<p>Triple Negative Breast Cancer (TNBC) is the most aggressive type of breast cancer. TNBC patients are resistant to virtually all target therapies and suffer a higher post-chemotherapy relapse with a worse overall survival compared with other types of breast cancers. Therefore, the development of an effective therapy is urgently needed. PKM2 plays a prominent role in mediating<b> </b>tumor glycolysis and PKM2 is often overexpressed in human cancers. However, whether PKM2 mediated glycolysis is necessary for cancer cell growth is questionable. Here, I have found that inhibition of PKM2 does not affect TNBC cell growth due to a metabolic switch from glycolysis to fatty acid oxidation (FAO). We show that PKM2 directly interacts with EZH2 to coordinately mediate epigenetic silencing of SLC16A9, transporter of a key player in FAO, Carnitine. Inhibition of either PKM2 or EZH2 increases levels of SLC16A9 and intracellular Carnitine to promote FAO and thereby sustains cancer cell growth. Direct inhibition of EZH2 using a clinically tested EZH2 inhibitor, GSK126, is able to elicit a previously unidentified vulnerability to a clinically tested FAO inhibitor, Etomoxir. As a result, combined GSK126-Etomoxir treatment synergistically abolishes TNBC xenograft tumor growth in vivo. Together, this study uncovers PKM2-EZH2 mediated metabolic reprogramming that leads to a new drug combination therapy by dual targeting of EZH2 and FAO for effective treatment of TNBC.<b> </b></p> <p> </p> <p>Furthermore, Dendritic Cell (DC) vaccination has shown promise in treating cancer patients. However, the <i>in vitro</i> generation of a fully functional DC remains a big challenge in this field. EZH2 inhibition has shown to be able to create an immunologically ‘hot’ tumors. Nonetheless, the role of EZH2 in regulation of DC function is still unclear. I found that the expression levels of EZH2 and its functional maker, H3K27Me3, are enhanced following maturation from immature DC (iDC) into two functional DCs, α-type 1-polarized-DC (αDC) and gold standard DC (sDC). Moreover, inhibition of EZH2 by GSK126 treatment elicits a dependency of sDC on FAO. These results suggest that EZH2 plays a role in maturation of DC through metabolic reprogramming, which may also provide new DC based immunotherapy of TNBC. </p>

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RNA interference (RNAi) is an important pathway that regulates gene expression in several organisms. The role of RNAi in post-transcriptional gene silencing in the cytoplasm is well characterized. In contrast, the role of RNAi components in the nucleus remains to be elucidated. Previous reports have indicated that RNAi components (Dicer and Argonaute proteins) and small RNAs act in the nucleus to regulate various pathways including heterochromatin formation, transposable elements repression, RNA Pol II processivity and alternative splicing. Nuclear Ago1 and Dicer have also been found to associate with active promoters and enhancers in mammalian cells, however their functional roles and mechanisms remain elusive. In this work, I investigated the functional role of nuclear RNAi components in gene expression regulation during skeletal muscle differentiation. To address this question, I undertook genomic and biochemical approaches applied to myogenic cells (C2C12) as a model system. I found that Ago1 and Dicer are present in the nucleus of C2C12 cells and expressed during differentiation. Chromatin Immunoprecipitation (ChIP) coupled with high throughput sequencing and quantitative real-time PCR indicate that Ago1 and Dicer are enriched at promoters and enhancer regions of myogenic genes. Interestingly, I found that depletion of Ago1 and Dicer reduces enhancer RNAs (eRNAs) levels at enhancer regions and expression of MyoD during differentiation. I observed that loss of Ago1 impacts differentiation, whereas, loss of Dicer leads to cell death and has severe effects on C2C12 cells. Moreover, using Chromosome Conformation Capture (3C), I revealed that Ago1 is involved in enhancer-promoter interaction at MyoD locus. The knockdown of Ago1 destabilizes these interactions and decreases the expression of MyoD. Finally, I demonstrated that Ago1 binds to eRNAs and interacts with CBP Acetyl-transferase in the nucleus of myotube cells. Ago1 depletion leads to loss of eRNA-CBP interaction and consequent impairment of CBP acetyltransferase activity and failure of MyoD mediated activation of the myogenic program. Taken together, these finding indicate that nuclear Ago1 together with eRNAs and CBP regulates MyoD expression by stimulating histone acetylation during differentiation. This study uncovered a novel function of chromatin associated Ago1 in gene expression regulation during mammalian skeletal muscle differentiation.

There is a genome in a cell, as everyone knows, but there is also an epigenome. The epigenome regulates the transcription of the underlying genome. In the last decade, it was discovered that the epigenome state and its regulation are important for differentiation and development. Correlation studies with aging samples had led to the hypothesis that misregulation of the epigenome causes aging and cancer. Furthermore, diseases were identified which are caused by errors in the epigenome state and its regulation. Identification of erroneous epigenome states and misregulation requires the prior knowledge of the common state. Several studies aim at measuring epigenome states in different organisms and cell types and thus, provide a huge amount of data. In this dissertation, a pipeline is developed to analyze and characterize histone modifications with respect to different cell types. Application of this pipeline is shown for a published data set of mouse consisting of data for H3K4me3, H3K27me3, and H3K9me3 measured in embryonic stem cells, embryonic fibroblasts and neuronal progenitors. Furthermore, methods for the detection of the epigenetic patterns are presented in this dissertation. Therefore, a segmentation method is developed to segment the genome guided by the data sets. Based on this segmentation, the epigenome states as well as epigenetic variation can be studied. Different visualization methods are developed to highlight the epigenetic patterns in the segmentation data. Application of the segmentation AND visualization methods to the mouse data set had resulted in not only colorful squares but also in biological conclusions! It demonstrate the power of the developed methods. Although the studied data set in this dissertation contains only ordinary tissue cells, the methods are not restricted to study the reference epigenome state. Comparison of normal and disease cells as well as comparison with aged cells are possible with all of the methods. Finally, the methods are compared based on the obtained results. It shows that all methods highlight different aspects of the data. Thus, applying all methods to the same data sets, deep insights into the epigenome in murine embryonic stem cells, embryonic fibroblasts and neuronal progenitor cells are gained. For example, it had been found that several mechanisms exist setting H3K4me3 marks. Furthermore, not all mechanisms are found in all cell types. Strong evidence had been found that catalysis of H3K4me3 and H3K27me3 is coupled.

Neurodevelopmental risk factors have assumed a critical role in prevailing notions concerning the etiopathogenesis of neuropsychiatric disorders. Staging, diagnostic elements at which phase of disease is determined, provides a means of conceptualizing the degree and extent of factors affecting brain development trajectories, but is concurrently specified through the particular interactions of genes and environment unique to each individual case. For present purposes, staging perspectives in neurodevelopmental aspects of the disease processes are considered from conditions giving rise to neurodevelopmental staging in affective states, adolescence, dopamine disease states, and autism spectrum disorders. Three major aspects influencing the eventual course of individual developmental trajectories appear to possess an essential determinant influence upon outcome: (i) the type of agent that interferes with brain development, whether chemical, immune system activating or absent (anoxia/hypoxia), (ii) the phase of brain development at which the agent exerts disruption, whether prenatal, postnatal, or adolescent, and (iii) the age of expression of structural and functional abnormalities. Clinical staging may be assumed at any or each developmental phase. The present perspective offers both a challenge to bring further order to diagnosis, intervention, and prognosis and a statement regarding the extreme complexities and interwoven intricacies of epigenetic factors, biomarkers, and neurobehavioral entities that aggravate currents notions of the neuropsychiatric disorders.

La télomérase est présente dans un nombre limité de cellules, telles que la plupart des cellules cancéreuses où son activité est indispensable pour l’immortalisation de ces dernières. C’est pourquoi cette enzyme a été proposée comme cible prometteuse pour des thérapies anticancéreuses. Ainsi, il est d’un intérêt certain d’identifier les mécanismes par lesquels elle est régulée, notamment via sa sous-unité catalytique, hTERT. Les rétinoïdes sont des inducteurs bien connus de la maturation granulocytaire associée à une répression de hTERT dans les blastes de leucémie aiguë promyélocytaire (LAP). Dans une lignée cellulaire LAP résistant à la maturation induite par les rétinoïdes (NB4-LR1), a précédemment été identifiée une nouvelle voie de répression transcriptionnelle de hTERT en absence de différenciation. De plus, mon laboratoire d’accueil a isolé un variant de la lignée NB4-LR1 résistant à cette répression transcriptionnelle de hTERT, la lignée NB4-LR1SFD. Ensemble, ces lignées cellulaires, qui se comportent différemment face à un traitement à l’ATRA, fournissent un outil unique et puissant pour obtenir plus d’informations sur plusieurs problèmes de la régulation de la biologie moléculaire de la télomérase. Dans cette étude, en utilisant plusieurs approches complémentaires (immunoprécipitation de la chromatine combinée à une technique d’analyse à haut débit du positionnement des nucléosomes et de la méthylation de l’ADN et une approche de FISH), j’ai pu obtenir une vue intégrée des événements épigénétiques qui promeuvent la transition du promoteur de hTERT d’un état silencieux à un état actif et inversement. Cette information sera cruciale pour le développement de stratégies anticancéreuses ciblant l’expression de hTERT. / Telomerase is present in a limited number of cells, most of them cancerous where its activity is crucial for their immortalisation. Thus, that enzyme has been proposed as a promising target for anticancer therapies. Therefore, it is of great interest to identify the mechanisms by which it is regulated, notably through its catalytic subunit hTERT. Retinoids are well-known inducers of granulocytic maturation associated with hTERT repression in acute promyelocytic leukemia (APL) blasts. However, in NB4-LR1, a maturation-resistant APL cell line, was previously identified a new pathway of retinoid-induced hTERT transcriptional repression independent of differentiation. Furthermore, my host lab reported the isolation of a variant of NB4-LR1 cells resistant to this repression: NB4-LR1SFD. These two cell lines, which behave distinctly in response to ATRA treatment, provide a unique and interesting tool to gain further insights into the molecular biology of telomerase regulation. In this thesis project, using several complementary approaches (chromatin immunoprecipitation combined to a high-resolution, single-molecule nucleosome positioning assay and DNA methylation, and a FISH approach) allowed me to shed more light on the integrated epigenetic events that lead to hTERT promoter transition from its silent to its active state and vice versa. The information obtained could be crucial for the development of anticancer strategies targeting hTERT expression.

Orientador: Lourdes Campaner dos Santos / Resumo: Os microrganismos são considerados uma fonte promissora de substâncias com potencial biológico e de alta capacidade biossintética para produção de novas substâncias com aplicação em diversas áreas tais como agricultura, medicina e alimentos. Os fungos endofíticos colonizam o interior das plantas e tem demonstrado grande importânica na produção de metabólitos secundários bioativos. Dessa forma, este trabalho foi idealizado objetivando a bioprospecção dos extratos produzidos por fungos endofíticos associados à Paepalanthus planifolius, espécie vegetal do Cerrado, e a avaliação epigenética em Aspergillus terreus, isolado de espécie vegetal do Deserto de Sonora, na obtenção de novas substâncias. Os fungos endofíticos isolados de P. planifolius (15 linhagens) foram cultivados em escala reduzida em meio líquido de batata e dextrose (PDB), a 25 oC, sob modo estático para obtenção dos respectivos extratos brutos em AcOEt. A avaliação das atividades antimicrobiana e citotóxica foram realizadas, sendo que a bioprospecção inicial conduziu a seleção de dois fungos endofíticos identificados como Paraphaeosphaeria sporulosa e Cochliobolus eragrostidis. Estes, foram cultivados em diferentes meios líquidos e sólidos (escala reduzida) para novamente avaliar a atividade biológica dos extratos e selecionar os mais promissores para isolamento e determinação/elucidação estrutural dos metabólitos secundários em escala ampliada. Do cultivo de P. sporulosa no meio sólido de arroz foram isoladas seis... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Microorganisms are considered a promising source of substances with biological potential and high biosynthetic capacity to produce new substances with application in various areas such as agriculture, medicine and food. Endophytic fungi colonize the interior of plants and have shown great importance in the production of bioactive secondary metabolites. Thus, this work was conceived aiming the bioprospection of extracts produced from endophytic fungi associated with Paepalanthus planifolius, a Cerrado plant species, and the epigenetic evaluation in Aspergillus terreus, isolated from Sonora Desert plant species, to obtain new substances. The isolated endophytic fungi of P. planifolius (15 strains) were cultivated in small scale in potato and dextrose liquid medium (PDB) at 25 oC, under static mode to obtain the respective EtOAc crude extracts. Antimicrobial and cytotoxic activities were evaluated and the initial bioprospection led to the selection of two endophytic fungi identified as Paraphaeosphaeria sporulosa and Cochliobolus eragrostidis. These were cultivated in different liquid and solid media (reduced scale) to again evaluate the biological activity of the extracts and select the most promising ones for isolation and structural determination/elucidation of the secondary metabolites on larger scale. From the cultivation of P. sporulosa in the solid medium of rice, six new substances, sporulosaldeins A-F (1-6) were isolated, with good antifungal activity (MIC <100 µg/mL) a... (Complete abstract click electronic access below) / Doutor

La santé et la fertilité des vaches laitières sont au cœur des préoccupations de la filière professionnelle dans un objectif d’efficience, de quantité et de qualité de la production de lait. La mise en place d’une lactation performante se superpose aux profonds changements hormonaux et métaboliques de la période postpartum, se traduisant par une balance énergétique négative. Les conséquences en sont souvent une altération de la fertilité et une immunodépression qui accroit la susceptibilité aux pathologies. Dans les élevages, il existe encore une grande variabilité d’état général et de performances chez les vaches laitières malgré la sélection génomique. Il est proposé que des modifications de la méthylation de l’ADN puissent contribuer à cette variabilité phénotypique individuelle. En effet, la méthylation de l’ADN, en tant que processus épigénétique, est impliquée dans la régulation transcriptionnelle des gènes, et présente une certaine plasticité face aux contraintes environnementales. Nous avons fait l’hypothèse que des signatures épigénétiques portées par les cellules du sang, pourraient refléter l’état de santé des vaches et pourraient être modifiées en réponse à différents facteurs intrinsèques (parité, stades physiologiques…) et aux contraintes environnementales. Ces signatures ont été recherchées dans une population de cellules du sang particulière : les monocytes. Ces cellules, accessibles par prélèvements sanguins et purification en présence d’un anticorps spécifique, constituent la première ligne de réponse d’immunité innée face aux infections aigües participant à la dégradation de l’état de santé des vaches en postpartum. Pour tester l’hypothèse de signatures épigénétiques monocytaires, une analyse du méthylome par « Reduced Representation Bisulfite Sequencing », (RRBS) dans diverses situations d’élevage a été réalisée. En utilisant des ADN génomiques de vaches incluses dans plusieurs protocoles, 22 banques ont été construites et séquencées. Leur analyse a été réalisée en utilisant un pipeline d’analyses bioinformatique et biostatistique développé au laboratoire.En moyenne 1 250 000 CpG sont pris en considération et permettent l’identification et la localisation de cytosines différentiellement méthylées (DMC) : i) 27143 DMC en comparant les méthylomes de différents types cellulaires (monocytes versus fibroblastes et PBMC) ii) 4788 DMC en réponse à un challenge nutritionnel basé sur la distribution du complément alimentaire GENIAL®, fabriqué et distribué en élevage par nos partenaires PILARDIERE et XR-Repro. iii) 2615 et 4616 DMC en réponse au challenge infectieux pour le groupe de vaches témoins et le groupe en restriction alimentaire respectivement (protocole coordonné par Christine Leroux et José Pires (RUMINFLAME, INRA, Theix) combinant une restriction alimentaire et un challenge immunitaire, par injection de LipoPolySaccharide). iv) 4420 DMC issues de la comparaison entre méthylomes de vaches à génome constant (issues du transfert nucléaire, clones) et de vaches à génome variable mais de même âge et élevées dans les mêmes conditions que les clones. Pour certaines régions différentiellement méthylées (DMR) ciblant le promoteur de gènes, le statut de méthylation a été confirmé par conversion bisulfite et pyroséquençage. L’expression des gènes associés a été étudiée. Une anti corrélation significative est observée entre méthylation et expression signant la fonctionnalité de ces régions.En comparant les 11 méthylomes monocytaires, il est montré que 21% des CpG sont extrêmement stables et ne présentent qu’une faible variation de méthylation entre échantillons ( 20%). L’ensemble de ces informations peut être pris en considération pour la conception d’un outil d’épigénotypage. A l’avenir, il serait aussi possible d’utiliser cet outil en routine afin d’appréhender les variations du méthylome monocytaire dans différentes conditions d’élevage. / In dairy breeding, the health and fertility of cows are the main concern with the aims to maintain milk quantity and quality and to reduce the interval between calving in a high competitive economical context. Postpartum period is marked by major hormonal and metabolic changes that affect productivity, immune responses and fertility. The consequences of immune response deterioration are an increasing susceptibility to diseases (mastitis, metritis, endometritis…). Genomic selection in livestock improves the performance of the population but does not exclude phenotypic variability at the level of livestock and the individual. It is proposed that DNA methylation could contribute to this individual phenotype variability. Indeed, DNA methylation is an epigenetic process involved in transcriptional regulation of genes displaying certain plasticity in front of environmental constraints.We assumed the epigenetic signatures carried by blood cells, could reflect overall health and could be modified in response to intrinsic factors (parity, stages …) and to environmental changes. These signatures were researched in a particular blood cells subpopulation: the monocytes. These cells, obtained by blood sampling and purification with a specific antibody, are the first line of defense against acute infections participating in health status deterioration of postpartum cows.To test the monocyte epigenetic signatures hypothesis, monocyte methylome were analyzed by « Reduced Representation Bisulfite Sequencing » (RRBS), in various breeding conditions. Using genomic DNA form cows included in several protocols, 22 libraries were constructed and sequenced. Their analyses were accomplished using a « homemade » pipeline which integrates bioinformatics and biostatistics analyses. On average, 1 250 000 CpGs were analyzed in order to identify differentially methylated cytosines (DMCs): i) 27143 DMC by comparison between different cells types (monocytes versus fibroblasts and PBMC) ii) 4788 DMCs in response to nutritional challenge based on the dietary supplement, GENIAL®, produced and distributed in breeding by our partner PILARDIERE and XR-Repro (in collaboration with Marion Boutinaud, INRA, Rennes). iii) 2615 and 4616 DMCs in response to infectious challenge with LipoPolySaccharide injection for control cows group fed normal diet and for dietary restriction cows group, respectively (collaboration with Christine Leroux and José Pires, RUMINFLAME, INRA, Theix; and Gilles Foucras (ENVT, Toulouse)). iv) 4420 DMCs from the comparison between constant genomic cow (Somatic cell nuclear transfer, clones) and variable genomic cows but with the same age and raised in the same conditions than clones.From DMCs, we identified differentially methylated regions (DMRs) defined as region with at least 3 DMCs inside 100 bp. For some DMRs targeting gene promoter, the methylation status was validated by bisulfite conversion and pyrosequencing. Gene associated expression were also investigated. A significant negative correlation has been observed between methylation and expression, highlighting the functional relevance of these DMRs in gene transcription control.By comparing the 11 monocyte methylomes, 21% of CpGs present a remarkable constant methylation level with weak variability between samples (20%).Taking together, these data can provide a list of relevant DMCs for an epigenetic tool conception. In the future, it would be possible to use this tool for a routine analysis in order to grasp monocyte methylome variations in different breeding management.