Impact des microARNs sur la lactation et la régulation nutritionnelle de leur expression dans la glande mammaire

Nutrition significantly affects the secretion and the composition of milk which determine its nutritional quality. In the mammary gland, regulation of these processes involves numerous genes which expression can be affected by nutrition. However, their regulations remain unclear. MicroRNAs (miRNA) are small non coding RNA which can bind mRNAs and regulate their expression of target genes. Consequently, they offer opportunities to understand the regulation of gene expression in response to nutrition. The first step of my PhD aimed to obtain a better knowledge of miRNA expressed in the mammary gland. Mammary miRNome were established from the lactating mouse, cow and goat using high-throughput sequencing. Later, the effect of nutrition on the expression of miRNA in the mammary gland was analyzed for the first time. Two models in ruminants, a food deprivation (“extreme” model) and a lipid supplementation (model similar to breeding conditions) highlighted 30 and 2 nutriregulated miRNA, respectively. The analysis of nutriregulated miRNA’s predicted targets, in silico, revealed their potential role in lipid metabolism. Some of those target genes have been previously identified as differently expressed in the same conditions and could thus be involved in the regulation of the expression of genes essential for the mammary gland function, such as ESR1. Finally, three nutriregulated miRNA were selected and used in a preliminary study of their functions in vitro in bovine mammary epithelial cells. These works bring first evidences in understanding the nutritional regulation of gene expression in the mammary gland as well as the role of miRNA in lactation.Le facteur nutritionnel affecte de façon significative la sécrétion et la composition des constituants du lait qui conditionnent sa qualité nutritionnelle. Dans la glande mammaire, ces processus font intervenir de nombreux gènes dont l’expression est modulée par l’alimentation, cependant les mécanismes de régulation sous-jacents ne sont pas connus. Les microARNs (miARN) sont des petits ARN non codants qui se lient sur leurs ARNm cibles pour en réguler l’expression. Ils ouvrent donc des pistes d’investigation pour la compréhension de ces mécanismes. La première partie de mon travail de thèse a consisté à obtenir une meilleure connaissance des miARN exprimés dans la glande mammaire, notamment en dressant les miRNomes de référence par séquençage haut débit chez la souris, la vache et la chèvre. Ensuite, pour la première fois, l’impact de la nutrition sur l’expression des miARN mammaires a été étudié. Deux modèles ruminants, un modèle dit « extrême » et un modèle de supplémentation lipidique proche des conditions d’élevage, ont permis d’identifier 30 et 2 miARN, respectivement, dont l’expression est nutrirégulée. L’analyse in silico des cibles des miARN nutrirégulés a révélé un rôle potentiel de ceux-ci dans le métabolisme des lipides. Certaines des cibles sont effectivement différentiellement exprimées dans ces modèles, parmi celles-ci certains gènes sont essentiels pour la lactation tels que ESR1. Enfin, une étude pilote de la fonction de trois miARN nutrigulés a été initiée in vitro dans des cellules épithéliales mammaires bovines. Ces travaux permettent donc d’apporter des premiers éléments pour la compréhension de la régulation de l’expression des gènes en réponse à la nutrition et de l’impact des miARN sur la lactation

Nutritional regulation of microRNAs in the mammary gland and their impact on the lactation

Le facteur nutritionnel affecte de façon significative la sécrétion et la composition des constituants du lait qui conditionnent sa qualité nutritionnelle. Dans la glande mammaire, ces processus font intervenir de nombreux gènes dont l’expression est modulée par l’alimentation, cependant les mécanismes de régulation sous-jacents ne sont pas connus. Les microARNs (miARN) sont des petits ARN non codants qui se lient sur leurs ARNm cibles pour en réguler l’expression. Ils ouvrent donc des pistes d’investigation pour la compréhension de ces mécanismes. La première partie de mon travail de thèse a consisté à obtenir une meilleure connaissance des miARN exprimés dans la glande mammaire, notamment en dressant les miRNomes de référence par séquençage haut débit chez la souris, la vache et la chèvre. Ensuite, pour la première fois, l’impact de la nutrition sur l’expression des miARN mammaires a été étudié. Deux modèles ruminants, un modèle dit « extrême » et un modèle de supplémentation lipidique proche des conditions d’élevage, ont permis d’identifier 30 et 2 miARN, respectivement, dont l’expression est nutrirégulée. L’analyse in silico des cibles des miARN nutrirégulés a révélé un rôle potentiel de ceux-ci dans le métabolisme des lipides. Certaines des cibles sont effectivement différentiellement exprimées dans ces modèles, parmi celles-ci certains gènes sont essentiels pour la lactation tels que ESR1. Enfin, une étude pilote de la fonction de trois miARN nutrigulés a été initiée in vitro dans des cellules épithéliales mammaires bovines. Ces travaux permettent donc d’apporter des premiers éléments pour la compréhension de la régulation de l’expression des gènes en réponse à la nutrition et de l’impact des miARN sur la lactation.Nutrition significantly affects the secretion and the composition of milk which determine its nutritional quality. In the mammary gland, regulation of these processes involves numerous genes which expression can be affected by nutrition. However, their regulations remain unclear. MicroRNAs (miRNA) are small non coding RNA which can bind mRNAs and regulate their expression of target genes. Consequently, they offer opportunities to understand the regulation of gene expression in response to nutrition. The first step of my PhD aimed to obtain a better knowledge of miRNA expressed in the mammary gland. Mammary miRNome were established from the lactating mouse, cow and goat using high-throughput sequencing. Later, the effect of nutrition on the expression of miRNA in the mammary gland was analyzed for the first time. Two models in ruminants, a food deprivation (“extreme” model) and a lipid supplementation (model similar to breeding conditions) highlighted 30 and 2 nutriregulated miRNA, respectively. The analysis of nutriregulated miRNA’s predicted targets, in silico, revealed their potential role in lipid metabolism. Some of those target genes have been previously identified as differently expressed in the same conditions and could thus be involved in the regulation of the expression of genes essential for the mammary gland function, such as ESR1. Finally, three nutriregulated miRNA were selected and used in a preliminary study of their functions in vitro in bovine mammary epithelial cells. These works bring first evidences in understanding the nutritional regulation of gene expression in the mammary gland as well as the role of miRNA in lactation

Le mélanome uvéal

Le mélanome uvéal est un cancer rare de l’adulte, dont les événements oncogéniques très stéréotypés ont été décryptés ces 10 dernières années. Ses particularités épidémiologiques, génétiques et transcriptionnelles en font un modèle remarquable de l’oncogenèse. La transformation maligne implique de façon presque mutuellement exclusive de grands processus biologiques, comme la régulation chromatinienne par inactivation de BAP1, l’épissage par mutations de SF3B1, et la traduction par mutations d’EIF1AX. L’étude du mélanome uvéal a permis de découvrir les mécanismes de l’épissage anormal lié aux mutations de SF3B1. La compréhension du lien entre ces anomalies et la transformation maligne sera la prochaine étape, dans l’espoir d’en déduire de nouvelles pistes thérapeutiques

Nutritional regulation of microRNAs in the lactating goat mammary gland

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Food deprivation affects the miRNome in the lactating goat mammary gland

Nutrition affects milk composition thus influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not fully understood. MicroRNAs (miRNA) are small non coding RNA which are important post-transcriptional regulators of gene expression by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, which may provide clues to deciphering regulations of the biosynthesis and secretion of milk components. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland were established from lactating goats fed ad libitum or deprived of food for 48h affecting milk production and composition. High throughput miRNA sequencing revealed 30 miRNA with an expression potentially modulated by food deprivation; 16 were down-regulated and 14 were up-regulated. Diana-microT predictive tools suggested a potential role for several nutriregulated miRNA in lipid metabolism. Among the putative targets, 19 were previously identified as differently expressed genes (DEG). The functions of these 19 DEG revealed, notably, their involvement in tissue remodelling. In conclusion, this study offers the first evidence of nutriregulated miRNA in the ruminant mammary gland. Characterization of these 30 miRNA could contribute to a clearer understanding of gene regulation in the mammary gland in response to nutrition

Delayed muscle development in small pig fetuses around birth cannot be rectified by maternal early feed restriction and subsequent overfeeding during gestation

Intrauterine variations in nutrient allowance can alter body composition and tissue features of the porcine offspring around birth. This study aimed to determine the effects of fetal weight variations between littermates and of maternal dietary regimen during gestation on fetal muscle traits just before birth. Fourteen pregnant gilts were reared under a conventional (control, CTL; n = 7) or an experimental (treatment, TRT; n = 7) dietary regimen during gestation. The dietary treatment provided 70% of the protein and digestible energy contents of the CTL diet during the first 70 days of gestation and then, 115% of the protein and digestible energy contents up to farrowing. At 110 days of gestation, sows were sacrificed and one fetus having a low (824 ± 140 g) and one having a normal (1218 ± 192 g) BW per litter were sampled. Irrespective of maternal dietary regimen, the longissimus muscle of the small fetuses exhibited higher expression levels of DLK1/Pref1 and NCAM1/CD56, two genes known to be downregulated during normal skeletal muscle development. Expression levels of the embryonic isoform of the myosin heavy chain (MyHC), both at the mRNA and at the protein levels, were also higher in small fetuses. In addition, the ratios of perinatal to embryonic and of adult fast to developmental MyHC isoforms were generally lower in light fetuses compared with their medium-weight littermates. These modifications suggest a delayed myofiber development in spontaneous growth-retarded fetuses. Finally, GLUT1 was expressed to a lesser extent in the muscle of small v. normal fetuses, suggesting decreased ability for glucose uptake in muscle. Initial feed restriction and subsequent overfeeding of sows during gestation led to a lower expression of the myogenic factor MYOD1, a prerequisite for myogenic initiation in skeletal muscle. This maternal strategy was also associated with a lower expression level of insulin-like growth factor 1 receptor (IGFR) but an upregulation of IGF2. This suggests an altered susceptibility of muscle cells to IGFs’ signal in fetuses from treated sows. Altogether, intrauterine growth restriction impaired fetal muscle development, and restricted feeding followed by overfeeding of gestating sows did not allow small fetuses to recover normal contractile and metabolic characteristics

multi-layer depth peeling via fragment sort

IEEE, Natl Nat Sci Fdn China, Zhejiang ProvWe present an accelerated depth peeling algorithm for order-independent transparency rendering on graphics hardware. Unlike traditional depth peeling which only peels one layer of transparent pixels per rendering pass, our algorithm peels multiple layers simultaneously per rendering pass. Our acceleration is achieved via our fragment program which sorts and writes multiple fragment colors and depths via MRT. A notable :feature of our algorithm is that it is robust against the unreliable parallel read-after-write behavior in current graphics hardware, guaranteeing correct transparency ordering. For ordinary scenes rendered under RGBA8 color precision, we achieve up to 8 x speed-up over conventional depth peeling with current generation graphics hardware. Our algorithm is simple to implement on current GPU without any hardware modification. In addition, it does not require applications to perform any pre-sorting of transparent geometry