Hundreds of variants clustered in genomic loci and biological pathways affect human height.

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Genetic evidence for a role of adiponutrin in the metabolism of apolipoprotein B-containing lipoproteins.

Adiponutrin (PNPLA3) is a predominantly liver-expressed transmembrane protein with phospholipase activity that is regulated by fasting and feeding. Recent genome-wide association studies identified PNPLA3 to be associated with hepatic fat content and liver function, thus pointing to a possible involvement in the hepatic lipoprotein metabolism. The aim of this study was to examine the association between two common variants in the adiponutrin gene and parameters of lipoprotein metabolism in 23,274 participants from eight independent West-Eurasian study populations including six population-based studies [Bruneck (n = 800), KORA S3/F3 (n = 1644), KORA S4/F4 (n = 1814), CoLaus (n = 5435), SHIP (n = 4012), Rotterdam (n = 5967)], the SAPHIR Study as a healthy working population (n = 1738) and the Utah Obesity Case-Control Study including a group of 1037 severely obese individuals (average BMI 46 kg/m2) and 827 controls from the same geographical region of Utah. We observed a strong additive association of a common non-synonymous variant within adiponutrin (rs738409) with age-, gender-, and alanine-aminotransferase-adjusted lipoprotein concentrations: each copy of the minor allele decreased levels of total cholesterol on average by 2.43 mg/dl (P = 8.87 x 10(-7)), non-HDL cholesterol levels by 2.35 mg/dl (P = 2.27 x 10(-6)) and LDL cholesterol levels by 1.48 mg/dl (P = 7.99 x 10(-4)). These associations remained significant after correction for multiple testing. We did not observe clear evidence for associations with HDL cholesterol or triglyceride concentrations. In conclusion, our study suggests that adiponutrin is involved in the metabolism of apoB-containing lipoproteins.

Hereditary hepatic and systemic amyloidosis caused by a new deletion/insertion mutation in the apolipoprotein AI gene.

We report a Spanish family with autosomal-dominant non-neuropathic hereditary amyloidosis with a unique hepatic presentation and death from liver failure, usually by the sixth decade. The disease is caused by a previously unreported deletion/insertion mutation in exon 4 of the apolipoprotein AI (apoAI) gene encoding loss of residues 60-71 of normal mature apoAI and insertion at that position of two new residues, ValThr. Affected individuals are heterozygous for this mutation and have both normal apoAI and variant molecules bearing one extra positive charge, as predicted from the DNA sequence. The amyloid fibrils are composed exclusively of NH2-terminal fragments of the variant, ending mainly at positions corresponding to residues 83 and 92 in the mature wild-type sequence. Amyloid fibrils derived from the other three known amyloidogenic apoAI variants are also composed of similar NH2-terminal fragments. All known amyloidogenic apoAI variants carry one extra positive charge in this region, suggesting that it may be responsible for their enhanced amyloidogenicity. In addition to causing a new phenotype, this is the first deletion mutation to be described in association with hereditary amyloidosis and it significantly extends the value of the apoAI model for investigation of molecular mechanisms of amyloid fibrillogenesis.

A Mendelian randomization approach to assess the causal relationship of gamma-glutamyl transferase with blood pressure and insulin

Background: Elevated levels of g-glutamyl transferase (GGT) have been associated with subsequent risk of elevated blood pressure (BP), hypertension and diabetes. However, the causality of these relationships has not been addressed. Mendelian randomization refers to the random allocation of alleles at the time of gamete formation. Such allocation is expected to be independent of any behavioural and environmental factors (known or unknown), allowing the analysis of largely unconfounded risk associations that are not due to reverse causation. Methods: We performed a cross-sectional analysis among 4361 participants to the population based CoLaus study. Associations of sex-specific GGT quartiles with systolic BP, diastolic BP and insulin levels were assessed using multivariable linear regression analyses. The rs2017869 GGT1 variant, which explained 1.6% of the variance in GGT levels, was used as an instrument to perform a Mendelian randomization analysis. Results: Median age of the study population was 53 years. After age and sex adjustment, GGT quartiles were strongly associated with systolic and diastolic BP (all p for linear trend <0.0001). After multivariable adjustment, these relationships were significantly attenuated, but remained significant for systolic (b(95%CI)¼1.30 (0.32;2.03), p¼0.007) and diastolic BP (b (95%CI)¼0.57 (0.02;1.13), p¼0.04). Using Mendelian randomization, we observed no positive association of GGT with either systolic BP (b (95%CI)¼-5.68 (-11.51-0.16), p¼0.06) or diastolic BP (b (95%CI)¼ -2.24 (-5.98;1.49) p¼0.24). The association of GGT with insulin was also attenuated after multivariable adjustment. Nevertheless, a strong linear trend persisted in the fully adjusted model (b (95%CI)¼0.07 (0.04;0.09), p<0.0001). Using Mendelian randomization, we observed a similar positive association of GGT with insulin (b (95%CI)¼0.19 (0.01-0.37), p¼0.04). Conclusion: In this study, we found evidence for a direct causal relationship between GGT and insulin, suggesting that oxidative stress may be causally implicated in the pathogenesis of type 2 diabetes mellitus.

Up-regulation of macrophage migration inhibitory factor gene and protein expression in glial tumor cells during hypoxic and hypoglycemic stress indicates a critical role for angiogenesis in glioblastoma multiforme.

Glioblastoma multiforme (GBM) is the most malignant variant of human glial tumors. A prominent feature of this tumor is the occurrence of necrosis and vascular proliferation. The regulation of glial neovascularization is still poorly understood and the characterization of factors involved in this process is of major clinical interest. Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine released by leukocytes and by a variety of cells outside of the immune system. Recent work has shown that MIF may function to regulate cellular differentiation and proliferation in normal and tumor-derived cell lines, and may also contribute to the neovascularization of tumors. Our immunohistological analysis of MIF distribution in GBM tissues revealed the strong MIF protein accumulation in close association with necrotic areas and in tumor cells surrounding blood vessels. In addition, MIF expression was frequently associated with the presence of the tumor-suppressor gene p53. To substantiate the concept that MIF might be involved in the regulation of angiogenesis in GBM, we analyzed the MIF gene and protein expression under hypoxic and hypoglycemic stress conditions in vitro. Northern blot analysis showed a clear increase of MIF mRNA after hypoxia and hypoglycemia. We could also demonstrate that the increase of MIF transcripts on hypoxic stress can be explained by a profound transcriptional activation of the MIF gene. In parallel to the increase of MIF transcripts, we observed a significant rise in extracellular MIF protein on angiogenic stimulation. The data of our preliminary study suggest that the up-regulation of MIF expression during hypoxic and hypoglycemic stress might play a critical role for the neovascularization of glial tumors.

The role of dynamical polarization of the ligand-to-metal charge transfer excitations in the ab initio determination of effective exchange parameters

The role of the bridging ligand on the effective Heisenberg coupling parameters is analyzed in detail. This analysis strongly suggests that the ligand-to-metal charge transfer excitations are responsible for a large part of the final value of the magnetic coupling constant. This permits us to suggest a variant of the difference dedicated configuration interaction (DDCI) method, presently one of the most accurate and reliable for the evaluation of magnetic effective interactions. This method treats the bridging ligand orbitals mediating the interaction at the same level than the magnetic orbitals and preserves the high quality of the DDCI results while being much less computationally demanding. The numerical accuracy of the new approach is illustrated on various systems with one or two magnetic electrons per magnetic center. The fact that accurate results can be obtained using a rather reduced configuration interaction space opens the possibility to study more complex systems with many magnetic centers and/or many electrons per center.

Trade policy and regional inequalities

This paper aims to analyse the effects of trade policies in the pattern of regional inequalities within a country. Inspired firstly, by the debate concerning the role of protectionist policies in the settlement of a pattern of striking regional inequalities in the Spanish industrialisation process and secondly, by current evidence of an increase in these inequalities following the entry of Spain in the EU (1986), we set a model that shows that trade liberalisation increases regional inequalities.

Trilateral retinoblastoma with suprasellar tumor and associated pineal cyst

Trilateral retinoblastoma (TRb) is a well-known syndrome associating hereditary retinoblastoma (Rb) with an intracranial neuroblastic tumor arising usually in the pineal region, rarely at the suprasellar or parasellar site. It develops in most cases after diagnosis of Rb. The outcome is usually fatal because of secondary spinal dissemination. Pineal cysts have recently been reported as a benign variant of TRb. We report the unusual presentation of a TRb in a 12-month-old boy with extensive bilateral Rb, a voluminous suprasellar tumor, pineal cyst, and leptomeningeal disease. The special features of this "quadrilateral" Rb are discussed.

La planification anticipée du projet thérapeutique (P.A.P.T.) auprès des personnes hébergées en établissement médico-social

Introduction Les interventions proposées pour promouvoir les directives anticipées (D.A.) n'ont que partiellement atteint leurs objectifs malgré les bénéfices anticipés. L'expérience internationale montre que, quand bien même l'institutionnalisation des D.A. est importante, les pratiques n'ont que peu évolué au cours des trois dernières décennies avec un taux de rédaction entre 15 à 30 %, variant modestement selon les publics, contextes et stratégies. Ce constat nécessite un changement de paradigme car la question des D.A. a trop fréquemment été conçue dans la perspective d'une allocation de ressources, avec une sélection de traitements à envisager en fonction de l'état de santé. Le déplacement souhaité implique de mettre en oeuvre une intervention de type Planification Anticipée du Projet Thérapeutique (P.A.P.T), centrée sur les objectifs et finalités des soins, selon les valeurs et priorités singulières à chaque patient. But L'étude pilote a permis dans un premier temps de développer et tester l'effet d'une intervention de P.A.P.T. menée par une infirmière auprès de résidants nouvellement admis en établissement médico-social (EMS) et de leurs proches significatifs. Dans un deuxième temps, la faisabilité et l'acceptabilité de cette intervention infirmière pour cette population spécifique a été évaluée. Méthode Au total 44 dyades (âge résidants M = 85,01 ans et proches M = 57,42) ont été recrutées pour participer entre mai 2011 et mai 2012 avec un suivi sur six mois dès l'admission du résidant. Un devis pré-post à groupe unique a évalué la qualité de la communication avec l'infirmière sur les soins à la fin de la vie (résidant/proche), les préférences et options de soins (résidant/proche) et la perception du fardeau chez le proche à l'entrée dans l'étude (semaine 5) et trois mois après l'intervention (semaine 25 après l'admission). L'intervention de P.A.P.T. sous forme de trois entretiens a été conduite par l'infirmière, durant le premier trimestre (semaines 6 à 13). Elle a pris connaissance de l'histoire de vie, des croyances et valeurs générales du résidant, clarifié les dix priorités jugées les plus importantes à la fin de sa vie sélectionnées et classées à l'aide d'un jeu de cartes ; elle a identifié, chez le proche, les représentations qu'il se faisait des préférences du résidant et discuté les options de soins au sein de la dyade. Après l'intervention, l'existence de traces dans les dossiers sur les priorités et souhaits de soins ainsi que la présence de D.A. rédigées ont été colligées. Des analyses descriptives et bivariées des données ont été effectuées. Résultats Aucune différence significative n'a été retrouvée après l'intervention par rapport à la qualité de la communication avec l'infirmière sur les soins à la fin de la vie chez le résidant (p = 0,32) et la similitude globale dans la dyade vis-à-vis des options de soins (p = 0,50). La concordance (degré d'accord mesuré avec l'indice K) entre résidant et proche par scénario vis-à-vis des options de soins s'est améliorée pour un des cinq scénarios et a diminué pour les quatre autres (p < 0,001). Pour le proche il a été constaté une amélioration de la qualité de la communication avec l'infirmière (p = 0,000) et de la perception du fardeau global (p - 0,007). Des traces de la P.A.P.T. ont été identifiées dans deux tiers des dossiers alors que des D.A. sont signalées pour 11 résidants. L'intervention s'est avérée faisable et a été bien acceptée par les dyades et les infirmières ayant conduit les entretiens. Conclusion L'intervention infirmière de P.A.P.T. en EMS parait efficace surtout auprès du proche. D'autres études interventionnelles à large échelle sont nécessaires pour confirmer ces résultats préliminaires chez la dyade.

A comparison of three methods of Mendelian randomization when the genetic instrument, the risk factor and the outcome are all binary.

The method of instrumental variable (referred to as Mendelian randomization when the instrument is a genetic variant) has been initially developed to infer on a causal effect of a risk factor on some outcome of interest in a linear model. Adapting this method to nonlinear models, however, is known to be problematic. In this paper, we consider the simple case when the genetic instrument, the risk factor, and the outcome are all binary. We compare via simulations the usual two-stages estimate of a causal odds-ratio and its adjusted version with a recently proposed estimate in the context of a clinical trial with noncompliance. In contrast to the former two, we confirm that the latter is (under some conditions) a valid estimate of a causal odds-ratio defined in the subpopulation of compliers, and we propose its use in the context of Mendelian randomization. By analogy with a clinical trial with noncompliance, compliers are those individuals for whom the presence/absence of the risk factor X is determined by the presence/absence of the genetic variant Z (i.e., for whom we would observe X = Z whatever the alleles randomly received at conception). We also recall and illustrate the huge variability of instrumental variable estimates when the instrument is weak (i.e., with a low percentage of compliers, as is typically the case with genetic instruments for which this proportion is frequently smaller than 10%) where the inter-quartile range of our simulated estimates was up to 18 times higher compared to a conventional (e.g., intention-to-treat) approach. We thus conclude that the need to find stronger instruments is probably as important as the need to develop a methodology allowing to consistently estimate a causal odds-ratio.

A common biological basis of obesity and nicotine addiction.

Smoking influences body weight such that smokers weigh less than non-smokers and smoking cessation often leads to weight increase. The relationship between body weight and smoking is partly explained by the effect of nicotine on appetite and metabolism. However, the brain reward system is involved in the control of the intake of both food and tobacco. We evaluated the effect of single-nucleotide polymorphisms (SNPs) affecting body mass index (BMI) on smoking behavior, and tested the 32 SNPs identified in a meta-analysis for association with two smoking phenotypes, smoking initiation (SI) and the number of cigarettes smoked per day (CPD) in an Icelandic sample (N=34,216 smokers). Combined according to their effect on BMI, the SNPs correlate with both SI (r=0.019, P=0.00054) and CPD (r=0.032, P=8.0 × 10(-7)). These findings replicate in a second large data set (N=127,274, thereof 76,242 smokers) for both SI (P=1.2 × 10(-5)) and CPD (P=9.3 × 10(-5)). Notably, the variant most strongly associated with BMI (rs1558902-A in FTO) did not associate with smoking behavior. The association with smoking behavior is not due to the effect of the SNPs on BMI. Our results strongly point to a common biological basis of the regulation of our appetite for tobacco and food, and thus the vulnerability to nicotine addiction and obesity.

Autoimmunity-Associated LYP-W620 Does Not Impair Thymic Negative Selection of Autoreactive T Cells.

A C1858T (R620W) variation in the PTPN22 gene encoding the tyrosine phosphatase LYP is a major risk factor for human autoimmunity. LYP is a known negative regulator of signaling through the T cell receptor (TCR), and murine Ptpn22 plays a role in thymic selection. However, the mechanism of action of the R620W variant in autoimmunity remains unclear. One model holds that LYP-W620 is a gain-of-function phosphatase that causes alterations in thymic negative selection and/or thymic output of regulatory T cells (Treg) through inhibition of thymic TCR signaling. To test this model, we generated mice in which the human LYP-W620 variant or its phosphatase-inactive mutant are expressed in developing thymocytes under control of the proximal Lck promoter. We found that LYP-W620 expression results in diminished thymocyte TCR signaling, thus modeling a "gain-of-function" of LYP at the signaling level. However, LYP-W620 transgenic mice display no alterations of thymic negative selection and no anomalies in thymic output of CD4(+)Foxp3(+) Treg were detected in these mice. Lck promoter-directed expression of the human transgene also causes no alteration in thymic repertoire or increase in disease severity in a model of rheumatoid arthritis, which depends on skewed thymic selection of CD4(+) T cells. Our data suggest that a gain-of-function of LYP is unlikely to increase risk of autoimmunity through alterations of thymic selection and that LYP likely acts in the periphery perhaps selectively in regulatory T cells or in another cell type to increase risk of autoimmunity.

Metabolic syndrome according to different definitions in a rapidly developing country of the African region

Rapport de synthèseLe syndrome métabolique représente un ensemble de facteurs de risque métaboliques souvent présents simultanément et il est associé à un risque accru de développer des maladies cardiovasculaires. La prevalence du syndrome métabolique est à la hausse au niveau mondial comme cela a souvent été documenté, en particulier dans les pays développés. Pourtant, les données concernant le syndrome métabolique dans les pays de la région sub-saharienne restent rares.Au cours des dernières années, plusieurs définitions du syndrome métabolique ont été formulées, dont celle du 'National Cholesterol Education Program Adult Treatment Panel III', celle de 1 Organisation Mondiale de la Santé et celle du 'International Diabetes Federation'. Parmi les controverses au sujet du syndrome métabolique persiste la question de l'utilité de rechercher la présence du syndrome métabolique chez les patients diabétiques, étant donné que la présence d'un diabète en soit suffit pour identifier un individu à haut risque de faire un événement cardiovasculaire.L'objectif de ce travail de thèse a été de déterminer la prévalence du syndrome métabolique selon les trois définitions majeures mentionnées ci-dessus, grâce à une étude de population transversale, réalisée aux Seychelles en 2004 dans un échantillon représentatif de la population âgée de 24-65 ans (n=1255, taux de participation de 80.3%). L'intérêt d'examiner cette question dans ce pays était d'obtenir des informations dans un pays en transition épidémiologique.Les résultats de ce travail montrent que la prévalence du syndrome métabolique aux Seychelles est élevée, quelque soit la définition utilisée. Selon la définition utilisée, cette prévalence était d'environ 25% chez les hommes et variant entre 25 et 35% chez les femmes.Cependant, malgré des prévalences semblables selon ces trois définitions, la concordance entre ces définitions n'était pas bonne, impliquant que ces différentes définitions classifient, à un certain degré, des individus différents comme étant porteurs du syndrome métabolique.En outre, la plupart (environ 80%) des individus diabétiques avaient un syndrome métabolique. Après exclusion des individus diabétiques, la prévalence du syndrome métabolique dans la population est réduite d'environ un tiers, à environ 20-25%.Ces résultats montrent que, d'une part, le fardeau de maladie dû au syndrome métabolique aux Seychelles, un pays en voie de développement, est considérable. Cette observation peut potentiellement s'appliquer à d'autres pays à un stade de développement semblable. Cela renforce le besoin de mettre en oeuvre des stratégies de santé publique afin de cibler les causes de ces désordres métaboliques, tels que le surpoids et la sédentarité. D'un point de vue du diagnostic, les trois définitions du syndrome métabolique semblent classifier un nombre semblable de personnes atteints du syndrome métabolique dans cette population. Par contre, la relativement mauvaise concordance entre ces définitions - certaines personnes identifiés comme porteurs du syndrome métabolique selon une définition ne le sont pas selon une autre - confirme la nécessité de clarifier la signification de ces différentes définitions et/ou éventuellement de développer une définition unifiée et fiable du syndrome métabolique.

Copy number variation of KIR genes influences HIV-1 control.

A genome-wide screen for large structural variants showed that a copy number variant (CNV) in the region encoding killer cell immunoglobulin-like receptors (KIR) associates with HIV-1 control as measured by plasma viral load at set point in individuals of European ancestry. This CNV encompasses the KIR3DL1-KIR3DS1 locus, encoding receptors that interact with specific HLA-Bw4 molecules to regulate the activation of lymphocyte subsets including natural killer (NK) cells. We quantified the number of copies of KIR3DS1 and KIR3DL1 in a large HIV-1 positive cohort, and showed that an increase in KIR3DS1 count associates with a lower viral set point if its putative ligand is present (p = 0.00028), as does an increase in KIR3DL1 count in the presence of KIR3DS1 and appropriate ligands for both receptors (p = 0.0015). We further provide functional data that demonstrate that NK cells from individuals with multiple copies of KIR3DL1, in the presence of KIR3DS1 and the appropriate ligands, inhibit HIV-1 replication more robustly, and associated with a significant expansion in the frequency of KIR3DS1+, but not KIR3DL1+, NK cells in their peripheral blood. Our results suggest that the relative amounts of these activating and inhibitory KIR play a role in regulating the peripheral expansion of highly antiviral KIR3DS1+ NK cells, which may determine differences in HIV-1 control following infection.

CD3 delta establishes a functional link between the T cell receptor and CD8.

T cells expressing T cell receptor (TCR) complexes that lack CD3 delta, either due to deletion of the CD3 delta gene, or by replacement of the connecting peptide of the TCR alpha chain, exhibit severely impaired positive selection and TCR-mediated activation of CD8 single-positive T cells. Because the same defects have been observed in mice expressing no CD8 beta or tailless CD8 beta, we examined whether CD3 delta serves to couple TCR.CD3 with CD8. To this end we used T cell hybridomas and transgenic mice expressing the T1 TCR, which recognizes a photoreactive derivative of the PbCS 252-260 peptide in the context of H-2K(d). We report that, in thymocytes and hybridomas expressing the T1 TCR.CD3 complex, CD8 alpha beta associates with the TCR. This association was not observed on T1 hybridomas expressing only CD8 alpha alpha or a CD3 delta(-) variant of the T1 TCR. CD3 delta was selectively co-immunoprecipitated with anti-CD8 antibodies, indicating an avid association of CD8 with CD3 delta. Because CD8 alpha beta is a raft constituent, due to this association a fraction of TCR.CD3 is raft-associated. Cross-linking of these TCR-CD8 adducts results in extensive TCR aggregate formation and intracellular calcium mobilization. Thus, CD3 delta couples TCR.CD3 with raft-associated CD8, which is required for effective activation and positive selection of CD8(+) T cells.