Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth

<p>Abstract</p> <p>Background</p> <p>The antenno-maxilary complex (AMC) forms the chemosensory system of the <it>Drosophila </it>larva and is involved in gustatory and olfactory perception. We have previously shown that a mutant allele of the homeodomain transcription factor Prospero (<it>prosVoila1</it>, <it>V1</it>), presents several developmental defects including abnormal growth and altered taste responses. In addition, many neural tracts connecting the AMC to the central nervous system (CNS) were affected. Our earlier reports on larval AMC did not argue in favour of a role of <it>pros </it>in cell fate decision, but strongly suggested that <it>pros </it>could be involved in the control of other aspect of neuronal development. In order to identify these functions, we used microarray analysis of larval AMC and CNS tissue isolated from the wild type, and three other previously characterised <it>prospero </it>alleles, including the <it>V1 </it>mutant, considered as a null allele for the AMC.</p> <p>Results</p> <p>A total of 17 samples were first analysed with hierarchical clustering. To determine those genes affected by loss of <it>pros </it>function, we calculated a discriminating score reflecting the differential expression between <it>V1 </it>mutant and other <it>pros </it>alleles. We identified a total of 64 genes in the AMC. Additional manual annotation using all the computed information on the attributed role of these genes in the <it>Drosophila </it>larvae nervous system, enabled us to identify one functional category of potential Prospero target genes known to be involved in neurite outgrowth, synaptic transmission and more specifically in neuronal connectivity remodelling. The second category of genes found to be differentially expressed between the null mutant AMC and the other alleles concerned the development of the sensory organs and more particularly the larval olfactory system. Surprisingly, a third category emerged from our analyses and suggests an association of <it>pros </it>with the genes that regulate autophagy, growth and insulin pathways. Interestingly, EGFR and Notch pathways were represented in all of these three functional categories. We now propose that Pros could perform all of these different functions through the modulation of these two antagonistic and synergic pathways.</p> <p>Conclusions</p> <p>The current data contribute to the clarification of the <it>prospero </it>function in the larval AMC and show that <it>pros </it>regulates different function in larvae as compared to those controlled by this gene in embryos. In the future, the possible mechanism by which Pros could achieve its function in the AMC will be explored in detail.</p

PGC-1-Related Coactivator Modulates Mitochondrial-Nuclear Crosstalk through Endogenous Nitric Oxide in a Cellular Model of Oncocytic Thyroid Tumours

BACKGROUND:The PGC-1 related coactivator (PRC), which shares structural and functional features with PGC-1alpha, is believed to regulate several metabolic pathways as well as mitochondrial biogenesis. Its involvement in the early programming of cell proliferation suggests the existence of finely regulated crosstalk between mitochondrial functions and the cell cycle status. METHODOLOGY/PRINCIPAL FINDINGS:PRC-regulated pathways were explored in a cell-line model derived from mitochondrial-rich tumours with an essentially oxidative metabolism and specifically high PRC expression. The functional status of mitochondria was compared to the results of microarray analysis under conditions of temporal PRC inhibition. To specify the fine PRC regulation, the expression levels of the genes and proteins involved in the oxidative phosphorylation process were studied by real time quantitative PCR and western blotting. As in earlier studies on PGC-1alpha, we investigated the role of nitric oxide in PRC-regulated mitochondrial biogenesis and determined its action in the control of the phosphorylation status of the mitogen-activated protein kinase pathway. CONCLUSION/SIGNIFICANCE:We found that nitric oxide rapidly influences PRC expression at the transcriptional level. Focusing on mitochondrial energetic metabolism, we observed that PRC differentially controls respiratory chain complexes and coupling efficiency in a time-dependent manner to maintain mitochondrial homeostasis. Our results highlight the key role of PRC in the rapid modulation of metabolic functions in response to the status of the cell cycle

Increasing the Number of Thyroid Lesions Classes in Microarray Analysis Improves the Relevance of Diagnostic Markers

BackgroundGenetic markers for thyroid cancers identified by microarray analysis have offered limited predictive accuracy so far because of the few classes of thyroid lesions usually taken into account. To improve diagnostic relevance, we have simultaneously analyzed microarray data from six public datasets covering a total of 347 thyroid tissue samples representing 12 histological classes of follicular lesions and normal thyroid tissue. Our own dataset, containing about half the thyroid tissue samples, included all categories of thyroid lesions. Methodology/Principal Findings Classifier predictions were strongly affected by similarities between classes and by the number of classes in the training sets. In each dataset, sample prediction was improved by separating the samples into three groups according to class similarities. The cross-validation of differential genes revealed four clusters with functional enrichments. The analysis of six of these genes (APOD, APOE, CLGN, CRABP1, SDHA and TIMP1) in 49 new samples showed consistent gene and protein profiles with the class similarities observed. Focusing on four subclasses of follicular tumor, we explored the diagnostic potential of 12 selected markers (CASP10, CDH16, CLGN, CRABP1, HMGB2, ALPL2, ADAMTS2, CABIN1, ALDH1A3, USP13, NR2F2, KRTHB5) by real-time quantitative RT-PCR on 32 other new samples. The gene expression profiles of follicular tumors were examined with reference to the mutational status of the Pax8-PPARγ, TSHR, GNAS and NRAS genes. Conclusion/Significance We show that diagnostic tools defined on the basis of microarray data are more relevant when a large number of samples and tissue classes are used. Taking into account the relationships between the thyroid tumor pathologies, together with the main biological functions and pathways involved, improved the diagnostic accuracy of the samples. Our approach was particularly relevant for the classification of microfollicular adenomas

De la génomique fonctionnelle vers la génomique intégrative de pathologies humaines

L'achèvement du séquençage du génome humain ainsi que celui de nombreux organismes a contribué à l'explosion de la génomique. Cette discipline s'attache notamment à la façon dont un génome s'exprime, au mode d'action des gènes, à l'étude de l'ensemble des produits qu'il code dans un système biologique donné. Des technologies de mesure du statut du génome à grande échelle, comme les biopuces que nous avons utilisées dans cette thèse, ont été mises en oeuvre. Ce travail a porté sur l'étude des variations du transcriptome dans différentes conditions physiologiques ou pathologiques. Nous avons pu mesurer l'influence de facteurs génétiques et environnementaux, détecter des biomarqueurs ou des profils d'expression spécifiques de sous-classe pathologiques dans des lymphomes et dans des maladies thyroïdiennes. Afin de comprendre des mécanismes moléculaires sous-jacents de ces modifications d'expression, nous avons progressivement intégré d'autres données génomiques. Ceci incluait la détection de délétions ou d'amplifications de régions génomiques par puces CGH, ou l'identification de sites de liaison de facteurs de transcription sur l'ADN par analyse bioinformatique ou par ChIP-chip. Par cette approche combinée, une modélisation de réseaux biologiques est alors envisageable. Elle permettra de mieux comprendre le fonctionnement d'un système biologique, suscitant de nombreux espoirs dans la recherche de cibles thérapeutiques encore plus pertinentes.The complete human genome sequence has contributed to the expansion of genomics. This field notably describes how a genome is expressed, how some sets of genes and their products work together in biological systems. High-throughput technologies for genome research, like microarrays which were used in this thesis, were set up. This work deals with transcriptomic variations observed in different physiological or pathological conditions. We appreciated the effect of genetic and environmental factors on expression profiles, to detect biomarkers specific to pathological subclasses of lymphoma and thyroid lesions. To understand molecular mechanisms underlying these gene expression modifications, we integrated gradually other genomic data. This included detections of genomic deletions or amplifications using CGH arrays, or the identification of transcription factor binding sites by sequence analysis or by ChIP-chip methodology. With this combined approach, modeling biological networks modeling is then conceivable. It will allow a better understanding of a biological system and to detect more reliable therapeutic targets.NANTES-BU Médecine pharmacie (441092101) / SudocSudocFranceF

Inhibition of GST-pi nuclear transfer increases mantle cell lymphoma sensitivity to cisplatin, cytarabine, gemcitabine, bortezomib and doxorubicin.

International audiencePURPOSE: Mantle cell lymphoma (MCL) is a chemoresistant lymphoma overexpressing the class pi glutathione-S-transferase (GST-pi). The nuclear localisation of GST-pi is induced by chemotherapy and is correlated to cell resistance. In this study, the effect of the Agaricus bisporus lectin (ABL), a GST-pi nuclear transfer inhibitor, on the chemosensitivity of MCL cells was investigated. METHODS: The proliferation of three MCL cell lines was evaluated in the presence of doxorubicin (DOX), cisplatin (CDDP), cytarabine (Ara-C), gemcitabine (GEM) or bortezomib with or without ABL pre-treatment. RESULTS: The cytotoxic activities of CDDP, Ara-C, GEM and bortezomib were increased in all cell lines. The DOX cytotoxic activity was enhanced in two of three cell lines. The inhibition of GST-pi nuclear transfer led to the potentialisation of all drug combinations. CONCLUSION: The inhibition of the nuclear transfer of GST-pi increases the MCL sensitivity to DOX, CDDP, Ara-C, GEM and bortezomib, alone or in combination

Inhibition of GST-pi nuclear transfer increases mantle cell lymphoma sensitivity to cisplatin, cytarabine, gemcitabine, bortezomib and doxorubicin.

International audiencePURPOSE: Mantle cell lymphoma (MCL) is a chemoresistant lymphoma overexpressing the class pi glutathione-S-transferase (GST-pi). The nuclear localisation of GST-pi is induced by chemotherapy and is correlated to cell resistance. In this study, the effect of the Agaricus bisporus lectin (ABL), a GST-pi nuclear transfer inhibitor, on the chemosensitivity of MCL cells was investigated. METHODS: The proliferation of three MCL cell lines was evaluated in the presence of doxorubicin (DOX), cisplatin (CDDP), cytarabine (Ara-C), gemcitabine (GEM) or bortezomib with or without ABL pre-treatment. RESULTS: The cytotoxic activities of CDDP, Ara-C, GEM and bortezomib were increased in all cell lines. The DOX cytotoxic activity was enhanced in two of three cell lines. The inhibition of GST-pi nuclear transfer led to the potentialisation of all drug combinations. CONCLUSION: The inhibition of the nuclear transfer of GST-pi increases the MCL sensitivity to DOX, CDDP, Ara-C, GEM and bortezomib, alone or in combination

Hierarchical clustering of cross-validated differential genes.

<p>The heatmap shows gene-expression levels in the Fontaine dataset for the tissue classes common to the Giordano dataset (104 genes). Functional enrichments are shown for five identified gene clusters on the right, followed by p-values and the genes involved. The black text represents Level 3 Gene Ontology terms; the blue text represents canonical Ingenuity pathways. Gene profiles of the differential genes reflect the class similarities observed. WT: wild type tissue; PTC: papillary thyroid carcinoma; FTA: macrofollicular thyroid adenoma; FTC: follicular thyroid carcinoma; OTA: oncocytic thyroid adenoma; and OTC: oncocytic thyroid carcinoma.</p

Cross validated differential genes from the two main datasets (n = 104).

<p>Cross validated differential genes from the two main datasets (n = 104).</p

Inter-dataset cross-validations. Positive accuracies of the classifiers defined by the Fontaine dataset in five other datasets.

<p>FTA: macrofollicular thyroid adenoma; FTC: follicular thyroid carcinoma; OTA: oncocytic thyroid adenoma; OTC: oncocytic thyroid carcinoma; and PTC: papillary thyroid carcinoma.</p