assays have indicated a 1.91 fold increase in promoter activity of the A fragment as compared to the G fragment (-256 to +397). The difference in promoter activity was, however, highly dependent on the particular fragment used, as no difference was observed between the alleles when a fragment {-256 to +68) was used. In this study elements were identified in the region +68 to +397 that causes a reduction in the promoter activity of the G allele by 3.6 fold, whilst reducing the A allele activity by 2 fold. This data would suggest that the point mutation functionally alters the apoAI promoter activity via its interaction with other sequences especially in the region +68 to +397.

Antibiotic-resistant bacterial infections account for millions of human fatalities each year, with drug susceptibility testing (DST) affordability being limited by instrumentational constraints, monetary and/or time expenses. Molecular diagnostics performed at the point of care can provide a solution. Split probes coupled with label-free reporters like Fluorescent Light-up APtamers (FLAPs) are promising for point-of-care DST as they offer the needed selectivity towards point mutations inducive of drug resistance. This project aims at bridging the gap in FLAP applications for molecular diagnostics with a focus on multiplexing the analysis. Due to the limited number of DNA FLAPs available, we explored the ability of one of the most efficient DNA FLAPs - dapoxyl binding aptamer (DAP) - to bind fluorogens with different spectral properties. We performed the rational mutagenesis of the DAP dye-binding core to reveal any sequence-function correlations and to identify prospective orthogonal FLAP-dye pairs. Orthogonal FLAPs were used as scaffolds to design split dapoxyl aptameric (SDA) probes, which targeted a fragment of the katG gene from Mycobacterium tuberculosis complex associated with bacterial resistance to a first-line antituberculous drug isoniazid (INH). The probes were tested to differentiate the nucleic acid targets with single-nucleotide variations corresponding to isoniazid-susceptible (INHS) and isoniazid-resistant (INHR) bacterial phenotype in a multiplex fashion. With proper optimization of the probes, they can find an application in ratiometric analysis of heterogeneous bacterial populations composed of both drug-susceptible and drug-resistant strains and thus help in initial diagnosing of infectious diseases and in monitoring the therapy outcomes.

Due to the misuse of antibiotics, multi-drug resistant (MDR) bacteria have become more rampant in our society; these MDR have given rise to diseases that are not readily curable. One such agent is the Mycobacterium tuberculosis complex, which is a causative agent of tuberculosis (TB). Timely diagnostics of the bacterial infection and detection of bacterial drug-susceptibility profiles helps to initiate the necessary treatment in a timely fashion and to limit transmission of the disease. For more affordable detection of bacterial diseases, such as TN, tag-free split aptamer probes are advantageous. This proposal aims at designing split aptamer probes for detection of point mutations in the rpoB and katG genes of M. tuberculosis that are associated with resistance to two front-line antibiotics – rifampin and isoniazid, respectively, which causes MDR-TB. The probes will be designed and tested with synthetic oligonucleotide mimics of the bacterial genes in terms of their limit of detection and selectivity in discriminating the targets with single-nucleotide substitutions.

Tesis por compendio / [EN] The determination of genetic biomarkers is progressively becoming more extended and popular, being commercialized even in kits for personalized medicine. Establishing specific genotype variations for each patient, such as single nucleotide polymorphisms (SNPs), could be a fundamental tool in the field of diagnosis, prognosis and therapy selection. However, the use of DNA testing is not fully implemented in general healthcare, mainly due to technical and economic barriers associated to the current technologies, which are limited only to specialized centers and large hospitals. In this thesis, the main goal was to overcome these obstacles by developing simpler, faster and more affordable point-of-care (POC) genotyping systems. Allele discrimination was achieved by employing isothermal enzymatic reactions, like recombinase polymerase amplification (RPA), ligation of oligonucleotides and loop-mediated isothermal amplification (LAMP). These processes were integrated to colorimetric indicators and immunoenzymatic assays, in a microarray format. Using compact discs and polycarbonate chips as platforms, the detection was achieved through widespread electronics, like disc-reader, flatbed scanner and smartphone. To demonstrate their capacities, the resulting systems were applied for identifying SNPs in human samples, associated to therapies for tobacco smoking cessation, major depression disorder and blood clotting-related diseases. After selecting the proper conditions, all studied strategies discriminated SNPs in samples containing as low as 100 copies of genomic DNA, with an error rate below 15%. Most importantly, the developed methods have reduced assays times varying between 70 and 140 minutes, at a cost similar to a conventional PCR-based analog, but maintaining or raising amplification efficiency and eliminating the need of specialized temperature cyclers and fluorescence scanners. In conclusion, the biosensors based in isothermal reactions and consumer electronics devices greatly improve the competitivity of POC DNA analysis. It was demonstrated that the technologies developed in this thesis could support genotyping assays in low-resource areas, such as primary healthcare centers and emerging countries. Through this democratization of genetic testing and by performing adequate association studies, molecular diagnostics and personalized medicine practices could have their application extended to the clinical routine. / [ES] La determinación de biomarcadores genéticos es cada vez más extensa y popular, estando incluso comercializándose kits para medicina personalizada. Establecer las variaciones específicas en el genotipo de cada paciente, como los polimorfismos de un solo nucleótido (SNP) podría ser una herramienta fundamental en el campo del diagnóstico, pronóstico y selección de la terapia. Sin embargo, el uso de pruebas de ADN no se encuentra completamente implementado en la atención médica general, principalmente debido a las barreras técnicas y económicas asociadas a las tecnologías actuales, limitadas solamente a centros especializados y grandes hospitales. En esta tesis, el objetivo principal fue superar estos obstáculos mediante el desarrollo de sistemas de genotipado point-of-care (POC), más simples, rápidos y asequibles. La discriminación alélica se logró mediante el uso de reacciones enzimáticas isotermas, como la amplificación de la recombinasa polimerasa (RPA), la ligación de oligonucleótidos y la amplificación isotérmica mediada por bucle (LAMP). Estos procesos se integraron a indicadores colorimétricos y ensayos inmunoenzimáticos en formato de micromatriz. Utilizando discos compactos y chips de policarbonato como plataforma de ensayo, se ha logrado la detección mediante dispositivos electrónicos de consumo, como un lector de discos, escáner documental y teléfono móvil. Para demostrar sus capacidades, los sistemas resultantes se aplicaron a la identificación de SNPs en muestras humanas, asociados a terapias antitabaquismo, para depresión y enfermedades relacionadas con la coagulación de la sangre. Tras seleccionar las condiciones adecuadas, todas las estrategias estudiadas discriminaron SNPs en muestras conteniendo tan solo 100 copias de ADN genómico, con una tasa de error inferior al 15%. Más importante, los métodos desarrollados han reducido los tiempos de ensayo a valores entre 70 y 140 minutos, a un coste similar a un análogo convencional basado en la reacción en cadena de la polimerasa (PCR), pero manteniendo o aumentando la eficiencia de amplificación y eliminando la necesidad de termocicladores y escáneres de fluorescencia. En conclusión, los biosensores basados en reacciones isotérmicas y dispositivos de electrónica de consumo mejoran en gran medida la competitividad del análisis POC de ADN. Se ha demostrado que las tecnologías desarrolladas en esta tesis podrían apoyar los ensayos de genotipado en áreas de recursos escasos, como centros de atención primaria y países emergentes. A través de esta democratización de las pruebas genéticas y realización estudios de asociación adecuados, el diagnóstico molecular y las prácticas en medicina personalizada podrían extender su aplicación a la rutina clínica. / [CA] La determinació de biomarcadors genètics és cada vegada més extensa i popular, estant fins i tot comercialitzant-se kits per a medicina personalitzada. Establir les variacions específiques en el genotip de cada pacient, com els polimorfismes d'un sol nucleòtid (SNP) podria ser una eina fonamental en el camp del diagnòstic, pronòstic i selecció de la teràpia. No obstant això, l'ús de proves d'ADN no es troba completament implementat en l'atenció mèdica general, principalment a causa de les barreres tècniques i econòmiques associades a les tecnologies actuals, limitades solament a centres especialitzats i grans hospitals. En aquesta tesi, l'objectiu principal va ser superar aquests obstacles mitjançant el desenvolupament de sistemes de genotipat point-of-care (POC), més simples, ràpids i assequibles. La discriminació al·lèlica es va aconseguir mitjançant l'ús de reaccions enzimàtiques isotermes, com l'amplificació de la recombinasa polimerasa (RPA), la lligació de oligonucleòtids i l'amplificació isotèrmica mediada per bucle (LAMP). Aquests processos es van integrar a indicadors colorimètrics i assajos inmunoenzimàtics en format de micromatriu. Utilitzant discos compactes i xips de policarbonat com a plataforma d'assaig, s'ha conseguit la detecció mitjançant dispositius electrònics de consum, com un lector de discos, escàner documental i telèfon mòbil. Per a demostrar les seues capacitats, els sistemes resultants es van aplicar a la identificació de polimorfismes en mostres humanes, associats a teràpies antitabaquisme, per a depressió i malalties relacionades amb la coagulació de la sang. Després de seleccionar les condicions adequades, totes les estratègies estudiades van ser capaces de discriminar SNPs en mostres contenint tan sols 100 còpies d'ADN genòmic, amb una taxa d'error inferior al 15%. Més important, els mètodes desenvolupats han reduït els temps d'assaig a valors entre 70 i 140 minuts, a un cost similar a un anàleg convencional basat en la reacció en cadena de la polimerasa (PCR), però mantenint o augmentant l'eficiència d'amplificació i eliminant la necessitat de termocicladors i escàners de fluorescència. En conclusió, els biosensors basats en reaccions isotèrmiques i dispositius d'electrònica de consum milloren en gran manera la competitivitat de l'anàlisi POC del ADN. S'ha demostrat que les tecnologies desenvolupades en aquesta tesi podrien donar suport als assajos de genotipat en àrees de recursos escassos, com a centres d'atenció primària i països emergents. A través d'aquesta democratització de les proves genètiques i realització estudis d'associació adequats, el diagnòstic molecular i les pràctiques en medicina personalitzada podrien estendre la seua aplicació a la rutina clínica. / [PT] A determinação de biomarcadores genéticos está tornando-se cada vez mais extensa e popular, sendo comercializada até em kits para medicina personalizada. O estabelecimento de variações específicas de genotipo para cada paciente, tais como os polimorfismo de nucleotídeo único, pode ser uma ferramenta fundamental no campo do diagnóstico, prognóstico e seleção de terapias. No entanto, o uso de testes de DNA ainda não encontra-se totalmente implementado na área de saúde geral, principalmente devido às barreiras técnicas e econômicas associadas às tecnologias atuais, limitadas apenas a centros especializados e grandes hospitais. Nesta tese, o principal objetivo foi superar esses obstáculos desenvolvendo sistemas de genotipagem point-of-care (POC) de DNA, mais simples, rápidos e acessíveis. A discriminação de alelos foi alcançada empregando reações enzimáticas isotérmicas, como amplificação por recombinase polimerase (RPA), ligação de oligonucleotídeos e amplificação isotérmica mediada por loop (LAMP). Tais processos foram integrados a indicadores colorimétricos e ensaios imunoenzimáticos, em formato micromatriz. Usando discos compactos e chips de policarbonato como plataforma de ensaio, os analitos foram detectados através de dispositivos eletrônicos de consumo, como leitor de disco, scanner de mesa e smartphone. Para demonstrar suas capacidades, os sistemas resultantes foram aplicados para identificação de polimorfismos em amostras de DNA humano, associados a terapias antitabagismo, para depressão e doenças relacionadas à coagulação do sangue. Após a seleção das condições adequadas, todas as estratégias estudadas foram capazes de discriminar SNPs em amostras contendo até 100 cópias de DNA genômico, com uma taxa de erro inferior a 15%. Mais importante, os métodos desenvolvidos reduziram o tempo de ensaio a valores entre 70 e 140 minutos, com um custo similar a um método análogo baseado em reação em cadeia da polimerase (PCR), mas mantendo ou aumentando a eficiência da amplificação e eliminando a necessidade de cicladores de temperatura e scanners de fluorescência especializados. Em conclusão, os biosensores baseados em reações enzimáticas isotérmicas e dispositivos eletrônicos de consumo incrementam grandemente a competitividade da análise POC de DNA. Foi demonstrado que as tecnologias desenvolvidas nesta tese poderiam dar suporte a ensaios de genotipagem em lugares com poucos recursos, como centros de atenção primária e países emergentes. Através desta democratização dos testes genéticos e com a realização de estudos de associação adequados, o diagnóstico molecular e as práticas de medicina personalizada poderiam ter sua aplicação extendida à rotina clínica. / The authors acknowledge the financial support received from the Generalitat Valenciana (GVA-PROMETEOII/2014/040 Project and GRISOLIA/2014/024 PhD grant) and the Spanish Ministry of Economy and Competitiveness (MINECO CTQ2013-45875-R project) / Yamanaka, ES. (2020). Isothermal-based DNA biosensors for application in pharmacogenetics [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/148366 / Compendio

Pour se défendre des effets délétères des éléments transposables, les pezizomycotina ont développé un système de défense génétique et épigénétique appelé « Repeat Induced Point Mutation » (RIP). Chez N. crassa, le RIP survient dans la cellule dicaryotique avant la caryogamie et conduit à la méthylation de novo des cytosines (5mC) inclues dans les séquences répétées de chacun des noyaux parentaux haploïdes. De plus, certaines de ces cytosines sont la cible d’un processus de mutation qui les transforme en thymines. Cette étape est suivie par la mise en place locale de l’hétérochromatine constitutive permettant une répression transcriptionnelle durable des séquences cibles du RIP au cours des divisions nucléaires. L’acteur majeur du RIP correspond à une cytosine méthyltransférase putative appelée RID (RIP Defective). Bien que son génome ne montre pas une quantité significative de 5mC, l’inactivation de PaRid chez Podospora anserina aboutit à un blocage du développement sexué survenant après la fécondation. Dans ce contexte, nous avons voulu déterminer si la fonction de PaRid dans le développement sexué consiste à éteindre l’expression de gènes cibles via l’installation de foyers d’hétérochromatine constitutive aux loci concernés. Pour ce faire, nous avons identifié les gènes PaKmt1 et PaHP1, codant respectivement l’histone méthyltransférase PaKmt1 (l’homologue de SU(VAR)39 qui catalyse la tri-méthylation du résidu H3K9 (H3K9me3) et PaHP1 (l’homologue de Heterochromatin Protein 1 qui se lie à H3K9me3). Les deux protéines interviennent dans une même voie de régulation qui aboutit à la mise en place de l’hétérochromatine constitutive. Par opposition, PaKmt6, homologue de l’histone méthyltransférase E(Z), correspond à la sous-unité catalytique du complexe PRC2 qui catalyse la marque H3K27me3 pour permettre l’établissement de l’hétérochromatine facultative. Nos résultats ont montré que l’absence de PaKmt1 et PaHP1 ne provoquent que des défauts mineurs. A l’inverse, l’inactivation du gène PaKmt6 conduit à un ensemble de défauts sévères : croissance végétative altérée, surproduction des gamètes mâles, malformations critiques des fructifications, production très réduite d’ascospores dont la germination est pour partie déficiente. Une étude d’épistasie a montré que les protéines PaRid et PaKmt6 interviennent chacune dans deux voies développementales distinctes. Par ailleurs, nous avons établi par immuno-précipitation de la chromatine les profils de distribution à l’échelle du génome entier des modifications H3K9me3, H3K27me3 et H3K4me3. Caractéristique rare, la marque H3K9me3 colocalise avec H3K27me3 sur des gènes transcriptionnellement réprimés et les séquences répétées ripées. Conformément à sa fonction canonique, H3K4me3 est présente en 5’ des gènes transcrits et est exclue des domaines H3K9me3 et H3K27me3. Comme attendue, PaKmt6 est essentielle à la mise en place de la marque H3K27me3, mais, de manière surprenante, elle serait aussi impliquée dans le dépôt et/ou le maintien d’une partie des marques H3K9me3, dévoilant ainsi une voie de méthylation non canonique de ces résidus. / In pezizomycotina, transposable elements are targeted by a genome defense system named Repeat Induced Point Mutation (RIP). First described in Neurospora crassa, RIP occurs before karyogamy in each parental haploid nucleus of the dikaryotic cells and results, within the repeats, in de novo methylation of cytosine (5mC) and mutations, mainly C to T transitions. This initial step triggers local assembly of constitutive heterochromatin, which allows transcriptional gene silencing. RID (RIP Defective) is a putative cytosine methyltransferase essential for RIP. Despite the absence of 5mC in its genome, PaRid inactivation in Podospora anserina results in sexual reproduction arrest right after fertilization. In this context, we asked whether PaRid is required to silence expression of some of sexual development-specific genes by nucleation of constitutive heterochromatin. To this end, we identified PaKmt1 and PaHp1 genes encoding respectively the histone methyltransferase PaKmt1 (SU(VAR)39 homologue protein) and the heterochromatin protein 1 (PaHP1). To assemble constitutive heterochromatin, PaKmt1 catalyses tri-methylation of H3K9 (H3K9me3), latter on bound by PaHP1. By contrast, the E(Z) histone methyltransferase homologue PaKmt6, as part of the PRC2 complex, catalyses tri-methylation of H3K27 (H3K27me3) to form facultative heterochromatin. Our results showed that loss of either PaKmt1 or PaHP1 does not cause major defects. Conversely, PaKmt6 gene inactivation results in severe defects: altered mycelium and vegetative growth rate, overproduction of male gamete, development of crippled fructifications, reduced production ascospores, part of which does not germinate. Furthermore, epistatic study showed that PaRid and PaKmt6 likely act in two different developmental pathways, with respect to sexual reproduction. In addition, using chromatin immuno-precipitation we characterized H3K9me3, H3K27me3 and H3K4me3 genome-wide distribution patterns. We observed an uncommon overlapping distribution between H3K9me3 and H3K27me3 on transcriptionally repressed genes and RIP target repeats. As expected, H3K4me3 localizes in 5’ of the transcribed genes and is excluded from the H3K9me3 and H3K27me3 domains. As expected, PaKmt6 is essential for H3K27me3 modification, but surprisingly, could also be responsible for some of the H3K9me3 setting up or maintenance.

A great challenge in bioinformatics is to accurately predict protein structure and function from its amino acid sequence, including annotation of protein domains, identification of protein disordered regions and detecting protein stability changes resulting from amino acid mutations. The combination of bioinformatics, genomics and proteomics becomes essential for the investigation of biological, cellular and molecular aspects of disease, and therefore can greatly contribute to the understanding of protein structures and facilitating drug discovery. In this thesis, a PREDICTOR, which consists of three machine learning methods applied to three different but related structure bioinformatics tasks, is presented: using profile Hidden Markov Models (HMMs) to identify remote sequence homologues, on the basis of protein domains; predicting order and disorder in proteins using Conditional Random Fields (CRFs); applying Support Vector Machines (SVMs) to detect protein stability changes due to single mutation. To facilitate structural instability and disease studies, these methods are implemented in three web servers: FISH, OnD-CRF and ProSMS, respectively. For FISH, most of the work presented in the thesis focuses on the design and construction of the web-server. The server is based on a collection of structure-anchored hidden Markov models (saHMM), which are used to identify structural similarity on the protein domain level. For the order and disorder prediction server, OnD-CRF, I implemented two schemes to alleviate the imbalance problem between ordered and disordered amino acids in the training dataset. One uses pruning of the protein sequence in order to obtain a balanced training dataset. The other tries to find the optimal p-value cut-off for discriminating between ordered and disordered amino acids.  Both these schemes enhance the sensitivity of detecting disordered amino acids in proteins. In addition, the output from the OnD-CRF web server can also be used to identify flexible regions, as well as predicting the effect of mutations on protein stability. For ProSMS, we propose, after careful evaluation with different methods, a clustered by homology and a non-clustered model for a three-state classification of protein stability changes due to single amino acid mutations. Results for the non-clustered model reveal that the sequence-only based prediction accuracy is comparable to the accuracy based on protein 3D structure information. In the case of the clustered model, however, the prediction accuracy is significantly improved when protein tertiary structure information, in form of local environmental conditions, is included. Comparing the prediction accuracies for the two models indicates that the prediction of mutation stability of proteins that are not homologous is still a challenging task. Benchmarking results show that, as stand-alone programs, these predictors can be comparable or superior to previously established predictors. Combined into a program package, these mutually complementary predictors will facilitate the understanding of structural instability and disease from protein sequence.

Orientadores: Fabíola Traina, Sara Teresinha Olalla Saad / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-27T21:37:05Z (GMT). No. of bitstreams: 1 Campos_PauladeMelo_D.pdf: 6042513 bytes, checksum: b12134db0721f177eb0c2116e7fdf5e2 (MD5) Previous issue date: 2015 / Resumo: As neoplasias mieloproliferativas crônicas BCR-ABL1 negativas (NMP) apresentam como característica comum a ocorrência de proliferação celular exacerbada, mantendo a capacidade de diferenciação mieloide terminal. Em parcela significativa dos casos, a ativação da proliferação celular ocorre pelo aumento da atividade tirosinoquinase de proteínas específicas. Entretanto, a heterogeneidade molecular observada nos pacientes e as respostas clínicas insatisfatórias observadas em parte dos casos com os tratamentos vigentes sugerem que mecanismos adicionais, como interações proteicas não descritas e novas mutações, possam estar envolvidos na fisiopatologia destas neoplasias. Neste trabalho, objetivamos estudar as vias de ativação tirosinoquinase em policitemia vera (PV), trombocitemia essencial (TE) e mielofibrose primária (MFP) (subprojeto 1), e em mastocitose sistêmica (subprojeto 2). O foco principal do subprojeto 1 consistiu em avaliar, em NMP, a associação JAK2/IRS2, previamente descrita em células não hematológicas após estímulo, bem como o envolvimento de IRS2 em vias de proliferação celular e apoptose. Utilizamos modelos de linhagens celulares leucêmicas humanas com JAK2 mutado (JAK2V617F) e JAK2 selvagem (JAK2WT), submetendo-as a inibição gênica por shRNA entregue por lentivírus e ao tratamento com o inibidor seletivo de JAK1/2 ruxolitinib. As células foram então submetidas à avaliação da viabilidade celular por MTT, e da apoptose por citometria de fluxo (anexina V/PI e caspase-3) e por imunobloting (caspase-3 clivada). A expressão do mRNA de IRS2 foi avaliada por PCR em tempo real em amostras de células CD34+ de sangue periférico de 99 pacientes com diagnóstico de PV, TE e MFP, e em 28 doadores normais. Através de imunoprecipitação e microscopia confocal, observamos a associação constitutiva entre JAK2 e IRS2 nas células JAK2V617F, mas não nas células JAK2WT. Em células JAK2V617F, a inibição de IRS2 por lentivírus diminuiu significativamente a fosforilação de STAT5, reduziu a viabilidade celular, aumentou as taxas de apoptose, e potencializou os efeitos de ruxolitinib. Não houve mudanças nas taxas de viabilidade celular e apoptose nas células JAK2WT inibidas para IRS2. A expressão do mRNA de IRS2 foi significativamente maior nos pacientes com TE em relação aos doadores normais, e em pacientes com NMP portadores da mutação JAK2V617F em relação aos pacientes com JAK2WT. Estas evidências sugerem que IRS2 possa participar das vias de sinalização celular nas NMP através de interação direta com JAK2. A inibição farmacológica de IRS2, isoladamente ou em conjunto com ruxolitinib, é ferramenta potencial no tratamento de pacientes com PV, TE e MFP. No subprojeto 2, nosso objetivo consistiu em investigar mutações no gene KIT em um caso de mastocitose sistêmica familiar seguido em nosso serviço, em que mãe (caso 1) e filha (caso 2) apresentavam extensa infiltração cutânea e da medula óssea por mastócitos, bem como avaliar a sensibilidade dos mastócitos neoplásicos ao tratamento com os inibidores de tirosinoquinase (ITK) imatinibe, dasatinibe e PKC412. Através de sequenciamento por Sanger, identificamos a mutação KITK509I em células de medula óssea total, CD3+ de sangue periférico e mucosa oral de ambas pacientes. Os pais do caso 1 apresentaram KIT selvagem. O tratamento in vitro por 4, 8 ou 12 dias de células totais de medula óssea dos casos 1 e 2 com os ITK avaliados resultou em menor viabilidade celular, avaliada por MTT, e em redução da fosforilação de P70S6K com todas as drogas testadas. Entretanto, apenas o imatinibe evidenciou resposta consistente na indução de apoptose. Foi iniciado tratamento dos casos 1 e 2 com imatinibe 400mg/dia via oral. Três meses após o início, houve normalização da pele e da medula óssea; após dois anos de seguimento, as pacientes mantêm-se em remissão. Embora rara, a mutação KITK509I deve ser pesquisada em todos os casos de mastocitose sistêmica familiar. O imatinibe pode ser considerado como droga de primeira escolha nestes casos / Abstract: The BCR-ABL1 negative chronic myeloproliferative neoplasms (MPN) are characterized by increased cellular proliferation with preserved terminal myeloid differentiation. In most cases, the activation of cell proliferation is caused by an increased tyrosine kinase activity of specific proteins. However, patients' molecular heterogeneity and the incomplete clinical responses observed in part of the cases using the current treatments suggest that additional mechanisms, such as unknown protein interactions and new mutations, can be involved in the pathophysiology of MPN. In this study, our main goal was to investigate tyrosine kinase activation pathways in polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF) (subproject 1), and in systemic mastocytosis (subproject 2). The focus of subproject 1 consisted in the investigation of JAK2/IRS2 association in MPN, already described in non-hematological cells following extrinsic stimulus, and in evaluating IRS2 function in MPN cell proliferation and apoptosis. JAK2 wild-type (JAK2WT) and JAK mutated (JAK2V617F) human leukemia cell lines were transduced with lentivirus-mediated shRNA targeting IRS2, and treated with vehicle (DMSO) or with the selective JAK1/2 inhibitor ruxolitinib. Cells were then submitted to evaluation of cell viability (MTT) and apoptosis (anexin V/PI and caspase-3 by flow cytometry, and cleaved caspase-3 by immunoblotting). IRS2 mRNA expression was evaluated by real time quantitative PCR in CD34+ peripheral blood cells of 99 patients with PV, ET and PMF, and in 28 healthy donors. Through immunoprecipitation/immunobloting and confocal microscopy, we observed the constitutive JAK2/IRS2 association in JAK2V617F cells, but not in JAK2WT cell lines. In JAK2V617F, IRS2 silencing significantly decreased phospho-STAT5, reduced cell viability, induced apoptosis, and potentiated the effects of ruxolitinib treatment. No differences in cell viability and apoptosis ratios were observed in IRS2 silenced JAK2WT cells. IRS2 mRNA expression was significantly higher in ET patients when compared to healthy donors, and in patients harboring JAK2V617F mutation in relation to JAK2WT. These evidence suggest that IRS2 participate in MPN cell signaling pathways through its interaction with JAK2. IRS2 pharmacological inhibition, alone or in combination with ruxolitinib, may be a potential tool in the treatment of PV, ET and PMF patients. In subproject 2, our main goal was to seek for KIT mutations in a case of systemic familial mastocytosis, followed in our outpatient clinics, in which the mother (case 1) and the daughter (case 2) had extensive skin and bone marrow infiltration by mast cells. Also, we aimed to evaluate in vitro sensitivity of neoplastic mast cells to the treatment with the tyrosine kinase inhibitors (TKI) imatinibe, dasatinibe and PKC412. Using Sanger sequencing analysis, we identified the KITK509I mutation in total bone marrow, peripheral blood CD3+ and oral mucosa cells in both patients. The parents of case 1 had wild type KIT. The in vitro treatment of total bone marrow cells of cases 1 and 2 with TKI for 4, 8 and 12 days resulted in reduced cell viability, as evaluated by MTT, and in reduced phosphorylation of P70S6K for all tested drugs. However, only imatinibe consistently induced apoptosis in both cases. Patients were started on imatinibe 400mg orally per day. Three months following imatinibe treatment, there was a complete reversion of skin and bone marrow mast cells infiltration; after two years of follow-up, cases 1 and 2 remain in complete remission of the systemic mastocytosis. Although rare, KITK509I mutation should be investigated in all cases of familial systemic mastocytosis. Imatinibe is a good first choice for the treatment of these cases / Doutorado / Fisiopatologia Médica / Doutora em Ciências

Die Grünalge Chlamydomonas reinhardtii ist ein Modellorganismus, der nach der Entdeckung von zwei Photorezeptoren, den Kanalrhodopsinen, eine Schlüsselrolle bei der Entwicklung der Optogenetik spielte. Kanalrhodopsine sind lichtinduzierte Ionenkanäle, die für das photoinduzierte Verhalten von Chlamydomonas verantwortlich sind. Aufgrund der Herausforderungen bei der gentechnischen Modifizierung in diesem Organismus konnte ihre Funktion in Phototaxis und photophober Reaktion bisher nicht umfassend untersucht werden. In dieser Arbeit präsentiere ich eine CRISPR-Cas9-basierte Technik, die einen zielgerichteten Austausch einzelner Nukleotide in einem ausgewählten Gen in vivo ermöglicht. Hierfür wird gezielt ein DNA-Doppelstrangbruch innerhalb des Gens induziert und anschließend wieder durch Aktivierung des Homologie-gesteuerten Reparaturmechanismus der Alge behoben, bei dem eine ausgewählte Punktmutation integriert wird. Diese Technik habe ich anschließend verwendet, um die Funktion der Kanalrhodopsine ChR1 und ChR2 in vivo aufzuklären. Dazu habe ich die codierenden Gene jeweils im Chlamydomonas Wildtyp-Stamm ausgeschaltet und Punktmutationen im verbleibenden Kanalrhodopsin eingeführt. Die so erzeugten Kanalmutanten weisen Veränderungen in ihrer Photozykluskinetik und Ionenselektivität auf, die das lichtabhängige Verhalten der Alge beeinflussen sollten. Die Ergebnisse zeigten zum einen, dass sowohl ChR1 als auch ChR2 Photorezeptoren sind, die die Phototaxis steuern, und zum anderen, dass eine Erhöhung der ChR2-Expression nach Deletion von ChR1 die phototaktische Aktivität der Algen wiederherstellt. Darüber hinaus wiesen die mutierten Chlamydomonas-Stämme mit veränderter Photozykluskinetik und reduzierter Kalzium-Permeabilität eine fast 100-fache Verringerung der Photosensitivität, eine verminderte photophobische Reaktion und schnellere Lichtadaptation auf. Zudem führte die Umkehr der Selektivität vom Channelrhodopsin von Kationen zu Anionen zum kompletten Verlust der Photoreaktion der Algen. Nicht zuletzt konnte diese Studie die Bedeutung der Proton-Leitfähigkeit der Kanalrhodopsine für das photoinduzierte Verhalten von Chlamydomonas aufzeigen. / The green alga Chlamydomonas reinhardtii is a model organism that played a key role in the development of optogenetics, after discovery of two photoreceptors called channelrhodopsins. Channelrhodopsins are light-gated ion channels that are responsible for photo-induced behavior of Chlamydomonas. Untill now, their functionality in algal photoresponses such as phototaxis and photophobic reaction has not been extensively studied, primarily due to the challenges connected to genetic editing in the organism. In this work, I presented a CRISPR-Cas9-based technique allowing a targeted exchange of single nucleotides in a gene of interest in vivo. It is based on targeted induction of DNA double-stranded breaks in the gene and on subsequent engagement of homologous recombination to repair the damage and integrate a selected point mutation. To elucidate the function of channelrhodopsins ChR1 and ChR2 in vivo, I created channelrhodopsin single knockouts in the wild-type Chlamydomonas strain and integrated point mutations in the remaining channelrhodopsin gene. The selected mutations affected photocycle kinetics and ion selectivity. It was shown that, first, both ChR1 and ChR2 are photoreceptors that mediate phototaxis and second, the upregulation of ChR2 upon the deletion of ChR1 rescues phototactic activity of the algae. Further, the mutant Chlamydomonas strains with altered photocycle kinetics and lower calcium permeability exhibited nearly 100-fold reduction of photosensitivity, a diminished photophobic reaction and faster light adaptation rates. Moreover, the conversion of channelrhodopsin selectivity to anions aborted algal photoresponse. In addition, the study highlighted the importance of proton conductance in the photo-induced behavior of Chlamydomonas.

A síndrome de McCune Albrigth (SMA) é uma doença genética não hereditária, com incidência estimada entre 1/100.000 e 1/1.000.000 casos/ano. A SMA caracteriza-se clinicamente pela tríade: displasia óssea fibrosa (FD), manchas cutâneas café-com-leite e hiperfunção endócrina tais como: síndrome de Cushing, pseudo-puberdade precoce, hipertiroidismo, acromegalia. O diagnóstico da SMA clássica é usualmente baseado no quadro clínico associado a dosagens hormonais e exames de imagem, principalmente cintilografia do esqueleto. No entanto, quadros atípicos e formas parciais muitas vezes dificultam o diagnóstico preciso da síndrome. O objetivo deste estudo foi padronizar dentre as técnicas de PNA (peptide nucleic acid) e PCT em Tempo Real, para a detecção de polimorfismos de base única (SNPs), a técnica mais sensível para a discriminação das mutações ativadoras da subunidade da proteína G. Para este estudo foram selecionados 32 pacientes, 1 masculino e 31 femininos, com SMA, todos em seguimento no Hospital das Clínicas da Faculdade de Medicina da USP. Como resultado positivo, apresentamos nesse trabalho pela primeira vez o uso do RT-PCR genotipagem na detecção das mutações ativadoras da proteína G, em DNA extraído de tecidos afetados e em leucócitos de sangue periférico, sendo a técnica considerada sensível o suficiente para discriminar de forma simples e rápida as mutações ativadoras da PGs. Sugerimos nesse estudo o uso da técnica de discriminação alélica pelo sistema Taqman. Essa técnica possibilita a detecção destas mutações gsp no sangue periférico mesmo numa baixa porcentagem, uma vez que nem sempre o tecido afetado (gônada, osso, hipófise) é disponível. / The McCune-Albright Syndrome (MAS) is a genetic disease, with incidence estimated at 1/100.000 and 1/1000000 cases per year. MAS is clinically characterized by the triad: bone fibrous dysplasia (FD) café-au-lait skin spots and endocrine hyperfunction, such as: precocious puberty (PP), Cushing's syndrome, hyperthyroidism and acromegaly. The diagnosis of MAS is originally based on clinical characteristics associated with hormonal and imaging studies. However, atypical and partial forms often hamper the accurate diagnosis of the syndrome. For this study we selected 32 patients, 1male and 31 females, all being treated in Hospital das Clínicas, School of Medicine, University of São Paulo. As a positive result, we showed for the first time the use of Real Time PCR/genotyping for the detection of activating mutations of the stimulatory G protein, using blood leucocytes DNA. This technique was sensible and can bring fast results for the patient and the physician, making the diagnosis easier. Our study proposes the use of allelic discrimination by Taqman system, which can be used as a probe that allows the identification of specific genotypes. These techniques could help detect these mutations in peripheral blood when the affected tissue is not available.

Le glutamate est accumulé dans des vésicules synaptiques par des transporteurs vésiculaires du glutamate appelés VGLUT1-3. VGLUT1 et VGLUT2 sont utilisés par les neurones glutamatergiques «classiques» corticaux et sous-corticaux. VGLUT3 est présent dans des sous-populations de neurones utilisant d’autres neurotransmetteurs que le glutamate. Dans la cochlée, VGLUT3 permet la transmission glutamatergique entre les cellules ciliées internes et les neurones du nerf auditif. Le travail mené par l’équipe du Pr Puel a permis de découvrir l’implication de VGLUT3 dans une pathologie héréditaire de l’audition chez l’Homme. Une mutation p.A211V du gène codant VGLUT3 humain est responsable d’une surdité progressive à transmission autosomique. Il s’agit de la première mutation d’un VGLUT associé à une pathologie humaine. Mon travail de thèse a consisté à caractériser l’impact de cette mutation sur le SNC d’une lignée de souris exprimant cette mutation. Nous avons observé que cette mutation avait des effets complexes sur VGLUT3. La mutation p.A211V entraine une baisse marquée de l’expression de VGLUT3 dans les terminaisons nerveuses qui semble liée à une dégradation accélérée de VGLUT3. 20% d’expression résiduelle de VGLUT3 suffisent à assurer la majeure partie des fonctions du transporteur. L’activité de VGLUT3 ne semble donc pas être linéairement corrélée à son expression. De plus, la réduction de VGLUT3 au niveau des synapses semble s’accompagner d’une réduction du nombre de vésicules VGLUT3-positives et d’une réduction du nombre de copies de VGLUT3 par vésicule. Dans l’ensemble, mon travail de thèse a permis d’acquérir une meilleure connaissance de la régulation de VGLUT3. / Glutamate is the major excitatory neurotransmitter in the Central Nervous System (CNS) and is accumulated into synaptic vesicles by proton-dependent transporters named VGLUT1-3. VGLUT1 and VGLUT2-positive neurons are respectively found in cortical and subcortical glutamatergic neurons. In contrast, VGLUT3 is localized in a small population of neurons using other neurotransmitter than glutamate i.e.: cholinergic interneurons in the striatum, subpopulation of GABAergic interneurons in the hippocampus and cortex and serotoninergic neurons. Furthermore, VGLUT3 is also expressed by sensory inner hear cells (IHCs).In the cochlea, VGLUT3 accumulates glutamate into synaptic vesicles of the IHCs. A mutation of the gene that encodes VGLUT3 is responsible for a progressive, high-frequency deafness. It is the first mutation of a VGLUT that was demonstrated to be responsible for a human pathology.We investigated the effects of the p.A211V mutation on VGLUT3 in the CNS of a mouse line expressing this mutation. We observed that this mutation had complex effects on VGLUT3. The p.A211V mutation causes a 80% decrease of VGLUT3 in nerve endings. 20% residual expression of VGLUT3 is sufficient to fulfill most part of its functions. Contrary to prevailing views, VGLUT3 global activity is not linearly correlated to VGLUT3 quantity. Futhermore, VGLUT3 reduction seems to be associated with a diminution of VGLUT3-positive vesicles accompanied by an homogenous reduction of VGLUT3 copy number per vesicle.Overall, my thesis allowed to acquire a better understanding of the regulation of VGLUT3. This work will deepen our understanding of the involvement of VGLUTs in various pathologies.