Pathway-Based Analysis of a Melanoma Genome-Wide Association Study: Analysis of Genes Related to Tumour-Immunosuppression

Systemic immunosuppression is a risk factor for melanoma, and sunburn-induced immunosuppression is thought to be causal. Genes in immunosuppression pathways are therefore candidate melanoma-susceptibility genes. If variants within these genes individually have a small effect on disease risk, the association may be undetected in genome-wide association (GWA) studies due to low power to reach a high significance level. Pathway-based approaches have been suggested as a method of incorporating a priori knowledge into the analysis of GWA studies. In this study, the association of 1113 single nucleotide polymorphisms (SNPs) in 43 genes (39 genomic regions) related to immunosuppression have been analysed using a gene-set approach in 1539 melanoma cases and 3917 controls from the GenoMEL consortium GWA study. The association between melanoma susceptibility and the whole set of tumour-immunosuppression genes, and also predefined functional subgroups of genes, was considered. The analysis was based on a measure formed by summing the evidence from the most significant SNP in each gene, and significance was evaluated empirically by case-control label permutation. An association was found between melanoma and the complete set of genes (pemp = 0.002), as well as the subgroups related to the generation of tolerogenic dendritic cells (pemp = 0.006) and secretion of suppressive factors (pemp = 0.0004), thus providing preliminary evidence of involvement of tumour-immunosuppression gene polymorphisms in melanoma susceptibility. The analysis was repeated on a second phase of the GenoMEL study, which showed no evidence of an association. As one of the first attempts to replicate a pathway-level association, our results suggest that low power and heterogeneity may present challenges

Desflurane-induced postconditioning of diabetic human right atrial myocardium in vitro

AIM: We tested the hypothesis that brief exposure to desflurane at the time of reoxygenation might be able to protect against hypoxia-reoxygenation injury in human myocardium from diabetic (insulin-dependent, ID; and non-insulin-dependent, NID) patients and non-diabetic (ND) subjects. METHODS: The force of contraction (34 degrees C, stimulation frequency 1Hz) in the right atrial trabeculae was recorded during 30min of hypoxia followed by 60min of reoxygenation. Desflurane (at 3, 6 and 9%) was administered during the first 5min of reoxygenation. The force of contraction at the end of the 60-min reoxygenation period (FoC(60)) was compared in the study groups (means+/-SD). RESULTS: In the ND group, desflurane at 3, 6 and 9% (FoC(60): respectively 78+/-10%, 84+/-4% and 85+/-12% of baseline) enhanced the recovery of FoC(60) compared with the ND-controls (53+/-7% of baseline; P<0.05). In the ID group, desflurane at 3% (61+/-4%) did not modify the recovery of FoC(60) compared with the ID-controls (54+/-6%), whereas desflurane at 6 and 9% (75+/-11% and 81+/-8%, respectively) enhanced the recovery of FoC(60)vs the controls (P<0.05). In the NID group, desflurane at 3% (57+/-5%) also failed to modify the recovery of FoC(60) compared with the NID-controls (52+/-10%), while desflurane at 6 and 9% (80+/-10% and 79+/-7%, respectively) enhanced the recovery of FoC(60)vs the controls (P<0.05). CONCLUSION: Desflurane in vitro was able to postcondition diabetic (both ID and NID) human myocardium at 6 and 9%, but not at 3%

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Role of 70-kDa ribosomal protein S6 kinase, nitric oxide synthase, glycogen synthase kinase-3 beta, and mitochondrial permeability transition pore in desflurane-induced postconditioning in isolated human right atria

Desflurane during early reperfusion has been shown to postcondition human myocardium. Whether it involves "reperfusion injury salvage kinase" pathway remains incompletely studied. The authors tested the involvement of 70-kDa ribosomal protein S6 kinase, nitric oxide synthase, glycogen synthase kinase (GSK)-3beta, and mitochondrial permeability transition pore in desflurane-induced postconditioning

Traceability of values for catalytic activity concentration of enzymes : a certified reference material for aspartate transaminase

Background: A new reference material for the liver enzyme aspartate transaminase (AST) (L-aspartate: 2-oxoglutarate-aminotransferase, EC 2.6.1.1), also called aspartate aminotransferase (ASAT), has been developed under the code ERM-AD457/IFCC. This certified reference material (CRM) for AST has been produced from a human type recombinant AST expressed in Escherichia coli and a buffer containing bovine serum albumin, and has been lyophilised. Methods: The homogeneity and the stability of the material have been tested and the catalytic activity concentration has been characterised by 12 laboratories using the reference procedure for AST at 37 degrees C from the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). Results: The certified catalytic activity concentration and certified uncertainty of AST in the reconstituted material are (1.74 +/- 0.05) mkat/L or (104.6 +/- 2.7) U/L (with a coverage factor k = 2; 95% confidence interval). Conclusions: Both the certified value and uncertainty are traceable to the International System of Units (SI). The material is aiming to control the IFCC reference procedure for AST at 37 degrees C, which will then be used to assign values to calibrants and control materials. The present paper highlights the scientific challenges and innovations which were encountered during the development of this new CRM

Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome

Oilseed rape (Brassica napus L.) was formed 3c7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782Peer reviewed: YesNRC publication: Ye

Coordination of research on internal dosimetry in Europe: The CONRAD project

The EUropean RAdiation DOSimetry Group (EURADOS) initiated in 2005 the CONRAD Project, a Coordinated Network for Radiation Dosimetry funded by the European Commission (EC), within the 6th Framework Programme (FP). The main purpose of CONRAD is to generate a European Network in the field of Radiation Dosimetry and to promote both research activities and dissemination of knowledge. The objective of CONRAD Work Package 5 (WP5) is the coordination of research on assessment and evaluation of internal exposures. Nineteen institutes from 14 countries participate in this action. Some of the activities to be developed are continuations of former European projects supported by the EC in the 5th FP (OMINEX and IDEAS). Other tasks are linked with ICRP activities, and there are new actions never considered before. A collaboration is established with CONRAD Work Package 4, dealing with Computational Dosimetry, to organise an intercomparison on Monte Carlo modelling for in vivo measurements of 241Am deposited in a knee phantom. Preliminary results associated with CONRAD WP5 tasks are presented here. © The Author 2007. Published by Oxford University Press. All rights reserved

Candida bloodstream infections in intensive care units: analysis of the extended prevalence of infection in intensive care unit study

To provide a global, up-to-date picture of the prevalence, treatment, and outcomes of Candida bloodstream infections in intensive care unit patients and compare Candida with bacterial bloodstream infection. DESIGN: A retrospective analysis of the Extended Prevalence of Infection in the ICU Study (EPIC II). Demographic, physiological, infection-related and therapeutic data were collected. Patients were grouped as having Candida, Gram-positive, Gram-negative, and combined Candida/bacterial bloodstream infection. Outcome data were assessed at intensive care unit and hospital discharge. SETTING: EPIC II included 1265 intensive care units in 76 countries. PATIENTS: Patients in participating intensive care units on study day. INTERVENTIONS: None. MEASUREMENT AND MAIN RESULTS: Of the 14,414 patients in EPIC II, 99 patients had Candida bloodstream infections for a prevalence of 6.9 per 1000 patients. Sixty-one patients had candidemia alone and 38 patients had combined bloodstream infections. Candida albicans (n = 70) was the predominant species. Primary therapy included monotherapy with fluconazole (n = 39), caspofungin (n = 16), and a polyene-based product (n = 12). Combination therapy was infrequently used (n = 10). Compared with patients with Gram-positive (n = 420) and Gram-negative (n = 264) bloodstream infections, patients with candidemia were more likely to have solid tumors (p < .05) and appeared to have been in an intensive care unit longer (14 days [range, 5-25 days], 8 days [range, 3-20 days], and 10 days [range, 2-23 days], respectively), but this difference was not statistically significant. Severity of illness and organ dysfunction scores were similar between groups. Patients with Candida bloodstream infections, compared with patients with Gram-positive and Gram-negative bloodstream infections, had the greatest crude intensive care unit mortality rates (42.6%, 25.3%, and 29.1%, respectively) and longer intensive care unit lengths of stay (median [interquartile range]) (33 days [18-44], 20 days [9-43], and 21 days [8-46], respectively); however, these differences were not statistically significant. CONCLUSION: Candidemia remains a significant problem in intensive care units patients. In the EPIC II population, Candida albicans was the most common organism and fluconazole remained the predominant antifungal agent used. Candida bloodstream infections are associated with high intensive care unit and hospital mortality rates and resource use