Genomics

Publications

Year of publication 2011

Debbie Montjean, Pierre De La Grange, David Gentien, Audrey Rapinat, Stéphanie Belloc, Paul Cohen-Bacrie, Yves Menezo, Moncef Benkhalifa (2011 Oct 13)

Sperm transcriptome profiling in oligozoospermia.

Journal of assisted reproduction and genetics : 3-10 : DOI : 10.1007/s10815-011-9644-3 Learn more
Summary

Investigate in what extent sperm transcriptome of infertile men is different from that of fertile individuals.

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Year of publication 2009

Mathieu Clément-Ziza, David Gentien, Stanislas Lyonnet, Jean-Paul Thiery, Claude Besmond, Charles Decraene (2009 May 28)

Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling.

BMC genomics : 246 : DOI : 10.1186/1471-2164-10-246 Learn more
Summary

For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture microdissection is much too small to perform microarray studies. To address this issue, RNA amplification methods have been developed to generate sufficient targets from picogram amounts of total RNA to perform microarray hybridisation.

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Year of publication 2008

Clotilde Billottet, Marianne Tuefferd, David Gentien, Audrey Rapinat, Jean-Paul Thiery, Philippe Broët, Jacqueline Jouanneau (2008 Jan 15)

Modulation of several waves of gene expression during FGF-1 induced epithelial-mesenchymal transition of carcinoma cells.

Journal of cellular biochemistry : 826-39 : DOI : 10.1002/jcb.21667 Learn more
Summary

During epithelial-mesenchymal transition (EMT), epithelial cells are converted into isolated motile and invasive mesenchymal cells. In model systems, EMT is induced most often by the activation of tyrosine kinase receptors through signaling pathways involving translational and post-translational regulation. In this study, we have used the NBT-II bladder carcinoma cell system to investigate in vitro Fibroblast Growth Factor-1 (FGF-1)-induced EMT. Transcriptome analyses were performed on NBT-II cells stimulated for 2, 6, 24, and 48 h with FGF-1. As some phenotypic changes occurred around 6 h post-stimulation, a supervised analysis was designed to identify transcript variations across defined time-periods. Our results clearly indicate that immediately after FGF-1 stimulation a set of genes assigned to transcriptional regulation (e.g., jun-B and v-ets) and to EMT induction (e.g., Notch 1) is transiently up-regulated. A set of genes involved in proteolytic systems (e.g., MMP-13 and uPAR) is immediately up-regulated but subsequently maintained throughout FGF-1 stimulation. Then follows a second wave of gene expression that includes a strong but transient up-regulation of ephrin B1 and arginase I. Finally, a third group of genes is stably modulated over 48 h which consists primarily of down-regulated genes specifically associated with the EMT-based loss of the epithelial phenotype and maintenance of the mesenchymal and invasive phenotype of carcinoma cells. Using genome-wide oligoarray technology, we have identified novel expressions of immediate, immediate-early and later EMT biomarkers that are specifically activated downstream of the FGF/FGFR pathway and which might be significant prognostic factors for tumor progression of carcinoma.

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Year of publication 2007

Virginie N Dupont, David Gentien, Marine Oberkampf, Yann De Rycke, Nathalie Blin (2007 Apr 24)

A gene expression signature associated with metastatic cells in effusions of breast carcinoma patients.

International journal of cancer : 1036-46 Learn more
Summary

Malignant effusion in invasive breast carcinoma is associated with poor prognosis. To decipher molecular events leading to metastasis and to identify reliable markers for targeted therapies are of crucial need. Therefore, we have used cDNA microarrays to delineate molecular signatures associated with metastasis and relapse in breast carcinoma effusions. Taking advantage of an immunomagnetic method, we have purified to homogeneity EpCAM-positive cells from 34 malignant effusions. Immunopurified cells represented as much as 10% of the whole cell fraction and their epithelial and carcinoma features were confirmed by immunofluorescence labeling. Gene expression profiles of 19 immunopurified effusion samples, were analyzed using human pan-genomic microarrays, and compared with those of 4 corresponding primary tumors, 8 breast carcinoma effusion-derived cell lines, and 4 healthy mammary tissues. Principal component and multiple clustering analyses of microarray data, clearly identified distinctive molecular portraits corresponding to the 4 categories of specimens. Of uppermost interest, effusion samples were arranged in 2 subsets on the basis of their gene expression patterns. The first subset partly shares a gene expression signature with the different cell lines, and overexpresses CD24, CD44 and epithelial cytokeratins 8,18,19. The second subset overexpresses markers related to aggressive invasive carcinoma (uPA receptor, S100A4, vimentin, CXCR4). These findings demonstrate the importance of using pure cell fractions to accurately decipher in silico gene expression of clinical specimens. Further studies will lead to the identification of genes of oustanding importance to diagnose malignant effusion, predict survival and tailor appropriate therapies to the metastatic effusion disease in breast carcinoma patients.

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Year of publication 2006

Nicolas Cagnard, Franck Letourneur, Abdellatif Essabbani, Valérie Devauchelle, Sylvie Mistou, Audrey Rapinat, Charles Decraene, Catherine Fournier, Gilles Chiocchia (2006 Feb 9)

Interleukin-32, CCL2, PF4F1 and GFD10 are the only cytokine/chemokine genes differentially expressed by in vitro cultured rheumatoid and osteoarthritis fibroblast-like synoviocytes.

European cytokine network : 289-92 Learn more
Summary

Since cytokines and chemokines are important actors in rheumatoid arthritis (RA), the aim of this study was to compare the gene expression profiles in cultured fibroblast-like synoviocytes (FLS) obtained from patients with either RA, or osteoarthritis (OA), focusing our analysis on genes for cytokines and chemokines, and their respective receptors. Gene expression in cultured FLS (third passage) from eight patients with RA (RA-FLS) were compared with gene expression in cultured FLS from nine patients with OA (OA-FLS) using Affymetrix Human Genome U133 Plus 2.0 Array microarray, allowing analysis of over 54,000 transcripts. Among the 171 genes studied (241 probes), limiting the selection of differentially expressed genes to a significant value (p < 0.05), and a differential ratio of expression > 1.6, only four genes, namely IL-32, CCL2, PF4F1 and GDF10 were found to be differentially expressed. Out of these four genes, only higher expression of CCL2 has been reported previously in RA. The newly described cytokine IL-32 was the most prominently differentially expressed gene in the present study, with higher expression in RA-FLS than in OA-FLS (p < 0.0073). IL-32 might have a previously unidentified pivotal role in RA.

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Year of publication 1990

S M Neill, M Lessana-Leibowitch, M Pelisse, M Moyal-Barracco (1990 Jun 1)

Lichen sclerosus, invasive squamous cell carcinoma, and human papillomavirus.

American journal of obstetrics and gynecology : 1633-4 Learn more
Summary

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C Eugène, M Stablo, L Wesenfelder, M L Anciaux, A Fingerhut, J C Etienne, A Bergue (1990 Jan 1)

[Invalidating polyarthritis in chronic pancreatitis. Recovery by pancreaticojejunostomy].

Gastroenterologie clinique et biologique : 1019-22 Learn more
Summary

A 38 year-old man presented with migratory joint arthropathy. He complained of abdominal pain, diarrhea and weight loss for 2 years. Periarticular needle aspiration yielded cytosteatonecrosis. The diagnosis of chronic pancreatitis was based on the results of ultrasound, CT scan, and endoscopic retrograde pancreatography. The latter showed a dilated and moniliform main pancreatic duct. Failure of symptomatic medical treatment of arthritis led to perform pancreaticojejunostomy which was followed immediately by complete relief of arthritic symptoms. During pancreatic disease, whether malignant or benign, joint involvement is often associated with bone, cutaneous, serosal, and multiorgan involvement. The pathogenesis and therapy of joint lesions in pancreatic disease are controversed. Surgical treatment of the causative disease, and especially pancreaticojejunostomy should undoubtedly be considered more often.

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