Combinatorial effects of splice variants modulate function of Aiolos

The transcription factor Aiolos (also known as IKZF3), a member of the Ikaros family of zinc-finger proteins, plays an important role in the control of B lymphocyte differentiation and proliferation. Previously, multiple isoforms of Ikaros family members arising from differential splicing have been described and we now report a number of novel isoforms of Aiolos. It has been demonstrated that full-length Ikaros family isoforms localize to heterochromatin and that they can associate with complexes containing histone deacetylase (HDAC). In this study, for the first time we directly investigate the cellular localization of various Aiolos isoforms, their ability to heterodimerize with Ikaros and associate with HDAC-containing complexes, and the effects on histone modification and binding to putative targets. Our work demonstrates that the cellular activities of Aiolos isoforms are dependent on combinations of various functional domains arising from the differential splicing of mRNA transcripts. These data support the general principle that the function of an individual protein is modulated through alternative splicing, and highlight a number of potential implications for Aiolos in normal and aberrant lymphocyte function.

The ubiquitin-proteasome system and signal transduction pathways regulating Epithelial Mesenchymal transition of cancer.

Epithelial to Mesenchymal transition (EMT) in cancer, a process permitting cancer cells to become mobile and metastatic, has a signaling hardwire forged from development. Multiple signaling pathways that regulate carcinogenesis enabling characteristics in neoplastic cells such as proliferation, resistance to apoptosis and angiogenesis are also the main players in EMT. These pathways, as almost all cellular processes, are in their turn regulated by ubiquitination and the Ubiquitin-Proteasome System (UPS). Ubiquitination is the covalent link of target proteins with the small protein ubiquitin and serves as a signal to target protein degradation by the proteasome or to other outcomes such as endocytosis, degradation by the lysosome or specification of cellular localization. This paper reviews signal transduction pathways regulating EMT and being regulated by ubiquitination.

Study of the SRR1-gene family in Arabidopsis, yeast and mouse cells

Abstract: Light is a very important environmental cue for plants. In addition to the energy for photosynthesis, it also provides information that is essential for many processes including seed germination, seedlings development, neighbours detection or transition from the vegetative to the reproductive state. Plants evolved different photoreceptors, among which the phytochromes (PHY), which are red/far-red photoreceptors. This family is composed of 5 members in Arabidopsis thaliana, among which phyB plays the major role for detection of red light. Phytochromes are also able to reset the phase of the circadian clock, which is composed of a complicated network of genes able to produce rhythms of about 24 hours, even in constant conditions. SRR1 (Sensitivity to Red light Reduced) is a gene that was shown to act in the phyB pathway as well as in the circadian clock. It was proposed to play a role in the maintenance of rhythms of the core oscillator because of the circadian phenotype of the srr1 mutant in constant light and in constant darkness. In the present study, we present data confirming the role of SRR1 in the core oscillator. Moreover, we show that SRR1 levels are not limiting for circadian rhythms nor for light perception. We show that the protein levels, the sub-cellular localisation or the complex in which SRR1 is found are not regulated in a circadian manner. Orthologues of SRR1 exist in numerous eukaryotes, forming a new gene family. None of the members of this family have been described. Here, we present data suggesting that the mouse orthologue of SRR1 may not be required for oscillation of the circadian clock of mouse cells in culture. The yeast gene (called BER1 for Benomyl REsistant) was studied to understand the biochemical function of this gene family. Based on synthetic genetic screens, a role of Ber1 was inferred in microtubules dynamics, N-terminal acetylation of protein and proteasome biogenesis. The effect of Ber1 on microtubules was confirmed by the observation that the ber1Δ mutant is more resistant to microtubule-depolymerising drugs and microscopic examination of microtubules in ber 1 Δ mutants. Complementation assays of ber1 Δ mutants and srrl mutants failed to reveal any obvious functional conservation of the mouse, yeast and Arabidopsis orthologues. In conclusion, the SRR1 family might encode genes that either plays different roles in different organisms, or have similar biochemical function but are involved in diverse pathway. Résumé: La lumière est un des facteurs abiotiques les plus important pour les plantes. En plus de l'énergie fournie pour la photosynthèse, elle fourni également de l'information nécessaire pour différents processus comme la germination, le développement des jeunes plantules, la détection de plantes avoisinantes ou encore la transition entre le développement végétatif et reproductif. Plusieurs types de photorécepteurs sont apparus chez les plantes au cours de l'évolution, notamment les phytochromes (PHI, qui perçoivent la lumière rouge et rouge lointaine. Cette famille est composé de 5 membres chez Arabidopsis thaliana, parmi lesquels phyB est le principal récepteur pour la lumière rouge. Les phytochromes sont aussi utiles pour la synchronisation entre les cycles jour-nuit dus à la rotation de la terre et l'horloge circadienne. Cette dernière est composée d'un réseau compliqué qui permet la production de rythmes capables de perdurer même en conditions constantes. SRRI (Sensitivity to Red light Reduced) est un gène qui agit dans la voie de signalisation de phyB ainsi que dans l'horloge circadienne. Il a été proposé que SRRI joue un rôle dans la maintenance des rythmes de l'oscillateur principal à cause des phénotypes circadiens du mutant srrl observés en lumière et en obscurité continue. Dans ce travail, nous présentons des données confirmant le rôle de SRR1 dans l'oscillateur principal. Nous montrons que les niveaux d'expression de SRRI ne sont pas limitants pour les rythmes circadiens ou la perception de la lumière. Enfin, nous montrons que le niveau d'accumulation de la protéine, sa localisation subcellulaire ou encore la taille du complexe dans lequel SRRl est trouvé ne sont pas régulés de façon circadiennes. Des orthologues de SRRI existent chez de nombreux eucaryotes, formant une nouvelle famille de gènes. Aucun des membres de cette famille n'a été étudié avant ce travail. Nous présentons des données suggérant que l'orthologue de la souris n'est peut-être pas requis pour les oscillations de l'horloge circadienne de cellules de souris en culture. Le gène de la levure (appelé SERI pour Benomyl REsistant) a été étudié afin de mieux comprendre la fonction biochimique de cette famille de gène. Une analyse par crible synthétique léthal a révélé un rôle de Ber1 dans la dynamique des microtubules, l'acétylation des protéines en N-terminal et la biogenèse du protéasome. L'effet de Ber1 sur les microtubules a été confirmé par l'observation du mutant ber1 en présence de drogue capable de dépolymériser les microtubules. Celui-ci est plus résistant à ces drogues que le type sauvage. Des expériences de complémentation n'ont pas montré de conservation de la fonction entre SRRI et ses homologues de souris ou de levure. En conclusion, la famille SRRI code pour des gènes qui pourraient avoir soit des rôles différents selon les organismes, soit la même fonction biochimique mais qui serait utile pour des voies de signalisation différentes.

The role of gene duplication in the origin and evolution of new biological functions

Abstract : Gene duplication is an essential source of material for the origin of genetic novelty and the evolution of lineage- or species-specific phenotypic traits. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with a significant number of gene copies during the last ~63 million years (MYA) of primate evolution. We estimated that at least 1 new functional gene (retrogene) per MYA emerged by retroposition in the primate lineage leading to humans. Using a combination of comparative sequencing and evolutionary simulations, we obtained strong evidence of functionality for 7 primate specific retrogenes. Most of these genes are specifically expressed in testis suggesting that retroposition has contributed with genetic raw material necessary for the evolution ofmale-specific functions in primates. We characterized CDC14Bretro (identified in the previous survey) that originated from the retroposition of a cell cycle gene - CDC14B - in the common ancestor of humans and apes. We demonstrate that CDC14Bretro experienced a period of intense positive selection in the African ape ancestor. By virtue of the amino acid substitutions that occurred during this period CDC 14Bretro adapted to a new subcellular compartment in African apes. Further analyses indicate that this subcellular shift reflects the evolution of anew functional role of CDC 14Bretro. Prompted by this result, we used yeast (Saccharomyces cerevisiae) to investigate on a global scale the extent of functional diversification of duplicate genes through the subcellular adaptation of their encoded proteins. We found that duplicate proteins frequently evolved new cellular localization patterns, either by partitioning of ancestral localizations ("sublocalization"), or more frequently by relocalization to previously unoccupied compartments ("neolocalization"). Interestingly, proteins involved in processes with a wider subcellular distribution more frequently evolved new localization patterns suggesting that subcellular localization changes are dependent on progenitor gene functions. Relocated proteins adapted to their new subcellular environments and evolved new functional roles through changes of their physio-chemical properties, expression levels, and interaction partners. Our work suggests an important role of subcellular adaptation for the emergence of new gene functions.

The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review).

During the last 2 years, several novel genes that encode glucose transporter-like proteins have been identified and characterized. Because of their sequence similarity with GLUT1, these genes appear to belong to the family of solute carriers 2A (SLC2A, protein symbol GLUT). Sequence comparisons of all 13 family members allow the definition of characteristic sugar/polyol transporter signatures: (1) the presence of 12 membrane-spanning helices, (2) seven conserved glycine residues in the helices, (3) several basic and acidic residues at the intracellular surface of the proteins, (4) two conserved tryptophan residues, and (5) two conserved tyrosine residues. On the basis of sequence similarities and characteristic elements, the extended GLUT family can be divided into three subfamilies, namely class I (the previously known glucose transporters GLUT1-4), class II (the previously known fructose transporter GLUT5, the GLUT7, GLUT9 and GLUT11), and class III (GLUT6, 8, 10, 12, and the myo-inositol transporter HMIT1). Functional characteristics have been reported for some of the novel GLUTs. Like GLUT1-4, they exhibit a tissue/cell-specific expression (GLUT6, leukocytes, brain; GLUT8, testis, blastocysts, brain, muscle, adipocytes; GLUT9, liver, kidney; GLUT10, liver, pancreas; GLUT11, heart, skeletal muscle). GLUT6 and GLUT8 appear to be regulated by sub-cellular redistribution, because they are targeted to intra-cellular compartments by dileucine motifs in a dynamin dependent manner. Sugar transport has been reported for GLUT6, 8, and 11; HMIT1 has been shown to be a H+/myo-inositol co-transporter. Thus, the members of the extended GLUT family exhibit a surprisingly diverse substrate specificity, and the definition of sequence elements determining this substrate specificity will require a full functional characterization of all members.

Genomic roles of the HCF transcriptional regulator in "Drosophila"

Abstract : Transcriptional regulation is the result of a combination of positive and negative effectors, such as transcription factors, cofactors and chromatin modifiers. During my thesis project I studied chromatin association, and transcriptional and cell cycle regulatory functions of dHCF, the Drosophila homologue of the human protein HCF-1 (host cell factor-1). The human and Drosophila HCF proteins are synthesized as large polypeptides that are cleaved into two subunits (HCFN and HCFC), which remain associated with one another by non covalent interactions. Studies in mammalian cells over the past 20 years have been devoted to understanding the cellular functions of HCF-1 and have revealed that it is a key regulator of transcription and cell cycle regulation. In human cells, HCF-1 interacts with the histone methyltransferase Set1/Ash2 and MLL/Ash2 complexes and the histone deacetylase Sin3 complex, which are involved in transcriptional activation and repression, respectively. HCF-1 is also recruited to promoters to regulate G1 -to-S phase progression during the cell cycle by the activator transcription factors E2F1 and E2F3, and by the repressor transcription factor E2F4. HCF-1 protein structure and these interactions between HCP-1 and E2F transcriptional regulator proteins are also conserved in Drosophila. In this doctoral thesis, I use proliferating Drosophila SL2 cells to study both the genomic-binding sites of dHCF, using a combination of chromatin immunoprecipitation and ultra high throughput sequencing (ChIP-seq) analysis, and dHCF regulated genes, employing RNAi and microarray expression analysis. I show that dHCF is bound to over 7500 chromosomal sites in proliferating SL2 cells, and is located at +-200 bp relative to the transcriptional start sites of about 30% of Drosophila genes. There is also a direct relationship between dHCF promoter association and promoter- associated transcriptional activity. Thus, dHCF binding levels at promoters correlated directly with transcriptional activity. In contrast, expression studies showed that dHCF appears to be involved in both transcriptional activation and repression. Analysis of dHCF-binding sites identified nine dHCF-associated motifs, four of them linked dHCF to (i) two insulator proteins, GAGA and BEAF, (ii) the E-box motif, and (iii) a degenerated TATA-box. The dHCF-associated motifs allowed the organization of the dHCF-bound genes into five biological processes: differentiation, cell cycle and gene expression, regulation of endocytosis, and cellular localization. I further show that different mechanisms regulate dHCF association with chromatin. Despite that after dHCF cleavage the dHCFN and dHCFC subunits remain associated, the two subunits showed different affinities for chromatin and differential binding to a set of tested promoters, suggesting that dHCF could target specific promoters through each of the two subunits. Moreover, in addition to the interaction between dHCF and E2F transcription factors, the dHCF binding pattern is correlated with dE2F2 genomic 4 distribution. I show that dE2F factors are necessary for recruitment of dHCF to the promoter of a set of dHCF regulated genes. Therefore dHCF, as in mammals, is involved in regulation of G1 to S phase progression in collaboration with the dE2Fs transcription factors. In addition, gene expression arrays reveal that dHCF could indirectly regulate cell cycle progression by promoting expression of genes involved in gene expression and protein synthesis, and inhibiting expression of genes involved in cell-cell adhesion. Therefore, dHCF is an evolutionary conserved protein, which binds to many specific sites of the Drosophila genome via interaction with DNA of chromatin-binding proteins to regulate the expression of genes involved in many different cellular functions. Résumé : La regulation de la transcription est le résultat des effets positifs et négatifs des facteurs de transcription, cofacteurs et protéines effectrices qui modifient la chromatine. Pendant mon projet de thèse, j'ai étudié l'association a la chromatine, ainsi que la régulation de la transcription et du cycle cellulaire par dHCF, l'homologue chez la drosophile de la protéine humaine HCF-1 (host cell factor-1). Chez 1'humain et la V drosophile, les deux protéines HCF sont synthétisées sous la forme d'un long polypeptide, qui est ensuite coupé en deux sous-unités au centre de la protéine. Les deux sous-unités restent associées ensemble grâce a des interactions non-covalentes. Des études réalisées pendant les 20 dernières années ont permit d'établir que HCF-l et un facteur clé dans la régulation de la transcription et du cycle cellulaire. Dans les cellules humaines, HCF-1 active et réprime la transcription en interagissant avec des complexes de protéines qui activent la transcription en méthylant les histones (HMT), comme par Set1/Ash2 et MLL/Ash2, et d'autres complexes qui répriment la transcription et sont responsables de la déacétylation des histones (HDAC) comme la protéine Sin3. HCF-l est aussi recruté aux promoteurs par les activateurs de la transcription E2F l et E2F3a, et par le répresseur de la transcription E2F4 pour réguler la transition entre les phases G1 et S du cycle cellulaire. La structure de HCF-1 et les interactions entre HCF-l et les régulateurs de la transcription sont conservées chez la drosophile. Pendant ma these j'ai utilisé les cellules de la drosophile, SL2 en culture, pour étudier les endroits de liaisons de HCF-l à la chromatine, grâce a immunoprecipitation de la chromatine et du séquençage de l'ADN massif ainsi que les gènes régulés par dHCF 3 grâce a la technique de RNAi et des microarrays. Mes résultats on montré que dHCF se lie à environ 7565 endroits, et estimé a 1200 paire de bases autour des sites d'initiation de la transcription de 30% des gènes de la drosophile. J 'ai observe une relation entre dHCF et le niveau de la transcription. En effet, le niveau de liaison dHCF au promoteur corrèle avec l'activité de la transcription. Cependant, mes études d'expression ont montré que dHCF est implique dans le processus d'activation et mais aussi de répression de la transcription. L'analyse des séquences d'ADN liées par dHCF a révèle neuf motifs, quatre de ces motifs ont permis d'associer dl-ICF a deux protéines isolatrices GAGA et BEAF, au motif pour les E-boxes et a une TATA-box dégénérée. Les neuf motifs associes à dHCF ont permis d'associer les gènes lies par dHCF au promoteur a cinq processus biologiques: différentiation, cycle cellulaire, expression de gènes, régulation de l'endocytosis et la localisation cellulaire, J 'ai aussi montré qu'il y a plusieurs mécanismes qui régulent l'association de dHCF a la chromatine, malgré qu'après clivage, les deux sous-unites dHCFN and dHCFC, restent associées, elles montrent différentes affinités pour la chromatine et lient différemment un group de promoteurs, les résultats suggèrent que dHCF peut se lier aux promoteurs en utilisant chacune de ses sous-unitées. En plus de l'association de dHCF avec les facteurs de transcription dE2F s, la distribution de dHCF sur le génome corrèle avec celle du facteur de transcription dE2F2. J'ai aussi montré que les dE2Fs sont nécessaires pour le recrutement de dHCF aux promoteurs d'un sous-groupe de gènes régules par dHCF. Mes résultats ont aussi montré que chez la drosophile comme chez les humains, dl-ICF est implique dans la régulation de la progression de la phase G1 a la phase S du cycle cellulaire en collaboration avec dE2Fs. D'ailleurs, les arrays d'expression ont suggéré que dHCF pourrait réguler le cycle cellulaire de façon indirecte en activant l'expression de gènes impliqués dans l'expression génique et la synthèse de protéines, et en inhibant l'expression de gènes impliqués dans l'adhésion cellulaire. En conclusion, dHCF est une protéine, conservée dans l'évolution, qui se lie spécifiquement a beaucoup d'endroits du génome de Drosophile, grâce à l'interaction avec d'autres protéines, pour réguler l'expression des gènes impliqués dans plusieurs fonctions cellulaires.

Network-based scoring system for genome-scale metabolic reconstructions

Background: Network reconstructions at the cell level are a major development in Systems Biology. However, we are far from fully exploiting its potentialities. Often, the incremental complexity of the pursued systems overrides experimental capabilities, or increasingly sophisticated protocols are underutilized to merely refine confidence levels of already established interactions. For metabolic networks, the currently employed confidence scoring system rates reactions discretely according to nested categories of experimental evidence or model-based likelihood. Results: Here, we propose a complementary network-based scoring system that exploits the statistical regularities of a metabolic network as a bipartite graph. As an illustration, we apply it to the metabolism of Escherichia coli. The model is adjusted to the observations to derive connection probabilities between individual metabolite-reaction pairs and, after validation, to assess the reliability of each reaction in probabilistic terms. This network-based scoring system uncovers very specific reactions that could be functionally or evolutionary important, identifies prominent experimental targets, and enables further confirmation of modeling results. Conclusions: We foresee a wide range of potential applications at different sub-cellular or supra-cellular levels of biological interactions given the natural bipartivity of many biological networks.

Role of the epithelial sodium channel (ENaC) in the epidermal barrier function of the skin

Abstract In humans, the skin is the largest organ of the body, covering up to 2m2 and weighing up to 4kg in an average adult. Its function is to preserve the body from external insults and also to retain water inside. This barrier function termed epidermal permeability barrier (EPB) is localized in the functional part of the skin: the epidermis. For this, evolution has built a complex structure of cells and lipids sealing the surface, the stratum corneum. The formation of this structure is finely tuned since it is not only formed once at birth, but renewed all life long. This active process gives a high plasticity and reactivity to skin, but also leads to various pathologies. ENaC is a sodium channel extensively studied in organs like kidney and lung due to its importance in regulating sodium homeostasis and fluid volume. It is composed of three subunits α, ß and r which are forming sodium selective channel through the cell membrane. Its presence in the skin has been demonstrated, but little is known about its physiological role. Previous work has shown that αENaC knockout mice displayed an abnormal epidermis, suggesting a role in differentiation processes that might be implicated in the EPB. The principal aim of this thesis has been to study the consequences for EPB function in mice deficient for αENaC by molecular and physiological means and to investigate the underlying molecular mechanisms. Here, the barrier function of αENaC knockout pups is impaired. Apparently not immediately after birth (permeability test) but 24h later, when evident water loss differences appeared compared to wildtypes. Neither the structural proteins of the epithelium nor the tights junctions showed any obvious alterations. In contrary, stratum corneum lipid disorders are most likely responsible for the barrier defect, accompanied by an impairment of skin surface acidification. To analyze in details this EPB defect, several hypotheses have been proposed: reduced sensibility to calcium which is the key activator far epidermal formation, or modification of ENaC-mediated ion fluxes/currents inside the epidermis. The cellular localization of ENaC and the action in the skin of CAPl, a positive regulator of ENaC, have been also studied in details. In summary, this study clearly demonstrates that ENaC is a key player in the EPB maintenance, because αENaC knockout pups are not able to adapt to the new environment (ex utero) as efficiently as the wildtypes, most likely due to impaired of sodium handling inside the epidermis. Résumé Chez l'homme, la peau est le plus grand organe, couvrant presque 2m2 et pesant près de 4kg chez l'adulte. Sa fonction principale est de protéger l'organisme des agressions extérieures mais également de conserver l'eau à l'intérieur du corps. Cette fonction nommée barrière épithéliale est localisée dans la partie fonctionnelle de la peau : l'épiderme. A cette fin, l'évolution s'est dotée d'une structure complexe composée de cellules et de lipides recouvrant la surface, la couche cornée. Sa formation est finement régulée, car elle n'est pas seulement produite à la naissance mais constamment renouvelée tout au long de la vie, ce qui lui confère une grande plasticité mais ce qui est également la cause de nombreuses pathologies. ENaC est un canal sodique très étudié dans le rein et le poumon pour son importance dans la régulation de l'homéostasie sodique et la régulation du volume du milieu intérieur. Il est composé de 3 sous unités, α, ß et y qui forment un pore sélectif pour le sodium dans les membranes. Ce canal est présent dans la peau mais sa fonction n'y est pas connue. Des travaux précédents ont pu montrer que les souris dont le gène codant pour αENaC a été invalidé présentent un épiderme pathologique, suggérant un rôle dans la différentiation et pourrait même être impliqué dans la barrière épithéliale. Le but de cette thèse fut l'étude de la barrière dans ces souris knockouts avec des méthodes moléculaires et physiologiques et la caractérisation des mécanismes moléculaire impliqués. Dans ce travail, il a été montré que les souris mutantes présentaient un défaut de la barrière. Ce défaut n'est pas visible immédiatement à la naissance (test de perméabilité), mais 24h plus tard, lorsque les tests de perte d'eau transépithéliale montrent une différence évidente avec les animaux contrôles. Ni les protéines de structures ni les jonctions serrées de l'épiderme ne présentaient d'imperfections majeures. A l'inverse, les lipides de la couche cornée présentaient un problème de maturation (expliquant le phénotype de la barrière), certainement consécutif au défaut d'acidification à la surface de la peau que nous avons observé. D'autres mécanismes ont été explorées afin d'investiguer cette anomalie de la barrière, comme la réduction de sensibilité au calcium qui est le principal activateur de la formation de l'épiderme, ou la modification des flux d'ions entre les couches de l'épiderme. La localisation cellulaire d'ENaC, et l'action de son activateur CAPl ont également été étudiés en détails. En résumé, cette étude démontre clairement qu'ENaC est un acteur important dans la formation de la barrière épithéliale, car la peau des knockouts ne s'adapte pas aussi bien que celle des sauvages au nouvel environnement ex utero à cause de la fonction d'ENaC dans les mouvements de sodium au sein même de l'épiderme. Résumé tout public Chez l'homme, la peau est le plus grand organe, couvrant presque 2m2 et pesant près de 4kg chez l'adulte. Sa fonction principale est de protéger l'organisme des agressions extérieures mais également de conserver l'eau à l'intérieur du corps. Cette fonction nommée barrière épithéliale est localisée dans la partie fonctionnelle de la peau : l'épiderme. A cette fin, l'évolution s'est dotée d'une structure complexe composée de cellules et de lipides recouvrant la surface, la couche cornée. Sa formation est finement régulée, car elle n'est pas seulement produite à la naissance mais constamment renouvelée tout au long de la vie, ce qui lui confère une grande plasticité mais ce qui est également la cause de nombreuses maladies. ENaC est une protéine formant un canal qui permet le passage sélectif de l'ion sodium à travers la paroi des cellules. Il est très étudié dans le rein pour son importance dans la récupération du sel lors de la concentration de l'urine. Ce canal est présent dans la peau mais sa fonction n'y est pas connue. Des travaux précédents ont pu montrer que les souris où le gène codant pour αENaC a été invalidé présentent un épiderme pathologique, suggérant un rôle dans la peau et plus particulièrement la fonction de barrière de l'épiderme. Le but de cette thèse fut l'étude de la fonction de barrière dans ces souris mutantes, au niveau tissulaire et cellulaire. Dans ce travail, il a été montré que les souris mutantes présentaient une peau plus perméable que celle des animaux contrôles, grâce à une machine mesurant la perte d'eau à travers la peau. Ce défaut n'est visible que 24h après la naissance, mais nous avons pu montrer que les animaux mutants perdaient quasiment 2 fois plus d'eau que les contrôles. Au niveau moléculaire, nous avons pu montrer que ce défaut provenait d'un problème de maturation des lipides qui composent la barrière de la peau. Cette maturation est incomplète vraisemblablement à cause d'un défaut de mouvement des ions dans les couches les plus superficielles de l'épiderme, et cela à cause de l'absence du canal ENaC. En résumé, cette étude démontre clairement qu'ENaC est un acteur important dans la formation de la barrière épithéliale, car la peau des mutants ne s'adapte pas aussi bien que celle des sauvages au nouvel environnement ex utero à cause de la fonction d'ENaC dans les mouvements de sodium au sein même de l'épiderme.

Minimal analytical characterization of engineered nanomaterials needed for hazard assessment in biological matrices.

Abstract This paper presents the outcomes from a workshop of the European Network on the Health and Environmental Impact of Nanomaterials (NanoImpactNet). During the workshop, 45 experts in the field of safety assessment of engineered nanomaterials addressed the need to systematically study sets of engineered nanomaterials with specific metrics to generate a data set which would allow the establishment of dose-response relations. The group concluded that international cooperation and worldwide standardization of terminology, reference materials and protocols are needed to make progress in establishing lists of essential metrics. High quality data necessitates the development of harmonized study approaches and adequate reporting of data. Priority metrics can only be based on well-characterized dose-response relations derived from the systematic study of the bio-kinetics and bio-interactions of nanomaterials at both organism and (sub)-cellular levels. In addition, increased effort is needed to develop and validate analytical methods to determine these metrics in a complex matrix.

Processing of metacaspase into a cytoplasmic catalytic domain mediating cell death in Leishmania major.

Metacaspases are cysteine peptidases that could play a role similar to caspases in the cell death programme of plants, fungi and protozoa. The human protozoan parasite Leishmania major expresses a single metacaspase (LmjMCA) harbouring a central domain with the catalytic dyad histidine and cysteine as found in caspases. In this study, we investigated the processing sites important for the maturation of LmjMCA catalytic domain, the cellular localization of LmjMCA polypeptides, and the functional role of the catalytic domain in the cell death pathway of Leishmania parasites. Although LmjMCA polypeptide precursor form harbours a functional mitochondrial localization signal (MLS), we determined that LmjMCA polypeptides are mainly localized in the cytoplasm. In stress conditions, LmjMCA precursor forms were extensively processed into soluble forms containing the catalytic domain. This domain was sufficient to enhance sensitivity of parasites to hydrogen peroxide by impairing the mitochondrion. These data provide experimental evidences of the importance of LmjMCA processing into an active catalytic domain and of its role in disrupting mitochondria, which could be relevant in the design of new drugs to fight leishmaniasis and likely other protozoan parasitic diseases.

Extracellular microvesicles from astrocytes contain functional glutamate transporters: regulation by protein kinase C and cell activation.

Glutamate transport through astrocytic excitatory amino-acid transporters (EAAT)-1 and EAAT-2 is paramount for neural homeostasis. EAAT-1 has been reported in secreted extracellular microvesicles (eMV, such as exosomes) and because the protein kinase C (PKC) family controls the sub-cellular distribution of EAATs, we have explored whether PKCs drive EAATs into eMV. Using rat primary astrocytes, confocal immunofluorescence and ultracentrifugation on sucrose gradient we here report that PKC activation by phorbol myristate acetate (PMA) reorganizes EAAT-1 distribution and reduces functional [(3)H]-aspartate reuptake. Western-blots show that EAAT-1 is present in eMV from astrocyte conditioned medium, together with NaK ATPase and glutamine synthetase all being further increased after PMA treatment. However, nanoparticle tracking analysis reveals that PKC activation did not change particle concentration. Functional analysis indicates that eMV have the capacity to reuptake [(3)H]-aspartate. In vivo, we demonstrate that spinal astrocytic reaction induced by peripheral nerve lesion (spared nerve injury, SNI) is associated with a phosphorylation of PKC δ together with a shift of EAAT distribution ipsilaterally. Ex vivo, spinal explants from SNI rats release eMV with an increased content of NaK ATPase, EAAT-1 and EAAT-2. These data indicate PKC and cell activation as important regulators of EAAT-1 incorporation in eMV, and raise the possibility that microvesicular EAAT-1 may exert extracellular functions. Beyond a putative role in neuropathic pain, this phenomenon may be important for understanding neural homeostasis and a wide range of neurological diseases associated with astrocytic reaction as well as non-neurological diseases linked to eMV release.

Mechanisms of interaction of therapeutic nanoparticles with cells

Nanoparticles (NPs) have gained a lot of interest in recent years due to their huge potential for applications in industry and medicine. Their unique properties offer a large number of attractive possibilities in the biomedical field, providing innovative tools for diagnosis of diseases and for novel therapies. Nevertheless, a deep understanding of their interactions with living tissues and the knowledge about their possible effects in the human body are necessary for the safe use of nanoparticulate formulations. The aim of this PhD project was to study in detail the interactions of therapeutic NPs with living cells, including cellular uptake and release, cellular localization and transport across the cell layers. Moreover, the effects of NPs on the cellular metabolic processes were determined using adapted in vitro assays. We evaluated the biological effect of several NPs potentially used in the biomedical field, including titanium dioxide (Ti02) NPs, 2-sized fluorescent silica NPs, ultrasmall superparamagnetic iron oxide (USPIO) NPs, either uncoated or coated with oleic acid or with polyvinylamine (aminoPVA) and poly(lactic-co-glycolic acid) - polyethylene-oxide (PLGA-PEO) NPs. We have found that the NPs were internalized by the cells, depending on their size, chemical composition, surface coating and also depending on the cell line considered. The uptake of aminoPVA-coated USPIO NPs by endothelial cells was enhanced in the presence of an external magnetic field. None of the tested USPIO NPs and silica NPs was transported across confluent kidney cell layers or brain endothelial cell layers, even in the presence of a magnetic field. However, in an original endothelium-glioblastoma barrier model which was developed, uncoated USPIO NPs were directly transferred from endothelial cells to glioblastoma cells. Following uptake, Ti02 NPs and uncoated USPIO NPs were released by the kidney cells, but not by the endothelial cells. Furthermore, these NPs induced an oxidative stress and autophagy in brain endothelial cells, possibly associated with their enhanced agglomeration in cell medium. A significant DNA damage was found in brain endothelial cells after their exposure to TiO2NPs. Altogether these results extend the existing knowledge about the effects of NPs on living cells with regard to their physicochemical characteristics and provide interesting tools for further investigation. The development of the in vitro toxicological assays with a special consideration for risk evaluation aims to reduce the use of animal experiments. -Les nanoparticules (NPs) présentent beaucoup d'intérêt dans le domaine biomédical et industriel. Leurs propriétés uniques offrent un grand nombre de possibilités de solutions innovantes pour le diagnostique et la thérapie. Cependant, pour un usage sûr des NPs il est nécessaire d'acquérir une connaissance approfondie des mécanismes d'interactions des NPs avec les tissus vivants et de leur effets sur le corps humain. Le but de ce projet de thèse était d'étudier en détail les mécanismes d'interactions de NPs thérapeutiques avec des cellules vivantes, en particulier les mécanismes d'internalisation cellulaire et leur subséquente sécrétion par les cellules, leur localisation cellulaire, leur transport à travers des couches cellulaires, et l'évaluation des effets de NPs sur le métabolisme cellulaire, en adaptant les méthodes existante d'évaluation cyto-toxico logique s in vitro. Pour ces expériences, les effets biologiques de nanoparticules d'intérêt thérapeutique, telles que des NPs d'oxyde de titane (TiO2), des NPs fluorescents de silicate de 2 tailles différentes, des NPs, d'oxyde de fer super-para-magnétiques ultra-petites (USPIO), soit non- enrobées soit enrobées d'acide oléique ou de polyvinylamine (aminoPVA), et des NPs d'acide poly(lactique-co-glycolique)-polyethylene-oxide (PLGA-PEO) ont été évalués. Les résultats ont démontré que les NPs sont internalisées par les cellules en fonction de leur taille, composition chimique, enrobage de surface, et également du type de cellules utilisées. L'internalisation cellulaire des USPIO NPs a été augmentée en présence d'un aimant externe. Aucune des NPs de fer et de silicate n'a été transportée à travers des couches de cellules épithéliales du rein ou endothéliales du cerveau, même en présence d'un aimant. Cependant, en développant un modèle original de barrière endothélium-glioblastome, un transfert direct de NPs d'oxyde de fer de cellule endothéliale à cellule de glioblastome a été démontré. A la suite de leur internalisation les NPs d'oxyde de fer et de titane sont relâchées par des cellules épithéliales du rein, mais pas des cellules endothéliales du cerveau. Dans les cellules endothéliales du cerveau ces NPs induisent en fonction de leur état d'agglomération un stress oxydatif et des mécanismes d'autophagie, ainsi que des dommages à l'ADN des cellules exposées aux NPs d'oxyde de titane. En conclusion, les résultats obtenus élargissent les connaissances sur les effets exercés par des NPs sur des cellules vivantes et ont permis de développer les outils expérimentaux pour étudier ces effets in vitro, réduisant ainsi le recours à des expériences sur animaux.

Clinical implications in the shift of syndecan-1 expression from the cell membrane to the cytoplasm in bladder cancer

Background To determine the diagnostic and prognostic capability of urinary and tumoral syndecan-1 (SDC-1) levels in patients with cancer of the urinary bladder. Methods SDC-1 levels were quantitated by enzyme-linked immunosorbent assay (ELISA) in 308 subjects (102 cancer subjects and 206 non-cancer subjects) to assess its diagnostic capabilities in voided urine. The performance of SDC-1 was evaluated using the area under the curve of a receiver operating characteristic curve. In addition, immunohistochemical (IHC) staining assessed SDC-1 protein expression in 193 bladder specimens (185 cancer subjects and 8 non-cancer subjects). Outcomes were correlated to SDC-1 levels. Results Mean urinary levels of SDC-1 did not differ between the cancer subjects and the non-cancer subjects, however, the mean urinary levels of SDC-1 were reduced in high-grade compared to low-grade disease (p < 0.0001), and in muscle invasive bladder cancer (MIBC) compared to non-muscle invasive bladder cancer (NMIBC) (p = 0.005). Correspondingly, preliminary data note a shift from a membranous cellular localization of SDC-1 in normal tissue, low-grade tumors and NMIBC, to a distinctly cytoplasmic localization in high-grade tumors and MIBC was observed in tissue specimens. Conclusion Alone urinary SDC-1 may not be a diagnostic biomarker for bladder cancer, but its urinary levels and cellular localization were associated with the differentiation status of patients with bladder tumors. Further studies are warranted to define the potential role for SDC-1 in bladder cancer progression.

Clinical implications in the shift of syndecan-1 expression from the cell membrane to the cytoplasm in bladder cancer

Background To determine the diagnostic and prognostic capability of urinary and tumoral syndecan-1 (SDC-1) levels in patients with cancer of the urinary bladder. Methods SDC-1 levels were quantitated by enzyme-linked immunosorbent assay (ELISA) in 308 subjects (102 cancer subjects and 206 non-cancer subjects) to assess its diagnostic capabilities in voided urine. The performance of SDC-1 was evaluated using the area under the curve of a receiver operating characteristic curve. In addition, immunohistochemical (IHC) staining assessed SDC-1 protein expression in 193 bladder specimens (185 cancer subjects and 8 non-cancer subjects). Outcomes were correlated to SDC-1 levels. Results Mean urinary levels of SDC-1 did not differ between the cancer subjects and the non-cancer subjects, however, the mean urinary levels of SDC-1 were reduced in high-grade compared to low-grade disease (p < 0.0001), and in muscle invasive bladder cancer (MIBC) compared to non-muscle invasive bladder cancer (NMIBC) (p = 0.005). Correspondingly, preliminary data note a shift from a membranous cellular localization of SDC-1 in normal tissue, low-grade tumors and NMIBC, to a distinctly cytoplasmic localization in high-grade tumors and MIBC was observed in tissue specimens. Conclusion Alone urinary SDC-1 may not be a diagnostic biomarker for bladder cancer, but its urinary levels and cellular localization were associated with the differentiation status of patients with bladder tumors. Further studies are warranted to define the potential role for SDC-1 in bladder cancer progression.