Mechanisms of apoptosis in retinitis pigmentosa.

Mutations in humans are associated with several forms of inherited retinal dystrophies, such as Retinitis Pigmentosa which lead to retinal cell death and irreversible loss of vision. Genes involved in affected patients mainly encode proteins related to vision physiology including visual cycle and light-dependent phototransduction cascade. As reported in spontaneous and genetically engineered mouse models, apoptosis is a common fate in retinal degeneration, although the triggered signals to retinal apoptosis remain largely unraveled. Several studies highlighted that many of the molecular pathways involved in ocular diseases rely on caspase-dependent or -independent apoptotic mitochondrial pathway involving the Bcl-2 family of proteins. Anti- and pro-apoptotic Bcl-2 members are present in retinal tissues and are thought to play a role in the pathogenesis of several retinal disorders. Since almost no efficient treatments are available so far, it remains a great challenge to decipher the molecular pathways involved in retinal dystrophies and to develop alternative therapies to prevent or inhibit eye defect. Toward this goal, mutation-independent strategies such as molecular therapy provides promising and exciting approaches to deliver anti-apoptotic molecules targeting the Bcl-2 pathway through the use of cell permeable transport peptides. Modulation of common apoptotic signaling pathways may be of outstanding potential to target multiple retinal dystrophies regardless of the primary genetic defect.

Characterization of the PHO1 gene family and the responses to phosphate deficiency of Physcomitrella patens.

PHO1 was previously identified in Arabidopsis (Arabidopsis thaliana) as a protein involved in loading inorganic phosphate (Pi) into the xylem of roots and its expression was associated with the vascular cylinder. Seven genes homologous to AtPHO1 (PpPHO1;1-PpPHO1;7) have been identified in the moss Physcomitrella patens. The corresponding proteins harbor an SPX tripartite domain in the N-terminal hydrophilic portion and an EXS domain in the conserved C-terminal hydrophobic portion, both common features of the plant PHO1 family. Northern-blot analysis showed distinct expression patterns for the PpPHO1 genes, both at the tissue level and in response to phosphate deficiency. Transgenic P. patens expressing the beta-glucuronidase reporter gene under three different PpPHO1 promoters revealed distinct expression profiles in various tissues. Expression of PpPHO1;1 and PpPHO1;7 was specifically induced by Pi starvation. P. patens homologs to the Arabidopsis PHT1, DGD2, SQD1, and APS1 genes also responded to Pi deficiency by increased mRNA levels. Morphological changes associated with Pi deficiency included elongation of caulonemata with inhibition of the formation of side branches, resulting in colonies with greater diameter, but reduced mass compared to Pi-sufficient plants. Under Pi-deficient conditions, P. patens also increased the synthesis of ribonucleases and of an acid phosphatase, and increased the ratio of sulfolipids over phospholipids. These results indicate that P. patens and higher plants share some common strategies to adapt to Pi deficiency, although morphological changes are distinct, and that the PHO1 proteins are well conserved in bryophyte despite the lack of a developed vascular system.

Native folding of aggregation-prone recombinant proteins in Escherichia coli by osmolytes, plasmid- or benzyl alcohol-overexpressed molecular chaperones.

When massively expressed in bacteria, recombinant proteins often tend to misfold and accumulate as soluble and insoluble nonfunctional aggregates. A general strategy to improve the native folding of recombinant proteins is to increase the cellular concentration of viscous organic compounds, termed osmolytes, or of molecular chaperones that can prevent aggregation and can actively scavenge and convert aggregates into natively refoldable species. In this study, metal affinity purification (immobilized metal ion affinity chromatography [IMAC]), confirmed by resistance to trypsin digestion, was used to distinguish soluble aggregates from soluble nativelike proteins. Salt-induced accumulation of osmolytes during induced protein synthesis significantly improved IMAC yields of folding-recalcitrant proteins. Yet, the highest yields were obtained with cells coexpressing plasmid-encoded molecular chaperones DnaK-DnaJ-GrpE, ClpB, GroEL-GroES, and IbpA/B. Addition of the membrane fluidizer heat shock-inducer benzyl alcohol (BA) to the bacterial medium resulted in similar high yields as with plasmid-mediated chaperone coexpression. Our results suggest that simple BA-mediated induction of endogenous chaperones can substitute for the more demanding approach of chaperone coexpression. Combined strategies of osmolyte-induced native folding with heat-, BA-, or plasmid-induced chaperone coexpression can be thought to optimize yields of natively folded recombinant proteins in bacteria, for research and biotechnological purposes.

ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins

Background: Annotations of completely sequenced genomes reveal that nearly half of the genes identified are of unknown function, and that some belong to uncharacterized gene families. To help resolve such issues, information can be obtained from the comparative analysis of homologous genes in model organisms. Results: While characterizing genes from the retinitis pigmentosa locus RP26 at 2q31-q33, we have identified a new gene, ORMDL1, that belongs to a novel gene family comprising three genes in humans (ORMDL1, ORMDL2 and ORMDL3), and homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. The human genes are expressed ubiquitously in adult and fetal tissues. The Drosophila ORMDL homolog is also expressed throughout embryonic and larval stages, particularly in ectodermally derived tissues. The ORMDL genes encode transmembrane proteins anchored in the endoplasmic reticulum (ER). Double knockout of the two Saccharomyces cerevisiae homologs leads to decreased growth rate and greater sensitivity to tunicamycin and dithiothreitol. Yeast mutants can be rescued by human ORMDL homologs. Conclusions: From protein sequence comparisons we have defined a novel gene family, not previously recognized because of the absence of a characterized functional signature. The sequence conservation of this family from yeast to vertebrates, the maintenance of duplicate copies in different lineages, the ubiquitous pattern of expression in human and Drosophila, the partial functional redundancy of the yeast homologs and phenotypic rescue by the human homologs, strongly support functional conservation. Subcellular localization and the response of yeast mutants to specific agents point to the involvement of ORMDL in protein folding in the ER.

Distinct effects of inflammation on gliosis, osmohomeostasis, and vascular integrity during amyloid beta-induced retinal degeneration.

In normal retinas, amyloid-β (Aβ) accumulates in the subretinal space, at the interface of the retinal pigment epithelium, and the photoreceptor outer segments. However, the molecular and cellular effects of subretinal Aβ remain inadequately elucidated. We previously showed that subretinal injection of Aβ(1-42) induces retinal inflammation, followed by photoreceptor cell death. The retinal Müller glial (RMG) cells, which are the principal retinal glial cells, are metabolically coupled to photoreceptors. Their role in the maintenance of retinal water/potassium and glutamate homeostasis makes them important players in photoreceptor survival. This study investigated the effects of subretinal Aβ(1-42) on RMG cells and of Aβ(1-42)-induced inflammation on retinal homeostasis. RMG cell gliosis (upregulation of GFAP, vimentin, and nestin) on day 1 postinjection and a proinflammatory phenotype were the first signs of retinal alteration induced by Aβ(1-42). On day 3, we detected modifications in the protein expression patterns of cyclooxygenase 2 (COX-2), glutamine synthetase (GS), Kir4.1 [the inwardly rectifying potassium (Kir) channel], and aquaporin (AQP)-4 water channels in RMG cells and of the photoreceptor-associated AQP-1. The integrity of the blood-retina barrier was compromised and retinal edema developed. Aβ(1-42) induced endoplasmic reticulum stress associated with sustained upregulation of the proapoptotic factors of the unfolded protein response and persistent photoreceptor apoptosis. Indomethacin treatment decreased inflammation and reversed the Aβ(1-42)-induced gliosis and modifications in the expression patterns of COX-2, Kir4.1, and AQP-1, but not of AQP-4 or GS. Nor did it improve edema. Our study pinpoints the adaptive response to Aβ of specific RMG cell functions.

Genotype-phenotype interactions in primary dystonias revealed by differential changes in brain structure.

Our understanding of how genotype determines phenotype in primary dystonia is limited. Familial young-onset primary dystonia is commonly due to the DYT1 gene mutation. A critical question, given the 30% penetrance of clinical symptoms in DYT1 mutation carriers, is why the same genotype leads to differential clinical expression and whether non-DYT1 adult-onset primary dystonia, with and without family history share pathophysiological mechanisms with DYT1 dystonia. This study examines the relationship between dystonic phenotype and the DYT1 gene mutation by monitoring whole-brain structure using voxel-based morphometry. We acquired magnetic resonance imaging data of symptomatic and asymptomatic DYT1 mutation carriers, of non-DYT1 primary dystonia patients, with and without family history and control subjects with normal DYT1 alleles. By crossing the factors genotype and phenotype we demonstrate a significant interaction in terms of brain anatomy confined to the basal ganglia bilaterally. The explanation for this effect differs according to both gene and dystonia status: non-DYT1 adult-onset dystonia patients and asymptomatic DYT1 carriers have significantly larger basal ganglia compared to healthy subjects and symptomatic DYT1 mutation carriers. There is a significant negative correlation between severity of dystonia and basal ganglia size in DYT1 mutation carriers. We propose that differential pathophysiological and compensatory mechanisms lead to brain structure changes in non-DYT1 primary adult-onset dystonias and DYT1 gene carriers. Given the range of age of onset, there may be differential genetic modulation of brain development that in turn determines clinical expression. Alternatively, a DYT1 gene dependent primary defect of motor circuit development may lead to stress-induced remodelling of the basal ganglia and hence dystonia.

Les biomarqueurs prédictifs dans le cancer colorectal [Predictive biomarkers in colorectal cancer]

While for many years the diagnosis and therapy of colon cancer did not change drastically, recently new drugs (irinotecan and oxaliplatin, used in adjuvant or neo-adjuvant approaches) and even more recently the introduction of therapies targeting the epidermal growth factor receptor (EGFR) through the monoclonal antibodies cetuximab and panitumumab, are revolutionizing the field. The finding that only patients with a tumor with a wild type (non mutated) KRAS gene respond to anti-EGFR therapy has also affected the way pathologists address colorectal cancer. Molecular analysis of the KRAS gene has become almost a routine in a very short period of time. Pathologists will have to be prepared for a new era: from standard morphology based diagnostic procedures to the prediction of response to therapy using molecular tools.

A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in root growth vigor.

Quantitative trait loci analysis of natural Arabidopsis thaliana accessions is increasingly exploited for gene isolation. However, to date this has mostly revealed deleterious mutations. Among them, a loss-of-function allele identified the root growth regulator BREVIS RADIX (BRX). Here we present evidence that BRX and the paralogous BRX-LIKE (BRXL) genes are under selective constraint in monocotyledons as well as dicotyledons. Unexpectedly, however, whereas none of the Arabidopsis orthologs except AtBRXL1 could complement brx null mutants when expressed constitutively, nearly all monocotyledon BRXLs tested could. Thus, BRXL proteins seem to be more diversified in dicotyledons than in monocotyledons. This functional diversification was correlated with accelerated rates of sequence divergence in the N-terminal regions. Population genetic analyses of 30 haplotypes are suggestive of an adaptive role of AtBRX and AtBRXL1. In two accessions, Lc-0 and Lov-5, seven amino acids are deleted in the variable region between the highly conserved C-terminal, so-called BRX domains. Genotyping of 42 additional accessions also found this deletion in Kz-1, Pu2-7, and Ws-0. In segregating recombinant inbred lines, the Lc-0 allele (AtBRX(Lc-0)) conferred significantly enhanced root growth. Moreover, when constitutively expressed in the same regulatory context, AtBRX(Lc-0) complemented brx mutants more efficiently than an allele without deletion. The same was observed for AtBRXL1, which compared with AtBRX carries a 13 amino acid deletion that encompasses the deletion found in AtBRX(Lc-0). Thus, the AtBRX(Lc-0) allele seems to contribute to natural variation in root growth vigor and provides a rare example of an experimentally confirmed, hyperactive allelic variant.

Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF.

Understanding the molecular aberrations involved in the development and progression of metastatic melanoma (MM) is essential for a better diagnosis and targeted therapy. We identified breast cancer suppressor candidate-1 (BCSC-1) as a novel tumor suppressor in melanoma. BCSC-1 expression is decreased in human MM, and its ectopic expression in MM-derived cell lines blocks tumor formation in vivo and melanoma cell proliferation in vitro while increasing cell migration. We demonstrate that BCSC-1 binds to Sox10, which down regulates MITF, and results in a switch of melanoma cells from a proliferative to a migratory phenotype. In conclusion, we have identified BCSC-1 as a tumor suppressor in melanoma and as a novel regulator of the MITF pathway.

A chromosomal insertion toolbox for promoter probing, mutant complementation and pathogenicity studies in Ralstonia solanacearum

We describe here the construction of a delivery system for stable and directed insertion of gene constructs in a permissive chromosomal site of the bacterial wilt pathogen Ralstonia solanacearum. The system consists of a collection of suicide vectors the Ralstonia chromosome (pRC) series that carry an integration element flanked by transcription terminators and two sequences of homology to the chromosome of strain GMI1000, where the integration element is inserted through a double recombination event. Unique restriction enzyme sites and a GATEWAY cassette enable cloning of any promoter::gene combination in the integration element. Variants endowed with different selectable antibiotic resistance genes and promoter::gene combinations are described. We show that the system can be readily used in GMI1000 and adapted to other R. solanacearum strains using an accessory plasmid. We prove that the pRC system can be employed to complement a deletion mutation with a single copy of the native gene, and to measure transcription of selected promoters in monocopy both in vitro and in planta. Finally, the system has been used to purify and study secretion type III effectors. These novel genetic tools will be particularly useful for the construction of recombinant bacteria that maintain inserted genes or reporter fusions in competitive situations (i.e., during plant infection).

Reproductive ecology of the exotic tree Muntingia calabura L. (Muntingiaceae) in southeastern Brazil

The exotic tree Muntingia calabura L. (Muntingiaceae), a species native to Central America, is used as fish feed and fiber and cellulose production in Brazil. This study was carried out in urban areas and verified the reproductive biology of this plant species. Flower and fruit morphology, compatibility system, reproductive phenology, pollination and frugivore animals, and germination of disseminated seeds were recorded by standard field and laboratory procedures. This tree is self-compatible and autonomously self-pollinated, with its flowers being mainly visited by bees and its fruits consumed by birds and bats. Germination of its dispersed seeds is fast and occurs at a high rate. The results of this work suggest that M. calabura is very adaptable to cultivated areas,thus being an excellent choice for urban reforestation. However, its reproductive characteristics place this plant as an invasive species with significant potential in southeastern Brazil.

Évaluation neurobiologique des souris spontanément hypertendues : Du vieillissement à la génomique comparative

Le but de cette thèse est premièrement d’évaluer l’effet du vieillissement sur les fonctions psychomotrices des souches de souris sélectionnées génétiquement en fonction de leur tension artérielle (TA); deuxièmement, de localiser les déterminants génétiques des phénotypes psychophysiologiques à partir de souches recombinantes congéniques (RCS). Ces travaux ont mené à la publication de 4 articles. Le premier article décrit l’évaluation des fonctions psychomotrices des souches avec une tension artérielle élevée (HBP), basse (LBP) et normale (NBP). La performance aux épreuves d’exploration, d’habiletés motrices et d’apprentissage spatial, a été mesurée sur deux cohortes âgées respectivement de 12 mois et de trois mois. Indépendamment de l’âge, les HBPs sont hyperactives dans l’open-field (OF), mais pas dans le test d’exploration de trous. Inversement, les LBP explorent moins d’espaces que les NBP et, à trois mois seulement, sont hypoactives dans l’OF. Par ailleurs, les HBPs et les LBP présentent des déficits précoces de coordination motrice et des fonctions visuo-motrices. Le second article concerne l’évaluation longitudinale de la coordination motrice, de l’anxiété et de l’apprentissage spatial des souches HBP, LBP et NBP, à l’âge de deux mois et de 12 mois. Le vieillissement accentue l’hyperactivité des HBPs dans l’OF. Par contre, l’hypoactivité des souris LBP est détectable seulement à l’âge de deux mois. Indépendamment de l’âge, les souris HBP et LBP montrent une perception réduite du danger dans l’épreuve d’anxiété et des dysfonctions visuo-motrices au labyrinthe aquatique. Enfin, des déficits précoces de coordination motrice se manifestent seulement chez les HBPs. Il reste à déterminer si les déficits observés sont liés à des déterminants génétiques indépendants ou secondaires aux altérations de la tension artérielle. Le troisième article présente la comparaison entre les souches consanguines A/J et C57Bl/6J (B6) aux épreuves de l’OF, de la planche à trous, du labyrinthe aquatique et du cintre (coordination motrice). Les B6 explore d’avantage l’OF et la planche à trous. Les B6 sont moins rapides sur le cintre, mais supérieurs aux A/J dans le labyrinthe aquatique, avec une plate-forme invisible ou visible. Ces résultats démontrent l’implication de déterminants génétiques. Cette thèse se termine par un quatrième article sur la localisation des déterminants génétiques de la susceptibilité au stress dans les RCS, dérivées de A/J et B6, et présentant un agencement spécifique de 12.5% du génome. La réactivité émotionnelle est évaluée dans l’OF et le plus-maze; la réponse de stress est mesurée par radio télémétrie de la température interne pendant le stress d’immobilisation (SI) sous diète régulière et riche en sel; l’excrétion des électrolytes urinaires est dosée après 24 heures de diète salée. Les loci les plus significatifs sont situés dans les régions suivantes: de l’émotionalité dans l’OF (Emo1) sur le chr. 1 (LOD=4.6) correspondant à la région homologue impliquée dans la cohorte d’hypertension familiale du Saguenay; de la dopa décarboxylase (ddc) sur le chr. 11 pour l’émergence du plus-maze (LOD=4.7); de la protéine liant l’endotoxine (lbp) sur le chr. 2 pour l’hypothermie initiale en réponse au SI (LOD=4); et de HSP90 sur le chr. 12 pour l’excrétion de Ca++ (LOD=4.6). Des banques de données sont ensuite interrogées pour recenser les polymorphismes des régions régulatrices ou codantes des gènes candidats chez les souches ancestrales A/J et B6, dont les séquences sont disponibles pour le génome entier. Des utilitaires web permettent de dévoiler les changements dans la structure secondaire de l’ARNm, l’interférence avec des microARN ou avec d’autres motifs de liaison. Plusieurs SNPs fonctionnels ont été identifiés pour le QTL du chr. 1, particulièrement dans les éléments de régulation; ceux-ci impliquant des gènes reliés avec les réponses inflammatoire/immunitaire ou avec le système cardiovasculaire. La quantification par la PCR confirme une régulation à la baisse d’atp1a2 dans le cœur et le cerveau des souches susceptibles à l’anxiété. Ces résultats confirment l’intrication des altérations de la susceptibilité au stress et de la régulation de la TA.

Caractérisation et étude d'un élément régulateur du gène codant pour le récepteur à la vasopressine de type 2

Thèse réalisée en cotutelle avec l'Université Pierre et Marie Curie, Paris VI, France

Rôle du test génétique dans la cardiomyopathie arythmogène du ventricule droit. Étude sur une cohorte prospective unicentrique.

La cardiomyopathie/dysplasie arythmogène du ventricule droit (ARVC/D) est un désordre d’origine génétique caractérisé par le remplacement du myocarde par du tissus fibro-adipeux dans le ventricule droit. Ce désordre est responsable d’un grand pourcentage de mort subite, spécialement chez les plus jeunes. ARVC/D est difficile à diagnostiquer avec les outils cliniques actuels. Elle est causée en grande majorité par des mutations dans les protéines desmosomales. ARVC/D a donc des implications d’une grande importance chez les membres de la famille, qui peuvent sans le savoir, être aussi à risque de mort subite. Dans le but d’améliorer le diagnostique, un nouvel outil, le test génétique, est de plus en plus utilisé. Hypothèses: Dans le but d’évaluer la valeur du test génétique en complément du test clinique classique chez ARVC/D nous avons effectué une investigation clinique et génétique chez 23 cas-index atteints. Méthodes: Les cas-index sont diagnostiqué après une mort subite dans la famille ou après un examen clinique poussé pour arythmies. Le diagnostique d’ARVC/D a été fait avec les outils cliniques selon les critères. L’analyse génétique des protéines desmosomales associées à la maladie a été effectuée en séquençant leurs exons ainsi que les régions introniques nécessaires à l’épissage alternatif. Résultats: Le diagnostique clinique était clair dans 18/23 et incertain dans 5/23 des individus. Nous avons identifié 15 différentes mutations chez 10 cas-index. 64% des mutations n’avaient jamais été décrites. De plus, nous avons observé la présence de double ou triple mutant dans 40% des cas-index positifs. Les individus avec mutations sont plus jeunes et ont plus de symptômes que les individus sans mutation. Conclusion: Les tests génétiques sont positifs dans 43% des patients avec ARVC/D. L’utilisation de la technologie génétique basée sur l’identification de mutations connues a une valeur limitée vu le haut pourcentage des mutations nouvelles dans la maladie. La présence de double, même de triple mutant n’est pas associé avec un phénotype plus sévère, mais renforce l’idée de la nécessité d’un test génétique pour tous les gènes. Le test génétique est un outil fort utile à ajouter aux tests cliniques pour le diagnostique des patients qui ne remplissent pas tous les critères cliniques de la maladie. Mots clés: génétique, ARVC/D, mort subite, desmosome

Classes Alléliques d’Haplotypes et Sélection Positive dans le Génome Humain

L'identification de régions génomiques cibles de la sélection naturelle positive permet de mieux comprendre notre passé évolutif et de trouver des variants génétiques fonctionnels importants. Puisque la fréquence des allèles sélectionnés augmente dans la population, la sélection laisse des traces sur les séquences d'ADN et ces empreintes sont détectées lorsque la variabilité génétique d'une région est différente de celle attendue sous neutralité sélective. On propose une nouvelle approche pour analyser les données de polymorphismes : le calcul des classes alléliques d’haplotypes (HAC), permettant d'évaluer la diversité globale des haplotypes en étudiant leur composition allélique. L'idée de l'approche est de déterminer si un site est sous sélection positive récente en comparant les distributions des HAC obtenues pour les deux allèles de ce site. Grâce à l'utilisation de données simulées, nous avons étudié ces distributions sous neutralité et sous sélection en testant l'effet de différents paramètres populationnels. Pour tester notre approche empiriquement, nous avons analysé la variation génétique au niveau du gène de lactase dans les trois populations inclues dans le projet HapMap.