1
|
Sambroni E, Lareyre JJ, Le Gac F. Fsh controls gene expression in fish both independently of and through steroid mediation. PLoS One 2013; 8:e76684. [PMID: 24194844 PMCID: PMC3806798 DOI: 10.1371/journal.pone.0076684] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/29/2013] [Indexed: 01/07/2023] Open
Abstract
The mechanisms and the mediators relaying Fsh action on testicular functions are poorly understood. Unlike in mammals, in fish both gonadotropins (Fsh and Lh) are able to efficiently stimulate steroidogenesis, likely through a direct interaction with their cognate receptors present on the Leydig cells. In this context, it is crucial to understand if Fsh effects are mediated through the production of steroids. To address this issue we performed transcriptome studies after in vitro incubations of rainbow trout testis explants in the presence of Fsh alone or in combination with trilostane, an inhibitor of Δ4- steroidogenesis. Trilostane significantly reduced or suppressed the response of many genes to Fsh (like wisp1, testis gapdhs, cldn11, inha, vt1 or dmrt1) showing that, in fish, important aspects of Fsh action follow indirect pathways and require the production of Δ4-steroids. What is more, most of the genes regulated by Fsh through steroid mediation were similarly regulated by Lh (and/or androgens). In contrast, the response to Fsh of other genes was not suppressed in the presence of trilostane. These latter included genes encoding for anti-mullerian hormone, midkine a (pleiotrophin related), angiopoietine-related protein, cyclins E1 and G1, hepatocyte growth factor activator, insulin-like growth factor 1b/3. A majority of those genes were preferentially regulated by Fsh, when compared to Lh, suggesting that specific regulatory effects of Fsh did not depend on steroid production. Finally, antagonistic effects between Fsh and steroids were found, in particular for genes encoding key factors of steroidogenesis (star, hsd3b1, cyp11b2-2) or for genes of the Igf system (igf1b/3). Our study provides the first clear evidence that, in fish, Fsh exerts Δ4-steroid-independent regulatory functions on many genes which are highly relevant for the onset of spermatogenesis.
Collapse
Affiliation(s)
- Elisabeth Sambroni
- INRA, UR1037 LPGP, Testicular Physiology and Puberty, SFR BIOSIT, Biogenouest, Campus de Beaulieu, Rennes, France
| | - Jean-Jacques Lareyre
- INRA, UR1037 LPGP, Testicular Physiology and Puberty, SFR BIOSIT, Biogenouest, Campus de Beaulieu, Rennes, France
| | - Florence Le Gac
- INRA, UR1037 LPGP, Testicular Physiology and Puberty, SFR BIOSIT, Biogenouest, Campus de Beaulieu, Rennes, France
| |
Collapse
|
2
|
Sambroni E, Rolland AD, Lareyre JJ, Le Gac F. FSH and LH have common and distinct effects on gene expression in rainbow trout testis. J Mol Endocrinol 2013; 50:1-18. [PMID: 23045716 DOI: 10.1530/jme-12-0197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The general rules established from mammalian species for the regulation of spermatogenesis by gonadotropins may not be fully relevant in fish. Particularly, Fsh is as potent as Lh to stimulate steroidogenesis and the Fsh receptor is expressed in Leydig cells. In seasonal breeders, Fsh is likely the major gonadotropin involved in spermatogenesis onset and Lh is required to support spermatogenesis progression and gamete release. However, the genes that relay the action of Fsh and Lh have been poorly investigated in fish. The present study was aimed at identifying gonadotropin-dependent genes expressed in the testis during fish puberty. We cultured pubertal trout testicular explants for 96 h, with or without gonadotropin, and analyzed transcriptome variations using microarrays. Fsh and Lh had similar effects on a large group of genes while other genes were preferentially regulated by one or the other gonadotropin. We showed that most of the responsive genes were expressed in somatic cells and exhibited relevant patterns during the seasonal reproductive cycle. Some genes preferentially modulated by Lh could be involved in testicular cell fate (pvrl1 and bty) or sperm maturation (ehmt2 and racgap1) and will deserve further examination. Besides Fsh's effects on the steroidogenic pathway, our study demonstrates that Fsh coordinates relevant stimulatory and inhibitory paracrine factors known to regulate early germ cell proliferation and differentiation. Some of these genes belong to major regulatory pathways including the Igf pathway (igf1b/igf3 and igfbp6), the Tgfb pathway (amh, inha, inhba, and fstl3), the Wnt pathway (wisp1), and pleiotrophin (mdka).
Collapse
Affiliation(s)
- Elisabeth Sambroni
- INRA, UR1037, Laboratoire de Physiologie et Génomique des Poissons, Campus de Beaulieu, Testicular Physiology and Puberty, Biosit, Biogenouest, F-35000 Rennes, France
| | | | | | | |
Collapse
|
3
|
da Hora Junior BT, Poloni JDF, Lopes MA, Dias CV, Gramacho KP, Schuster I, Sabau X, Cascardo JCDM, Mauro SMZD, Gesteira ADS, Bonatto D, Micheli F. Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease. MOLECULAR BIOSYSTEMS 2012; 8:1507-19. [PMID: 22373587 DOI: 10.1039/c2mb05421c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This study reports on expression analysis associated with molecular systems biology of cacao-Moniliophthora perniciosa interaction. Gene expression data were obtained for two cacao genotypes (TSH1188, resistant; Catongo, susceptible) challenged or not with the fungus M. perniciosa and collected at three time points through disease. Using expression analysis, we identified 154 and 227 genes that are differentially expressed in TSH1188 and Catongo, respectively. The expression of some of these genes was confirmed by RT-qPCR. Physical protein-protein interaction (PPPI) networks of Arabidopsis thaliana orthologous proteins corresponding to resistant and susceptible interactions were obtained followed by cluster and gene ontology analyses. The integrated analysis of gene expression and systems biology allowed designing a general scheme of major mechanisms associated with witches' broom disease resistance/susceptibility. In this sense, the TSH1188 cultivar shows strong production of ROS and elicitors at the beginning of the interaction with M. perniciosa followed by resistance signal propagation and ROS detoxification. On the other hand, the Catongo genotype displays defense mechanisms that include the synthesis of some defense molecules but without success in regards to elimination of the fungus. This phase is followed by the activation of protein metabolism which is achieved with the production of proteasome associated with autophagy as a precursor mechanism of PCD. This work also identifies candidate genes for further functional studies and for genetic mapping and marker assisted selection.
Collapse
Affiliation(s)
- Braz Tavares da Hora Junior
- Centro de Biotecnologia e Genética-CBG, Departamento de Ciências Biológicas-DCB, Universidade Estadual de Santa Cruz-UESC, Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus-BA, Brasil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Liaubet L, Lobjois V, Faraut T, Tircazes A, Benne F, Iannuccelli N, Pires J, Glénisson J, Robic A, Le Roy P, Sancristobal M, Cherel P. Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism. BMC Genomics 2011; 12:548. [PMID: 22053791 PMCID: PMC3239847 DOI: 10.1186/1471-2164-12-548] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 11/04/2011] [Indexed: 01/03/2023] Open
Abstract
Background The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering. Results QTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs). Conclusion Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential.
Collapse
Affiliation(s)
- Laurence Liaubet
- Laboratoire de Génétique Cellulaire, INRA UMR444, Chemin de Borde Rouge, F-31326 Castanet-Tolosan, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Barbier M, Faille D, Loriod B, Textoris J, Camus C, Puthier D, Flori L, Wassmer SC, Victorero G, Alessi MC, Fusaï T, Nguyen C, Grau GE, Rihet P. Platelets alter gene expression profile in human brain endothelial cells in an in vitro model of cerebral malaria. PLoS One 2011; 6:e19651. [PMID: 21603600 PMCID: PMC3095604 DOI: 10.1371/journal.pone.0019651] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/12/2011] [Indexed: 01/16/2023] Open
Abstract
Platelet adhesion to the brain microvasculature has been associated with cerebral malaria (CM) in humans, suggesting that platelets play a role in the pathogenesis of this syndrome. In vitro co-cultures have shown that platelets can act as a bridge between Plasmodium falciparum-infected red blood cells (pRBC) and human brain microvascular endothelial cells (HBEC) and potentiate HBEC apoptosis. Using cDNA microarray technology, we analyzed transcriptional changes of HBEC in response to platelets in the presence or the absence of tumor necrosis factor (TNF) and pRBC, which have been reported to alter gene expression in endothelial cells. Using a rigorous statistical approach with multiple test corrections, we showed a significant effect of platelets on gene expression in HBEC. We also detected a strong effect of TNF, whereas there was no transcriptional change induced specifically by pRBC. Nevertheless, a global ANOVA and a two-way ANOVA suggested that pRBC acted in interaction with platelets and TNF to alter gene expression in HBEC. The expression of selected genes was validated by RT-qPCR. The analysis of gene functional annotation indicated that platelets induce the expression of genes involved in inflammation and apoptosis, such as genes involved in chemokine-, TREM1-, cytokine-, IL10-, TGFβ-, death-receptor-, and apoptosis-signaling. Overall, our results support the hypothesis that platelets play a pathogenic role in CM.
Collapse
Affiliation(s)
- Mathieu Barbier
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Dorothée Faille
- Unité de Recherche en Biologie et en Épidémiologie Parasitaires, UMR 6236-URMITE-IMTSSA, Institut de Recherche Biomédicale des Armées-Antenne Marseille, Marseille, France
- INSERM, UMR 626, Faculté de Médecine, Aix-Marseille Université, Marseille, France
- Vascular Immunology Unit, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Béatrice Loriod
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Julien Textoris
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Claire Camus
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Denis Puthier
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Laurence Flori
- Laboratoire de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, INRA AgroParisTech, Jouy-en-Josas, France
| | - Samuel Crocodile Wassmer
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | | | | | - Thierry Fusaï
- Unité de Recherche en Biologie et en Épidémiologie Parasitaires, UMR 6236-URMITE-IMTSSA, Institut de Recherche Biomédicale des Armées-Antenne Marseille, Marseille, France
| | - Catherine Nguyen
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Georges E. Grau
- Vascular Immunology Unit, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Pascal Rihet
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
- * E-mail:
| |
Collapse
|
6
|
Boone N, Loriod B, Bergon A, Sbai O, Formisano-Tréziny C, Gabert J, Khrestchatisky M, Nguyen C, Féron F, Axelrod FB, Ibrahim EC. Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia. PLoS One 2010; 5:e15590. [PMID: 21187979 PMCID: PMC3004942 DOI: 10.1371/journal.pone.0015590] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/13/2010] [Indexed: 12/29/2022] Open
Abstract
Background Familial dysautonomia (FD) is a hereditary neuropathy caused by mutations in the IKBKAP gene, the most common of which results in variable tissue-specific mRNA splicing with skipping of exon 20. Defective splicing is especially severe in nervous tissue, leading to incomplete development and progressive degeneration of sensory and autonomic neurons. The specificity of neuron loss in FD is poorly understood due to the lack of an appropriate model system. To better understand and modelize the molecular mechanisms of IKBKAP mRNA splicing, we collected human olfactory ecto-mesenchymal stem cells (hOE-MSC) from FD patients. hOE-MSCs have a pluripotent ability to differentiate into various cell lineages, including neurons and glial cells. Methodology/Principal Findings We confirmed IKBKAP mRNA alternative splicing in FD hOE-MSCs and identified 2 novel spliced isoforms also present in control cells. We observed a significant lower expression of both IKBKAP transcript and IKAP/hELP1 protein in FD cells resulting from the degradation of the transcript isoform skipping exon 20. We localized IKAP/hELP1 in different cell compartments, including the nucleus, which supports multiple roles for that protein. We also investigated cellular pathways altered in FD, at the genome-wide level, and confirmed that cell migration and cytoskeleton reorganization were among the processes altered in FD. Indeed, FD hOE-MSCs exhibit impaired migration compared to control cells. Moreover, we showed that kinetin improved exon 20 inclusion and restores a normal level of IKAP/hELP1 in FD hOE-MSCs. Furthermore, we were able to modify the IKBKAP splicing ratio in FD hOE-MSCs, increasing or reducing the WT (exon 20 inclusion):MU (exon 20 skipping) ratio respectively, either by producing free-floating spheres, or by inducing cells into neural differentiation. Conclusions/Significance hOE-MSCs isolated from FD patients represent a new approach for modeling FD to better understand genetic expression and possible therapeutic approaches. This model could also be applied to other neurological genetic diseases.
Collapse
Affiliation(s)
- Nathalie Boone
- NICN-CNRS UMR 6184, Université de la Méditerranée-Faculté de Médecine Nord, IFR Jean Roche, Marseille, France
| | | | | | - Oualid Sbai
- NICN-CNRS UMR 6184, Université de la Méditerranée-Faculté de Médecine Nord, IFR Jean Roche, Marseille, France
| | | | - Jean Gabert
- Plateforme Transcriptome, CRO2, Faculté de Médecine, Marseille, France
- Biochemistry and Molecular Biology, Hôpital Nord, AP-HM, Marseille, France
| | - Michel Khrestchatisky
- NICN-CNRS UMR 6184, Université de la Méditerranée-Faculté de Médecine Nord, IFR Jean Roche, Marseille, France
| | | | - François Féron
- NICN-CNRS UMR 6184, Université de la Méditerranée-Faculté de Médecine Nord, IFR Jean Roche, Marseille, France
| | - Felicia B. Axelrod
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
| | - El Chérif Ibrahim
- NICN-CNRS UMR 6184, Université de la Méditerranée-Faculté de Médecine Nord, IFR Jean Roche, Marseille, France
- * E-mail:
| |
Collapse
|
7
|
Gitaí DLG, Fachin AL, Mello SS, Elias CF, Bittencourt JC, Leite JP, Passos GADS, Garcia-Cairasco N, Paçó-Larson ML. The non-coding RNA BC1 is down-regulated in the hippocampus of Wistar Audiogenic Rat (WAR) strain after audiogenic kindling. Brain Res 2010; 1367:114-21. [PMID: 20974111 DOI: 10.1016/j.brainres.2010.10.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/21/2010] [Accepted: 10/17/2010] [Indexed: 01/08/2023]
Abstract
The aim of this study was to identify molecular pathways involved in audiogenic seizures in the epilepsy-prone Wistar Audiogenic Rat (WAR). For this, we used a suppression-subtractive hybridization (SSH) library from the hippocampus of WARs coupled to microarray comparative gene expression analysis, followed by Northern blot validation of individual genes. We discovered that the levels of the non-protein coding (npc) RNA BC1 were significantly reduced in the hippocampus of WARs submitted to repeated audiogenic seizures (audiogenic kindling) when compared to Wistar resistant rats and to both naive WARs and Wistars. By quantitative in situ hybridization, we verified lower levels of BC1 RNA in the GD-hilus and significant signal ratio reduction in the stratum radiatum and stratum pyramidale of hippocampal CA3 subfield of audiogenic kindled animals. Functional results recently obtained in a BC1⁻/⁻ mouse model and our current data are supportive of a potential disruption in signaling pathways, upstream of BC1, associated with the seizure susceptibility of WARs.
Collapse
Affiliation(s)
- Daniel Leite Goes Gitaí
- Department of Cellular and Molecular Biology, Ribeirão Preto School of Medicine, University of São Paulo, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Josset L, Textoris J, Loriod B, Ferraris O, Moules V, Lina B, N'Guyen C, Diaz JJ, Rosa-Calatrava M. Gene expression signature-based screening identifies new broadly effective influenza a antivirals. PLoS One 2010; 5. [PMID: 20957181 PMCID: PMC2949399 DOI: 10.1371/journal.pone.0013169] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/09/2010] [Indexed: 12/11/2022] Open
Abstract
Classical antiviral therapies target viral proteins and are consequently subject to resistance. To counteract this limitation, alternative strategies have been developed that target cellular factors. We hypothesized that such an approach could also be useful to identify broad-spectrum antivirals. The influenza A virus was used as a model for its viral diversity and because of the need to develop therapies against unpredictable viruses as recently underlined by the H1N1 pandemic. We proposed to identify a gene-expression signature associated with infection by different influenza A virus subtypes which would allow the identification of potential antiviral drugs with a broad anti-influenza spectrum of activity. We analyzed the cellular gene expression response to infection with five different human and avian influenza A virus strains and identified 300 genes as differentially expressed between infected and non-infected samples. The most 20 dysregulated genes were used to screen the connectivity map, a database of drug-associated gene expression profiles. Candidate antivirals were then identified by their inverse correlation to the query signature. We hypothesized that such molecules would induce an unfavorable cellular environment for influenza virus replication. Eight potential antivirals including ribavirin were identified and their effects were tested in vitro on five influenza A strains. Six of the molecules inhibited influenza viral growth. The new pandemic H1N1 virus, which was not used to define the gene expression signature of infection, was inhibited by five out of the eight identified molecules, demonstrating that this strategy could contribute to identifying new broad anti-influenza agents acting on cellular gene expression. The identified infection signature genes, the expression of which are modified upon infection, could encode cellular proteins involved in the viral life cycle. This is the first study showing that gene expression-based screening can be used to identify antivirals. Such an approach could accelerate drug discovery and be extended to other pathogens.
Collapse
Affiliation(s)
- Laurence Josset
- Centre National de la Recherche Scientifique (CNRS) FRE 3011 Virologie et Pathologie Humaine, Université Lyon 1, Lyon, France
- Laboratoire de Virologie Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
- * E-mail: (LJ); (MRC)
| | - Julien Textoris
- Institut National de la Santé et de la Recherche Médicale (INSERM) U928 Technologies Avancées pour le Génome et la Clinique, Université de la Méditerranée, Marseille, France
- Centre National de la Recherche Scientifique (CNRS) UMR 5534, Centre Léon Bérard, Centre de Génétique Moléculaire et Cellulaire, Université Lyon 1, Lyon, France
- Service d'anesthésie et de réanimation Hôpital Nord, Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Béatrice Loriod
- Institut National de la Santé et de la Recherche Médicale (INSERM) U928 Technologies Avancées pour le Génome et la Clinique, Université de la Méditerranée, Marseille, France
| | - Olivier Ferraris
- Centre National de la Recherche Scientifique (CNRS) FRE 3011 Virologie et Pathologie Humaine, Université Lyon 1, Lyon, France
| | - Vincent Moules
- Centre National de la Recherche Scientifique (CNRS) FRE 3011 Virologie et Pathologie Humaine, Université Lyon 1, Lyon, France
| | - Bruno Lina
- Centre National de la Recherche Scientifique (CNRS) FRE 3011 Virologie et Pathologie Humaine, Université Lyon 1, Lyon, France
- Laboratoire de Virologie Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Catherine N'Guyen
- Institut National de la Santé et de la Recherche Médicale (INSERM) U928 Technologies Avancées pour le Génome et la Clinique, Université de la Méditerranée, Marseille, France
| | - Jean-Jacques Diaz
- Centre National de la Recherche Scientifique (CNRS) UMR 5534, Centre Léon Bérard, Centre de Génétique Moléculaire et Cellulaire, Université Lyon 1, Lyon, France
| | - Manuel Rosa-Calatrava
- Centre National de la Recherche Scientifique (CNRS) FRE 3011 Virologie et Pathologie Humaine, Université Lyon 1, Lyon, France
- * E-mail: (LJ); (MRC)
| |
Collapse
|
9
|
Gene expression profiles characterize inflammation stages in the acute lung injury in mice. PLoS One 2010; 5:e11485. [PMID: 20628605 PMCID: PMC2900209 DOI: 10.1371/journal.pone.0011485] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 06/08/2010] [Indexed: 01/05/2023] Open
Abstract
Acute Lung Injury (ALI) carries about 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with mechanical ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis depends on two factors: the infection and the pre-existing inflammation. In this study, we described each stage of the inflammation process using a transcriptional approach and an animal model. Female C57BL6/J mice received an intravenous oleic acid injection to induce an acute lung injury (ALI). Lung expression patterns were analyzed using a 9900 cDNA mouse microarray (MUSV29K). Our gene-expression analysis revealed marked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early stage (1 hour–1.5 hours) is characterized by a pro-inflammatory immune response. Later (3 hours–4 hours), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of lung inflammation (18 hours–24 hours), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes and lipid metabolism. In this study, we described a global overview of critical events occurring during lung inflammation which is essential to understand infectious pathologies such as sepsis where inflammation and infection are intertwined. Based on these data, it becomes possible to isolate the impact of a pathogen at the transcriptional level from the global gene expression modifications resulting from the infection associated with the inflammation.
Collapse
|
10
|
Lopes MA, Hora BT, Dias CV, Santos GC, Gramacho KP, Cascardo JCM, Gesteira AS, Micheli F. Expression analysis of transcription factors from the interaction between cacao and Moniliophthora perniciosa (Tricholomataceae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1279-97. [PMID: 20623454 DOI: 10.4238/vol9-3gmr825] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cacao (Theobroma cacao) is one of the most important tropical crops; however, production is threatened by numerous pathogens, including the hemibiotrophic fungus Moniliophthora perniciosa, which causes witches' broom disease. To understand the mechanisms that lead to the development of this disease in cacao, we focused our attention on cacao transcription factors (TFs), which act as master regulators of cellular processes and are important for the fine-tuning of plant defense responses. We developed a macroarray with 88 TF cDNA from previously obtained cacao-M. perniciosa interaction libraries. Seventy-two TFs were found differentially expressed between the susceptible (Catongo) and resistant (TSH1188) genotypes and/or during the disease time course--from 24 h to 30 days after infection. Most of the differentially expressed TFs belonged to the bZIP, MYB and WRKY families and presented opposite expression patterns in susceptible and resistant cacao-M. perniciosa interactions (i.e., up-regulated in Catongo and down-regulated in TSH1188). The results of the macroarray were confirmed for bZIP and WRKY TFs by real-time PCR. These differentially expressed TFs are good candidates for subsequent functional analysis as well as for plant engineering. Some of these TFs could also be localized on the cacao reference map related to witches' broom resistance, facilitating the breeding and selection of resistant cacao trees.
Collapse
Affiliation(s)
- M A Lopes
- Laboratório de Genômica e Expressão Gênica, Departamento de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brasil
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Rolland AD, Lareyre JJ, Goupil AS, Montfort J, Ricordel MJ, Esquerré D, Hugot K, Houlgatte R, Chalmel F, Le Gac F. Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. BMC Genomics 2009; 10:546. [PMID: 19925684 PMCID: PMC2786911 DOI: 10.1186/1471-2164-10-546] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 11/20/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. RESULTS Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. CONCLUSION A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species.
Collapse
Affiliation(s)
| | | | | | - Jérôme Montfort
- INRA, UR1037, IFR-140, Ouest Genopole, Rennes, 35042, France
| | | | - Diane Esquerré
- INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France
- CEA, DSV, iRCM, SREIT, Laboratoire de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
- AgroParisTech, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Karine Hugot
- INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France
- CEA, DSV, iRCM, SREIT, Laboratoire de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
- AgroParisTech, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Rémi Houlgatte
- Inserm, U915, Université de Nantes, Faculté de Médecine, Nantes, 44035, France
| | - Fréderic Chalmel
- Inserm, U625, GERHM, Université de Rennes1, IFR-140, Ouest Genopole, Rennes, 35042, France
| | - Florence Le Gac
- INRA, UR1037, IFR-140, Ouest Genopole, Rennes, 35042, France
| |
Collapse
|
12
|
Guyonnet B, Marot G, Dacheux JL, Mercat MJ, Schwob S, Jaffrézic F, Gatti JL. The adult boar testicular and epididymal transcriptomes. BMC Genomics 2009; 10:369. [PMID: 19664223 PMCID: PMC2738690 DOI: 10.1186/1471-2164-10-369] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 08/07/2009] [Indexed: 12/30/2022] Open
Abstract
Background Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm gain their motility and fertility. Epididymis is a crescent shaped organ adjacent to the testis that can be divided in three gross morphological regions, head (caput), body (corpus) and tail (cauda). It contains a long and unique convoluted tubule connected to the testis via the efferent ducts and finished by joining the vas deferens in its caudal part. Results In this study, the testis, the efferent ducts (vas efferens, VE), nine distinct successive epididymal segments and the deferent duct (vas deferens, VD) of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9 K nylon microarray (AGENAE program; GEO accession number: GPL3729) spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoid (top down PAM) or hierarchical clustering (bottom up HCL) were combined for class discovery and gene expression analysis. Tissue clustering defined seven transcriptomic units: testis, vas efferens and five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically over-expressed (markers) in testis, VE or in each of the five transcriptomic units of the epididymis (including VD). The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology information. Conclusion This study described for the first time the complete transcriptomes of the testis, the epididymis, the vas efferens and the vas deferens on the same species. It described new genes or genes not yet reported over-expressed in these boar tissues, as well as new control mechanisms. It emphasizes and fulfilled the gap between studies done in rodents and human, and provides tools that will be useful for further studies on the biochemical processes responsible for the formation and maintain of the epididymal regionalization and the development of a fertile spermatozoa.
Collapse
Affiliation(s)
- Benoît Guyonnet
- UMR85 Physiologie de Reproduction et des Comportements, Institut National de Recherche Agronomique, F-37380 Nouzilly, France.
| | | | | | | | | | | | | |
Collapse
|
13
|
Pires ABL, Gramacho KP, Silva DC, Góes-Neto A, Silva MM, Muniz-Sobrinho JS, Porto RF, Villela-Dias C, Brendel M, Cascardo JCM, Pereira GAG. Early development of Moniliophthora perniciosa basidiomata and developmentally regulated genes. BMC Microbiol 2009; 9:158. [PMID: 19653910 PMCID: PMC2782264 DOI: 10.1186/1471-2180-9-158] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 08/04/2009] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The hemibiotrophic fungus Moniliophthora perniciosa is the causal agent of Witches' broom, a disease of Theobroma cacao. The pathogen life cycle ends with the production of basidiocarps in dead tissues of the infected host. This structure generates millions of basidiospores that reinfect young tissues of the same or other plants. A deeper understanding of the mechanisms underlying the sexual phase of this fungus may help develop chemical, biological or genetic strategies to control the disease. RESULTS Mycelium was morphologically analyzed prior to emergence of basidiomata by stereomicroscopy, light microscopy and scanning electron microscopy. The morphological changes in the mycelium before fructification show a pattern similar to other members of the order Agaricales. Changes and appearance of hyphae forming a surface layer by fusion were correlated with primordia emergence. The stages of hyphal nodules, aggregation, initial primordium and differentiated primordium were detected. The morphological analysis also allowed conclusions on morphogenetic aspects. To analyze the genes involved in basidiomata development, the expression of some selected EST genes from a non-normalized cDNA library, representative of the fruiting stage of M. perniciosa, was evaluated. A macroarray analysis was performed with 192 selected clones and hybridized with two distinct RNA pools extracted from mycelium in different phases of basidiomata formation. This analysis showed two groups of up and down-regulated genes in primordial phases of mycelia. Hydrophobin coding, glucose transporter, Rho-GEF, Rheb, extensin precursor and cytochrome p450 monooxygenase genes were grouped among the up-regulated. In the down-regulated group relevant genes clustered coding calmodulin, lanosterol 14 alpha demethylase and PIM1. In addition, 12 genes with more detailed expression profiles were analyzed by RT-qPCR. One aegerolysin gene had a peak of expression in mycelium with primordia and a second in basidiomata, confirming their distinctiveness. The number of transcripts of the gene for plerototolysin B increased in reddish-pink mycelium and indicated an activation of the initial basidiomata production even at this culturing stage. Expression of the glucose transporter gene increased in mycelium after the stress, coinciding with a decrease of adenylate cyclase gene transcription. This indicated that nutrient uptake can be an important signal to trigger fruiting in this fungus. CONCLUSION The identification of genes with increased expression in this phase of the life cycle of M. perniciosa opens up new possibilities of controlling fungus spread as well as of genetic studies of biological processes that lead to basidiomycete fruiting. This is the first comparative morphologic study of the early development both in vivo and in vitro of M. perniciosa basidiomata and the first description of genes expressed at this stage of the fungal life cycle.
Collapse
Affiliation(s)
- Acássia B L Pires
- Centro de Biotecnologia e Genética, Laboratório de Genômica e Expressão Gênica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, 45662-000, Ilhéus-Bahia, Brazil.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from seven RNA follicle pools and several technical replicates were made. The objective of this paper was to state the feasibility of a transcriptomic protocol for the study of folliculogenesis in the pig. A statistical analysis was chosen, relying on the linear mixed model (LMM) paradigm. Low variability within technical replicates was hence checked with a LMM. Relevant genes that might be involved in the studied process were then selected. For the most significant genes, statistical methods such as principal component analysis and unsupervised hierarchical clustering were applied to assess their relevance, and a random forest analysis proved their predictive value. The selection of genes was consistent with previous studies and also allowed the identification of new genes whose role in pig folliculogenesis will be further investigated.
Collapse
|
15
|
Bombonato-Prado KF, Bellesini LS, Junta CM, Marques MM, Passos GA, Rosa AL. Microarray-based gene expression analysis of human osteoblasts in response to different biomaterials. J Biomed Mater Res A 2009; 88:401-8. [PMID: 18306281 DOI: 10.1002/jbm.a.31701] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Several biomaterials have been widely used in bone regeneration/substitution procedures in orthopedic and oral surgery. However, how these biomaterials alter osteoblast gene expression is poorly understood. We therefore attempted to address this question by using cDNA microarray technique to identify genes that are differentially regulated in osteoblasts exposed to biomaterials comprehending the biocompatibility spectrum of bioactive (bioglass and hydroxyapatite), bioinert (Ti and stainless steel), and biotolerant (polymethylmethacrylate). By using a cDNA microarray containing 687 human IMAGE sequences, we identified in primary cultures of osteoblastic cells differentiated from the human bone marrow and exposed to these biomaterials, genes whose expression was significantly upregulated or downregulated. Among the differentially expressed genes we have found those involved with cell cycle regulation, cell differentiation and proliferation, apoptosis, cell adhesion, bone mineralization and skeletal development. These results can be relevant to a better understanding of the molecular mechanism underlying the behavior of osteoblasts in bone regenerative procedures.
Collapse
Affiliation(s)
- Karina F Bombonato-Prado
- Department of Morphology, Stomatology and Physiology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | |
Collapse
|
16
|
Bellesini LS, Beloti MM, Crippa GE, Bombonato-Prado KF, Junta CM, Marques MM, Passos GA, Rosa AL. The effect of TAK-778 on gene expression of osteoblastic cells is mediated through estrogen receptor. Exp Biol Med (Maywood) 2008; 234:190-9. [PMID: 19064943 DOI: 10.3181/0808-rm-246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study evaluated the effect of TAK-778 [(2R, 4S)-(-)-N-(4-diethoxyphosphorylmethylphenyl)-1,2,4,5-tetrahydro-4-methyl-7,8-methylenedioxy-5-oxo-3-benzothiepin-2-carboxamide)] on in vitro osteogenic events and on gene expression of osteoblastic cells derived from human alveolar bone and the participation of estrogen receptors (ERs) on such effect. Osteoblastic cells were subcultured, with or without TAK-778 (10(-5) M), to evaluate cell growth and viability, total protein content, and alkaline phosphatase (ALP) activity at 7, 14, and 21 days; bone-like formation at 21 days; and gene expression, using cDNA microarray, at 7 days. Also, osteoblastic cells were exposed to TAK-778 (10(-5) M) combined to ICI182,780, a nonspecific ER antagonist (10(-6) M), and gene expression was evaluated by real-time polymerase chain reaction (PCR) at 7 days. TAK-778 induced a reduction in culture growth and an increase in cell synthesis, ALP activity, and bone-like formation. The cDNA microarray showed genes associated with cell adhesion and differentiation, skeletal development, ossification, and transforming growth factor-beta receptor signaling pathway, with a tendency to be higher expressed in cells exposed to TAK-778. The gene expression of ALP, osteocalcin, Msh homeobox 2, receptor activator of NF-kappa B ligand, and intercellular adhesion molecule 1 was increased by TAK-778 as demonstrated by real-time PCR, and this effect was antagonized by ICI182,780. The present results demonstrated that TAK-778 acts at a transcriptional level to enhance the in vitro osteogenic process and that its effect on gene expression of osteoblastic cells is mediated, at least partially, through ERs. Based on these findings, TAK-778 could be considered in the treatment of bone metabolic disorders.
Collapse
Affiliation(s)
- Larissa S Bellesini
- Cell Culture Laboratory, Molecular Immunogenetics Group, Department of Genetics, School of Dentistry of Ribeirao Preto, University of Sao Paulo, Av do Cafe, s/n, 14040-904-Ribeirao Preto, SP, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Vendrell JA, Robertson KE, Ravel P, Bray SE, Bajard A, Purdie CA, Nguyen C, Hadad SM, Bieche I, Chabaud S, Bachelot T, Thompson AM, Cohen PA. A candidate molecular signature associated with tamoxifen failure in primary breast cancer. Breast Cancer Res 2008; 10:R88. [PMID: 18928543 PMCID: PMC2614524 DOI: 10.1186/bcr2158] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 10/13/2008] [Accepted: 10/17/2008] [Indexed: 01/25/2023] Open
Abstract
Introduction Few markers are available that can predict response to tamoxifen treatment in estrogen receptor (ER)-positive breast cancers. Identification of such markers would be clinically useful. We attempted to identify molecular markers associated with tamoxifen failure in breast cancer. Methods Eighteen initially ER-positive patients treated with tamoxifen requiring salvage surgery (tamoxifen failure [TF] patients) were compared with 17 patients who were disease free 5 years after surgery plus tamoxifen adjuvant therapy (control patients). cDNA microarray, real-time quantitative PCR, and immunohistochemistry on tissue microarrays were used to generate and confirm a gene signature associated with tamoxifen failure. An independent series of 33 breast tumor samples from patients who relapsed (n = 14) or did not relapse (n = 19) under tamoxifen treatment from a different geographic location was subsequently used to explore the gene expression signature identified. Results Using a screening set of 18 tumor samples (from eight control patients and 10 TF patients), a 47-gene signature discriminating between TF and control samples was identified using cDNA arrays. In addition to ESR1/ERα, the top-ranked genes selected by statistical cross-analyses were MET, FOS, SNCG, IGFBP4, and BCL2, which were subsequently validated in a larger set of tumor samples (from 17 control patients and 18 TF patients). Confirmation at the protein level by tissue microarray immunohistochemistry was observed for ER-α, γ-synuclein, and insulin-like growth factor binding protein 4 proteins in the 35 original samples. In an independent series of breast tumor samples (19 nonrelapsing and 14 relapsing), reduced expression of ESR1/ERα, IGFBP4, SNCG, BCL2, and FOS was observed in the relapsing group and was associated with a shorter overall survival. Low mRNA expression levels of ESR1/ERα, BCL2, and FOS were also associated with a shorter relapse-free survival (RFS). Using a Cox multivariate regression analysis, we identified BCL2 and FOS as independent prognostic markers associated with RFS. Finally, the BCL2/FOS signature was demonstrated to have more accurate prognostic value for RFS than ESR1/ERα alone (likelihood ratio test). Conclusions We identified molecular markers including a BCL2/FOS signature associated with tamoxifen failure; these markers may have clinical potential in the management of ER-positive breast cancer.
Collapse
|
18
|
Bonnet A, Lê Cao KA, Sancristobal M, Benne F, Robert-Granié C, Law-So G, Fabre S, Besse P, De Billy E, Quesnel H, Hatey F, Tosser-Klopp G. In vivo gene expression in granulosa cells during pig terminal follicular development. Reproduction 2008; 136:211-24. [PMID: 18456903 DOI: 10.1530/rep-07-0312] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ovarian antral follicular development is clearly dependent on pituitary gonadotrophins FSH and LH. Although the endocrine mechanism that controls ovarian folliculogenesis leading to ovulation is quite well understood, the detailed mechanisms and molecular determinants in the different follicular compartments remain to be clarified. The aim of this study was to identify the genes differentially expressed in pig granulosa cells along the terminal ovarian follicle growth, to gain a comprehensive view of these molecular mechanisms. First, we developed a specific micro-array using cDNAs from suppression subtractive hybridization libraries (345 contigs) obtained by comparison of three follicle size classes: small, medium and large antral healthy follicles. In a second step, a transcriptomic analysis using cDNA probes from these three follicle classes identified 79 differentially expressed transcripts along the terminal follicular growth and 26 predictive genes of size classes. The differential expression of 18 genes has been controlled using real-time PCR experiments validating the micro-array analysis. Finally, the integration of the data using Ingenuity Pathways Analysis identified five gene networks providing descriptive elements of the terminal follicular development. Specifically, we observed: (1) the down-expression of ribosomal protein genes, (2) the genes involved in lipid metabolism and (3) the down-expression of cell morphology and ion-binding genes. In conclusion, this study gives new insight into the gene expression during pig terminal follicular growth in vivo and suggested, in particular, a morphological change in pig granulosa cells accompanying terminal follicular growth.
Collapse
Affiliation(s)
- A Bonnet
- INRA, UMR 444, Génétique Cellulaire, F-31326 Castanet-Tolosan Cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Hepatic gene expression profiles in juvenile rainbow trout (Oncorhynchus mykiss) fed fishmeal or fish oil-free diets. Br J Nutr 2008; 100:953-67. [PMID: 18439330 DOI: 10.1017/s0007114508981411] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Reducing the reliance on fishery by-products as amino acid and fatty acid sources in feeds for farmed fish is a major objective today. We evaluated the effect of dietary fish oil or dietary fishmeal replacement by vegetable oils and plant proteins respectively through analysis of hepatic transcriptomes in rainbow trout (Oncorhynchus mykiss). Fish were fed right from first feeding with diets based on plant by-products before being killed. We analysed the hepatic gene profile using trout cDNA microarrays (9K). Our data showed that seventy-one and seventy-five genes were affected after fish oil and fishmeal replacement respectively. The major part of modified gene expression coding for proteins of the metabolic pathways was as follows: (i) a lower level of expression for genes of energy metabolism found in fish after fishmeal and fish oil replacement; (ii) a lower level of gene expression for fatty acid metabolism (biosynthesis) in fish fed with vegetable oils; (iii) a differential expression of actors of detoxification metabolism in trout fed with vegetable oils; (iv) a lower level of expression of genes involved in protein metabolism in fish fed with plant proteins. Overall, our data suggest that dietary fish oil replacement is linked to a decreased capacity of fatty acid biosynthesis (fatty acid synthase) and variation of detoxification metabolism (cytochrome P450s) whereas dietary fishmeal replacement may depress protein metabolism in the liver as reflected by glutamine synthetase.
Collapse
|
20
|
Hook SE, Skillman AD, Gopalan B, Small JA, Schultz IR. Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture. Toxicol Sci 2007; 102:42-60. [PMID: 18084045 DOI: 10.1093/toxsci/kfm293] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Among proposed uses for microarrays in environmental toxiciology is the identification of key contributors to toxicity within a mixture. However, it remains uncertain whether the transcriptomic profiles resulting from exposure to a mixture have patterns of altered gene expression that contain identifiable contributions from each toxicant component. We exposed isogenic rainbow trout Onchorynchus mykiss, to sublethal levels of ethynylestradiol, 2,2,4,4-tetrabromodiphenyl ether, and chromium VI or to a mixture of all three toxicants Fluorescently labeled complementary DNA (cDNA) were generated and hybridized against a commercially available Salmonid array spotted with 16,000 cDNAs. Data were analyzed using analysis of variance (p<0.05) with a Benjamani-Hochberg multiple test correction (Genespring [Agilent] software package) to identify up and downregulated genes. Gene clustering patterns that can be used as "expression signatures" were determined using hierarchical cluster analysis. The gene ontology terms associated with significantly altered genes were also used to identify functional groups that were associated with toxicant exposure. Cross-ontological analytics approach was used to assign functional annotations to genes with "unknown" function. Our analysis indicates that transcriptomic profiles resulting from the mixture exposure resemble those of the individual contaminant exposures, but are not a simple additive list. However, patterns of altered genes representative of each component of the mixture are clearly discernible, and the functional classes of genes altered represent the individual components of the mixture. These findings indicate that the use of microarrays to identify transcriptomic profiles may aid in the identification of key stressors within a chemical mixture, ultimately improving environmental assessment.
Collapse
Affiliation(s)
- Sharon E Hook
- Battelle, Marine Research Operations, West Sequim Bay Road, Sequim, Washington 98382, USA.
| | | | | | | | | |
Collapse
|
21
|
Shanker A, Verdeil G, Buferne M, Inderberg-Suso EM, Puthier D, Joly F, Nguyen C, Leserman L, Auphan-Anezin N, Schmitt-Verhulst AM. CD8 T Cell Help for Innate Antitumor Immunity. THE JOURNAL OF IMMUNOLOGY 2007; 179:6651-62. [DOI: 10.4049/jimmunol.179.10.6651] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
22
|
Ferré PJ, Liaubet L, Concordet D, SanCristobal M, Uro-Coste E, Tosser-Klopp G, Bonnet A, Toutain PL, Hatey F, Lefebvre HP. Longitudinal Analysis of Gene Expression in Porcine Skeletal Muscle After Post-Injection Local Injury. Pharm Res 2007; 24:1480-9. [PMID: 17380264 DOI: 10.1007/s11095-007-9266-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
Abstract
PURPOSE The purpose of this study is to describe the time course of gene expression in a skeletal muscle local injury induced by an intramuscular (IM) injection, and to compare the dynamics of gene expression with pathological events. MATERIALS AND METHODS Ten piglets received 4 IM injections of propylene glycol in the longissimus dorsi muscles 6 h, 2, 7, and 21 days before euthanasia, where control and injected muscle sites were sampled for RNA isolation and microscopic examination. The hybridization of nylon cDNA microarrays was carried out with radioactive probes obtained from the muscle RNA. RESULTS 153 genes were found under- or over-expressed at least once among the investigated time-conditions. The eight most discriminant genes were also identified: Two genes (GTP-binding protein RAD and Ankyrin repeat domain protein) were over-expressed at 6 h and six genes between 2 and 21 days (Osteonectin, Fibronectin, Matrix metalloproteinase-2, Collagen alpha 1(I) chain, Collagen alpha 2(I) chain, and Thymosin beta-4). Necrosis, inflammation and regeneration were observed through both the dynamics of gene expression profiles and through the microscopic examinations. CONCLUSION Our data demonstrate that several pathways are involved in post-injection muscle injury, and that necrosis, inflammation and regeneration are not sequential but occur in parallel.
Collapse
Affiliation(s)
- Pierre J Ferré
- UMR181 de Physiopathologie et Toxicologie Expérimentales, INRA, ENVT, National Veterinary School, 23 chemin des Capelles, BP 87614, Toulouse cedex 03, 31076, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Cathelin R, Lopez F, Klopp C. AGScan: a pluggable microarray image quantification software based on the ImageJ library. Bioinformatics 2006; 23:247-8. [PMID: 17092988 DOI: 10.1093/bioinformatics/btl564] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997-2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms. AVAILABILITY The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.
Collapse
Affiliation(s)
- R Cathelin
- INRA, Sigenae UR875 Biométrie et Intelligence Artificielle/Génétique Cellulaire, BP 52627, 31326 Castanet-Tolosan Cedex, France
| | | | | |
Collapse
|
24
|
Honoré P, Granjeaud S, Tagett R, Deraco S, Beaudoing E, Rougemont J, Debono S, Hingamp P. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. BMC Genomics 2006; 7:240. [PMID: 16987406 PMCID: PMC1592093 DOI: 10.1186/1471-2164-7-240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 09/20/2006] [Indexed: 01/08/2023] Open
Abstract
Background High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.
Collapse
Affiliation(s)
- Paul Honoré
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Samuel Granjeaud
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
| | - Rebecca Tagett
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Stéphane Deraco
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
- Now at CNRS – DSI, Tour Gaïa, rue Pierre-Gilles de Gennes, BP 21902, 31319 LABEGE CEDEX, France
| | - Emmanuel Beaudoing
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Jacques Rougemont
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stéphane Debono
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Pascal Hingamp
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at IGS, CNRS UPR 2589, 163 Avenue de Luminy Case 934, 13288 Marseille Cedex 09, France
| |
Collapse
|
25
|
Oh SJ, Hong BJ, Choi KY, Park JW. Surface Modification for DNA and Protein Microarrays. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:327-43. [PMID: 17069511 DOI: 10.1089/omi.2006.10.327] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.
Collapse
Affiliation(s)
- Soon Jin Oh
- Department of Biomedical Science and Technology, Institute of Biomedical Science and Technology, Konkuk University, Seoul, Korea.
| | | | | | | |
Collapse
|
26
|
Sousa Cardoso R, Magalhães DAR, Baião AMT, Junta CM, Macedo C, Marques MMC, Sakamoto-Hojo ET, Donadi EA, Passos GAS. Onset of promiscuous gene expression in murine fetal thymus organ culture. Immunology 2006; 119:369-75. [PMID: 16903901 PMCID: PMC1819582 DOI: 10.1111/j.1365-2567.2006.02441.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
T-cell differentiation and induction of tolerance to self-antigens occurs mainly in the thymus. Thymic stromal cells, specifically medullary thymic epithelial cells, express a diverse set of genes encoding parenchymal organ-specific proteins. This phenomenon has been termed promiscuous gene expression (PGE) and has been implicated in preventing organ-specific autoimmunity by inducing T-cell tolerance to self antigens. Early thymopoiesis and the critical factors involved in T-cell differentiation can be reproduced in vitro by murine fetal thymus organ culture (FTOC), which mimics the natural thymic microenvironment. To evaluate the occurrence of PGE in FTOC, gene expression profiling during in vitro thymic development in BALB/c mice was performed using a set of nylon cDNA microarrays containing 9216 sequences. The statistical analysis of the microarray data (sam program) revealed the temporal repression and induction of 57 parenchymal and seven lymphoid organ-specific genes. Most of the genes analysed are repressed during early thymic development (15-17 days post-coitum). The expression of the autoimmune regulator (AIRE) gene at 16 days post-coitum marks the onset of PGE. This precedes the induction of parenchymal organ genes during the late developmental phase at 20 days post-coitum. The mechanism of T-cell tolerance induction begins during fetal development and continues into adulthood. Our findings are significant because they show a fine demarcation of PGE onset, which plays a central role in induction of T-cell tolerance.
Collapse
Affiliation(s)
- Renato Sousa Cardoso
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Hook SE, Skillman AD, Small JA, Schultz IR. Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2006; 77:372-85. [PMID: 16488489 PMCID: PMC2494855 DOI: 10.1016/j.aquatox.2006.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 01/09/2006] [Accepted: 01/11/2006] [Indexed: 05/06/2023]
Abstract
The increased availability and use of DNA microarrays has allowed the characterization of gene expression patterns associated with exposure to different toxicants. An important question is whether toxicant induced changes in gene expression in fish are sufficiently diverse to allow for identification of specific modes of action and/or specific contaminants. In theory, each class of toxicant may generate a gene expression profile unique to its mode of toxic action. In this study, isogenic (cloned) rainbow trout Oncorhynchus mykiss were exposed to sublethal levels of a series of model toxicants with varying modes of action, including ethynylestradiol (xeno-estrogen), 2,2,4,4'-tetrabromodiphenyl ether (BDE-47, thyroid active), diquat (oxidant stressor), chromium VI, and benzo[a]pyrene (BaP) for a period of 1-3 weeks. An additional experiment measured trenbolone (anabolic steroid; model androgen) induced gene expression changes in sexually mature female trout. Following exposure, fish were euthanized, livers removed and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNA's. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up- and downregulated genes, as well as to determine gene clustering patterns that can be used as "expression signatures". The results indicate each toxicant exposure caused between 64 and 222 genes to be significantly altered in expression. Most genes exhibiting altered expression responded to only one of the toxicants and relatively few were co-expressed in multiple treatments. For example, BaP and Diquat, both of which exert toxicity via oxidative stress, upregulated 28 of the same genes, of over 100 genes altered by either treatment. Other genes associated with steroidogenesis, p450 and estrogen responsive genes appear to be useful for selectively identifying toxicant mode of action in fish, suggesting a link between gene expression profile and mode of toxicity. Our array results showed good agreement with quantitative real time polymerase chain reaction (qRT PCR), which demonstrates that the arrays are an accurate measure of gene expression. The specificity of the gene expression profile in response to a model toxicant, the link between genes with altered expression and mode of toxic action, and the consistency between array and qRT PCR results all suggest that cDNA microarrays have the potential to screen environmental contaminants for biomarkers and mode of toxic action.
Collapse
Affiliation(s)
- Sharon E Hook
- Battelle, Marine Research Operations, Sequim, WA, USA.
| | | | | | | |
Collapse
|
28
|
Tian YX, Chen C, Zou XY, Tan XC, Cai PX, Mo JY. Study on Fractal Characteristics of the Coding Sequences in DNA. CHINESE J CHEM 2006. [DOI: 10.1002/cjoc.200690081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
29
|
Ballester B, Ramuz O, Gisselbrecht C, Doucet G, Loï L, Loriod B, Bertucci F, Bouabdallah R, Devilard E, Carbuccia N, Mozziconacci MJ, Birnbaum D, Brousset P, Berger F, Salles G, Briére J, Houlgatte R, Gaulard P, Xerri L. Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas. Oncogene 2005; 25:1560-70. [PMID: 16288225 DOI: 10.1038/sj.onc.1209178] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The classification of peripheral T-cell lymphomas (PTCL) is still a matter of debate. To establish a molecular classification of PTCL, we analysed 59 primary nodal T-cell lymphomas using cDNA microarrays, including 56 PTCL and three T-lymphoblastic lymphoma (T-LBL). The expression profiles could discriminate angioimmunoblastic lymphoma, anaplastic large-cell lymphoma and T-LBL. In contrast, cases belonging to the broad category of 'PTCL, unspecified' (PTCL-U) did not share a single molecular profile. Using a multiclass predictor, we could separate PTCL-U into three molecular subgroups called U1, U2 and U3. The U1 gene expression signature included genes known to be associated with poor outcome in other tumors, such as CCND2. The U2 subgroup was associated with overexpression of genes involved in T-cell activation and apoptosis, including NFKB1 and BCL-2. The U3 subgroup was mainly defined by overexpression of genes involved in the IFN/JAK/STAT pathway. It comprised a majority of histiocyte-rich PTCL samples. Gene Ontology annotations revealed different functional profile for each subgroup. These results suggest the existence of distinct subtypes of PTCL-U with specific molecular profiles, and thus provide a basis to improve their classification and to develop new therapeutic targets.
Collapse
|
30
|
Grange T, Imbert J, Thieffry D. Epigenomics: large scale analysis of chromatin modifications and transcription factors/genome interactions. Bioessays 2005; 27:1203-5. [PMID: 16237667 DOI: 10.1002/bies.20319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thierry Grange
- Institut Jacques Monod, CNRS-Universités de PARIS 6 et 7, Paris, France
| | | | | |
Collapse
|
31
|
Application of microarray technology in pulmonary diseases. Respir Res 2004; 5:26. [PMID: 15585067 PMCID: PMC543572 DOI: 10.1186/1465-9921-5-26] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2004] [Accepted: 12/07/2004] [Indexed: 12/11/2022] Open
Abstract
Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.
Collapse
|
32
|
Puthier D, Joly F, Irla M, Saade M, Victorero G, Loriod B, Nguyen C. A General Survey of Thymocyte Differentiation by Transcriptional Analysis of Knockout Mouse Models. THE JOURNAL OF IMMUNOLOGY 2004; 173:6109-18. [PMID: 15528347 DOI: 10.4049/jimmunol.173.10.6109] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The thymus is the primary site of T cell lymphopoiesis. To undergo proper differentiation, developing T cells follow a well-ordered genetic program that strictly depends on the heterogeneous and highly specialized thymic microenvironment. In this study, we used microarray technology to extensively describe transcriptional events regulating alphabeta T cell fate. To get an integrated view of these processes, both whole thymi from genetically engineered mice together with purified thymocytes were analyzed. Using mice exhibiting various transcriptional perturbations and developmental blockades, we performed a transcriptional microdissection of the organ. Multiple signatures covering both cortical and medullary stroma as well as various thymocyte maturation intermediates were clearly defined. Beyond the definition of histological and functional signatures (proliferation, rearrangement), we provide the first evidence that such an approach may also highlight the complex cross-talk events that occur between maturing T cells and stroma. Our data constitute a useful integrated resource describing the main gene networks set up during thymocyte development and a first step toward a more systematic transcriptional analysis of genetically modified mice.
Collapse
MESH Headings
- Animals
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cell Line
- Cell Line, Transformed
- Cell Proliferation
- DNA Helicases
- Gene Expression Profiling/methods
- Gene Rearrangement, T-Lymphocyte
- Genes, T-Cell Receptor alpha/genetics
- Leukemia P388
- Mice
- Mice, Inbred C57BL
- Mice, Knockout/genetics
- Mice, Knockout/immunology
- Models, Animal
- Multigene Family/immunology
- Nuclear Proteins/biosynthesis
- Nuclear Proteins/genetics
- Oligonucleotide Array Sequence Analysis/methods
- Proto-Oncogene Proteins/deficiency
- Proto-Oncogene Proteins/genetics
- Receptor, Notch1
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Interleukin-2/biosynthesis
- Stromal Cells/immunology
- Stromal Cells/metabolism
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Thymus Gland/cytology
- Thymus Gland/immunology
- Thymus Gland/metabolism
- Transcription Factor RelB
- Transcription Factors/biosynthesis
- Transcription Factors/deficiency
- Transcription Factors/genetics
- Transcription Factors/physiology
- Up-Regulation/genetics
- Up-Regulation/immunology
Collapse
Affiliation(s)
- Denis Puthier
- Technologies Avancées pour le Génome et la Clinique/ERM 206, Parc Scientifique de Luminy, 13288 Marseille cedex 09, France
| | | | | | | | | | | | | |
Collapse
|