Cox proportional hazards survival regression in haplotype-based association analysis using the Stochastic-EM algorithm

It is now widely recognized that haplotype information inferred from genotypes can be of great interest to better characterize the role of a candidate gene in the etiology of a complex trait in the context of association studies. Several works have recently advocated the simultaneous estimation of haplotype frequencies and haplotype effects in order to get a better efficiency in parameter estimation. Most of the available models can deal with a binary or a quantitative phenotype, but none has yet discussed the application of haplotype-based association analysis to a survival outcome. We describe how the recently proposed Stochastic-EM (SEM) algorithm can be applied to estimate haplotype effects in censored data analysis using a standard Cox proportional hazards formulation. This model has been implemented in the THESIAS software freely available at http://www.genecanvas.org.     

The endothelial protein C receptor (PROCR) Ser219Gly variant and risk of common thrombotic disorders: a HuGE review and meta-analysis of evidence from observational studies

The endothelial protein C receptor (EPCR) limits thrombus formation by enhancing activation of the protein C anticoagulant pathway, and therefore may play a role in the etiology of thrombotic disorders. The rs867186 single-nucleotide polymorphism in the PROCR gene (g.6936A > G, c.4600A > G), resulting in a serine-to-glycine substitution at codon 219, has been associated with reduced activation of the protein C pathway, although its association with thrombosis risk remains unclear. The present study is a highly comprehensive systematic review and meta-analysis, including unpublished genome-wide association study results, conducted to evaluate the evidence for an association between rs867186 and 2 common thrombotic outcomes, venous thromboembolism (VTE) and myocardial infarction (MI), which are hypothesized to share some etiologic pathways. MEDLINE, EMBASE, and HuGE Navigator were searched through July 2011 to identify relevant epidemiologic studies, and data were summarized using random-effects meta-analysis. Twelve candidate genes and 13 genome-wide association studies were analyzed (11 VTE and 14 MI, including 37,415 cases and 84,406 noncases). Under the additive genetic model, the odds of VTE increased by a factor of 1.22 (95% confidence interval, 1.11-1.33, P < .001) for every additional copy of the G allele. No evidence for association with MI was observed.     

Deciphering the molecular basis of venous thromboembolism: where are we and where should we go?

Venous thromboembolism (VTE) is a frequent disease that has a major genetic component of risk. However, known identified genetic risk factors account for <30% of idiopathic (without any environmental origin) VTE cases. This article aims to review the lessons learnt during recent decades in the field of the genetics of VTE, describe the present state‐of‐art methods and discuss promising themes for finding new susceptibility loci.     

EphA2 as target of anticancer immunotherapy: identification of HLA-A*0201-restricted epitopes

EphA2 (Eck) is a tyrosine kinase receptor that is overexpressed in several human cancers such as breast, colon, lung, prostate, gastric carcinoma, and metastatic melanoma but not in nonmalignant counterparts. To validate EphA2 as a tumor antigen recognized by CD8+ T lymphocytes, we used reverse immunology approach to identify HLA-A*0201-restricted epitopes. Peptides bearing the HLA-A*0201-specific anchor motifs were analyzed for their capacity to bind and stabilize the HLA-A*0201 molecules. Two peptides, EphA2(58) and EphA2(550), with a high affinity for HLA-A*0201 were selected. Both peptides were immunogenic in the HLA-A*0201-transgenic HHD mice. Interestingly, peptide-specific murine CTLs cell lines responded to COS-7 cells coexpressing HLA-A*0201 and EphA2 and to EphA2-positive human tumor cells of various origin (renal cell, lung, and colon carcinoma and sarcoma). This demonstrates that EphA2(58) and EphA2(550) are naturally processed from endogenous EphA2. In addition, EphA2(58) and EphA2(550) stimulated specific CD8(+) T cells from healthy donor peripheral blood mononuclear cells. These T cells recognized EphA2-positive human tumor cells in an HLA-A*0201-restricted manner. Interestingly, EphA2-specific CD8+ T cells were detected in the peripheral blood mononuclear cells of prostate cancer patients. These results show for the first time that EphA2 is a tumor rejection antigen and lead us to propose EphA2(58) and EphA2(550) peptides for a broad-spectrum-tumor immunotherapy.     

Biological and genetic factors influencing plasma factor VIII levels in a healthy family population: results from the Stanislas cohort

The mechanisms underlying the variability of factor VIII (FVIII) levels are still poorly understood. The only receptor of FVIII identified so far is the lipoprotein receptor-related protein (LRP), which is thought to be involved in FVIII degradation. We aimed to characterize biological and genetic factors related to FVIII variability, focusing on coding polymorphisms of the LRP gene and polymorphisms potentially detected by molecular screening of the LRP-binding domains of the FVIII gene. Plasma FVIII coagulant activity (FVIII:C) and von Willebrand factor (VWF:Ag) antigen levels were measured in a sample of 100 healthy nuclear families (200 parents and 224 offspring). The ABO blood group and the three coding polymorphisms of the LRP gene (A217V, D2080N and C766T) were genotyped. Lipids and anthropometric factors poorly contributed to the variability of FVIII:C (<5%). A strong effect of ABO blood groups on FVIII:C levels was observed that remained significant after adjustment for VWF:Ag levels (P = 0.02). These two factors explained more than 50% of FVIII:C variability. After adjustment for VWF:Ag and ABO blood groups, a residual resemblance for FVIII:C persisted between biological relatives (rho = 0.13 +/- 0.06 between parents and offspring, rho = 0.24 +/- 0.09 between siblings) compatible with an additional genetic influence. The N allele of the LRP/D2080N polymorphism was associated with decreased levels of FVIII:C (90.4 +/- 8.7 vs. 102.2 +/- 3.5 IU/dl, P = 0.03) and VWF:Ag levels (109.1 +/- 11.2 vs. 125.4 +/- 4.4 IU/dl, P = 0.02). No polymorphism was detected in the LRP-binding domains of the FVIII gene. This study reinforces the hypothesis of a genetic influence of FVIII levels beyond the influence of VWF:Ag and ABO blood groups. The D2080N polymorphism of the LRP gene weakly contributed to the variability of FVIII:C levels in this healthy population.     

Human CalDAG-GEFI gene (RASGRP2) mutation affects platelet function and causes severe bleeding

The nature of an inherited platelet disorder was investigated in three siblings affected by severe bleeding. Using whole-exome sequencing, we identified the culprit mutation (cG742T) in the RAS guanyl-releasing protein-2 (RASGRP2) gene coding for calcium- and DAG-regulated guanine exchange factor-1 (CalDAG-GEFI). Platelets from individuals carrying the mutation present a reduced ability to activate Rap1 and to perform proper αIIbβ3 integrin inside-out signaling. Expression of CalDAG-GEFI mutant in HEK293T cells abolished Rap1 activation upon stimulation. Nevertheless, the PKC- and ADP-dependent pathways allow residual platelet activation in the absence of functional CalDAG-GEFI. The mutation impairs the platelet’s ability to form thrombi under flow and spread normally as a consequence of reduced Rac1 GTP-binding. Functional deficiencies were confined to platelets and megakaryocytes with no leukocyte alteration. This contrasts with the phenotype seen in type III leukocyte adhesion deficiency caused by the absence of kindlin-3. Heterozygous did not suffer from bleeding and have normal platelet aggregation; however, their platelets mimicked homozygous ones by failing to undergo normal adhesion under flow and spreading. Rescue experiments on cultured patient megakaryocytes corrected the functional deficiency after transfection with wild-type RASGRP2. Remarkably, the presence of a single normal allele is sufficient to prevent bleeding, making CalDAG-GEFI a novel and potentially safe therapeutic target to prevent thrombosis.Inherited platelet disorders are rare diseases that give rise to bleeding when platelets fail to fulfill their hemostatic function upon vessel injury. Clinical manifestations include mainly mucocutaneous bleeding, menometrorrhagia and excessive bleeding after surgical intervention or trauma. The study of these diseases allows a better understanding of normal platelet biochemistry and physiology. These inherited disorders include abnormalities of platelet receptors, granules, or signal transduction (Nurden and Nurden, 2011). Signal transduction dysfunction is thought to be the most common cause of platelet inherited disorders; however, only a few have been successfully genotyped.Here, we have identified and characterized the first mutation of RASGRP2 (RAS guanyl-releasing protein-2) in a family suffering severe bleeding. RASGRP2 codes for a major signaling molecule in platelets, calcium-and-DAG-regulated guanine exchange factor-1 (CalDAG-GEFI). It is a guanine nucleotide exchange factor (GEF) that is critical for Ras-like GTPase activation whose target is mainly Rap1 in platelets (Crittenden et al., 2004; Bergmeier et al., 2007; Cifuni et al., 2008; Stefanini et al., 2009). Rap1 is one of the most predominant small GTPases in platelets and constitutes a key signaling element that governs platelet activation by directly regulating integrin-mediated aggregation and granule secretion (Chrzanowska-Wodnicka et al., 2005; Zhang et al., 2011). Mice lacking CalDAG-GEFI not only have major defects in platelet function, with a reduced ability to form thrombi upon vascular injury, but they also have impaired neutrophil functions (Crittenden et al., 2004; Bergmeier et al., 2007; Carbo et al., 2010). To date, no pathological mutation in RASGRP2 has been reported in man and knowledge about the phenotype linked to human CalDAG-GEFI deficiency is lacking.     

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact

Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters.     

Polymorphisms of the lamina maturation pathway and their association with the metabolic syndrome: the DESIR prospective study

Laminopathies are rare monogenic diseases, some of them exhibiting features of the metabolic syndrome. These diseases are mainly due to mutations in LMNA, encoding A-type lamins. One LMNA polymorphism, rs4641, has been associated with the metabolic syndrome, but results have been controversial. We therefore investigated the effect of single nucleotide polymorphisms (SNPs) in the LMNA gene in combination with four other genes encoding enzymes influencing lamin post-translational maturation on risk of metabolic syndrome (MS). Twenty-three tagging SNPs characterising the haplotypic variability of five genes (LMNA, ICMT, ZMPSTE24, FNTA and FNTB) were genotyped in 3,916 French men and women who took part in the prospective DESIR study. Single locus and haplotype analyses were performed but did not detect any significant association with the risk of MS. No robust interaction between SNPs located in different genes on the risk of MS was identified. In conclusion, we did not observe any convincing evidence that common polymorphisms of the lamina pathway could modulate the risk of MS.