Image-based high-content screens (HCS) hold tremendous promise for cell-based phenotypic screens. Challenges related to HCS include not only storage and management of data, but critical analysis of the complex image-based data. I implemented a data storage and screen management framework and developed approaches for data analysis of a number high-content microscopy screen formats. I visualized and analysed pilot screens to develop a robust multi-parametric assay for the identification of genes involved in DNA damage repair in HeLa cells. Further, I developed and implemented new approaches for image processing and screen data normalization. My analyses revealed that the ubiquitin ligase RNF8 plays a central role in DNA-damage response and that a related ubiquitin ligase RNF168 causes the cellular and developmental phenotypes characteristic for the RIDDLE syndrome. My approaches also uncovered a role for the MMS22LTONSL complex in DSB repair and its role in the recombination-dependent repair of stalled or collapsed replication forks. The discovery of novel bioactive molecules is a challenge because the fraction of active candidate molecules is usually small and confounded by noise in experimental readouts. Cheminformatics can improve robustness of chemical high-throughput screens and functional genomics data sets by taking structure-activity relationships into account. I applied statistics, machine learning and cheminformatics to different data sets to discern novel bioactive compounds. I showed that phenothiazines and apomorphines are regulators for cell differentiation in murine embryonic stem cells. Further, I pioneered computational methods for the identification of structural features that influence the degradation and retention of compounds in the nematode C. elegans. I used chemoinformatics to assemble a comprehensive screening library of previously approved drugs for redeployment in new bioassays. A combination of chemical genetic interactions, cheminformatics and machine learning allowed me to predict novel synergistic antifungal small molecule combinations from sensitized screens with the drug library. In another study on the biological effects of commonly prescribed psychoactive compounds, I discovered a strong link between lipophilicity and bioactivity of compounds in yeast and unexpected off-target effects that could account for unwanted side effects in humans. I also investigated structure-activity relationships and assessed the chemical diversity of a compound collection that was used to probe chemical-genetic interactions in yeast. Finally, I have made these methods and tools available to the scientific community, including an open source software package called MolClass that allows researchers to make predictions about bioactivity of small molecules based on their chemical structure.

Endocytosis is an essential cellular process consisting of the internalization of extracellular cargo and its transport towards different intracellular destinations. Multiple endocytic routes are tailored for the internalization and trafficking of different types of cargo and multiple endocytic organelles provide specialized biochemical environments where different molecular events take place. Membrane receptors and cargo molecules are internalized by both Clathrin-dependent and –independent endocytosis into early endosomes. From here two main endocytic routes are followed: 1) the recycling route, mainly followed by membrane receptor and other molecules like Transferrin, brings the cargo back to the plasma membrane and 2) the degradative route, followed by molecules like Epidermal Growth Factor (EGF) and Lipoprotein particles (LDL), leads the cargo to degradation into late endosomes/lysosomes. In addition to the basic function of intracellular cargo transport, the endocytic system fulfils many other cellular and developmental functions such as transmission of proliferative and survival signals and defence against pathogens. In order for cells to properly perform their various and numerous functions in organs and tissues, the activity of the endocytic system needs to be coordinated between cells and, within individual cells, integrated with other cellular functions. Even though molecules orchestrating the endocytic sorting and transport of different types of cargo have long been investigated, our understanding of the molecular machinery underlying endocytosis and its coordination into the cellular systems remains fragmentary. The work presented in this thesis aimed at understanding how this high-order regulation and integration is achieved. This requires not only a comprehensive analysis of molecular constituents of the endocytic system but also an understanding of the general design principles underlying its function. To this end, in collaboration with several members of the Zerial group and with the HT-Technology Development Studio (TDS) at MPI-CBG, I developed a new strategy to accurately profile the activity of human genes with respect to Transferrin (Tfn) and Epidermal Growth Factor (EGF) endocytosis by combining genome-wide RNAi with several siRNA/esiRNA per gene, automated high-resolution confocal microscopy, quantitative multi-parametric image analysis and high-performance computing. This provided a rich and complex genomic dataset that was subsequently subjected to analysis with a combination of tools such as a multi-parametric correlation of oligo profiles, phenotypic clustering and pathways analysis, and a Bayesian network reconstruction of key endocytic features. Altogether, the genomic endeavour and the subsequent analyses provided a number of important results: first, they revealed a much higher extent of off-target effects from RNAi and provided novel tools to infer the specific effects of genes loss of function; second, they identified a large number of novel molecules exerting a regulatory role on the endocytic system, including uncharacterized genes and genes implicated in human diseases; third, they uncovered the regulatory activity of signalling pathways such as Wnt, Integrin, TGF-β, and Notch, and found new genes regulating the sorting of cargo to a specialized subset of early endosomes that function as intracellular signalling platforms; and fourth, a systems analysis by Bayesian networks revealed that the cell specifically regulates the number, size, concentration of cargo and intracellular position of endosomes, thus uncovering novel properties of the endocytic system. In conclusion, the work presented here not only provided a dataset extremely rich of information whose potential has just begun to be uncovered but also shows how genomic datasets can be used to reveal design principles governing the functioning of biological processes.

Adult mammalian central nervous system (CNS) neurons are unable to extend axons after injury, partially owing to the inhibitory myelin and chondroitin sulfate proteoglycans (CSPGs) present in the environment. A neuron's intrinsic state is also important for determining its regenerative potential. Peripheral nervous system (PNS) neurons, unlike their CNS counterparts, have increased ability to regrow their axons after injury, even in the presence of inhibitory molecules. With the goal of discovering novel regeneration associated genes, we have isolated the genes differentially expressed by PNS neurons. We then developed a high throughput neuronal transfection method to test whether these genes were sufficient to modify neurite growth in vitro. Using high content screening, we measured the ability of cerebellar neurons to initiate neurite outgrowth on inhibitory and permissive substrates. This combination of technologies (subtractive hybridization, microarray, high throughput electroporation and high content screening) allowed phenotypic examination of neurons after the overexpression of over a thousand genes. Additionally, kinases and phosphatases were assayed for their ability to modify neurite outgrowth in hippocampal neurons. Results from both of these large unbiased screens confirmed many of the existing candidates for neurite growth during development and regeneration. We also discovered many novel genes which promoted neurite outgrowth such as GPX3, EIF2B5, RBMX, CHKA, IRF6, and PKN2. To accurately interpret the large volume of data, new methods of analysis were performed. Finally, we developed novel techniques that took advantage of public databases to cluster genes and determine whether those clusters produced robust changes in neurite growth. In summary, we have provided a vast repository of functional data to study axon development and regeneration after injury as well as developing the tools needed to interpret that data.

The overall focus of this project has two parts: First, was to develop a protocol utilizing serum-free media formulations and defined plating and culture techniques to create functional in vitro myotubes derived from adult skeletal muscle satellite cells. The second was to manipulate the inherent muscle parameters such as force output and fatigue of these myotubes by employing exercise regimes or by small molecule application. The importance of serum-free medium use for in vitro cultures is becoming increasingly important in creating functional systems that can be validated for drug testing by the Food and Drug Administration (FDA). Also, the study of age related diseases as well as the potential for “personalized medicine” relies on the proliferation and maturation of satellite cells from adult derived tissue. For that purpose, a serum-free medium and culture system was designed to create mature striated myotubes in culture on a defined non-biological substrate N-1[3-trimethoxysilyl propyl] diethylenetriamine (DETA). These myotubes were evaluated by morphology, muscle specific protein expression, and by muscle functionality. After the thorough characterization of the resultant myotubes the functional output of the muscle was altered utilizing chemical means (creatine supplementation and PGC-1? agonists), chronic long term stimulation, and the use of PGC-1? deficient tissue. In this thesis presentation the utility of the newly developed medium formulation to create myotubes from a variety of adult derived muscle sources will be shown. A protocol in which to exercise skeletal muscle in vitro to alter endurance was developed and employed to manipulate skeletal muscle. Finally, small molecules were tested to validate this system for drug study use. This engineered system has the potential for high-throughput screening of drugs for efficacy and drug toxicity studies as well as general biological studies on muscle fatigue.

Como em diversos tumores sólidos, no câncer de cabeça e pescoço (HNSCC) a presença de metástases é um importante fator de mal prognóstico. Até o momento, estudos indicam que, no microambiente inflamatório tumoral, a estimulação com o Fator de Necrose Tumoral Alpha (TNF-?) leva à ativação de diferentes vias moleculares, como a via do Fator Nuclear Kappa-B (NF-kB) e PI3K/AKT, que inibem GSK3? e consequentemente, promovem a estabilização e translocação nuclear de SNAIL e betacatenina. De um modo geral, em diversos tipos de câncer, enquanto beta-catenina tem ação em promover a proliferação celular, membros da família SNAIL são capazes de induzir o processo de transição epitélio-mesenquimal (EMT). Sabe-se que os eventos de EMT estão envolvidos tanto na iniciação de metástases quanto na geração de célulastronco tumorais (CSCs), que por sua vez estão associadas à falha terapêutica e recidiva, devido à características que lhe conferem resistência aos tratamentos convencionais. Ao silenciar a expressão gênica de modo pós-transcricional, microRNAs (miRs) tem sido associados à regulação tanto da EMT quanto da geração de CSCs. Com uso da abordagem de High-Content Screening (HCS, análise celular multiparamétrica quantitativa por microscopia automatizada), buscamos investigar a capacidade de um grupo de 30 miRs humanos, muitos deles envolvidos em vias inflamatórias e na pluripotência, em modular aspectos relacionados a sobrevivência celular e EMT, em uma linhagem celular derivada de HNSCC (FADU) sob estímulo inflamatório. Inicialmente, avaliamos o potencial do TNF-? em modular parâmetros morfométricos, bem como a presença/localização de proteínas relacionadas com a EMT e capacidade migratória. Posteriormente, avaliamos o efeito de moléculas miméticas dos miRs em suprimir ou potencializar a sobrevivência celular e EMT em células estimuladas com TNF-?, seguido da identificação de transcritos alvos preditos (bem como das vias de sinalização enriquecidas para estes alvos) comumente alvejados por grupos de miRs que levaram a alterações multiparamétricas similares. De modo geral, miRs que alvejaram RELA e AKT2/AKT3 foram responsáveis pela redução na proliferação celular e EMT, enquanto o oposto foi observado em miRs que alvejaram GSK3B e ARHGAP5 (inibidor de RhoA). O silenciamento por siRNAs específicos contra RELA e CTNNB1, causou à redução na sobrevivência celular, enquanto que o silenciamento de AKT1 e CTNNB1 levou à redução na expressão proteica de SNAIL/SLUG. Finalmente, o silenciamento de RELA, AKT1, GSK3B e CTNNB1 levou a redução na sobrevivência celular e indução a apoptose mesmo na ausência de estimulação com TNF-?. Como um todo, nós demonstramos que a abordagem de HCS permitiu a identificação de miRs com efeitos fenotípicos similares (no contexto de proliferação e EMT) e que, a predição de alvos compartilhados por estes miRs, levou à identificação de alvos e vias de sinalização relevantes do ponto de vista terapêutico. / Like many solid cancers, in head and neck cancer (HNC) the presence of metastases is an important factor of poor prognosis. To date, studies indicate that, in the tumor inflammatory microenvironment, stimulation with Tumor Necrosis Factor Alpha (TNF-?) leads to the activation of different molecular pathways, such as the Nuclear Factor-Kappa B (NF-kB) and PI3K/AKT pathway, inhibiting GSK3? and the degradation of SNAIL and beta-catenin, stabilizing them promoting their nuclear translocation. In general, in several types of cancer, while beta-catenin acts to promote cell proliferation, members of the SNAIL family induce the epithelial-mesenchymal (EMT) transition process. It is known that EMT events are involved both in the initiation of metastases and generation of cancer stem cells (CSCs), which in turn are associated with therapeutic failure and relapse, due to its properties that confer resistance to conventional treatments. By silencing gene expression in a post-transcriptional fashion, microRNAs (miRs) have been associated with the regulation of both EMT and CSCs generation. Using the HighContent Screening (HCS) approach, we sought to investigate the ability of a group of 30 human miRs, many of them involved in inflammatory pathways and pluripotency, to modulate aspects related to cell survival and EMT, in a HNSCC-derived cell line (FADU) under inflammatory stimuli. Initially, we evaluated the potential of TNF-? in modulating morphometric parameters, as well as the presence/location of EMT-related proteins and migratory capacity. Subsequently, we evaluated the effect of miRs mimetic molecules on suppressing or potentiating cell survival and EMT in TNF-?-stimulated cells, followed by the identification of predicted target transcripts (as well as signaling pathways enriched for these targets) commonly targeted by groups of miRs that led to similar multiparametric changes. Overall, miRs that targeted RELA and AKT2/AKT3 were responsible for the reduction in cell proliferation and EMT, while the opposite was observed in miRs that targeted GSK3B and ARHGAP5 (RhoA inhibitor). Gene silencing by specific siRNAs against RELA and CTNNB1 caused a reduction in cell survival, while silencing of AKT1 and CTNNB1 led to reduced protein expression of SNAIL/SLUG. Finally, the silencing of RELA, AKT1, GSK3B and CTNNB1 led to a reduction in cell survival and induction of apoptosis even in the absence of TNF-? stimulation. As a whole, we demonstrated that the HCS approach allowed the identification of miRs with similar phenotypic effects (in the context of proliferation and EMT) and that the prediction of targets shared by these miRs led to the identification of relevant targets and signaling pathways from the therapeutic point of view.

Como em diversos tumores sólidos, no câncer de cabeça e pescoço (HNSCC) a presença de metástases é um importante fator de mal prognóstico. Até o momento, estudos indicam que, no microambiente inflamatório tumoral, a estimulação com o Fator de Necrose Tumoral Alpha (TNF-?) leva à ativação de diferentes vias moleculares, como a via do Fator Nuclear Kappa-B (NF-kB) e PI3K/AKT, que inibem GSK3? e consequentemente, promovem a estabilização e translocação nuclear de SNAIL e betacatenina. De um modo geral, em diversos tipos de câncer, enquanto beta-catenina tem ação em promover a proliferação celular, membros da família SNAIL são capazes de induzir o processo de transição epitélio-mesenquimal (EMT). Sabe-se que os eventos de EMT estão envolvidos tanto na iniciação de metástases quanto na geração de célulastronco tumorais (CSCs), que por sua vez estão associadas à falha terapêutica e recidiva, devido à características que lhe conferem resistência aos tratamentos convencionais. Ao silenciar a expressão gênica de modo pós-transcricional, microRNAs (miRs) tem sido associados à regulação tanto da EMT quanto da geração de CSCs. Com uso da abordagem de High-Content Screening (HCS, análise celular multiparamétrica quantitativa por microscopia automatizada), buscamos investigar a capacidade de um grupo de 30 miRs humanos, muitos deles envolvidos em vias inflamatórias e na pluripotência, em modular aspectos relacionados a sobrevivência celular e EMT, em uma linhagem celular derivada de HNSCC (FADU) sob estímulo inflamatório. Inicialmente, avaliamos o potencial do TNF-? em modular parâmetros morfométricos, bem como a presença/localização de proteínas relacionadas com a EMT e capacidade migratória. Posteriormente, avaliamos o efeito de moléculas miméticas dos miRs em suprimir ou potencializar a sobrevivência celular e EMT em células estimuladas com TNF-?, seguido da identificação de transcritos alvos preditos (bem como das vias de sinalização enriquecidas para estes alvos) comumente alvejados por grupos de miRs que levaram a alterações multiparamétricas similares. De modo geral, miRs que alvejaram RELA e AKT2/AKT3 foram responsáveis pela redução na proliferação celular e EMT, enquanto o oposto foi observado em miRs que alvejaram GSK3B e ARHGAP5 (inibidor de RhoA). O silenciamento por siRNAs específicos contra RELA e CTNNB1, causou à redução na sobrevivência celular, enquanto que o silenciamento de AKT1 e CTNNB1 levou à redução na expressão proteica de SNAIL/SLUG. Finalmente, o silenciamento de RELA, AKT1, GSK3B e CTNNB1 levou a redução na sobrevivência celular e indução a apoptose mesmo na ausência de estimulação com TNF-?. Como um todo, nós demonstramos que a abordagem de HCS permitiu a identificação de miRs com efeitos fenotípicos similares (no contexto de proliferação e EMT) e que, a predição de alvos compartilhados por estes miRs, levou à identificação de alvos e vias de sinalização relevantes do ponto de vista terapêutico. / Like many solid cancers, in head and neck cancer (HNC) the presence of metastases is an important factor of poor prognosis. To date, studies indicate that, in the tumor inflammatory microenvironment, stimulation with Tumor Necrosis Factor Alpha (TNF-?) leads to the activation of different molecular pathways, such as the Nuclear Factor-Kappa B (NF-kB) and PI3K/AKT pathway, inhibiting GSK3? and the degradation of SNAIL and beta-catenin, stabilizing them promoting their nuclear translocation. In general, in several types of cancer, while beta-catenin acts to promote cell proliferation, members of the SNAIL family induce the epithelial-mesenchymal (EMT) transition process. It is known that EMT events are involved both in the initiation of metastases and generation of cancer stem cells (CSCs), which in turn are associated with therapeutic failure and relapse, due to its properties that confer resistance to conventional treatments. By silencing gene expression in a post-transcriptional fashion, microRNAs (miRs) have been associated with the regulation of both EMT and CSCs generation. Using the HighContent Screening (HCS) approach, we sought to investigate the ability of a group of 30 human miRs, many of them involved in inflammatory pathways and pluripotency, to modulate aspects related to cell survival and EMT, in a HNSCC-derived cell line (FADU) under inflammatory stimuli. Initially, we evaluated the potential of TNF-? in modulating morphometric parameters, as well as the presence/location of EMT-related proteins and migratory capacity. Subsequently, we evaluated the effect of miRs mimetic molecules on suppressing or potentiating cell survival and EMT in TNF-?-stimulated cells, followed by the identification of predicted target transcripts (as well as signaling pathways enriched for these targets) commonly targeted by groups of miRs that led to similar multiparametric changes. Overall, miRs that targeted RELA and AKT2/AKT3 were responsible for the reduction in cell proliferation and EMT, while the opposite was observed in miRs that targeted GSK3B and ARHGAP5 (RhoA inhibitor). Gene silencing by specific siRNAs against RELA and CTNNB1 caused a reduction in cell survival, while silencing of AKT1 and CTNNB1 led to reduced protein expression of SNAIL/SLUG. Finally, the silencing of RELA, AKT1, GSK3B and CTNNB1 led to a reduction in cell survival and induction of apoptosis even in the absence of TNF-? stimulation. As a whole, we demonstrated that the HCS approach allowed the identification of miRs with similar phenotypic effects (in the context of proliferation and EMT) and that the prediction of targets shared by these miRs led to the identification of relevant targets and signaling pathways from the therapeutic point of view.

Endocytosis is an essential cellular process consisting of the internalization of extracellular cargo and its transport towards different intracellular destinations. Multiple endocytic routes are tailored for the internalization and trafficking of different types of cargo and multiple endocytic organelles provide specialized biochemical environments where different molecular events take place. Membrane receptors and cargo molecules are internalized by both Clathrin-dependent and –independent endocytosis into early endosomes. From here two main endocytic routes are followed: 1) the recycling route, mainly followed by membrane receptor and other molecules like Transferrin, brings the cargo back to the plasma membrane and 2) the degradative route, followed by molecules like Epidermal Growth Factor (EGF) and Lipoprotein particles (LDL), leads the cargo to degradation into late endosomes/lysosomes. In addition to the basic function of intracellular cargo transport, the endocytic system fulfils many other cellular and developmental functions such as transmission of proliferative and survival signals and defence against pathogens. In order for cells to properly perform their various and numerous functions in organs and tissues, the activity of the endocytic system needs to be coordinated between cells and, within individual cells, integrated with other cellular functions. Even though molecules orchestrating the endocytic sorting and transport of different types of cargo have long been investigated, our understanding of the molecular machinery underlying endocytosis and its coordination into the cellular systems remains fragmentary. The work presented in this thesis aimed at understanding how this high-order regulation and integration is achieved. This requires not only a comprehensive analysis of molecular constituents of the endocytic system but also an understanding of the general design principles underlying its function. To this end, in collaboration with several members of the Zerial group and with the HT-Technology Development Studio (TDS) at MPI-CBG, I developed a new strategy to accurately profile the activity of human genes with respect to Transferrin (Tfn) and Epidermal Growth Factor (EGF) endocytosis by combining genome-wide RNAi with several siRNA/esiRNA per gene, automated high-resolution confocal microscopy, quantitative multi-parametric image analysis and high-performance computing. This provided a rich and complex genomic dataset that was subsequently subjected to analysis with a combination of tools such as a multi-parametric correlation of oligo profiles, phenotypic clustering and pathways analysis, and a Bayesian network reconstruction of key endocytic features. Altogether, the genomic endeavour and the subsequent analyses provided a number of important results: first, they revealed a much higher extent of off-target effects from RNAi and provided novel tools to infer the specific effects of genes loss of function; second, they identified a large number of novel molecules exerting a regulatory role on the endocytic system, including uncharacterized genes and genes implicated in human diseases; third, they uncovered the regulatory activity of signalling pathways such as Wnt, Integrin, TGF-β, and Notch, and found new genes regulating the sorting of cargo to a specialized subset of early endosomes that function as intracellular signalling platforms; and fourth, a systems analysis by Bayesian networks revealed that the cell specifically regulates the number, size, concentration of cargo and intracellular position of endosomes, thus uncovering novel properties of the endocytic system. In conclusion, the work presented here not only provided a dataset extremely rich of information whose potential has just begun to be uncovered but also shows how genomic datasets can be used to reveal design principles governing the functioning of biological processes.

Os microRNAs (miRs) desempenham um papel importante na biologia das células-tronco por meio da interação com seus mRNAs alvos, induzindo inibição da tradução e/ou degradação destes transcritos. Durante a diferenciação de células pluripotentes, os miRs podem ser induzidos ou reprimidos, no entanto, suas funções específicas são amplamente inexploradas. Nós investigamos os papéis funcionais de um conjunto selecionado de miRs na pluripotência e diferenciação celular, usando microscopia de fluorescência quantitativa (High Content Analysis). Para isso, foram empregadas a NTera-2 (células de carcinoma embrionário humano, CCE) e a H1 (células-tronco embrionárias humanas, CTEh) como modelos. Essas células foram transfectadas reversamente com trinta moléculas de miRs distintas (individualmente) ou moléculas controles. Após 3-4 dias de cultura, as células foram fixadas, permeabilizadas e coradas com Hoechst / CellMask Blue (núcleo/citoplasma), anti-OCT4, anti-Ciclina B1 e imageadas com um sistema ImageXpress Micro HCA. O CellProfiler foi utilizado para quantificar vários parâmetros morfométricos e medidas de intensidade de OCT4 e Ciclina B1 em compartimentos nucleares e citoplasmáticos. Esses dados foram usados para gerar perfis fenotípicos multiparamétricos específicos de cada miR (usando KNIME) e o agrupamento desses dados levou à identificação de vias e processos envolvidos na indução de características de pluripotência ou diferenciação celular causadas por miRs com efeitos fenotípicos similares. Como exemplo, as vias de PI3K-AKT, WNT, TGF? e DICER foram encontradas como moduladas por alguns clusters fenotípicos e os transcritos de alguns alvos foram avaliados por qPCR para validar os achados. Parte do trabalho foi focada na regulação da via Notch por miRNAs em células pluripotentes, o que levou à observação de que o miR- 363-3p inibe a sinalização de Notch e promove pluripotência nessas células. A transfecção de miR-363-3p não apenas elevou as características de pluripotência em NTera-2 e H1, mas também protegeu as CCE da diferenciação induzida por cocultivo com OP9 expressando DLL1 e causou a diminuição no nível de transcritos de PSEN1. Em conclusão, o ensaio desenvolvido aqui provou ser uma ferramenta robusta na detecção de mecanismos moleculares, baseando-se na combinação de análises fenotípicas funcionais e bioinformáticas. / microRNAs (miRs) play an important role in stem cell\'s biology by binding to target mRNAs transcripts, inducing translation blockage and/or transcripts degradation. Upon differentiation of pluripotent cells, miRNAs can be induced or repressed, however, their specific roles are largely unexplored. We investigated the functional roles of a selected set of miRs in pluripotency and differentiation, using quantitative automated fluorescence microscopy (High Content Analysis). For this, we used NTera-2 (human embryonal carcinoma cells, ECC) and H1 (embryonic stem cells; ESC) as models. These cells were reverse-transfected with thirty distinct miRs mimics (individually) or control molecules. Following 3-4 days of culture, cells were fixed, permeabilized and stained with Hoechst/CellMask Blue (nucleus/cytoplasm), antiOCT4, anti-Cyclin B1 and imaged using an ImageXpress Micro HCA System. CellProfiler was used to quantify several morphometric parameters and intensity measurements of OCT4 and CYCB1 in nuclear and cytoplasmic compartments. Quantified parameters were used to generate miR-specific multiparametric phenotypic profiles (using KNIME) and clustering these data led to identification of pathways and processes involved in the induction of pluripotency or cell diferention features caused by miRs with similar phenotypic effects. As an example, PI3K-AKT, WNT, TGF? and DICER pathways were found to be regulated by some phenotypic clusters and transcripts level of some of miR targets were evaluated by qPCR to validate de findings. Part of the work was focused in the regulation of Notch pathway by miRNAs in pluripotent cells, which led the observation that miR-363-3p inhibits Notch signaling and promotes pluripotency feature, as the transfection with miR-363-3p mimic not only enhanced pluripotent phenotype in NTera-2 and H1, but also protected de ECCs from differentiation induced by coculture with OP9 expressing DLL1 and decreased PSEN1 transcripts level.In conclusion, The assay developed here proved to be a robust tool in the detection of molecular mechanisms based on combined functional phenotypic and bioinformatic analyzes.

Os microRNAs (miRs) desempenham um papel importante na biologia das células-tronco por meio da interação com seus mRNAs alvos, induzindo inibição da tradução e/ou degradação destes transcritos. Durante a diferenciação de células pluripotentes, os miRs podem ser induzidos ou reprimidos, no entanto, suas funções específicas são amplamente inexploradas. Nós investigamos os papéis funcionais de um conjunto selecionado de miRs na pluripotência e diferenciação celular, usando microscopia de fluorescência quantitativa (High Content Analysis). Para isso, foram empregadas a NTera-2 (células de carcinoma embrionário humano, CCE) e a H1 (células-tronco embrionárias humanas, CTEh) como modelos. Essas células foram transfectadas reversamente com trinta moléculas de miRs distintas (individualmente) ou moléculas controles. Após 3-4 dias de cultura, as células foram fixadas, permeabilizadas e coradas com Hoechst / CellMask Blue (núcleo/citoplasma), anti-OCT4, anti-Ciclina B1 e imageadas com um sistema ImageXpress Micro HCA. O CellProfiler foi utilizado para quantificar vários parâmetros morfométricos e medidas de intensidade de OCT4 e Ciclina B1 em compartimentos nucleares e citoplasmáticos. Esses dados foram usados para gerar perfis fenotípicos multiparamétricos específicos de cada miR (usando KNIME) e o agrupamento desses dados levou à identificação de vias e processos envolvidos na indução de características de pluripotência ou diferenciação celular causadas por miRs com efeitos fenotípicos similares. Como exemplo, as vias de PI3K-AKT, WNT, TGF? e DICER foram encontradas como moduladas por alguns clusters fenotípicos e os transcritos de alguns alvos foram avaliados por qPCR para validar os achados. Parte do trabalho foi focada na regulação da via Notch por miRNAs em células pluripotentes, o que levou à observação de que o miR- 363-3p inibe a sinalização de Notch e promove pluripotência nessas células. A transfecção de miR-363-3p não apenas elevou as características de pluripotência em NTera-2 e H1, mas também protegeu as CCE da diferenciação induzida por cocultivo com OP9 expressando DLL1 e causou a diminuição no nível de transcritos de PSEN1. Em conclusão, o ensaio desenvolvido aqui provou ser uma ferramenta robusta na detecção de mecanismos moleculares, baseando-se na combinação de análises fenotípicas funcionais e bioinformáticas. / microRNAs (miRs) play an important role in stem cell\'s biology by binding to target mRNAs transcripts, inducing translation blockage and/or transcripts degradation. Upon differentiation of pluripotent cells, miRNAs can be induced or repressed, however, their specific roles are largely unexplored. We investigated the functional roles of a selected set of miRs in pluripotency and differentiation, using quantitative automated fluorescence microscopy (High Content Analysis). For this, we used NTera-2 (human embryonal carcinoma cells, ECC) and H1 (embryonic stem cells; ESC) as models. These cells were reverse-transfected with thirty distinct miRs mimics (individually) or control molecules. Following 3-4 days of culture, cells were fixed, permeabilized and stained with Hoechst/CellMask Blue (nucleus/cytoplasm), antiOCT4, anti-Cyclin B1 and imaged using an ImageXpress Micro HCA System. CellProfiler was used to quantify several morphometric parameters and intensity measurements of OCT4 and CYCB1 in nuclear and cytoplasmic compartments. Quantified parameters were used to generate miR-specific multiparametric phenotypic profiles (using KNIME) and clustering these data led to identification of pathways and processes involved in the induction of pluripotency or cell diferention features caused by miRs with similar phenotypic effects. As an example, PI3K-AKT, WNT, TGF? and DICER pathways were found to be regulated by some phenotypic clusters and transcripts level of some of miR targets were evaluated by qPCR to validate de findings. Part of the work was focused in the regulation of Notch pathway by miRNAs in pluripotent cells, which led the observation that miR-363-3p inhibits Notch signaling and promotes pluripotency feature, as the transfection with miR-363-3p mimic not only enhanced pluripotent phenotype in NTera-2 and H1, but also protected de ECCs from differentiation induced by coculture with OP9 expressing DLL1 and decreased PSEN1 transcripts level.In conclusion, The assay developed here proved to be a robust tool in the detection of molecular mechanisms based on combined functional phenotypic and bioinformatic analyzes.

Les Tunneling nanotubes (TNT) sont des protrusions cellulaires à base d'actine qui médient la communication cellulaire en transférant des cargos cellulaires. Les différents types de communication intercellulaires sont de plus en plus considérés comme des cibles potentielles pour le traitement de différentes maladies, telles que les maladies infectieuses liées aux virus et bactéries, les cancers ou les maladies neurodégénératives. Des études récentes ont mis en évidence un mécanisme de propagation d'agrégats protéiques ressemblant à la propagation du prion dans diverses maladies neurodégénératives non infectieuses telles que la maladie d'Alzheimer (AD), la démence frontotemporelle (FTD), la maladie de Parkinson (PD) et la maladie de Huntington. Ces maladies se caractérisent par l'accumulation de protéines mal repliées dans le cerveau des patients. Ainsi, on peut envisager de nouvelles stratégies thérapeutiques pour bloquer la propagation des protéines anormales dans tout le cerveau. Il a été démontré que les TNT pourraient jouer un rôle essentiel dans la propagation des agrégats de prions au sein du système nerveux central (SNC) et périphérique. Par conséquent, l'étude du mécanisme de la formation de TNT pourrait fournir de nouvelles idées sur le mécanisme de propagation de la maladie et de nouvelles cibles thérapeutiques. L'objectif de ma thèse était d'étudier le rôle du transfert des agrégats de protéines par les TNT entre les cellules et d'étudier le mécanisme de formation des TNT. Dans notre laboratoire, nous avons déjà montré que les TNT permettent le transfert de prions entre les cellules. Dans la première partie de mon doctorat, j'ai confirmé que les transferts d'agrégats de prions entre les cellules de CAD neuronales se faisaient par les TNT à l'intérieur de vésicules endocytiques (Zhu et al., 2015). De plus, en collaboration avec un collègue, nous avons fourni des preuves que les agrégats de prions pourraient être transférés entre des astrocytes primaires et des neurones et que ce transfert était médié par un contact cellulaire (Victoria et al., 2016). J'ai également collaboré à une autre étude où nous avons montré que les agrégats d'α-synucléine (caractéristiques de la maladie de Parkinson) peuvent être transférés entre les cellules à l'intérieur des lysosomes, et que ce transfert intercellulaire est médié par les TNT (Abounit et al., 2016). Dans mon deuxième projet, afin d'étudier le mécanisme de la formation de TNT, j'ai effectué un crible à haut débit pour les Rab GTPase. J'ai trouvé que Rab8 et Rab11 peuvent favoriser la formation des TNT, et que les cascades Rab8-VAMP3, Rab11-ERM et Rab8-Rab11 sont impliquées dans la formation des TNT. Mes données suggèrent que la polymérisation de l'actine et le trafic de membranes sont impliqués dans la formation des TNT. Ces résultats permettent d'éclairer le mécanisme de la formation des TNT et de fournir des preuves moléculaires que les Rab GTPases régulent ce processus. / Tunneling nanotubes are actin-based cell protrusions that mediate cell-to-cell communication by transferring cellular cargos. The different types of intercellular communication are increasing by being considered as potential targets for the treatment of various diseases, such as infectious diseases linked to viruses and bacteria, cancers or neurodegenerative diseases. Recent studies have highlighted a prion-like mechanism of propagation of protein misfolding in a variety of common, non-infectious, neurodegenerative diseases such as Alzheimer’s disease (AD), Frontotemporal dementia (FTD), Parkinson’s disease (PD), and Polyglutamine (PolyQ) diseases, which are characterized by the accumulation of misfolded proteins in the brain of patients. Thus, new therapeutic strategies to block propagation of protein misfolding throughout the brain can be envisaged. It has been shown that TNTs might play a critical role in spreading of prion aggregates within the CNS and from the periphery. Therefore, the study of mechanism of TNT formation could provide new insights on the mechanism of disease propagation and novel therapeutic targets. The aim of my thesis was to study the role of TNT-mediate protein aggregates transfer between cells and to investigate the mechanism of TNT formation. In our lab, we already reported TNT mediate prion transfer between cells. In the first part of my PhD, I further confirmed that prion aggregates transfer between neuronal CAD cells through TNT inside endocytic vesicles (Zhu et al., 2015). Furthermore in collaboration with a colleague, we provided evidences that prion aggregates could transfer between primary astrocytes and neurons and the transfer was mediated by cell-to-cell contact (Victoria et al., 2016). I also collaborated to another study where we showed that α-synuclein aggregates (Parkinson’s disease) can transfer between cells inside lysosomes, and the intercellular transfer is mediated by TNTs (Abounit et al., 2016).In my second project, in order to investigate the mechanism of TNT formation, I performed a High-content screening of Rab GTPase. I found that Rab8 and Rab11 can promote TNT formation, that Rab8-VAMP3, Rab11-ERM and Rab8-Rab11 cascades are involved in TNT formation. My data suggests that both actin polymerization and membrane trafficking are involved in TNT formation. These results help to shed light on the mechanism of TNT formation, and provide molecular evidences that Rab GTPases regulate this process.