Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by the ectopic expression of defined factors. iPSCs hold great promise for pharmaceutical screening and regenerative medicine but the mechanism of reprogramming is not well understood. This work examines a component process of reprogramming that is the mesenchymal-to-epithelial transition (MET), an important step in the generation of iPS cells. In this thesis I demonstrate a connection between BMP signaling and the reprogramming factor Klf4 in the activation of the MET expression program. Using ChIP-Seq I mapped the binding of Klf4 and BMP Smads across the genome and linked their co-binding to a MET expression program determined by RNA-Seq. My work uncovers a thus-far unreported interaction between Klf4 and BMP signaling in cellular epithelialization that can directly improve the technical methods of reprogramming and have important implications for the induction of epithelial tissues in general.

Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by the ectopic expression of defined factors. iPSCs hold great promise for pharmaceutical screening and regenerative medicine but the mechanism of reprogramming is not well understood. This work examines a component process of reprogramming that is the mesenchymal-to-epithelial transition (MET), an important step in the generation of iPS cells. In this thesis I demonstrate a connection between BMP signaling and the reprogramming factor Klf4 in the activation of the MET expression program. Using ChIP-Seq I mapped the binding of Klf4 and BMP Smads across the genome and linked their co-binding to a MET expression program determined by RNA-Seq. My work uncovers a thus-far unreported interaction between Klf4 and BMP signaling in cellular epithelialization that can directly improve the technical methods of reprogramming and have important implications for the induction of epithelial tissues in general.

Pour comprendre comment les gènes du développement exercent de multiples fonctions temporelles, nous prenons comme modèle le facteur de transcription Otx2. Celui-ci est impliqué dans la gastrulation, le développement de l’œil, du système olfactif, de la glande pinéale, du thalamus et de la région cranio-faciale. Dans la rétine adulte, deux tissus distincts expriment Otx2 : l’épithélium pigmenté (RPE) et la rétine neurale, contenant les photorécepteurs. L’ablation globale du gène Otx2 entraîne la dégénérescence exclusive des photorécepteurs alors qu’elle modifie l’expression de gènes surtout dans le RPE. Ces faits suggèrent un mécanisme non autonome, confirmé par des expériences de gain et perte de fonction restreintes au RPE. Pour approcher les fonctions de la protéine Otx2 dans la rétine neurale et le RPE, une étude à grande échelle de ses cibles génomiques a été menée. Les profils distincts d’occupation du génome du RPE et de la rétine neurale suggèrent des fonctions différentes d’Otx2. Dans la rétine neurale, ce profil est très proche de celui du facteur paralogue Crx, indiquant une redondance fonctionnelle entre Otx2 et Crx. Nous avons émis l’hypothèse qu’une combinatoire de partenaires protéiques différents permet de moduler l’action d’Otx2 en sélectionnant des cibles génomiques distinctes. Pour identifier cette combinatoire in vivo et la corréler aux fonctions exercées par Otx2, nous avons créé une lignée de souris exprimant une protéine de fusion Otx2-TAP-tag à un niveau physiologique. Cet outil permettra la purification des complexes protéiques Otx2 in vivo et leur identification par analyse protéomique. / In the present work, we study the Otx2 transcription factor as a model to understand how developmental genes achieve multiple functions throughout time. Otx2 is first implied in gastrulation, and then participates to the development of the eye, the olfactory system, the pineal gland, the thalamus and the craniofacial region. Otx2 is expressed in two distinct tissues: retinal pigmented epithelium (RPE) and neural retina including photoreceptors. Global Otx2 gene ablation leads to exclusive photoreceptor degeneration although most of the affected genes are RPE specific. These elements suggest a non-cell-autonomous mechanism, confirmed by RPE restricted gain and loss of function. To understand Otx2 functions in the neural retina and in the RPE, a large scale study of its genomic targets has been yielded. Genome occupancy profiles in RPE and neural retina suggest different Otx2 functions. In the neural retina, Otx2 genome occupancy profile is very close to the one of its paralogue Crx, indicating functional redundancy between both transcription factors. We hypothesized that a different combination of protein partners allows modulating Otx2 action by selecting distinct target genes. To identify Otx2 combinatory in vivo and correlate it to Otx2 functions, we produced a mouse line expressing an Otx2-TAP-tag fusion protein at physiological level. This tool will allow purification of Otx2 protein complexes in vivo and their identification by proteomic analysis.

Cette thèse s’intéresse aux mécanismes permettant d’expliquer plusieurs des fonctions de l’homéogène Otx2 au cours du développement. Une première partie étudie l’importance de la régulation de son expression dans la régionalisation du système nerveux central. A la fin de la gastrulation la frontière d’expression postérieure d’Otx2 déterminera la position de l’organiseur isthmique responsable de l’induction du mésencéphale et du métencéphale. Un modèle murin a été mis au point dans lequel cette frontière est abolie au profit d’une présence uniforme du gène. A l’encontre du modèle actuel, l’isthme est alors correctement induit, et est de plus déplacé antérieurement, signe qu’un seuil net de concentration d’Otx2 est nécessaire à sa fonction régionalisante. Une seconde partie étudie l’importance du contexte cellulaire dans les modalités d’action d’Otx2 au niveau de la rétine adulte. Otx2 est exprimé dans les deux tissus qui composent cet organe, la neurorétine et le RPE. Une étude par ChIP-seq dans ces deux tissus a pu montrer que l’homéogène y occupait des sites de fixation très différents, suggérant des fonctions distinctes. L’écrasante majorité des sites occupés par Otx2 dans la neurorétine l’était également par son paralogue Crx, indice d’une redondance fonctionnelle. Une nouvelle lignée de souris a permis l’analyse des partenaires protéiques d’Otx2 dans la neurorétine, et pu démontrer qu’Otx2 ne formait pas d’interactions avec les autres facteurs de ce tissu, faisant en fait de Crx l’acteur principal de la famille Otx. Cette analyse a également dévoilé une série de partenaires jusque-là inconnus d’Otx2, potentiellement associée à de nouvelles fonctions de la protéine. / The molecular mechanisms explaining several functions of the homeogene Otx2 during embryonic development are the focus of this work. In a first part the importance of the regulation of its expression in the regionalisation of the central nervous system is studied. At the end of gastrulation the posterior border of Otx2 expression will position the isthmic organizer responsible for the induction of the midbrain and hindbrain. A mouse model was developed where this border is replaced by an ubiquitous expression of the gene. Contrary to the predictions of the current model, the organizer then correctly arises, and is shifted anteriorly. A concentration threshold of Otx2 thus appears necessary to its regionalising function. In a second part the importance of the cellular context in Otx2 function in the adult retina is examined. Otx2 is expressed in both tissues of this organ, the neural retina and RPE. A ChIP-seq analysis performed on both tissues revealed that this homeogene occupies very different sets of binding sites, which suggests distinct functions of the transcription factor. Most Otx2-bound sites in the neural retina were also bound by its paralogue Crx, with which a functional redundancy may therefore exist. A new mouse line finally allowed the study of the complete Otx2 interactome in the neural retina; this analysis showed that Otx2 does not interact with other important transcription factors of this tissue, and that Crx may therefore be the main actor of the Otx family in neural retina function. It also led to the discovery of a series of previously unknown partners of Otx2, which could be associated to new functions of this homeogene.

La ségrégation active des molécules d'ADN chez les bactéries compte sur l'assemblage d'une structure nucléoprotéique nucléée sur des sites centromerique localisés près de l'origine de réplication. Pour les systèmes de partition de type I, les seuls présent sur les chromosomes et le plus fréquents sur les plasmides a bas nombre de copie, la protéine qui se lie au centromère, ParB, montre la capacité de propagation sur l'ADN à partir de la nucléation au niveau du site centromerique pars. Ainsi, le complèxe de partition contient plus que 90% des ParB présent dans la cellule et interagit avec ParA, une ATPase dont l'activité dépend de ParB et de l'ADN. Deux modèles concurrents qui sont actuellement proposés pour expliquer le mécanisme d'assemblage du complèxe de partition : les modèles de 'spreading and bridging' (Graham et al., 2014), et le 'nucleation and caging' (Sanchez et al., 2015) . Nous avons utilisé le système de partition du plasmide F et pour déterminer si la mode d'assemblage était aussi conservée sur les chromosomes, nous avons étudié le système natif de Vibrio cholerae du chromosome 1. D'abord, nous avons exploré les mécanismes d'incompatibilité basé sur les sites centromériques pour comprendre l'assemblage des complèxes de partition dans les conditions de titrage ParB par le site parS. Ensuite, nous avons décrit un protocole optimisé de ChIP-sequencing à haut-débit, de la paillasse jusqu'à l'analyse des données. Puis, en utilisant le ChIP-sequencing, la microscopie à épifluorescence et la modélisation physico-mathématique, nous avons révélé que l'assemblage du complèxe de partition est robuste et cohérent avec le modèle de 'nucleation and caging' à la fois sur les chromosomes et les systèmes plasmidiques. / The active partition of low copy number plasmids and most bacterial chromosomes relies on the assembly of a nucleoprotein superstructure nucleated at centromere-like sites near the origin of replication. In the case of type I partition systems, the most widespread on plasmids and the only ones present on chromosomes, centromere binding proteins, ParB, display the capability to propagate along DNA from their nucleation point at the centromere-like site, parS. This structure, termed the partition complex, contains over 90% of the available ParB in the cell and interacts with ParA, a ParB- and DNA-dependent ATPase, to segregate and position replicons within the cell. Two concurrent models exist to explain the assembly mechanism of the partition complex: the spreading and bridging (Graham et al., 2014), and the nucleation and caging (Sanchez et al., 2015) models. We used the partition system of the archetypal plasmid F and the naturally occurring partition system of Vibrio cholerae's chromosome 1. First, we explored the mechanisms of centromere-based incompatibilities to gain insight into partition complex assembly in low levels of ParB through parS titration of ParB. Next, we describe an optimized a high- resolution ChIP-sequencing protocol from the lab bench to data analysis. Then, through ChIP-sequencing, epifluorescence microscopy and physico-mathematical modeling, we revealed that the partition complex assembly mechanism is robust and consistent with the nucleation and caging model on both chromosomal and plasmid systems.

De par sa taille (17 Gb), la complexité de son génome (allohexaploïde) ainsi que la forte proportion d’éléments répétés (>80%), l’étude du génome de blé tendre est une tâche particulièrement complexe et s’est souvent retrouvée confrontée aux limites technologies. Grâce une approche de tri de chromosomes, le chromosome 3B (995 Mb) a pu être isolé et séquencé. Ces données ont permis la construction d’une pseudomolécule. Mes travaux de thèse se sont basés sur des données de transcriptomique produites avec une approche RNA-Seq, afin d’investiguer l’impact de la taille de ce chromosome sur l’organisation de l’espace génique. L’annotation du chromosome 3B a permis de mettre en évidence : 5 326 gènes et 1 938 pseudogènes. L’analyse des librairies RNA-Seq pour 15 conditions de développement a permis de mettre en évidence l’expression de 71 % des gènes annotés, ainsi que 3 692 régions nouvellement transcrites (NTR). Nous avons aussi pu détecter des transcrits alternatifs pour 61% des gènes exprimés (en moyenne 6 isoformes). Nous avons donc pu mettre en évidence une structuration de l’espace génique pour le chromosome 3B. En effet, la transcription est répartie sur tout le chromosome, cependant les gènes sont organisés selon un gradient de densité croissant sur l’axe centromère-télomère. En nous basant sur le profil des données de recombinaison, nous avons divisé le chromosome en 3 régions : R1, R2 et R3. La région R2 correspondant à la région centrale du chromosome (647 Mb) où le taux de recombinaison est très faible voir absent. Les régions R1 (58 Mb) et R3 (69 Mb) correspondent respectivement aux parties distales du bras court et du bras long du chromosome, où le taux de recombinaison est le plus fort. Ces trois régions diffèrent par leur niveau et leur spécificité d'expression, ainsi que par leur structure génique (nombre d'exons, taille des introns …). En effet, les gènes ayant une expression tissu-spécifique, ainsi qu’un faible nombre de transcrits alternatifs sont retrouvés dans les régions R1 et R3. Deux modèles peuvent expliquer le lien observé entre la structure des gènes et leur niveau/spécificité d’expression : le modèle de la sélection pour l’économie et le modèle dessin génomique. En conclusion, ce travail a montré et ce, pour la première fois à l’échelle d’un chromosome entier de blé, l’impact de la taille du chromosome sur l’organisation ; mettant en relation la structure des gènes, leur niveau d’expression, leur spécificité d’expression, ainsi que leur nature évolutive. L’assemblage ainsi que l’annotation de pseudomolécules des autres chromosomes permettra de mettre en évidence si cette structure est conservée. Afin de mieux comprendre les mécanismes cellulaires impliqués dans la régulation de l’expression des gènes, une étude du paysage épigénomique a été engagée. / Genome-wide studies of the bread wheat are a complicated task due to its large size (17 Gb), its allohexaploidy and its high content in repeat sequences (>80%). Using a chromosome-specific approach, the chromosome 3B (995 Mb) was successfully isolated and sequenced leading to the assembly of one pseudomolecule. The work presented in this thesis investigated the impact of the 3B chromosome size on the gene space organization. Production of transcriptomic data was achieved using RNA-Seq approach. The chromosome 3B was annotated and we predicted 7 264 features, including 5 326 full genes and 1 938 pseudogenes. We constructed RNA-Seq libraries for 15 developmental wheat conditions. Using this data we detected expression of 71.4% of the predictions, and 3 692 novel transcribed regions (NTR). We also detected alternative transcripts for 61% of the expressed genes, with 5.8 isoforms on average for one gene. Using these transcriptional data, we highlighted a partitioning of the chromosome 3B gene space. Indeed, transcription was found all along the chromosome, but genes were organized according to an increasing density gradient along the centromere-telomere axis. Based on recombination profile, we segmented the chromosome in 3 major regions: R1, R2 and R3. The region R2 was identified with low or no recombination rate corresponding to the centromeric and peri-centromeric regions (647 Mb). The regions R1 and R3 were associated with a higher recombination rate, both localized on the distal part of the short arm (58 Mb) and the long arm (69 Mb) respectively, where the recombination rate is higher. All three regions showed distinct level and specificity of gene expression as well as unique gene structure (variation size, exon number, intron size). Indeed, genes expressed in a specific condition and with a small number of alternatives transcripts were localized on regions R1 and R3. We showed that two evolutionary model could explain the link between gene structure and the level/specificity of expression : “selection for economy” and “genome design”. In conclusion, a transcriptomic studies was achieved along the 3B chromosome for the first time. This study demonstrated a relationship between gene characteristics (structure, expression level, expression specificity and evolution) and the chromosome 3B organization. Future pseudomolecule assemblies will help us to assess the structural organization of these chromosomes. In order to better understand the cellular mechanisms of gene expression, an epigenomic study of the 3B chromosome was started.

The Nelore breed represents the vast majority of Brazilian Zebuine cattle (Bos taurus indicus). The great adaptability of the Nelore breed to Brazilian tropical climate, however, is not associated with meat tenderness (MT). It is known that MT is influenced by several environmental factors, but also genetic composition. In the first chapter, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® Bovine High Density SNP-chip data for a Nelore population of 723 males including 30 sires. We detected >2600 CNV regions (CNVRs) representing ≈6.5% of the Bos taurus genome. The CNVR size was 65 kb on average, ranging from 5 kb to 4.3 Mb. A total of 1155 CNVRs (43.6%) overlapped 2750 genes. They are enriched for important functions such as immune response, olfactory reception and processes involving guanosine triphosphate (GTP). The GTP processes have known influence in skeletal muscle physiology and morphology. Quantitative trait loci for MT, partly specific for Nelore, overlapped a substantial fraction of CNVRs and two CNVRs were found proximal to glutathione metabolism genes that are associated with MT as well. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). We selected 9 CNVRs that overlapped regions associated with MT and we validated them in all 30 sires by qPCR. There was identified many genomic regions of structural variation in Nelore with important implications on the MT phenotype. In the second chapter, a total of 34 animals of the population were subjected to transcriptome analysis and meat tenderness (MT) phenotyping. We identified 170 CNV fragments (CNVFs) residing in 20 CNVRs, which occurred in different frequencies between animals with tougher and softer meat genetic potential. A considerable fraction of the identified CNVFs affected gene expression of the MT genes, which play important roles in glycogen metabolism, connective tissue turnover, membrane transporters and glutathione pathways. We also detected that several CNVRs substantially influenced the expression of overlapped and nearby genes, where the increase or decrease of copy number correlated well with the change in gene expression. Among them are two CNVRs at chromosomes 12 and 23, which are in the vicinity of previously described QTLs for MT in Nelore breed. Several CNVFs, which are more frequent in animals with genetic potential for softer or tougher MT, showed significant differences in gene expression. Those regions are linked to important biological functions with highly relevant influences on MT and skeletal muscle physiology. / A raça Nelore é predominante no rebanho zebuíno brasileiro (Bos taurus indicus). A grande adaptabilidade da raça Nelore ao clima tropical brasileiro, no entanto, não está associada à maciez de carne (MT). Sabe-se que MT é influenciada por vários fatores ambientais e pela composição genética. Foi realizada uma análise de todo o genoma para inferir Variação no Número de Cópias de Segmentos Genômicos (Copy Number Variation - CNV) a partir de dados oriundos de chip de SNP (Illumina® Bovine High Density), para uma população de 723 machos Nelore, incluindo 30 ancentrais da população. Foram detectadas >2600 regiões de CNV (CNVRs) representando ≈6.5% do genoma bovino. O tamanho médio do CNVR foi de 65 kb, variando de 5 kb até 43 Mb. Um total de 1155 CNVRs (43.6%) obtiveram sobreposição com 2750 genes. Estes genes foram enriquecidos para as funções importantes, tais como resposta imunológica, recepção olfativa e processos que envolvem o trifosfato de guanosina (GTP). As vias metabólicas do GTP conhecidamente influenciam a fisiologia e a morfologia do músculo esquelético. Loci de características quantitativas (QTLs) para MT, alguns específicos para Nelore, sobrepuseram uma fração substancial das CNVRs encontradas. Dois CNVRs foram encontrados em região proximal à genes do metabolismo da glutationa os quais também são associados com MT. Comparando os resultados com estudos anteriores ≈1400 CNVRs (>50%) foram sobrepostos. Nove CNVRs em regiões associadas com MT foram validados nos 30 ancentrais por qPCR. Em conclusão, foram identificadas regiões genômicas de variação estrutural no Nelore, com potenciais implicações sobre o fenótipo MT. No segundo capítulo, um total de 34 animais da população foi submetido à análise do transcriptoma e análise de potencial genético para MT. Foram identificados 170 fragmentos de CNV (CNVFs) mapeados em 20 CNVRs, os quais mostraram frequências significativamente diferentes entre animais com potencial genético para carne mais dura ou mais macia. Uma fração considerável dos CNVFs identificados afetaram a expressão gênica de genes MT (anteriormente descritos como associados à MT ou fisiologia do músculo esquelético), os quais desempenham um papel importante no metabolismo de glicogênio, volume do tecido conjuntivo, transportadores de membrana e vias metabólicas da glutationa. Um número considerável de CNVRs foram associados à expressão de genes sobrepostos e nas proximidades, onde o aumento ou diminuição do número de cópias foi associado com a mudança na expressão gênica. Dois CNVRs associados foram mapeados para os cromossomo 12 e 23, estando próximos a QTLs anteriormente descritos para MT na raça Nelore. Vários CNVFs, entre animais com potencial genético para carne mais macia ou dura, mostraram diferenças significativas na expressão gênica. Essas regiões estão ligadas a importantes funções biológicas com influências altamente relevantes para MT e para a fisiologia do músculo esquelético.

Submitted by ELKIN FERNANDO RODAS MENDOZA null (elferodas@yahoo.es) on 2016-09-24T23:11:18Z No. of bitstreams: 1 Tese Final.pdf: 4482779 bytes, checksum: 749ee0c558bf2e2ec8bbdc14d079523e (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-09-27T14:22:47Z (GMT) No. of bitstreams: 1 mendoza_efr_dr_jabo.pdf: 4482779 bytes, checksum: 749ee0c558bf2e2ec8bbdc14d079523e (MD5) / Made available in DSpace on 2016-09-27T14:22:47Z (GMT). No. of bitstreams: 1 mendoza_efr_dr_jabo.pdf: 4482779 bytes, checksum: 749ee0c558bf2e2ec8bbdc14d079523e (MD5) Previous issue date: 2016-08-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Xanthomonas citri subsp. citri (Xac) é o agente causal do cancro cítrico, uma das principais doenças que acometem a citricultura mundial. Atualmente não há uma maneira eficiente de controle do cancro, e novos métodos devem ser desenvolvidos para o tratamento desta doença. Assim, o estudo dos mecanismos utilizados pela Xac durante o processo infeccioso pode revelar novos alvos para o desenvolvimento de compostos farmacológicos que possam eliminar ou controlar o patógeno. Neste estudo, a técnica de RNA-Seq foi utilizada para a identificação de genes diferencialmente expressos (GDE) na Xac em condições in vivo e in vitro. Para isso, cinco variedades de citros com níveis diferentes de suscetibilidade ao cancro cítrico, e meios de cultura indutores de fatores de virulência foram utilizados. Muitos dos genes que codificam para proteínas relacionadas ao sistema de secreção tipo 3 (T3SS), enzimas extracelulares, resposta ao estresse oxidativo, transportadores de ferro e fósforo foram induzidos pela Xac nas condições in vivo. No entanto, in vitro, os perfis de expressão para estes mesmos genes foram diferentes. Estes dados permitiram compreender melhor o ambiente intracelular do hospedeiro, e como este se relaciona com os mecanismos de ativação dos fatores de virulência e patogenicidade de Xac. Neste sentido, os dados apresentados neste estudo mostraram que o T3SS é o principal fator de virulência expresso por esta bactéria em condições in vivo. Além disso, nossos resultados sugerem também que as baixas concentrações de fósforo inorgânico (Pi) e nitrogênio que a bactéria percebe no apoplasto das plantas, são interpretadas como sinais para a ativação do T3SS. Mutações realizadas em genes relacionados com o transporte de Pi (∆phoR e ∆pstB) em Xac demostraram a perda de virulência por alteração na expressão dos genes do T3SS. Assim, estes dados demostram pela primeira vez em Xac um possível mecanismo de regulação entre o sistema de transporte de Pi e o T3SS. Este estudo revelou diferentes fatores de virulência e patogenicidade utilizados pela Xac para vencer as defesas da planta, o que permitirá levantar hipóteses sobre a identificação de possíveis alvos quimioterapêuticos para o tratamento do cancro. / Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker, a major disease affecting citrus worldwide. Currently there is no effective way of cancer control, and new methods must be developed for the treatment of this disease. Thus, the study of the mechanisms used by Xac during the infectious process can reveal new targets for the development of pharmacologic compounds that can eliminate or control the pathogen. In this study, RNA-Seq technique was used to identify Xac differentially expressed genes (DEG) in vivo and in vitro conditions. For this purpose, five citrus varieties with different levels of susceptibility to citrus canker and culture mediums inducing virulence factors were used. Many of the genes encoding proteins of the type 3 protein secretion system (T3SS), extracellular enzymes, oxidative stress response, iron and phosphorus transport were induced in Xac in vivo conditions. However, the expression profiles for these same genes were different than observed in vitro conditions. These data allowed us to better understand the intracellular environment of the host, and how this relates to the activation mechanisms of pathogenicity and virulence factors in Xac. In this context, the data presented in this study show the T3SS as the main virulence factor expressed by the bacteria in vivo conditions. Furthermore, our results also suggest that low concentrations of inorganic phosphorus (Pi) and nitrogen, that bacteria sense in the plant apoplast, are interpreted as signals to activation of the T3SS. In this respect, mutations carried out in genes related to the transport of Pi (ΔphoR and ΔpstB) in Xac demonstrated loss of virulence by altering the expression of T3SS genes. Thus, these data identifies for the first time in Xac a possible regulatory mechanism between Pi transport system and T3SS. This study revealed different virulence and pathogenicity factors used by Xac to overcome the plant defenses. These discoveries allow raise hypotheses about the identification of potential chemotherapeutic targets to canker treatment.

A melatonina é um antioxidante muito eficaz e protege as células contra o estresse oxidativo causado pelas espécies reativas, e indiretamente, modula a expressão de genes associados ao ciclo celular, metabolismo oxidativo e apoptose celular. Deste modo, a suplementação da melatonina ao meio de maturação in vitro, a torna uma alternativa para promover melhorias na viabilidade das células germinativas e embrionárias. O estudo 1 avaliou o efeito da adição de melatonina ao meio de maturação por meio da maturação nuclear (progressão meiótica) e citoplasmática (migração de grânulos corticais) e dos níveis de ROS em oócitos suínos maturados in vitro. A suplementação do meio de maturação com melatonina estimulou a progressão da meiose, a migração de grânulos corticais e reduziu os níveis intracelulares de ROS nos oócitos. O estudo 2 avaliou o efeito da melatonina na expressão de genes antioxidantes (Catalase, SOD1, SOD2 e GPX) envolvidos na proteção celular de oócitos e células do cumulus. A adição da melatonina ao meio de maturação influenciou positivamente a expressão dos genes antioxidantes nos oócitos e células do cumulus. O estudo 3 avaliou o efeito da melatonina nos processos biológicos por meio do perfil de trascriptomas, via RNA-Seq, em células do cumulus oriundas de oócitos suínos maturados in vitro. A partir da análise de expressão diferencial foi possível identificar que a adição da melatonina ao meio de maturação influenciou 80 genes associados a nove processos biológicos (ciclo celular; proteólise; organização de citoesqueleto; via energética; adesão e transporte celular; via de sinalização; fator de transcrição; metabolismo oxidativo e apoptose; e componente celular). A suplementação do meio de maturação com melatonina potencialmente influencia a viabilidade e o funcionamento celular, uma vez que modulou a expressão de genes associados à processos fisiológicos essenciais, tais como: divisão celular, metabolismo energético e oxidativo, vias de sinalização e apoptose. O estudo 4, avaliou o efeito da melatonina sobre os genes associados à viabilidade oocitária e o subsequente desenvolvimento embrionário por meio do perfil de trascriptomas, via RNA-Seq, de células do cumulus oriundas de oócitos suínos. A adição da melatonina ao meio de maturação influenciou 59 genes associados a nove funções biológicas (expansão do cumulus, comunicação em COCs, maturação nuclear, maturação citoplasmática, reparo e integridade do DNA, viabilidade oocitária, esteroidogênese, fertilização e embriogênese). Em conclusão, a suplementação do meio de maturação com melatonina influencia positivamente a maturação oócitária, reduz os níveis intracelulares de ROS, aumenta a expressão de genes antioxidantes, em adição, interfere no transcriptoma de um número expressivo de genes associados à aquisição da competência oócitária, da viabilidade embrionária e desenvolvimento subsequente. / Melatonin is a very effective antioxidant and protects cells against oxidative stress caused by reactive species, and indirectly modulates expression of genes associated with cell cycle, oxidative metabolism, and apoptosis. Thus, melatonin supplementation to in vitro maturation media becomes an alternative to improve the viability of germ and embryonic cells. The first study assessed the effects of adding melatonin to the maturation medium on nuclear (meiotic progression) and cytoplasmic (cortical granules migration) maturation and ROS levels in in vitro matured porcine cumulus-oocyte complexes (COCs). Melatonin supplementation stimulated meiosis progression and cortical granules migration, and reduced intracellular ROS levels in oocytes. The second study evaluated the effects of melatonin on the expression of antioxidant genes (Catalase, SOD1, SOD2, and GPX) involved in cellular protection in oocytes and cumulus cells. The addition of melatonin to the maturation medium positivity influence the expression of antioxidant genes in oocytes and cumulus cells. The third study evaluated the effect of melatonin on genes associated with biological processes through transcriptomic profile via RNA-Seq in cumulus cells derived from porcine COCs in vitro matured. Melatonin addition to maturation medium differentially affected expression of 80 genes associated with nine biological processes (cell cycle, proteolysis, cytoskeletal organization, energy pathaway, cell adhesion and transport, signalling pathway, transcription factor, oxidative metabolism and apoptosis, and cell components). The fourth study assessed the effect of melatonin on genes associated with oocyte viability and subsequent embryo development through transcriptomic profile via RNA-Seq in cumulus cells derived from porcine COCs. Melatonin in the maturation medium affected 59 genes associated with nine biological functions related with oocyte viability and embryo development (cumulus expansion, communication between cumulus cells and oocytes, nuclear maturation, cytoplasmic maturation, DNA repair and integrity, oocyte viability, steroidogenesis, fertilization and embryogenesis). In conclusion, supplementation of melatonin to maturation environment influences oocyte nuclear and cytoplasmic maturation, reduces intracellular ROS levels, positivity influence the expression of antioxidant and also interferes in the transcriptome of a significant number of genes associated with oocyte competence acquisition, embryo viability and subsequent development.

As leishmanioses são um conjunto de doenças causadas pela infecção com protozoários do gênero Leishmania. No Brasil, o parasita L. infantum provoca a manifestação de uma doença sistêmica e crônica, conhecida como leishmaniose visceral (VL), que, quando não tratada, pode levar o indivíduo à óbito. A gravidade da leishmaniose visceral vem sendo associada ao aumento do nível sistêmico de IL- 6 em pacientes sintomáticos. Ainda não está claro como o aumento dessa citocina coordena a progressão da doença. Nós demonstramos durante a infecção por L. infantum experimental há produção dessa citocina nos órgãos alvos. Em decorrência dessa via, animais deficientes para IL-6 (IL-6-/-) são suscetíveis a infecção por apresentar maior número de parasitos nos órgãos alvo e por desenvolverem uma fraca resposta inflamatória em função da diminuição do infiltrado inflamatório. Como consequência, há o aumento de CXCL2 que medeia o recrutamento de neutrófilos no baço. Apesar de aumentada em animais IL-6-/- os neutrófilos apresentam um estado menos ativado. A produção dos principais mediadores de morte dos parasitos, como espécies reativas de oxigênio (ROS) e o óxido nítrico (NO), estão comprometidas e favorecem a disseminação do parasito em animais IL-6-/-. Por outro lado, a Il-6 não interfere na produção de citocinas pró-inflamatórias e na proliferação de linfócitos Th1, atuando somente em linfócitos Th17 no início da infecção, sugerindo que o controle da resposta inflamatória é dependente de mecanismos inatos. Em humanos, identificamos dois genes modulados pela via de sinalização da IL-6. Os genes Hsbp1 e AR estão up-regulados em pacientes com a doença ativa e são genes associados com a migração e a produção de neutrófilos na medula óssea, possivelmente envolvidos com a neutropenia em pacientes com LV. Juntos, os dados mostram que a via de sinalização da IL-6 tem papel importante na modulação da resposta imune de neutrófilos, e em promover proteção durante a LV. / Leishmaniasis is a group of diseases caused by infection with protozoa of the genus Leishmania. In Brazil, the parasite L. infantum causes the manifestation of a systemic and chronic disease, known as visceral leishmaniasis (VL), which, when left untreated, can lead to death. The severity of visceral leishmaniasis has been associated with an increase in the systemic level of IL-6 in symptomatic patients. It is not yet clear how the increase in this cytokine coordinates the progression of the disease. We demonstrated during the infection by experimental L. infantum there is production of this cytokine in the target organs. As a result of this pathway, IL-6 ( IL- 6-/-) deficient animals are susceptible to infection because they present a higher number of parasites in the target organs and they develop a poor inflammatory response due to the decrease of the inflammatory infiltrate. As a consequence, there is an increase in CXCL2 that mediates the recruitment of neutrophils in the spleen. Although increased in IL-6-/- animals the neutrophils have a less activated state. The production of the main mediators of parasite death, such as reactive oxygen species (ROS) and nitric oxide (NO), are compromised and favor the spread of the parasite in IL-6-/- animals. On the other hand, IL-6 does not interfere in the production of proInflammatory cytokines and Th1 lymphocyte proliferation, acting only on Th17 lymphocytes at the beginning of the infection, suggesting that the control of the inflammatory response is dependent on innate mechanisms. In humans, we identified two genes modulated by the IL-6 signaling pathway. The Hsbp1 and AR genes are up-regulated in patients with the active disease and are genes associated with the migration and production of neutrophils in the bone marrow, possibly involved with neutropenia in patients with VL. Together, the data show that the IL-6 signaling pathway plays an important role in modulating the neutrophil immune response, and in promoting protection during LV.