Etiologic impact of known cancer susceptibility genes

The impact of a gene variant on the population burden of cancer can be measured by the population attributable fraction (PAF), which depends on the risk conferred by the variant, genotype relative risk (GRR), the frequency of the variant in the population and the mode of inheritance. PAF defines the proportion of the disease in the study population due to a gene variant, hence the synonymic term, etiologic fraction. After a review of the literature, 27 confirmed cancer susceptibility genes, groups of genes and loci were selected for analysis on the basis of their prevalence and availability of validated GRR data. The covered variants represent the most common established cancer susceptibility genes; those not included have marginal PAFs on common cancers. The PAF due to known genes at the covered sites was highest for brain hemangioblastoma (19%), conferred by the VHL gene. For colorectal cancer, the PAF estimates amounted to 7.0%. Including genes and identified loci from whole genome scans, PAFs for both breast and prostate cancers summed up to 70%. The derived estimates should rectify common overstatements on the contribution of individual high penetrance genes on common cancers at the population level. More dramatically, the estimates show the large PAFs conferred by the recently discovered breast, prostate and colorectal cancer loci, most of which are not known to alter coding sequences or expression patterns and they thus act through yet unexplained mechanisms. Although of low risk, these common variants appear to explain large proportions of breast and prostate cancers in the population.     

A gene-wide investigation on polymorphisms in the ABCG2/BRCP transporter and susceptibility to colorectal cancer

ATP-binding cassette (ABC) transporters actively export a wide variety of molecules from cells, contributing to reduce the local cellular burden of toxic compounds. ABCG2/BCRP is abundantly expressed in epithelial cells of the intestine and colon. The expression and activity of this transporter in the gut differ between individuals, due at least in part to genetic polymorphisms, which may thus affect the risk of colorectal cancer (CRC). We selected 15 tagging SNPs, covering all the known genetic variation of the gene, and typed them in 680 CRC cases and 593 controls. We found that heterozygous carriers of the minor alleles of SNPs rs2622621 and rs1481012 had a decreased risk of CRC, respectively, with odds ratios of 0.73 (95% confidence interval 0.56-0.94; P(value)=0.017), and 0.72 (95% CI 0.53-0.97; P(value)=0.03). Thus, we found no strong and clearcut association between ABCG2 polymorphisms and CRC risk. To our knowledge this is the first report on ABCG2 and CRC risk.     

Human-mediated lineage admixture in an expanding Ponto-Caspian crustacean species <Emphasis Type="Italic">Paramysis lacustris</Emphasis> created a novel genetic stock that now occupies European waters

Identifying the origins and colonization routes of alien species is critical to understanding the mechanisms, consequences and management of invasions. This study aims to demonstrate and explain conflicting genetic signals in a widespread invasive Ponto-Caspian mysid Paramysis lacustris using mitochondrial DNA and microsatellite markers. Native Black Sea populations of P. lacustris are divided into three distinct phylogeographic groups: Danube–Dniester region, coastal Danube lakes, and Dnieper River delta. In the 1950s–1970s the species has been extensively used for relatively well documented transplantations in Eastern Europe. However, the populations in the newly established distribution area do not match any of the known native groups, and their genetic signal does not correspond with the recorded transplantation history. Using Bayesian Approximate Computation we explore alternative scenarios that could explain the unexpected mitochondrial and nuclear signals in the introduced populations. We suggest that reservoir construction and break-up of natural dispersal barriers on the River Dnieper have brought about a novel stock, probably admixed from a previously isolated and unknown “relict” population in the middle Dnieper and the genetically distinct Dnieper delta lineage. Through further intentional transfers this new P. lacustris lineage is now widely present in Eastern Europe and is likely to have new gene and trait combinations. The conflicting mitochondrial-nuclear signal in non-native populations also highlights the importance of using multiple genetic markers when tracing invasion sources and pathways.     

Vasodepressor reaction induced by inferior vena caval occlusion and isoproterenol.

Testing for the susceptibility for vasodepressor reaction in humans involves the combination of restriction of venous return by passive upright tilting and the administration of isoproterenol. To explore the basis of the vasodepressor test in humans, the present experiment examined whether a reduced cardiac volume coupled with adrenergic stimulation causes a vasodepressor reaction in rats. Vasodepressor reaction was defined as paradoxical heart rate slowing in conjunction with hypotension during inferior vena caval occlusion. Inferior vena caval occlusion was performed for 60 s and the maximum changes in R-R were measured during seven states as follows. (A) Under control conditions inferior vena caval occlusion alone accelerated the rate in 32 of 32 rats (delta R-R, -13.9 +/- 1.7 ms, p less than 0.001). (B) When inferior vena caval occlusion was performed during an infusion of isoproterenol (0.5-1.0 micrograms.min-1), a vasodepressor reaction was observed in all rats as the heart rate slowed (delta R-R, +138.1 +/- 14.8 ms, p less than 0.001). The vasodepressor reaction was further examined during isoproterenol and inferior vena caval occlusion under five additional states. (C) After atropine the vasodepressor reaction was unchanged (delta R-R, +132.7 +/- 24.8 ms, p less than 0.001). (D) After bilateral vagotomy the paradoxical slowing was eliminated. (E) After intrapericardial lidocaine the paradoxic slowing was eliminated. (F) After bilateral stellectomy nonsignificant slowing was still present, but this was markedly reduced when compared with B (p less than 0.001). (G) Following chronic chemical sympathetic denervation with 6-hydroxydopamine the paradoxic bradycardia was eliminated. Conclusions: (1) Reduced cardiac volume combined with adrenergic stimulation can stimulate a vasodepressor reaction; (2) the vasodepressor reaction requires signalling by the afferent but not efferent vagal fibers; (3) the bradycardia is mainly due to withdrawal of sympathetic efferent tone.     

A cross-scale framework to support a mechanistic understanding and modelling of marine climate-driven species redistribution,from individuals to communities

Climate-driven species redistribution is pervasive and accelerating, yet the complex mechanisms at play remain poorly understood. The implications of large-scale species redistribution for natural systems and human societies have resulted in a large number of studies exploring the effects on individual species and ecological communities worldwide. Whilst many studies have investigated discrete components of species redistribution, the integration required for a more complete mechanistic understanding is lacking. In this paper, we provide a framework for synthesising approaches to more robustly understand and predict marine species redistributions. We conceptualise the stages and processes involved in climate-driven species redistribution at increasing levels of biological organisation, and synthesize the laboratory, field and modelling approaches used to study redistribution related processes at individual, population and community levels. We then summarise links between scales of biological organisation and methodological approaches in a hierarchical framework that represents an integrated mechanistic assessment of climate-driven species redistributions. In a rapidly expanding field of research, this framework provides direction for: 1) guiding future research, 2) highlighting key knowledge gaps, 3) fostering data exchange and collaboration between disciplines and 4) improving shared capacity to predict and therefore, inform the proactive management of climate impacts on natural systems.     

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I,II, VII,XII, and XIII

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation.     

A Coding IRAK2 Protein Variant Compromises Toll-like receptor (TLR) Signaling and Is Associated with Colorectal Cancer Survival

Within innate immune signaling pathways, interleukin-1 receptor-associated kinases (IRAKs) fulfill key roles downstream of multiple Toll-like receptors and the interleukin-1 receptor. Although human IRAK4 deficiency was shown to lead to severe immunodeficiency in response to pyogenic bacterial infection during childhood, little is known about the role of human IRAK2. We here identified a non-synonymous IRAK2 variant, rs35060588 (coding R214G), as hypofunctional in terms of NF-κB signaling and Toll-like receptor-mediated cytokine induction. This was due to reduced ubiquitination of TRAF6, a key step in signal transduction. IRAK2 rs35060588 occurs in 3–9% of individuals in different ethnic groups, and our studies suggested a genetic association of rs35060588 with colorectal cancer survival. This for the first time implicates human IRAK2 in a human disease and highlights the R214G IRAK2 variant as a potential novel and broadly applicable biomarker for disease or as a therapeutic intervention point.     

The balance between heritable and environmental aetiology of human disease

The Human Genome Project and the ensuing International HapMap Project were largely motivated by human health issues. But the distance from a DNA sequence variation to a novel disease gene is considerable; for complex diseases, closing this gap hinges on the premise that they arise mainly from heritable causes. Using cancer as an example of complex disease, we examine the scientific evidence for the hypothesis that human diseases result from interactions between genetic variants and the environment.     

Acute changes in intermediary metabolism in cerebellum and contralateral hemisphere following middle cerebral artery occlusion in rat

Focal ischemia leads to functional deafferentation of regions connected to the ischemic area via fiber tracts. Using i.v. administration of ¹³C-labeled glucose and acetate combined with ex vivo ¹³C MR spectroscopy and HPLC of brain extracts we identify the effect of middle cerebral artery occlusion (MCAO) on neurotransmitter synthesis and turnover, and on neuro-astrocytic interactions in the non-ischemic cerebellum and in contralesional lateral caudoputamen plus lower parietal cortex (LPC), and upper frontoparietal cortex (UFPCx) in the rat after 30, 60, 120 and 240 min of ischemia. In all regions, there was a significant persisting loss of glutamate, and in LCP and UFPCx also of glutamine, but only in LCP was GABA reduced at all times. Metabolism and blood flow were uncoupled in all regions. In cerebellum, glucose metabolism as well as utilization of intermediates derived from astrocytic tricarboxylic acid cycle activity were significantly decreased at all times in both glutamatergic and GABAergic neurons. In LCP and UFPCx, there were normal or increased enrichment in glutamate and GABA from glucose. Glutamate derived from astrocytic acetate metabolism was increased, but GABA synthesis from acetate was initially impaired. The results showed that both the type of afferent connection, i.e., glutamatergic and/or GABAergic, and local cytoarchitecture, determined the effect MCAO had on metabolic activity in the non-ischemic regions. In conclusion, it was primarily excitatory input into non-ischemic regions that was affected by MCAO, perhaps enabling resetting of the excitatory/inhibitory balance, aiding reshaping of the receptive fields and thus facilitating recovery.     

Unveiling the spatial distribution of aflatoxin B1 and plant defense metabolites in maize using AP-SMALDI mass spectrometry imaging

In order to cope with the presence of unfavorable compounds, plants can biotransform xenobiotics, translocate both parent compounds and metabolites, and perform compartmentation and segregation at the cellular or tissue level. Such a scenario also applies to mycotoxins, fungal secondary metabolites with a pre-eminent role in plant infection. In this work, we aimed to describe the effect of the interplay between Zea mays (maize) and aflatoxin B1 (AFB1) at the tissue and organ level. To address this challenge, we used atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) to investigate the biotransformation, localization and subsequent effects of AFB1 on primary and secondary metabolism of healthy maize plants, both in situ and from a metabolomics standpoint. High spatial resolution (5 µm) provided fine localization of AFB1, which was located within the root intercellular spaces, and co-localized with its phase-I metabolite aflatoxin M2. We provided a parallel visualization of maize metabolic changes, induced in different organs and tissues by an accumulation of AFB1. According to our untargeted metabolomics investigation, anthocyanin biosynthesis and chlorophyll metabolism in roots are most affected. The biosynthesis of these metabolites appears to be inhibited by AFB1 accumulation. On the other hand, metabolites found in above-ground organs suggest that the presence of AFB1 may also activate the biochemical response in the absence of an actual fungal infection; indeed, several plant secondary metabolites known for their antimicrobial or antioxidant activities were localized in the outer tissues, such as phenylpropanoids, benzoxazinoids, phytohormones and lipids.