The methylation status of the O 6 -methylguanine-DNA methyltransferase ( MGMT ) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Recent studies in anaplastic glioma suggest a prognostic value for MGMT methylation. Investigation of pathogenetic and epigenetic features of this intriguingly distinct behavior requires accurate MGMT classification to assess high throughput molecular databases. Promoter methylation-mediated gene silencing is strongly dependent on the location of the methylated CpGs, complicating classification. Using the HumanMethylation450 (HM - 450K) BeadChip interrogating 176 CpGs annotated for the MGMT gene, with 14 located in the promoter, two distinct regions in the CpG island of the promoter were identified with high importance for gene silencing and outcome prediction. A logistic regression model (MGMT-STP27) comprising probes cg1243587 and cg12981137 provided good classification properties and prognostic value (kappa = 0.85; log-rank p < 0.001) using a training-set of 63 glioblastomas from homogenously treated patients, for whom MGMT methylation was previously shown to be predictive for outcome based on classification by methylation-specific PCR. MGMT-STP27 was successfully validated in an independent cohort of chemo-radiotherapy-treated glioblastoma patients ( n = 50; kappa = 0.88; outcome, log-rank p < 0.001). Lower prevalence of MGMT methylation among CpG island methylator phenotype (CIMP) positive tumors was found in glioblastomas from The Cancer Genome Atlas than in low grade and anaplastic glioma cohorts, while in CIMP-negative gliomas MGMT was classified as methylated in approximately 50 % regardless of tumor grade. The proposed MGMT-STP27 prediction model allows mining of datasets derived on the HM - 450K or HM-27K BeadChip to explore effects of distinct epigenetic context of MGMT methylation suspected to modulate treatment resistance in different tumor types. Electronic supplementary material The online version of this article (doi:10.1007/s00401-012-1016-2) contains supplementary material, which is available to authorized users.

Summary 1. The application of environmental policy and legislation across large‐scale administrative units creates a growing need for standard tools to assess and monitor the ‘ecological health’ of rivers, a requirement that can be achieved through the description of ecological functions of lotic invertebrate species in river communities. 2. To assess alternative metrics, we tested how the functional structure (described by 14 biological traits) of invertebrate communities in 190 large river reaches differed with respect to differences in taxonomic resolution (species, genus, family), taxa weighting of traits (raw abundance, ln‐transformed abundance, presence–absence data) and consideration of alien species (inclusion or exclusion), and how these differences influenced the potential of functional descriptions to discriminate river reaches across a gradient of multiple human impacts. 3. Functional descriptions derived at the level of species, genera and families were very similar, whereas functional descriptions derived from raw abundances differed significantly from those derived from both ln‐transformed abundances and presence–absence data. Functional descriptions after the exclusion of alien species differed considerably from those including alien species. 4. Generally, the functional descriptions significantly discriminated river reaches according to the level of human impact. Taxonomic resolution scarcely influenced the discrimination of impact levels, whereas the use of raw abundances decreased impact discrimination in comparison with ln‐transformed abundances and presence–absence data. Exclusion of alien species also decreased discrimination of impact levels. 5. When considered separately, individual biological traits describing maximal size, number of descendants per reproductive cycle, number of reproductive cycles per individual, life duration of adults, reproductive method, parental care, body form and feeding habits had the highest potential to discriminate the level of human impact. 6. Our findings indicate that genus or perhaps family identifications are sufficient for large‐river biomonitoring using invertebrate traits. Although raw abundances could provide a better discrimination of low levels of human impact, presence–absence data should be sufficient to discriminate functional community changes caused by elevated levels of human impact across Europe.

This study provides the evidence that a 10-15-minute BAI does not decrease alcohol use and health resource utilization in hazardous drinkers treated in the ED, and demonstrates that commonly found decreases in hazardous alcohol use in control groups cannot be attributed to the baseline alcohol assessment.

BackgroundHOX genes are a family of developmental genes that are expressed neither in the developing forebrain nor in the normal brain. Aberrant expression of a HOX-gene dominated stem-cell signature in glioblastoma has been linked with increased resistance to chemo-radiotherapy and sustained proliferation of glioma initiating cells. Here we describe the epigenetic and genetic alterations and their interactions associated with the expression of this signature in glioblastoma.ResultsWe observe prominent hypermethylation of the HOXA locus 7p15.2 in glioblastoma in contrast to non-tumoral brain. Hypermethylation is associated with a gain of chromosome 7, a hallmark of glioblastoma, and may compensate for tumor-driven enhanced gene dosage as a rescue mechanism by preventing undue gene expression. We identify the CpG island of the HOXA10 alternative promoter that appears to escape hypermethylation in the HOX-high glioblastoma. An additive effect of gene copy gain at 7p15.2 and DNA methylation at key regulatory CpGs in HOXA10 is significantly associated with HOX-signature expression. Additionally, we show concordance between methylation status and presence of active or inactive chromatin marks in glioblastoma-derived spheres that are HOX-high or HOX-low, respectively.ConclusionsBased on these findings, we propose co-evolution and interaction between gene copy gain, associated with a gain of chromosome 7, and additional epigenetic alterations as key mechanisms triggering a coordinated, but inappropriate, HOX transcriptional program in glioblastoma.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0583-7) contains supplementary material, which is available to authorized users.

Amplification of the epidermal growth factor receptor (EGFR) gene is one of the most common oncogenic alterations in glioblastoma (45%) making it a prime target for therapy. However, small molecule inhibitors of the EGFR tyrosine kinase showed disappointing efficacy in clinical trials for glioblastoma. Here we aimed at investigating the molecular effects of the tyrosine kinase inhibitor gefitinib on the EGFR signaling pathway in human glioblastoma. Twenty-two patients selected for reoperation of recurrent glioblastoma were treated within a phase II trial for 5 days with 500 mg gefitinib before surgery followed by postoperative gefitinib until recurrence. Resected glioblastoma tissues exhibited high concentrations of gefitinib (median, 4

1. Multiple biological invertebrate traits (e.g. body size, body form, dispersal potential) each described through multiple categories (e.g. small, intermediate or large body size) could serve as indicators of particular types of human impacts on large rivers. The trait composition of natural invertebrate communities is scarcely constrained by taxonomic differences among them, i.e. individual trait categories could be used to discriminate various types of human impacts across large geographic areas, which would require the definition of trait patterns for conditions of relatively low human impact. 2. Using large databases to link 14 biological traits (described through 66 categories) of invertebrate genera to their occurrence in running water reaches with known environmental conditions, we examined the accuracy of various approaches to predict expected trait variation across least impacted river reaches (LIRRs) of Europe in a stepwise analytical procedure. This procedure included Monte Carlo simulations and ultimately the assignment of test-LIRRs (reaches not used in previous analyses) to the previously defined LIRR conditions. 3. Distance from the source was an integrative variable capturing some (but not all) landscape features (e.g. altitude) or habitat variables (e.g. reach shear stress). Correspondingly, the relative abundance of many trait categories changed along 13 European running waters, although particularly the intensity of these changes differed among these 13 running waters. 4. 'Downstream models' (using only distance from the source as predictor) provided the least accurate predictions of expected invertebrate trait patterns when compared with 'landscape models' (using distance from the source in combination with altitude and/or latitude) or 'habitat models' (using reach shear stress, mean annual air temperature and/or pH of the water). Landscape models provided more accurate predictions than habitat models, but the improvement of predictions of expected invertebrate traits patterns obtained using landscape models was negligible in comparison with a simpler 'mean-model' approach, suggesting that defining LIRR conditions through simple descriptions of frequency distributions would be sufficient for the future biomonitoring of large European rivers. 5. To define these LIRR conditions, we used the average of the relative abundance of each trait category from 68 LIRRs ( ‡40 m wide) as expected LIRR values, and computed LIRR frequency distributions that described the deviations of the 68 individual LIRRs from these expected values. Computing such deviations from the expected LIRR values for 57 testLIRRs (also ‡40 m wide), 57 trait categories correctly assigned >90% of the test-LIRRs to LIRR conditions if the latter were defined through the entire range of the LIRR frequency distributions. To the 90%-range enveloped by the LIRR frequency distributions, 42 trait categories correctly assigned >80% and 12 categories >90% of the test-LIRRs. 6. Using a framework that required no regionalisation of a large geo...

1. Studies on biodiversity and ecosystem function require considering metrics for accurately describing the functional diversity of communities. The number of taxa (richness) is commonly used to characterise biological diversity. The disadvantage of richness as a measure of biological diversity is that all taxa are taken into account on an equal basis regardless of their abundance, their biological characteristics or their function in the ecosystem. 2. To circumvent this problem, we applied a recently described measure of biological diversity that incorporates dissimilarities among taxa. Dissimilarities were defined from biological traits (e.g. life history, morphology, physiology and behaviour) of stream invertebrate taxa and the resulting biological diversity index was considered as a surrogate for functional diversity. 3. As sampling effort is known to affect the number of taxa collected within a reach, we investigated how change in functional diversity is affected by sampling effort. We used stream invertebrate community data from three large European rivers to model accumulation curves and to assess the number of samples required to estimate (i.e. closeness to the maximal value) functional diversity and genera richness. We further evaluated the precision of estimates (i.e. similarity of temporal or spatial replicates) of the total functional diversity. 4. As expected, richness estimates were strongly dependent on sampling effort, and 10 replicate samples were found to underestimate actual richness. Moreover, richness estimates showed much variation with season and location. In contrast, functional diversity had greater accuracy with less sampling effort and the precision of the estimates was higher than richness both across sampling occasions and sampling reaches. These results are further arguments towards conducting research on the design of a biomonitoring tool based on biological traits.

We assessed the temporal changes in and the relationships between the structures of the macroinvertebrate communities and the environmental conditions of the French Rhône River (the river from Lake Geneva to the Mediterranean Sea) over the last 20 years (1985-2004). Multisite environmental and biological datasets were analysed using multiple CO-inertia analysis (MCOA) and Procrustean analysis. Changes in environmental conditions were mainly marked by an improvement in water quality between 1985 and 1991 and by an increase in water temperature from 1985 onwards due to climate change. Improvement in water quality seemed to delay changes in community structures under global warming. We then observed trends in community structures coupled with high temperatures and a decrease in oxygen content. Interestingly, we observed both gradual changes and rapid switches in community states. These shifts seemed coupled to extreme hydroclimatic events (i.e. pulse disturbances). Floods and the 2003 heatwave enhanced the development of eurytolerant and invasive taxa which were probably able to take advantage of gradual warming environmental conditions. Despite various site-specific "press" constraints (e.g. hydropower schemes, nuclear power plants), similar changes in community structures were observed along the French Rhône River. Such consistency in temporal processes at large geographical scales underlined the strength of hydroclimatic constraints on community dynamics compared to specific local disturbances. Finally, community structures did not show any sign of recovery, and their relative sensitivities to extreme hydroclimatic events seemed to increase with time. Thus, our results suggest that global changes may reduce the resilience of current community states.