A Generic Solution for Automated Collecting and Integration of Biological Data from Web Sources

Session Posters. Colloque avec actes et comité de lecture. internationale.International audienceWe present here a work dealing with automated collecting and integration of data along a user-defined scenario. Aspects such as query construction, query submission, parsing of returned document, filtering of desired data and storing them in a structured document have been considered as well as the chaining between the various steps of the scenario. Automation of the process allows to refresh the data in a time-saving manner in order to take into account the frequent changes in source contents. A configuration module distinct from the execution module allows to modify the scenario steps according to user preferences and/or source changes

Immunoselection and characterization of a human genomic PPAR binding fragment located within POTE genes

Peroxisome proliferator-activated receptors (PPARs) are ligand-inducible transcription factors and belong to the nuclear hormone receptor superfamily. They form heterodimers with retinoid X receptor (RXR) and bind to specific PPAR-response elements. To identify novel PPAR target genes, we developed an affinity method to isolate human genomic fragments containing binding sites for PPARs. For this, an antibody raised against all PPAR subtypes was used. Immunoselected fragments were amplified and sequenced. One of them, ISF1029, was mapped by BLAT and BLAST searches on different human chromosomes, downstream of several POTE genes. ISF1029 contained three hexamers strongly related to the AGGTCA motif organized according to a DR0/3 motif. The latter was found to bind to PPARΑ in gel mobility shift and supershift assays and to exhibit a downregulation potentiality in transfection experiments under clofibrate treatment. POTE genes were shown to be highly expressed in human Caco-2 colorectal adenocarcinoma cells and downregulated by fenofibrate and 9-cis-retinoic acid, as attested by RT-PCR assays. Microarray analysis confirmed and extended to the human T98-G glioblastoma cells, the downregulation of several POTE genes expression by Wy-14,643, a potent PPARΑ activator. Our data provide new insights about the pleiotropic action of PPARs

Damaged DNA Binding Protein 2 Plays a Role in Breast Cancer Cell Growth

The Damaged DNA binding protein 2 (DDB2), is involved in nucleotide excision repair as well as in other biological processes in normal cells, including transcription and cell cycle regulation. Loss of DDB2 function may be related to tumor susceptibility. However, hypothesis of this study was that DDB2 could play a role in breast cancer cell growth, resulting in its well known interaction with the proliferative marker E2F1 in breast neoplasia. DDB2 gene was overexpressed in estrogen receptor (ER)-positive (MCF-7 and T47D), but not in ER-negative breast cancer (MDA-MB231 and SKBR3) or normal mammary epithelial cell lines. In addition, DDB2 expression was significantly (3.0-fold) higher in ER-positive than in ER-negative tumor samples (P = 0.0208) from 16 patients with breast carcinoma. Knockdown of DDB2 by small interfering RNA in MCF-7 cells caused a decrease in cancer cell growth and colony formation. Inversely, introduction of the DDB2 gene into MDA-MB231 cells stimulated growth and colony formation. Cell cycle distribution and 5 Bromodeoxyuridine incorporation by flow cytometry analysis showed that the growth-inhibiting effect of DDB2 knockdown was the consequence of a delayed G1/S transition and a slowed progression through the S phase of MCF-7 cells. These results were supported by a strong decrease in the expression of S phase markers (Proliferating Cell Nuclear Antigen, cyclin E and dihydrofolate reductase). These findings demonstrate for the first time that DDB2 can play a role as oncogene and may become a promising candidate as a predictive marker in breast cancer

Amphibian intestinal ontogenesis : importance of metamorphosis. Comparison with other vertebrates

Metamorphosis is a characteristic event of Anuran Amphibian post-embryonic development It is related to a change in environment and in feeding behaviour. Among many transformations, intestine undergoes remarkable modifications : it shortens, loses its coiled shape and a folded secondary epithelium is put in place of larval epithelial cell lining. In parallel with epithelium substitution, at cellular level, quantitative and qualitative changes in genes expression are noted, triggered by thyroid hormones. Microvillar proteins are concerned as membrane-bound enzymes or structural cytoskeleton components (for example, villin). Such a late intestinal maturation is also observed in other Vertebrates, especially during Agnathans metamorphosis, Birds hatching or Mammalians birth and weaningLe développement post-embryonnaire des Amphibiens Anoures est caractérisé par la métamorphose, qui coïncide avec un changement de milieu et de régime alimentaire. Les nombreuses transformations que subit l'organisme concernent en particulier l'intestin : il se raccourcit, se déspiralise et sa paroi est profondément remaniée (plissement, renouvellement épithélial). A l'échelle cellulaire, parallèlement à la substitution épithéliale, se produit une modification quantitative et qualitative de l'expression du génome des épithéliocytes, sous contrôle des hormones thyroïdiennes. Les protéines des microvillosités sont affectées, qu'elles soient membranaires (par exemple les enzymes de la bordure en brosse) ou composantes du cytosquelette (par exemple les protéines de structure telles la villine). Une maturation intestinale tardive est également remarquée chez les autres Vertébrés, lors de la métamorphose chez les Cyclostomes, à l'éclosion chez les Oiseaux ou à la naissance et au sevrage chez les Mammifère

The human Semaphorin 6B gene is down regulated by PPARs

Article dans revue scientifique avec comité de lecture. internationale.International audienceThe peroxisome proliferator-activated receptors (PPARs) are ligand-inducible transcription factors and belong to the nuclear hormone receptor superfamily. They form heterodimers with the retinoid X receptor and bind to specific peroxisome proliferator-response elements. The latter are direct repeat elements of two hexanucleotides with the consensus sequence TG(A/T)CCT separated by a single nucleotide spacer. Such a sequence, or a similar one, has been found in numerous PPAR-inducible genes. We developed an affinity method to isolate human genomic fragments containing binding sites for PPARs and to identify novel PPAR target genes. For this, an antibody raised against all PPAR subtypes was used. Immunoselected fragments were amplified and sequenced and one of them, ISF5148, was found to bind specifically to PPARs in gel mobility shift, supershift, and competition assays and to exhibit a down transregulation potentiality in transfection experiments under clofibrate (a PPARalpha agonist) treatment. ISF5148 was mapped by BLAST analysis 8.5 kb upstream of the human semaphorin 6B [(HSA)SEMA6B] gene. The latter encodes a member of the semaphorin family of axon guidance molecules. Expression of this gene in human glioblastoma T98G cells was strongly down regulated after treatment with clofibrate or Wy-14,643, two PPARalpha agonists. Our study establishes for the first time that PPAR activators diminish the expression of the human (HSA)SEMA6B gene. These data are relevant to the fact that PPARs are implicated in brain development, neuronal differentiation, and lipid metabolism in the central nervous system. In addition, cross talk between the peroxisome proliferator and retinoic acid pathways is suggested

A plant steroid, diosgenin, induces apoptosis, cell cycle arrest and COX activity in osteosarcoma cells

International audienceCyclooxygenases (COXs) are key enzymes in the conversion of arachidonic acid into prostanoids which are involved in apoptosis and inflammation. Two distinct COXs have been identified: COX-1 which is constitutively expressed and COX-2 which is induced by different products such as tumor promoters or growth factors. Previously, we demonstrated that a plant steroid, diosgenin, was a new megakaryocytic differentiation inducer of human erythroleukemia cells. In our study, we investigated the effect of diosgenin on the proliferation rate, cell cycle distribution and apoptosis in the human osteosarcoma 1547 cell line. The effects of this compound were also tested on COX expression and COX activities. Diosgenin treatment caused an inhibition of 1547 cell growth with a cycle arrest in G1 phase and apoptosis induction. Moreover, we found a correlation between p53, p21 mRNA expression and nuclear factor-kappaB activation and we observed a time-dependent increase in PGE2 synthesis after diosgenin treatment

Different contribution of apoptosis to the antiproliferative effects of diosgenin and other plant steroids, hecogenin and tigogenin, on human 1547 osteosarcoma cells.

International audienceRegulation of growth arrest and apoptosis are, in part, controlled by the tumor suppressor p53 after its phosphorylation which causes a determinant role in its functional activation. Moreover, PPAR regulate many functions such as proliferation and apoptosis. We compared the biological activity of diosgenin with hecogenin and tigogenin, plant steroids structurally close to diosgenin, on proliferation rate, cell cycle distribution and apoptosis in human 1547 osteosarcoma cells. We found that all three molecules have an antiproliferative effect but gel shift analysis demonstrated that none of the plant steroids transactivated PPAR in human 1547 osteosarcoma cells whereas these molecules induced NF-kappaB binding to DNA. Although these plant steroids have a very close structure, only diosgenin caused a cell cycle arrest associated with strong apoptosis. This biological action seems correlated with a large increase of p53 protein expression. This fact was showed by immunofluorescence analysis which confirmed that diosgenin strongly enhanced the activation of p53 in contrast to hecogenin and tigogenin actions

Constitutive NF-κB activity influences basal apoptosis and radiosensitivity of head-and-neck carcinoma cell lines

Purpose: Nuclear factor-κB (NF-κB) has been implicated in anti-apoptotic gene transactivation, according to its transcriptional activity. The present study was designed to investigate whether constitutive NF-κB activity could modulate basal apoptosis and intrinsic radiosensitivity of KB head-and-neck carcinoma cell line and KB3 subline. The KB3 subline was more radiosensitive (SF2 = 0.48, α = 0.064) than the radioresistant KB parental cell line (SF2 = 0.80, α = 0.114). Methods and Materials: Constitutive NF-κB DNA-binding activity was determined using electrophoretic mobility shift assay. Modulation of NF-κB activity was performed by exposing both cell lines to tumor necrosis factor α or dexamethasone. Apoptotic cell population was analyzed using flow cytometry (annexin V/propidium iodide). Radiosensitivity was assessed from determination of the surviving fraction at 2 Gy (SF2), and α and β parameters were determined using the linear-quadratic model. Results: Constitutive NF-κB activity was found to be significantly lower in KB3 than in KB. KB cell line exposure to dexamethasone significantly decreased NF-κB DNA-binding activity and, consequently, enhanced baseline apoptosis and radiosensitivity (α values: 0.114 vs. 0.052). Conversely, exposure of KB3 cells to tumor necrosis factor α increased NF-κB DNA-binding activity and resulted in a significant decrease (50%) in rate of apoptosis and in radiosensitivity (SF2 values: 0.48 vs. 0.63). Conclusions: Modulation of NF-κB DNA-binding activity influences baseline apoptosis and intrinsic radiosensitivity. © 2001 Elsevier Science Inc.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

PPAR et interactions des cellules entre elles ou avec la matrice extracellulaire

Les récepteurs activés par les proliférateurs de peroxysomes (PPAR) sont des facteurs de transcription qui appartiennent à la superfamille des récepteurs nucléaires. Trois gènes, répartis sur des chromosomes différents, ont été identifiés : PPARα, PPARβ/δ et PPARγ. La protéine PPARα joue un rôle clé dans le contrôle du métabolisme et de l’homéostasie lipidiques. PPARβ/δ est une isoforme ubiquitaire, qui est fortement impliquée dans la physiologie des muscles. Les récepteurs PPARβ/δ et PPARγ sont des facteurs importants pour le développement et le fonctionnement du placenta, et pour l’implantation de l’embryon. PPARγ est un partenaire capital du processus d’adipogenèse. Les PPAR codent aussi des protéines qui interviennent à des degrés divers dans les processus de prolifération, de différenciation et d’apoptose cellulaires. Assez curieusement, le rôle de ces facteurs transcriptionnels dans les processus d’interactions entre cellules et/ ou entre cellules et matrice extracellulaire est rarement souligné, exception faite de leur action anti-inflammatoire. Pourtant, via des mécanismes souvent indirects et incomplètement élucidés, de nouveaux rôles des PPAR se dessinent, qui pourraient, s’ils se précisent, élargir encore la notion de cible thérapeutique associée à ces récepteurs