Évaluation de la contribution de gènes de susceptibilité et de gènes candidats du cancer du sein chez des familles canadiennes françaises à risque élevé

Le cancer du sein est une maladie comportant à la fois une composante environnementale et une composante génétique. Dans le cadre de mes études doctorales je me suis intéressé à la composante génétique du cancer du sein. Puisque la distribution de l'héritabilité chez les familles présentant plusieurs cas de cancer du sein suggère la prédominance de facteurs génétiques afin d'expliquer l'agrégation familiale de ce type de cancer, mes études ont porté sur des cas de cancer du sein provenant de familles à risque élevé non porteuses de mutations délétères dans les gènes BRCA1 et BRCA2. Deux volets principaux ont été abordés. Le premier volet, intitulé ± évaluation de la contribution de gènes de susceptibilité au cancer du sein ¿, m'a amené à évaluer la contribution des gènes de susceptibilité à forte penetrance PTENet STK11. Ces gènes sont respectivement responsables des syndromes de Cowden et de Peutz-Jeghers avec lesquels un risque accru de cancer du sein a été associé. Trois autres gènes de susceptibilité au cancer du sein, soit CHEK2, BRIP1 et PALB2, ont également été analysés. Des mutations dans ces gènes confèrent un risque modéré de cancer du sein.Lors du deuxième volet de mon projet, "identification de gènes de susceptibilité au cancer du sein", quatre gènes candidats du cancer du sein ont été analysés. Ces gènes ont été sélectionnés sur la base de leur interaction avec BRCA1. En effet, puisque les protéines encodées par ces gènes interagissent avec BRCA1, elles pourraient réguler ses diverses fonctions. Les gènes AURKA, BAP1, BARD1 et DHX9, encodant respectivement une kinase, une ubiquitine hydrolase, une ubiquitine ligase et une hélicase à ARN, ont été sélectionnés pour leur rôle possible dans la modulation de l'activité de BRCA1 dans la réparation couplée à la transcription. L'étude de ces gènes a permis de mettre en évidence une implication possible d'un variant de BARD1 dans la susceptibilité au cancer du sein. L'étude de ces gènes a permis d'acquérir une meilleure connaissance de la contribution de ceux-ci à la susceptibilité au cancer du sein chez les familles à risque élevé provenant de la population canadienne-française

Reconstructing Plants in 3D from a Single Image Using Analysis-by-Synthesis

International audienceMature computer vision techniques allow the reconstruction of challenging 3D objects from images. However, due to high complexity of plant topology, dedicated methods for generating 3D plant models must be devised. We propose to generate a 3D model of a plant, using an analysis-by-synthesis method mixing information from a single image and a priori knowledge of the plant species. First, our dedicated skeletonisation algorithm generates a possible branch- ing structure from the foliage segmentation. Then, a 3D generative model, based on a parametric model of branching systems that takes into ac- count botanical knowledge is built. The resulting skeleton follows the hierarchical organisation of natural branching structures. An instance of a 3D model can be generated. Moreover, varying parameter values of the generative model (main branching structure of the plant and foliage), we produce a series of candidate models. The reconstruction is improved by selecting the model among these proposals based on a matching criterion with the image. Realistic results obtained on di erent species of plants illustrate the performance of the proposed method

Reconstruction de modèles virtuels de vignes à partir d'images

National audienceWe propose a method for recontructing virtual model of vines from images. For this, an analysis by synthesis method is used and consist in characterizing an image using a number of a priori knowledge about the 3D scene. Initially, we get an approximation of the plant modeled in 3D. Then, comparing its reprojection with the original image, we refine this model though an iterative optimisation process. To be efficient, our method do not optimize positionning of individual leaves but rather a realistic foliage consistent with the images.Nous présentons ici une méthode de reconstruction de modèles virtuels de pieds de vignes à partir d'images. Pour cela, nous utilisons une technique d'analyse par synthèse qui consiste à caractériser une image à partir d'un certain nombre de connaissances a priori sur la scène 3D. Tout d'abord, à partir d'une première analyse des images, nous obtenons une approximation initiale de la plante modélisée en 3D. Puis, nous affinons cette modélisation par un processus d'optimisation où la projection du modèle reconstruit est comparée avec l'image d'origine. Pour être efficace, notre méthode n'optimise pas le positionnement de chacune des feuilles mais un feuillage réaliste et cohérent avec les images

Modélisation de vignes à partir d'une séquence d'images

National audienceCet article présente des travaux sur la modélisation de plantes à géométries fortement contraintes à partir d'images. A partir de séquences d'images acquises dans un vignoble, nous instancions un modèle paramétré des parcelles, des rangs, et des pieds de vignes. Le modèle est déduit des connaissances a priori ; à partir des images, des paramètres sont extraits. Ces paramètres sont ensuite fournis au modèle qui génère une représentation de la plante, du rang ou de la parcelle filmée

Acute effects of single doses of bonito fish peptides and vitamin D on whole blood gene expression levels : a randomized controlled trial

Fish contains high quality proteins and essential nutrients including 25-hydroxyvitamin D (25(OH)D). Fish peptide consumption can lower cardiovascular disease (CVD) risk factors, and studies have shown an association between 25(OH)D deficiency, CVD and CVD risk factors, such as diabetes. This study investigated acute effects of a single dose of cholecalciferol (VitD3), bonito fish peptide hydrolysate (BPH), or a combination of both on CVD risk factors and whole blood gene expression levels. A randomized, crossover, placebo controlled trial was conducted in 22 adults. They ingested, in random order and at 7-day intervals, 1000 IU of VitD3, 3 g of BPH, a combination of both, or a placebo. A 180 min oral glucose tolerance test was performed. Differences in whole-genome expression levels after versus before each supplementation were computed for 18 subjects. We observed that 16, 1 and 5 transcripts were differentially expressed post- vs. pre-ingestion for VitD3, BPH or VitD3 + BPH treatments, respectively. VitD3-containing treatments affected the expression of the solute carrier family 25 member 20 (SLC25A20) gene involved in fatty acid oxidation, various transcription factors and genes related to glucose metabolism. These results suggest that VitD3 rapidly modulates genes related to CVD risk factors in blood while BPH seems to moderately modulate gene expression levels

Genetic and common environmental contributions to familial resemblances in plasma carotenoid concentrations in healthy families

Carotenoids have shown an interindividual variability that may be due to genetic factors. The only study that has reported heritability of serum α- and β-carotene has not considered the environmental component. This study aimed to estimate the contribution of both genetic and common environmental effects to the variance of carotenoid concentrations and to test whether their phenotypic correlations with cardiometabolic risk factors are explained by shared genetic and environmental effects. Plasma carotenoid concentrations (α-carotene, β-carotene, β-cryptoxanthin, lutein, lycopene, zeaxanthin, and total carotenoids) of 48 healthy subjects were measured. Heritability estimates of carotenoid concentrations were calculated using the variance component method. Lutein and lycopene showed a significant familial effect (p = 6 × 10−6 and 0.0043, respectively). Maximal heritability, genetic heritability, and common environmental effect were computed for lutein (88.3%, 43.8%, and 44.5%, respectively) and lycopene (45.2%, 0%, and 45.2%, respectively). Significant phenotypic correlations between carotenoid concentrations and cardiometabolic risk factors were obtained for β-cryptoxanthin, lycopene, and zeaxanthin. Familial resemblances in lycopene concentrations were mainly attributable to common environmental effects, while for lutein concentrations they were attributable to genetic and common environmental effects. Common genetic and environmental factors may influence carotenoids and cardiometabolic risk factors, but further studies are needed to better understand the potential impact on disease development

Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

Background: Variability in circulating carotenoids may be attributable to several factors including, among others, genetic variants and lipid profile. However, relatively few studies have considered the impact of gene expression in the inter-individual variability in circulating carotenoids. Most studies considered expression of genes individually and ignored their high degree of interconnection. Weighted gene co-expression network analysis (WGCNA) is a systems biology method used for finding gene clusters with highly correlated expression levels and for relating them to phenotypic traits. The objective of the present observational study is to examine the relationship between plasma total carotenoid concentrations and lipid profile using WGCNA. Results: Whole blood expression levels of 533 probes were associated with plasma total carotenoids. Among the four WGCNA distinct modules identified, turquoise, blue, and brown modules correlated with plasma high-density lipoprotein cholesterol (HDL-C) and total cholesterol. Probes showing a strong association with HDL-C and total cholesterol were also the most important elements of the brown and blue modules. A total of four and 29 hub genes associated with total carotenoids were potentially related to HDL-C and total cholesterol, respectively. Conclusions: Expression levels of 533 probes were associated with plasma total carotenoid concentrations. Using WGCNA, four modules and several hub genes related to lipid and carotenoid metabolism were identified. This integrative analysis provides evidence for the potential role of gene co-expression in the relationship between carotenoids and lipid concentrations. Further studies and validation of the hub genes are needed

Network Analysis of the potential role of DNA methylation in the relationship between plasma carotenoids and lipid profile

Abstract: Variability in plasma carotenoids may be attributable to several factors including genetic variants and lipid profile. Until now, the impact of DNA methylation on this variability has not been widely studied. Weighted gene correlation network analysis (WGCNA) is a systems biology method used for finding gene clusters (modules) with highly correlated methylation levels and for relating them to phenotypic traits. The objective of the present study was to examine the role of DNA methylation in the relationship between plasma total carotenoid concentrations and lipid profile using WGCNA in 48 healthy subjects. Genome-wide DNA methylation levels of 20,687 out of 472,245 CpG sites in blood leukocytes were associated with total carotenoid concentrations. Using WGCNA, nine co-methylation modules were identified. A total of 2734 hub genes (17 unique top hub genes) were potentially related to lipid profile. This study provides evidence for the potential implications of gene co-methylation in the relationship between plasma carotenoids and lipid profile. Further studies and validation of the hub genes are needed

Genome-wide association study of dietary pattern scores

Dietary patterns, representing global food supplies rather than specific nutrients or food intakes, have been associated with cardiovascular disease (CVD) incidence and mortality. The contribution of genetic factors in the determination of food intakes, preferences and dietary patterns has been previously established. The current study aimed to identify novel genetic factors associated with reported dietary pattern scores. Reported dietary patterns scores were derived from reported dietary intakes for the preceding month and were obtained through a food frequency questionnaire and genome-wide association study (GWAS) conducted in a study sample of 141 individuals. Reported Prudent and Western dietary patterns demonstrated nominal associations (p < 1 × 10−5) with 78 and 27 single nucleotide polymorphisms (SNPs), respectively. Among these, SNPs annotated to genes previously associated with neurological disorders, CVD risk factors and obesity were identified. Further assessment of SNPs demonstrated an impact on gene expression levels in blood for SNPs located within/near BCKDHB (p = 0.02) and the hypothalamic glucosensor PFKFB3 (p = 0.0004) genes, potentially mediated through an impact on the binding of transcription factors (TFs). Overrepresentations of glucose/energy homeostasis and hormone response TFs were also observed from SNP-surrounding sequences. Results from the current GWAS study suggest an interplay of genes involved in the metabolic response to dietary patterns on obesity, glucose metabolism and food-induced response in the brain in the adoption of dietary patterns

Structure determination of the (3sqrt{3}x3sqrt{3}) reconstructed alpha-Al_2O_3(0001)

Grazing-incidence X-ray diffraction data are combined with energy-minimization calculations to analyse the atomic structure of the Al-rich (3sqrt{3} x 3sqrt{3})R 30 deg reconstructed surface of sapphire alpha-Al_2O_3(0001). The experiments on the BM32 beamline of the ESRF provide the non-integer-order diffraction intensities and, after Fourier transform, an incomplete Patterson map. The computer simulations are implemented to obtain structural information from this map. In the simulations, the interactions between the Al overlayer atoms were described with the Sutton-Chen potential and the interactions between the overlayer and the sapphire substrate with a laterally modulated Lennard-Jones potential. We have shown that the hexagonal reconstructed unit cell is composed of triangles where the two layers of Al adatoms are FCC(111) ordered whereas between the triangles the stacking is FCC(001).Comment: 9 pages, incl. 4 figures; submitted to Surface Science Letter