Identification of MET genomic amplification, protein expression and alternative splice isoforms in neuroblastomas

Crizotinib, a dual anaplastic lymphoma kinase (ALK) and mesenchymal-epithelial transition (MET) tyrosine kinase inhibitor, is currently being evaluated for the treatment of neuroblastoma. Its effects are thought to be mediated mainly via its activity against ALK. Although MET genomic/protein expression status might conceivably affect crizotinib efficacy, this issue has hitherto not received attention in neuroblastomas.

Peer effects in UK adolescent substance use: Never mind the classmates?

This article estimates peer influences on the alcohol, tobacco and cannabis use of UK adolescents. We present evidence of large, positive and statistically significant peer effects in all three behaviours when classmates are taken as the reference group. We also find large, positive and statistically significant associations between own substance use and friends' substance use. When both reference groups are considered simultaneously, the influence of classmates either disappears or is much reduced, whereas the association between own and friends' behaviours does not change. The suggestion is that classmate behaviour is primarily relevant only inasmuch as it proxies for friends' behaviour.

Climate Change, national politics and grassroots action: an introduction

Climate change continues to dominate academic work within green/environmental politics. Indeed, there appears to be almost an inverse relationship between the lack of political leadership on tackling climate change and the growth in ever more sophisticated academic analyses of this complex and multifaceted problem. There is an increasing disjunction between the growth in our knowledge and understanding of the ethical, political, economic, sociological, cultural, and psychological aspects of climate change and the lack of political achievement in putting in place clear and binding targets, an agreed decarbonisation roadmap, and associated regulatory and policy instruments with enforcement. This gap might be taken as evidence that we do not need more reports on climate change. To quote that most unlikely of green politicians, Arnold Schwarzenegger, former Governor of California: ‘The debate is over. We know the science. We see the threat. And we know that the time for action is now’ (California Energy Commission 2007, p. 1). This special issue focuses on a variety of ways in which climate change is conceptualised in normative political and ethical theory, and addressed in policy and regulations.

Anniversaries

The hundredth anniversary of the outbreak of the First World War is only the first of a large number of major European historical anniversaries that will occur in the coming four years. Other twentieth-century anniversaries include that of the Russian Revolution and the Easter Uprising; notable corollaries from earlier centuries include the Battle of Bannockburn, the Hanoverian succession, the Battle of Waterloo and, perhaps most significant of all, the five hundredth anniversary of the Lutheran Reformation. Rather than commission special issues or other features to tie in to individual anniversaries centred on or relevant to German history in a manner which repeats unthinkingly the conventions of scholarly and popular culture, the editors elected to reflect more fundamentally on what might be at stake in major anniversaries for professional scholars of history. In anticipation of the major wave of scholarly and popular publications, commemorative activities and memory conflicts that each of these will generate, and in order to reflect upon the dynamics of German history, memory and commemoration in a more overtly comparative context, the editors invited a number of scholars working on different national histories to reflect on the possibilities and potential pitfalls such anniversaries offer to historians who tie their work in to such moments. They are Jörg Arnold (Nottingham), Thomas A. Brady (Berkeley), Fearghal McGarry (Queen’s University, Belfast), Tim Grady (Chester) and Dan Healey (St Antony’s College, Oxford). The questions were posed by the editors.

Biomass-derived Oxymethylene Ethers as Diesel Additives: A Thermodynamic Analysis

Conversion of biomass for production of liquid fuels can help in reducing the greenhouse gas (GHG) emissions which are predominantly generated by combustion of fossil fuels. Adding oxymethylene ethers (OMEs) in conventional diesel fuel has the potential to reduce soot formation during the combustion in a diesel engine. OMEs are downstream products of syngas, which can be generated by the gasification of biomass. In this research, a thermodynamic analysis has been conducted through development of data intensive process models of all the unit operations involved in production of OMEs from biomass. Based on the developed model, the key process parameters affecting the OMEs production including equivalence ratio, H2/CO ratio, and extra water flow rate were identified. This was followed by development of an optimal process design for high OMEs production. It was found that for a fluidized bed gasifier with heat capacity of 28 MW, the conditions for highest OMEs production are at an air amount of 317 tonne/day, at H2/CO ratio of 2.1, and without extra water injection. At this level, the total OMEs production is 55 tonne/day (13 tonne/day OME3 and 9 tonne/day OME4). This model would further be used in a techno-economic assessment study of the whole biomass conversion chain to determine the most attractive pathways.

Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes.

The opportunistic human pathogen Propionibacterium acnes is comprised of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II and III, that vary in their production of putative virulence factors, inflammatory potential, as well as biochemical, aggregative and morphological characteristics. Although Multilocus Sequence Typing (MLST) currently represents the gold standard for unambiguous phylogroup classification, and individual strain identification, it is a labour and time-consuming technique. As a consequence, we have developed a multiplex touchdown PCR assay that will, in a single reaction, confirm species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA (all isolates), ATPase (type IA1, IA2, IC), sodA (type IA2, IB), atpD (type II) and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterised by MLST, and representing type IA1 (n=145), IA2 (n=20), IB (n=65), IC (n=7), II (n=45) and III (n=30), the multiplex displayed 100% sensitivity and 100% specificity for the detection of isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. The multiplex assay will provide researchers with a rapid, high-throughput and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, as well as a pre-screening tool to maximise the number of genetically diverse isolates selected for downstream, higher resolution sequence-based analyses.

CCAAT/enhancer binding protein α predicts poorer prognosis and prevents energy starvation-induced cell death in hepatocellular carcinoma

CCAAT enhancer binding protein α (C/EBPα) plays an essential role in cellular differentiation, growth, and energy metabolism. Here, we investigate the correlation between C/EBPα and hepatocellular carcinoma (HCC) patient outcomes and how C/EBPα protects cells against energy starvation. Expression of C/EBPα protein was increased in the majority of HCCs examined (191 pairs) compared with adjacent nontumor liver tissues in HCC tissue microarrays. Its upregulation was correlated significantly with poorer overall patient survival in both Kaplan-Meier survival (P = 0.017) and multivariate Cox regression (P = 0.028) analyses. Stable C/EBPα-silenced cells failed to establish xenograft tumors in nude mice due to extensive necrosis, consistent with increased necrosis in human C/EBPα-deficient HCC nodules. Expression of C/EBPα protected HCC cells in vitro from glucose and glutamine starvation-induced cell death through autophagy-involved lipid catabolism. Firstly, C/EBPα promoted lipid catabolism during starvation, while inhibition of fatty acid beta-oxidation significantly sensitized cell death. Secondly, autophagy was activated in C/EBPα-expressing cells, and the inhibition of autophagy by ATG7 knockdown or chloroquine treatment attenuated lipid catabolism and subsequently sensitized cell death. Finally, we identified TMEM166 as a key player in C/EBPα-mediated autophagy induction and protection against starvation.

CONCLUSION: The C/EBPα gene is important in that it links HCC carcinogenesis to autophagy-mediated lipid metabolism and resistance to energy starvation; its expression in HCC predicts poorer patient prognosis.

Analysis of wntless (WLS) expression in gastric, ovarian, and breast cancers reveals a strong association with HER2 overexpression

The oncogenic role of WNT is well characterized. Wntless (WLS) (also known as GPR177, or Evi), a key modulator of WNT protein secretion, was recently found to be highly overexpressed in malignant astrocytomas. We hypothesized that this molecule may be aberrantly expressed in other cancers known to possess aberrant WNT signaling such as ovarian, gastric, and breast cancers. Immunohistochemical analysis using a TMA platform revealed WLS overexpression in a subset of ovarian, gastric, and breast tumors; this overexpression was associated with poorer clinical outcomes in gastric cancer (P=0.025). In addition, a strong correlation was observed between WLS expression and human epidermal growth factor receptor 2 (HER2) overexpression. Indeed, 100% of HER2-positive intestinal gastric carcinomas, 100% of HER2-positive serous ovarian carcinomas, and 64% of HER2-positive breast carcinomas coexpressed WLS protein. Although HER2 protein expression or gene amplification is an established predictive biomarker for trastuzumab response in breast and gastric cancers, a significant proportion of HER2-positive tumors display resistance to trastuzumab, which may be in part explainable by a possible mechanistic link between WLS and HER2.

DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach

BACKGROUND: Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.

METHODS: The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.

RESULTS: A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.

CONCLUSIONS: High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.