105 research outputs found

    Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

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    Deciphering transcription factor networks from microarray data remains difficult. This study presents a simple method to infer the regulation of transcription factors from microarray data based on well-characterized target genes. We generated a catalog containing transcription factors associated with 2720 target genes and 6401 experimentally validated regulations. When it was available, a distinction between transcriptional activation and inhibition was included for each regulation. Next, we built a tool (www.tfacts.org) that compares submitted gene lists with target genes in the catalog to detect regulated transcription factors. TFactS was validated with published lists of regulated genes in various models and compared to tools based on in silico promoter analysis. We next analyzed the NCI60 cancer microarray data set and showed the regulation of SOX10, MITF and JUN in melanomas. We then performed microarray experiments comparing gene expression response of human fibroblasts stimulated by different growth factors. TFactS predicted the specific activation of Signal transducer and activator of transcription factors by PDGF-BB, which was confirmed experimentally. Our results show that the expression levels of transcription factor target genes constitute a robust signature for transcription factor regulation, and can be efficiently used for microarray data mining

    Hepatocyte MyD88 affects bile acids, gut microbiota and metabolome contributing to regulate glucose and lipid metabolism

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    OBJECTIVE: To examine the role of hepatocyte myeloid differentiation primary-response gene 88 (MyD88) on glucose and lipid metabolism. DESIGN: To study the impact of the innate immune system at the level of the hepatocyte and metabolism, we generated mice harbouring hepatocyte-specific deletion of MyD88. We investigated the impact of the deletion on metabolism by feeding mice with a normal control diet or a high-fat diet for 8 weeks. We evaluated body weight, fat mass gain (using time-domain nuclear magnetic resonance), glucose metabolism and energy homeostasis (using metabolic chambers). We performed microarrays and quantitative PCRs in the liver. In addition, we investigated the gut microbiota composition, bile acid profile and both liver and plasma metabolome. We analysed the expression pattern of genes in the liver of obese humans developing non-alcoholic steatohepatitis (NASH). RESULTS: Hepatocyte-specific deletion of MyD88 predisposes to glucose intolerance, inflammation and hepatic insulin resistance independently of body weight and adiposity. These phenotypic differences were partially attributed to differences in gene expression, transcriptional factor activity (ie, peroxisome proliferator activator receptor-α, farnesoid X receptor (FXR), liver X receptors and STAT3) and bile acid profiles involved in glucose, lipid metabolism and inflammation. In addition to these alterations, the genetic deletion of MyD88 in hepatocytes changes the gut microbiota composition and their metabolomes, resembling those observed during diet-induced obesity. Finally, obese humans with NASH displayed a decreased expression of different cytochromes P450 involved in bioactive lipid synthesis. CONCLUSIONS: Our study identifies a new link between innate immunity and hepatic synthesis of bile acids and bioactive lipids. This dialogue appears to be involved in the susceptibility to alterations associated with obesity such as type 2 diabetes and NASH, both in mice and humans

    Environmental hypoxia favors myoblast differentiation and fast phenotype but blunts activation of protein synthesis after resistance exercise in human skeletal muscle

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    We hypothesized that a single session of resistance exercise performed in moderate hypoxic (FiO2: 14%) environmental conditions would potentiate the anabolic response during the recovery period spent in normoxia. Twenty subjects performed a 1-leg knee extension session in normoxic or hypoxic conditions. Muscle biopsies were taken 15 min and 4 h after exercise in the vastus lateralis of the exercised and the nonexercised legs. Blood and saliva samples were taken at regular intervals before, during, and after the exercise session. The muscle fractional-protein synthetic rate was determined by deuterium incorporation into proteins, and the protein-degradation rate was determined by methylhistidine release from skeletalmuscle.Wefoundthat:1)hypoxiablunted the activation of protein synthesis after resistance exercise; 2) hypoxia down-regulated the transcriptional program of autophagy; 3) hypoxia regulated the expression of genes involved in glucose metabolism at rest and the genes involved in myoblast differentiation and fusion and in muscle contraction machinery after exercise; and 4) the hypoxia-inducible factor-1alpha pathway was not activated at the time points studied. Contrary to our hypothesis, environmental hypoxia did not potentiate the short-term anabolic response after resistance exercise, but it initiated transcriptional regulations that could potentially translate into satellite cell incorporation and higher force production in the long term

    Signal transduction by the interleukin-9 receptor

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    Interleukin-9 (IL-9) is a pleiotropic TH2 cytokine involved in anti-parasite immunity, asthma and lymphoma development. It regulates survival, growth, and differentiation of target cells, such as lymphocytes and mast cells. The present work aimed at identifying intracellular signals triggered by the binding of IL-9 to its membrane receptor. This receptor is a complex composed of two proteins: the IL-9 receptor itself (IL-9R), and the Îłc chain. Both proteins are associated with a tyrosine kinase of the JAK family, JAK1 and JAK3, respectively. These enzymes, which are activated in the presence of IL-9, are most likely responsible for the phosphorylation a single IL-9R tyrosine that we identified by mutagenesis. Our data suggest that this phosphoryled amino-acid is recognized by three transcription factors of the STAT family; i.e. STAT1, STAT3 and STAT5. Based on the literature, receptor-associated STATs are activated by JAK kinases, dissociate from the receptor, dimerize and migrate to the nucleus, where they regulate gene transcription. We showed that most genes regulated but IL-9 are controlled by this pathways. It is the case if Lys-6A/E, a gene involved in lymphocyte activation. Some of these genes are regulated by a specific STAT factor, whereas others are equally induced via STAT1, STAT3 or STAT5. These observations provide an explanation for differences in gene regulation by IL-2, IL-3, IL-6, IL-9 and interferon Îł in our system. Our results also indicated that STAT transcription factors play a key role in IL-9-medaited cell proliferation and inhibition of apoptosis induced by glucocorticoids. It is likely that these effects of IL0 are also mediated by regulation of genes, the nature of which is still unknown, however. Implication of STATs in cell survival and proliferation prompted us to investigate their activation in tumorigenic clones derived from IL-9 dependent cell lines. In two murine models established in our laboratory, we observed that constitutive STAT activation was associated with tumorgenesis. These models should help us to identify STAT-regulated genes involved in proliferation. Taken together, our results point to a role for STAT factors in lymphocytic oncogenesis. Future studies will have to determine whether STATs are useful target in lymphoma and leukemia therapyL’interleukine-9 (IL-9) est une cytokine impliquĂ©e dans les rĂ©ponses immunitaires de type TH2, responsables des rĂ©actions contre les parasites et de certaines formes d’asthme. IL-9 pourrait Ă©galement favoriser le dĂ©veloppement de lymphomes et leucĂ©mies. Elle rĂ©gule la survie, la multiplication et la diffĂ©renciation de nombreuses cellules, notamment des mastocytes et des lymphocytes. Notre but Ă©tait d’identifier les signaux intracellulaires activĂ©s par la fixation de l’IL-9 sur son rĂ©cepteur. Celui-ci est formĂ© de deux protĂ©ines transmembranaires : le rĂ©cepteur de l’IL-9 proprement dit (IL-9R), et Îłc, qui est Ă©galement associĂ©e aux rĂ©cepteurs des interleukines 2, 4, 7 et 15. Chacune de ces deux xhaĂŻnes est liĂ©e Ă  une tyrosine kinase de la famille des JAK : JAK1 et JAK3, respectivement. Nous avons pu montrer que ces enzymes sont activĂ©es en prĂ©sence d’IL-9, et phosphorylent une seule tyrosine d’IL-9R, identifiĂ©e par mutagĂšne. AprĂšs phosphorylation, cet acide aminĂ© est reconnu par des facteurs de transcriptions de la famille STAT : STAT1, STAT3 et STAT5. Ces protĂ©ines sont probablement activĂ©es directement par JAK1 ou JAK3, ce qui permet leur dimĂ©risation et leur migration vers le noyau de la cellule, oĂč elles rĂ©gulent la transcription de certains gĂšnes, en se fixant sur leur partie promotrice. Nous avons dĂ©montrĂ© que cette voie de transduction du signal joue un rĂŽle majeur dans le contrĂŽle de l’expression des gĂšnes par l’IL-9. Certains de ces gĂšnes comme ly-6A/E, sont rĂ©gulĂ©s plus spĂ©cifiquement par certains facteurs STAT activĂ©s par l’IL-9, alors que d’autres, comme pim1, sont induits indiffĂ©remment via STAT1, STAT3 ouSTAT5. Ces observations permettent d’expliquer les diffĂ©rences entre les effets de l’IL-2, l’IL-3, l’IL-6, l’IL-9 et l’interfĂ©ron-Îł dans notre systĂšme, en fonction du type de STATS qu’ils activent. Nos rĂ©sultats indiquent que les protĂ©ines STAT sont Ă©galement les mĂ©diateurs des activitĂ©s de l’IL-9 sur les lymphomes et les lignĂ©es lymphoĂŻdes : la stimulation de la croissance cellulaire et l’inhibition de l’apoptose induite par les glucocorticoĂŻdes. Ces effets dĂ©pendent probablement aussi de l’activation de gĂšnes, dont la nature reste Ă  dĂ©terminer. Ces observations nous ont poussĂ©s Ă  Ă©tudier le rĂŽle des STAT dans l’oncogĂšne des lymphocytes. Dans deux modĂšles murins Ă©tablis dans notre laboratoire, nous avons observĂ© que l’activation constitutive de STAT5 Ă©tait corrĂ©lĂ©e avec la transformation de cellules en clones tumoraux. Des recherches ultĂ©rieures devront dĂ©terminer si les STAT sont des cibles thĂ©rapeutiques de choix pour le traitement de certains types de lymphomes et leucĂ©miesThĂšse de doctorat en sciences pharmaceutiques (mĂ©decine expĂ©rimentale) -- UCL, 199

    No PDGF receptor signal in pericytes without endosialin?

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    Solid tumors contain non-transformed cells of critical importance for disease progression. These cells form the tumor stroma, including blood vessel and fibroblasts. Being more genetically stable than cancer cells, stromal cells have drawn much interest as potential therapeutic targets, leading to the concepts of anti-angiogenic and anti-stromal drugs. In this context, researchers have been seeking new stromal cell markers. Endosialin (CD248, TEM-1) and PDGF Receptor beta are two of them

    Interleukin 9 and its receptor: an overview of structure and function.

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    Interleukin-9 (IL-9) is a multifunctional cytokine produced by activated TH2 clones in vitro and during TH2-like T cell responses in vivo. Although IL-9 was initially described as a T cell growth factor, its role in T cell responses is still unclear. While freshly isolated normal T cells do not respond to IL-9, this cytokine induces the proliferation of murine T cell lymphomas in vitro, and in vivo overexpression of IL-9 results in the development of thymic lymphomas. In the human, the existence of an IL-9 mediated autocrine loop has been suggested for some malignancies such as Hodgkin's disease. Various observations indicate that IL-9 is actively involved in mast cells responses by inducing the proliferation and differentiation of these cells. Other potential biological targets for IL-9 include B lymphocytes, and hematopoietic progenitors, for which higher responses were observed with foetal or transformed cells as compared to normal adult progenitors. The IL-9 receptor is a member of the hemopoietin receptor superfamily and interacts with the gamma chain of the IL-2 receptor for signaling. Signal transduction studies have stressed the role of the Jak-STAT pathway in various IL-9 bioactivities, whereas the 4PS/IRS2 adaptor protein might also play a significant role in IL-9 signaling

    Platelet-derived growth factors and their receptors in normal and malignant hematopoiesis

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    Platelet-derived growth factors (PDGF) bind to two closely related receptor tyrosine kinases, PDGF receptor α and ÎČ, which are encoded by the PDGFRA and PDGFRB genes. Aberrant activation of PDGF receptors occurs in myeloid malignancies associated with hypereosinophilia, due to chromosomal alterations that produce fusion genes, such as ETV6-PDGFRB or FIP1L1-PDGFRA. Most patients are males and respond to low dose imatinib, which is particularly effective against PDGF receptor kinase activity. Recently, activating point mutations in PDGFRA were also described in hypereosinophilia. In addition, autocrine loops have been identified in large granular lymphocyte leukemia and HTLV-transformed lymphocytes, suggesting new possible indications for tyrosine kinase inhibitor therapy. Although PDGF was initially purified from platelets more than 30 years ago, its physiological role in the hematopoietic system remains unclear. Hematopoietic defects in PDGF-deficient mice have been reported but appear to be secondary to cardiovascular and placental abnormalities. Nevertheless, PDGF acts directly on several hematopoietic cell types in vitro, such as megakaryocytes, platelets, activated macrophages and, possibly, certain lymphocyte subsets and eosinophils. The relevance of these observations for normal human hematopoiesis remains to be established