Infections and functionnal impairment in nursing home residents : a reciprocal relationship

RESUME: Contexte : l'objectif de cette étude de cohorte prospective était de déterminer la relation entre la survenue d'infections et la dépendance fonctionnelle chez des résidents d'établissements de long séjour durant une période de 6 mois. Population et méthode : les patients inclus (1324 résidents) étaient âgés de 65 ans et plus (âge moyen 85.7 ans, 76.6% de femmes), étaient des résidents de 39 EMS du canton de Vaud. Au baseline, des données démographiques, médicales, concernant les facteurs de risque et protecteurs des infections ont été récoltées. Au cours du suivi de 6 mois, les infirmières des EMS ont documenté la survenue de symptômes et signes d'infection en utilisant les critères développés spécifiquement par l'APIC pour les établissements de long séjour. Les mesures du status fonctionnel ont été évaluées au baseline, à 3 mois et à 6 mois. Deux outcomes différents ont été utilisés : a) le déclin fonctionnel défini comme le décès ou une diminution des capacités fonctionnelles au suivi, b) le status fonctionnel mesuré par une échelle standardisée. Résultats : à la fin du suivi, la mortalité était de 14.6%, similaire pour les résidents avec et sans infection (16.2% versus 13.1%, P .11). Durant les 2 périodes de suivi de 3 mois, les sujets ayant présenté une ou plusieurs infections avaient des odds de déclin fonctionnel plus élevés, y compris après ajustement pour les caractéristiques démographiques, médicales et fonctionnelles du baseline, ainsi que la survenue de nouvelles maladies (odds ratio ajustés (OR) = 1.6, intervalle de confiance à 95% (IC) = 1.2-2.2, P = .002 et OR = 1.5, 95% IC= 1.1-2.0, P= .008, respectivement). Comparés aux résidents non infectés, les odds de déclin fonctionnel augmentaient significativement et graduellement chez ceux ayant eu une, respectivement 2 infections ou plus. L'analyse prédisant le score fonctionnel (restreinte aux sujets ayant survécu) a donné des résultats similaires. Finalement, une analyse de survie prédisant le temps jusqu'à la première infection a confirmé une augmentation progressive de la probabilité d'infection chez les sujets avec dépendance fonctionnelle modérée, respectivement sévère, comparés aux sujets indépendants à la ligne de base. Conclusion : chez les résidents de long séjour, les infections sont à la fois cause et conséquence de la dépendance fonctionnelle. Des études futures devraient être entreprises pour investiguer si des programmes de prévention des infections peuvent également contribuer à prévenir le déclin fonctionnel, un facteur important pour la qualité de vie de ces résidents. ABSTRACT: Objectives: To determine the relationship between infections and functional impairment in nursing home residents. Design: Prospective cohort study (follow-up period, 6 months). Setting: Thirty-nine nursing homes in western Switzerland. Participants: A total of 1,324 residents aged 65 and older (mean age 85.7; 76.6% female) who agreed to participate, or their proxies, by oral informed consent. Measurements: Functional status measured every 3 months. Two different outcomes were used: (a) functional decline defined as death or decreased function at follow-up and (b) functional status score using a standardized measure. Results: At the end of follow-up, mortality was 14.6%, not different for those with and without infection (16.2% vs 13.1%, P= .11) During both 3-month periods, subjects with infection had higher odds of functional decline, even after adjustment for baseline characteristics and occurrence of a new illness (adjusted odds ratio (AOR) = 1.6, 95% confidence interval (CI) = 1.2-2.2, P = .002, and AOR 1.5, 95% CI 1.1-2.0, P .008, respectively). The odds of decline increased in a stepwise fashion in patients with zero, one, and two or more infections. The analyses predicting functional status score (restricted to subjects who survived) gave similar results. A survival analysis predicting time to first infection confirmed a stepwise greater likelihood of infection in subjects -with moderate and severe impairment at baseline than in subjects with no or mild functional impairment at baseline. Conclusion: Infections appear to be both a cause and a consequence of functional impairment in nursing home residents. Further studies should be undertaken to investigate whether effective infection control programs can also contribute to preventing functional decline, an important component of these residents' quality of life.

Can MRI replace CT in evaluating semicircular canal dehiscence?

BACKGROUND AND PURPOSE: Patients with symptoms of semicircular canal dehiscence often undergo both CT and MR imaging. We assessed whether FIESTA can replace temporal bone CT in evaluating patients for SC dehiscence. MATERIALS AND METHODS: We retrospectively reviewed 112 consecutive patients (224 ears) with vestibulocochlear symptoms who underwent concurrent MR imaging and CT of the temporal bones between 2007 and 2009. MR imaging protocol included a FIESTA sequence covering the temporal bone (axial 0.8-mm section thickness, 0.4-mm spacing, coronal/oblique reformations; 41 patients at 1.5T, 71 patients at 3T). CT was performed on a 64-row multidetector row scanner (0.625-mm axial acquisition, with coronal/oblique reformations). Both ears of each patient were evaluated for dehiscence of the superior and posterior semicircular canals in consensual fashion by 2 neuroradiologists. Analysis of the FIESTA sequence and reformations was performed first for the MR imaging evaluation. CT evaluation was performed at least 2 weeks after the MR imaging review, resulting in a blinded comparison of CT with MR imaging. CT was used as the reference standard to evaluate the MR imaging results. RESULTS: For SSC dehiscence, MR imaging sensitivity was 100%, specificity was 96.5%, positive predictive value was 61.1%, and negative predictive value was 100% in comparison with CT. For PSC dehiscence, MR imaging sensitivity was 100%, specificity was 99.1%, positive predictive value was 33.3%, and negative predictive value was 100% in comparison with CT. CONCLUSIONS: MR imaging, with a sensitivity and negative predictive value of 100%, conclusively excludes SSC or PSC dehiscence. Negative findings on MR imaging preclude the need for CT to detect SC dehiscence. Only patients with positive findings on MR imaging should undergo CT evaluation.

Double-blind comparison of indapamide with a placebo in hypertensive patients treated by practicing physicians.

The antihypertensive effect of indapamide (2.5 mg/day) was compared to that obtained with a placebo in a controlled trial carried out by 11 physicians in their private practice. Thirty-one patients with uncomplicated essential hypertension were included. After a run-in period of 3 weeks without any treatment, either indapamide (n = 16) or a placebo (n = 15) were administered for 8 weeks in double-blind fashion. Blood pressure decreased in both groups. In patients treated with indapamide, systolic pressure was significantly lower than in those given the placebo at 3 out of the 4 follow-up visits; diastolic pressure, however, was significantly lower only at the end of the trial. Both the active drug and the placebo were well tolerated. No significant change in body weight, plasma potassium and uric acid occurred during the study in either group of patients. It appears therefore that indapamide, at a dose which apparently has no major diuretic effect, may be useful for practitioners in managing patients with mild to moderate hypertension.

An allele-specific, stochastic gene expression process controls the expression of multiple Ly49 family genes and generates a diverse, MHC-specific NK cell receptor repertoire.

Mouse NK cells express MHC class I-specific inhibitory Ly49 receptors. Since these receptors display distinct ligand specificities and are clonally distributed, their expression generates a diverse NK cell receptor repertoire specific for MHC class I molecules. We have previously found that the Dd (or Dk)-specific Ly49A receptor is usually expressed from a single allele. However, a small fraction of short-term NK cell clones expressed both Ly49A alleles, suggesting that the two Ly49A alleles are independently and randomly expressed. Here we show that the genes for two additional Ly49 receptors (Ly49C and Ly49G2) are also expressed in a (predominantly) mono-allelic fashion. Since single NK cells can co-express multiple Ly49 receptors, we also investigated whether mono-allelic expression from within the tightly linked Ly49 gene cluster is coordinate or independent. Our clonal analysis suggests that the expression of alleles of distinct Ly49 genes is not coordinate. Thus Ly49 alleles are apparently independently and randomly chosen for stable expression, a process that directly restricts the number of Ly49 receptors expressed per single NK cell. We propose that the Ly49 receptor repertoire specific for MHC class I is generated by an allele-specific, stochastic gene expression process that acts on the entire Ly49 gene cluster.

Myelin basic protein content of aggregating rat brain cell cultures treated with cytokines and/or demyelinating antibody: effects of macrophage enrichment.

The demyelinative potential of the cytokines interleukin-1 alpha (IL-1 alpha), interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha) has been investigated in myelinating aggregate brain cell cultures. Treatment of myelinated cultures with these cytokines resulted in a reduction in myelin basic protein (MBP) content. This effect was additively increased by anti-myelin/oligodendrocyte glycoprotein (alpha-MOG) in the presence of complement. Qualitative immunocytochemistry demonstrated that peritoneal macrophages, added to the fetal telencephalon cell suspensions at the start of the culture period, successfully integrated into aggregate cultures. Supplementing the macrophage component of the cultures in this fashion resulted in increased accumulation of MBP. The effect of IFN-gamma on MBP content of cultures was not affected by the presence of macrophages in increased numbers.

Hormone signalling crosstalk in plant growth regulation.

The remarkable plasticity of plant ontogeny is shaped by hormone pathways, which not only orchestrate intrinsic developmental programs, but also convey environmental inputs. Several classes of plant hormones exist, and among them auxin, brassinosteroid and gibberellin are central for the regulation of growth in general and of cell elongation in particular. Various growth phenomena can be modulated by each of the three hormones, in a sometimes synergistic fashion, suggesting physiological redundancy and/or crosstalk between the different pathways. Whether this means that they target a common and unique transcriptome module, or rather separate growth-promoting transcriptome modules, remains unclear, however. Nevertheless, while surprisingly few molecular mediators of direct crosstalk in the proper sense have been isolated, evidence is accumulating for complex cross-regulatory relations between hormone pathways at the level of transcription, as exemplified in root meristem growth. The growing number of available genome sequences from the green lineage offers first glimpses at the evolution of hormone pathways, which can aid in understanding the multiple relationships observed between these pathways in angiosperms. The available analyses suggest that auxin, gibberellin and brassinosteroid signalling arose during land plant evolution in this order, correlating with increased morphological complexity and possibly conferring increased developmental flexibility.

Detection of smuggled cocaine in cargo using MDCT.

OBJECTIVE: Smuggling dissolved drugs, especially cocaine, in bottled liquids is an ongoing problem at borders. Common fluoroscopy of packages at the border cannot detect contaminated liquids. The objective of our study was to develop an MDCT screening method to detect cocaine-containing vessels that are hidden between uncontaminated ones in a shipment. MATERIALS AND METHODS: Studies were performed on three wine bottles containing cocaine solutions that were confiscated at the Swiss border. Reference values were obtained by scans of different sorts of commercially available wine and aqueous solutions of dissolved sugar. All bottles were scanned using MDCT, and data evaluation was performed by measuring the mean peak of Hounsfield units. To verify the method, simulated testing was performed. RESULTS: Using measurements of the mean peak of Hounsfield units enables the detection of dissolved cocaine in wine bottles in a noninvasive and rapid fashion. Increasing opacity corresponds well with the concentration of dissolved cocaine. Simulated testing showed that it is possible to distinguish between cocaine-contaminated and uncontaminated wine bottles. CONCLUSION: The described method is an efficacious screening method to detect cocaine-contaminated bottles that are hidden between untreated bottles in cargo. The noninvasive examination of cargo allows a questionable delivery to be tracked without arousing the suspicion of the smugglers.

Arbuscular mycorrhizal fungi mediate below-ground plant-herbivore interactions: a phylogenetic study

Ecological interactions are complex networks, but have typically been studied in a pairwise fashion. Examining how third-party species can modify the outcome of pairwise interactions may allow us to better predict their outcomes in realistic systems. For instance, arbuscular mycorrhizal fungi (AMF) can affect plant interactions with other organisms, including below-ground herbivores, but the mechanisms underlying these effects remain unclear. Here, we use a comparative, phylogenetically controlled approach to test the relative importance of mycorrhizal colonization and plant chemical defences (cardenolides) in predicting plant survival and the abundance of a generalist below-ground herbivore across 14 species of milkweeds (Asclepias spp.). Plants were inoculated with a mixture of four generalist AMF species or left uninoculated. After 1month, larvae of Bradysia sp. (Diptera: Sciaridae), a generalist below-ground herbivore, colonized plant roots. We performed phylogenetically controlled analyses to assess the influence of AMF colonization and toxic cardenolides on plant growth, mortality and infestation by fungus gnats. Overall, plants inoculated with AMF exhibited greater survival than did uninoculated plants. Additionally, surviving inoculated plants had lower numbers of larvae in their roots and fewer non-AM fungi than surviving uninoculated plants. In phylogenetic controlled regressions, gnat density in roots was better predicted by the extent of root colonized by AMF than by root cardenolide concentration. Taken as a whole, AMF modify the effect of below-ground herbivores on plants in a species-specific manner, independent of changes in chemical defence. This study adds to the growing body of literature demonstrating that mycorrhizal fungi may improve plant fitness by conferring protection against antagonists, rather than growth benefits. In addition, we advocate using comparative analyses to disentangle the roles of shared history and ecology in shaping trait expression and to better predict the outcomes of complex multitrophic interactions.

Increased vulnerability to kainic acid-induced epileptic seizures in mice underexpressing the scaffold protein Islet-Brain 1/JIP-1.

Islet-Brain 1, also known as JNK-interacting protein-1 (IB1/JIP-1) is a scaffold protein mainly involved in the regulation of the pro-apoptotic signalling cascade mediated by c-Jun-N-terminal kinase (JNK). IB1/JIP-1 organizes JNK and upstream kinases in a complex that facilitates JNK activation. However, overexpression of IB1/JIP-1 in neurons in vitro has been reported to result in inhibition of JNK activation and protection against cellular stress and apoptosis. The occurrence and the functional significance of stress-induced modulations of IB1/JIP-1 levels in vivo are not known. We investigated the regulation of IB1/JIP-1 in mouse hippocampus after systemic administration of kainic acid (KA), in wild-type mice as well as in mice hemizygous for the gene MAPK8IP1, encoding for IB1/JIP-1. We show here that IB1/JIP-1 is upregulated transiently in the hippocampus of normal mice, reaching a peak 8 h after seizure induction. Heterozygous mutant mice underexpressing IB1/JIP-1 showed a higher vulnerability to the epileptogenic properties of KA, whereas hippocampal IB1/JIP-1 levels remained unchanged after seizure induction. Subsequently, an increasing activation of JNK in the 8 h following seizure induction was observed in IB1/JIP-1 haploinsufficient mice, which also underwent more severe excitotoxic lesions in hippocampal CA3, as assessed histologically 3 days after KA administration. Taken together, these data indicate that IB1/JIP-1 in hippocampus participates in the regulation of the neuronal response to excitotoxic stress in a level-dependent fashion.

Global invasion history of the fire ant Solenopsis invicta.

The fire ant Solenopsis invicta is a significant pest that was inadvertently introduced into the southern United States almost a century ago and more recently into California and other regions of the world. An assessment of genetic variation at a diverse set of molecular markers in 2144 fire ant colonies from 75 geographic sites worldwide revealed that at least nine separate introductions of S. invicta have occurred into newly invaded areas and that the main southern U.S. population is probably the source of all but one of these introductions. The sole exception involves a putative serial invasion from the southern United States to California to Taiwan. These results illustrate in stark fashion a severe negative consequence of an increasingly massive and interconnected global trade and travel system.

The renal hemodynamic effects of Aspirin in newborn and young adult rabbits.

A group of neonatal (n=10) and 12-week-old (n=12) anesthetized, ventilated New Zealand white rabbits received an acute i.v. dose (40 mg/kg body weight) of acetylsalicylic acid (ASA, Aspirin). In the neonatal animals, i.v. ASA caused within 20 min a significant (P<0.01) fall in renal blood flow and glomerular filtration rate (GFR), with an equally significant (P<0.01) increase in filtration fraction and renal vascular resistance. The latter indicates greatly augmented renal vasconstriction or more precisely reduction in intrarenal vasodilatation by inhibition of vasodilatory prostaglandin (PG) synthesis. Urine volume decreased. The 12-week-old young adult animals responded in a similar, but significantly attenuated fashion. These experiments demonstrate that inhibition of PG synthesis in neonatal animals causes very rapid, reversible vasoconstriction, with a reduction in GFR. In addition, this study confirms previous observations that the renal hemodynamic response to the inhibition of PG synthesis is far more pronounced in neonatal animals than in (young) adult rabbits.

Administration of growth hormone to underweight patients with chronic obstructive pulmonary disease. A prospective, randomized, controlled study.

Patients with chronic obstructive pulmonary disease (COPD) often develop weight loss, which is associated with increased mortality. Recombinant human growth hormone (rhGH) treatment has been proposed to improve nitrogen balance and to increase muscle strength in these patients. The aim of this study was to assess the effects of rhGH administration on the nutritional status, resting metabolism, muscle strength, exercise tolerance, dyspnea, and subjective well-being of underweight patients with stable COPD. Sixteen patients attending a pulmonary rehabilitation program (age: 66 +/- 9 yr; weight: 77 +/- 7% of ideal body weight; FEV1: 39 +/- 13% of predicted) were randomly treated daily with either 0.15 IU/kg rhGH or placebo during 3 wk in a double-blind fashion. Measurements were made at the beginning (DO) and at the end (D21) of treatment and 2 mo later (D81). Body weight was similar in the two groups during the study, but lean body mass was significantly higher in the rhGH group at D21 (p < 0.01) and D81 (p < 0.05). The increase in lean body mass was 2.3 +/- 1.6 kg in the rhGH group and 1.1 +/- 0.9 kg in the control group at D21 and 1.9 +/- 1.6 kg in the rhGH group and 0.7 +/- 2.1 kg in the control group at D81. At D21, the resting energy expenditure was increased in the rhGH group (107.8% of DO, p < 0.001 compared with the control group). At D21 and D81, the changes in maximal respiratory pressures, handgrip strength, maximal exercise capacity, and subjective well-being were similar in the two groups. At D21, the 6-min walking distance decreased in the rhGH group (-13 +/- 31%) and increased in the control group (+10 +/- 14%; p < 0.01). We conclude that the daily administration of 0.15 IU/kg rhGH during 3 wk increases lean body mass but does not improve muscle strength or exercise tolerance in underweight patients with COPD.

Computational and statistical analysis of copy number variants in normal and cancer genomes

AbstractAlthough the genomes from any two human individuals are more than 99.99% identical at the sequence level, some structural variation can be observed. Differences between genomes include single nucleotide polymorphism (SNP), inversion and copy number changes (gain or loss of DNA). The latter can range from submicroscopic events (CNVs, at least 1kb in size) to complete chromosomal aneuploidies. Small copy number variations have often no (lethal) consequences to the cell, but a few were associated to disease susceptibility and phenotypic variations. Larger re-arrangements (i.e. complete chromosome gain) are frequently associated with more severe consequences on health such as genomic disorders and cancer. High-throughput technologies like DNA microarrays enable the detection of CNVs in a genome-wide fashion. Since the initial catalogue of CNVs in the human genome in 2006, there has been tremendous interest in CNVs both in the context of population and medical genetics. Understanding CNV patterns within and between human populations is essential to elucidate their possible contribution to disease. But genome analysis is a challenging task; the technology evolves rapidly creating needs for novel, efficient and robust analytical tools which need to be compared with existing ones. Also, while the link between CNV and disease has been established, the relative CNV contribution is not fully understood and the predisposition to disease from CNVs of the general population has not been yet investigated.During my PhD thesis, I worked on several aspects related to CNVs. As l will report in chapter 3, ! was interested in computational methods to detect CNVs from the general population. I had access to the CoLaus dataset, a population-based study with more than 6,000 participants from the Lausanne area. All these individuals were analysed on SNP arrays and extensive clinical information were available. My work explored existing CNV detection methods and I developed a variety of metrics to compare their performance. Since these methods were not producing entirely satisfactory results, I implemented my own method which outperformed two existing methods. I also devised strategies to combine CNVs from different individuals into CNV regions.I was also interested in the clinical impact of CNVs in common disease (chapter 4). Through an international collaboration led by the Centre Hospitalier Universitaire Vaudois (CHUV) and the Imperial College London I was involved as a main data analyst in the investigation of a rare deletion at chromosome 16p11 detected in obese patients. Specifically, we compared 8,456 obese patients and 11,856 individuals from the general population and we found that the deletion was accounting for 0.7% of the morbid obesity cases and was absent in healthy non- obese controls. This highlights the importance of rare variants with strong impact and provides new insights in the design of clinical studies to identify the missing heritability in common disease.Furthermore, I was interested in the detection of somatic copy number alterations (SCNA) and their consequences in cancer (chapter 5). This project was a collaboration initiated by the Ludwig Institute for Cancer Research and involved other groups from the Swiss Institute of Bioinformatics, the CHUV and Universities of Lausanne and Geneva. The focus of my work was to identify genes with altered expression levels within somatic copy number alterations (SCNA) in seven metastatic melanoma ceil lines, using CGH and SNP arrays, RNA-seq, and karyotyping. Very few SCNA genes were shared by even two melanoma samples making it difficult to draw any conclusions at the individual gene level. To overcome this limitation, I used a network-guided analysis to determine whether any pathways, defined by amplified or deleted genes, were common among the samples. Six of the melanoma samples were potentially altered in four pathways and five samples harboured copy-number and expression changes in components of six pathways. In total, this approach identified 28 pathways. Validation with two external, large melanoma datasets confirmed all but three of the detected pathways and demonstrated the utility of network-guided approaches for both large and small datasets analysis.RésuméBien que le génome de deux individus soit similaire à plus de 99.99%, des différences de structure peuvent être observées. Ces différences incluent les polymorphismes simples de nucléotides, les inversions et les changements en nombre de copies (gain ou perte d'ADN). Ces derniers varient de petits événements dits sous-microscopiques (moins de 1kb en taille), appelés CNVs (copy number variants) jusqu'à des événements plus large pouvant affecter des chromosomes entiers. Les petites variations sont généralement sans conséquence pour la cellule, toutefois certaines ont été impliquées dans la prédisposition à certaines maladies, et à des variations phénotypiques dans la population générale. Les réarrangements plus grands (par exemple, une copie additionnelle d'un chromosome appelée communément trisomie) ont des répercutions plus grave pour la santé, comme par exemple dans certains syndromes génomiques et dans le cancer. Les technologies à haut-débit telle les puces à ADN permettent la détection de CNVs à l'échelle du génome humain. La cartographie en 2006 des CNV du génome humain, a suscité un fort intérêt en génétique des populations et en génétique médicale. La détection de différences au sein et entre plusieurs populations est un élément clef pour élucider la contribution possible des CNVs dans les maladies. Toutefois l'analyse du génome reste une tâche difficile, la technologie évolue très rapidement créant de nouveaux besoins pour le développement d'outils, l'amélioration des précédents, et la comparaison des différentes méthodes. De plus, si le lien entre CNV et maladie a été établit, leur contribution précise n'est pas encore comprise. De même que les études sur la prédisposition aux maladies par des CNVs détectés dans la population générale n'ont pas encore été réalisées.Pendant mon doctorat, je me suis concentré sur trois axes principaux ayant attrait aux CNV. Dans le chapitre 3, je détaille mes travaux sur les méthodes d'analyses des puces à ADN. J'ai eu accès aux données du projet CoLaus, une étude de la population de Lausanne. Dans cette étude, le génome de plus de 6000 individus a été analysé avec des puces SNP et de nombreuses informations cliniques ont été récoltées. Pendant mes travaux, j'ai utilisé et comparé plusieurs méthodes de détection des CNVs. Les résultats n'étant pas complètement satisfaisant, j'ai implémenté ma propre méthode qui donne de meilleures performances que deux des trois autres méthodes utilisées. Je me suis aussi intéressé aux stratégies pour combiner les CNVs de différents individus en régions.Je me suis aussi intéressé à l'impact clinique des CNVs dans le cas des maladies génétiques communes (chapitre 4). Ce projet fut possible grâce à une étroite collaboration avec le Centre Hospitalier Universitaire Vaudois (CHUV) et l'Impérial College à Londres. Dans ce projet, j'ai été l'un des analystes principaux et j'ai travaillé sur l'impact clinique d'une délétion rare du chromosome 16p11 présente chez des patients atteints d'obésité. Dans cette collaboration multidisciplinaire, nous avons comparés 8'456 patients atteint d'obésité et 11 '856 individus de la population générale. Nous avons trouvés que la délétion était impliquée dans 0.7% des cas d'obésité morbide et était absente chez les contrôles sains (non-atteint d'obésité). Notre étude illustre l'importance des CNVs rares qui peuvent avoir un impact clinique très important. De plus, ceci permet d'envisager une alternative aux études d'associations pour améliorer notre compréhension de l'étiologie des maladies génétiques communes.Egalement, j'ai travaillé sur la détection d'altérations somatiques en nombres de copies (SCNA) et de leurs conséquences pour le cancer (chapitre 5). Ce projet fut une collaboration initiée par l'Institut Ludwig de Recherche contre le Cancer et impliquant l'Institut Suisse de Bioinformatique, le CHUV et les Universités de Lausanne et Genève. Je me suis concentré sur l'identification de gènes affectés par des SCNAs et avec une sur- ou sous-expression dans des lignées cellulaires dérivées de mélanomes métastatiques. Les données utilisées ont été générées par des puces ADN (CGH et SNP) et du séquençage à haut débit du transcriptome. Mes recherches ont montrées que peu de gènes sont récurrents entre les mélanomes, ce qui rend difficile l'interprétation des résultats. Pour contourner ces limitations, j'ai utilisé une analyse de réseaux pour définir si des réseaux de signalisations enrichis en gènes amplifiés ou perdus, étaient communs aux différents échantillons. En fait, parmi les 28 réseaux détectés, quatre réseaux sont potentiellement dérégulés chez six mélanomes, et six réseaux supplémentaires sont affectés chez cinq mélanomes. La validation de ces résultats avec deux larges jeux de données publiques, a confirmée tous ces réseaux sauf trois. Ceci démontre l'utilité de cette approche pour l'analyse de petits et de larges jeux de données.Résumé grand publicL'avènement de la biologie moléculaire, en particulier ces dix dernières années, a révolutionné la recherche en génétique médicale. Grâce à la disponibilité du génome humain de référence dès 2001, de nouvelles technologies telles que les puces à ADN sont apparues et ont permis d'étudier le génome dans son ensemble avec une résolution dite sous-microscopique jusque-là impossible par les techniques traditionnelles de cytogénétique. Un des exemples les plus importants est l'étude des variations structurales du génome, en particulier l'étude du nombre de copies des gènes. Il était établi dès 1959 avec l'identification de la trisomie 21 par le professeur Jérôme Lejeune que le gain d'un chromosome supplémentaire était à l'origine de syndrome génétique avec des répercussions graves pour la santé du patient. Ces observations ont également été réalisées en oncologie sur les cellules cancéreuses qui accumulent fréquemment des aberrations en nombre de copies (telles que la perte ou le gain d'un ou plusieurs chromosomes). Dès 2004, plusieurs groupes de recherches ont répertorié des changements en nombre de copies dans des individus provenant de la population générale (c'est-à-dire sans symptômes cliniques visibles). En 2006, le Dr. Richard Redon a établi la première carte de variation en nombre de copies dans la population générale. Ces découvertes ont démontrées que les variations dans le génome était fréquentes et que la plupart d'entre elles étaient bénignes, c'est-à-dire sans conséquence clinique pour la santé de l'individu. Ceci a suscité un très grand intérêt pour comprendre les variations naturelles entre individus mais aussi pour mieux appréhender la prédisposition génétique à certaines maladies.Lors de ma thèse, j'ai développé de nouveaux outils informatiques pour l'analyse de puces à ADN dans le but de cartographier ces variations à l'échelle génomique. J'ai utilisé ces outils pour établir les variations dans la population suisse et je me suis consacré par la suite à l'étude de facteurs pouvant expliquer la prédisposition aux maladies telles que l'obésité. Cette étude en collaboration avec le Centre Hospitalier Universitaire Vaudois a permis l'identification d'une délétion sur le chromosome 16 expliquant 0.7% des cas d'obésité morbide. Cette étude a plusieurs répercussions. Tout d'abord elle permet d'effectuer le diagnostique chez les enfants à naître afin de déterminer leur prédisposition à l'obésité. Ensuite ce locus implique une vingtaine de gènes. Ceci permet de formuler de nouvelles hypothèses de travail et d'orienter la recherche afin d'améliorer notre compréhension de la maladie et l'espoir de découvrir un nouveau traitement Enfin notre étude fournit une alternative aux études d'association génétique qui n'ont eu jusqu'à présent qu'un succès mitigé.Dans la dernière partie de ma thèse, je me suis intéressé à l'analyse des aberrations en nombre de copies dans le cancer. Mon choix s'est porté sur l'étude de mélanomes, impliqués dans le cancer de la peau. Le mélanome est une tumeur très agressive, elle est responsable de 80% des décès des cancers de la peau et est souvent résistante aux traitements utilisés en oncologie (chimiothérapie, radiothérapie). Dans le cadre d'une collaboration entre l'Institut Ludwig de Recherche contre le Cancer, l'Institut Suisse de Bioinformatique, le CHUV et les universités de Lausanne et Genève, nous avons séquencés l'exome (les gènes) et le transcriptome (l'expression des gènes) de sept mélanomes métastatiques, effectués des analyses du nombre de copies par des puces à ADN et des caryotypes. Mes travaux ont permis le développement de nouvelles méthodes d'analyses adaptées au cancer, d'établir la liste des réseaux de signalisation cellulaire affectés de façon récurrente chez le mélanome et d'identifier deux cibles thérapeutiques potentielles jusqu'alors ignorées dans les cancers de la peau.

Fecal calprotectin more accurately reflects endoscopic activity of ulcerative colitis than the Lichtiger Index, CRP, and blood leukocytes

Background: Thus far, the correlation of noninvasive markers with endoscopic activity in ulcerative colitis (UC) according to the modified Baron Index is unknown. We aimed to evaluate the correlation between endoscopic activity and fecal calprotectin (FC), C-reactive protein (CRP), blood leukocytes, and the Lichtiger Index (clinical score). Methods: UC patients undergoing complete colonoscopy were prospectively enrolled and scored clinically and endoscopically in an independent fashion. Fecal and blood samples were analyzed in UC patients and controls. Results: We enrolled 228 UC patients and 52 controls. Endoscopic disease activity correlated best with FC (Spearman's rank correlation coefficient r = 0.821), followed by the Lichtiger Index (r = 0.682), CRP (r = 0.556), and leukocytes (r = 0.401). FC was the only marker discriminating between different grades of endoscopic activity (grade 0, 20}11 mg/g; grade 1, 44}34 mg/g; grade 2, 111}74 mg/g; grade 3, 330}332 mg/g; grade 4, 659}319 mg/g; P = 0.0018 for discriminating grade 0 vs. 1 and P < 0.001 for discriminating all other grades). FC had the highest overall accuracy (91%) to detect endoscopically active disease (modified Baron Index _2), followed by the Lichtiger Index of _4 (77%), CRP larger than 5 mg/L (69%) and blood leukocytosis (58%). Conclusions: FC better correlated with the endoscopic disease activity than clinical activity, CRP, and blood leukocytes. The strong correlation with endoscopic disease activity suggests that FC represents a useful biomarker for noninvasive monitoring of disease activity in UC patients.

Detection of Leishmania RNA virus in Leishmania parasites.

BACKGROUND: Patients suffering from cutaneous leishmaniasis (CL) caused by New World Leishmania (Viannia) species are at high risk of developing mucosal (ML) or disseminated cutaneous leishmaniasis (DCL). After the formation of a primary skin lesion at the site of the bite by a Leishmania-infected sand fly, the infection can disseminate to form secondary lesions. This metastatic phenotype causes significant morbidity and is often associated with a hyper-inflammatory immune response leading to the destruction of nasopharyngeal tissues in ML, and appearance of nodules or numerous ulcerated skin lesions in DCL. Recently, we connected this aggressive phenotype to the presence of Leishmania RNA virus (LRV) in strains of L. guyanensis, showing that LRV is responsible for elevated parasitaemia, destructive hyper-inflammation and an overall exacerbation of the disease. Further studies of this relationship and the distribution of LRVs in other Leishmania strains and species would benefit from improved methods of viral detection and quantitation, especially ones not dependent on prior knowledge of the viral sequence as LRVs show significant evolutionary divergence. METHODOLOGY/PRINCIPAL FINDINGS: This study reports various techniques, among which, the use of an anti-dsRNA monoclonal antibody (J2) stands out for its specific and quantitative recognition of dsRNA in a sequence-independent fashion. Applications of J2 include immunofluorescence, ELISA and dot blot: techniques complementing an arsenal of other detection tools, such as nucleic acid purification and quantitative real-time-PCR. We evaluate each method as well as demonstrate a successful LRV detection by the J2 antibody in several parasite strains, a freshly isolated patient sample and lesion biopsies of infected mice. CONCLUSIONS/SIGNIFICANCE: We propose that refinements of these methods could be transferred to the field for use as a diagnostic tool in detecting the presence of LRV, and potentially assessing the LRV-related risk of complications in cutaneous leishmaniasis.