Chromosomal translocations in cancer

Genetic alterations in DNA can lead to cancer when it is present in proto-oncogenes, tumor suppressor genes, DNA repair genes etc. Examples of such alterations include deletions, inversions and chromosomal translocations. Among these rearrangements chromosomal translocations are considered as the primary cause for many cancers including lymphoma, leukemia and some solid tumors. Chromosomal translocations in certain cases can result either in the fusion of genes or in bringing genes close to enhancer or promoter elements, hence leading to their altered expression. Moreover, chromosomal translocations are used as diagnostic markers for cancer and its therapeutics. In the first part of this review, we summarize the well-studied chromosomal translocations in cancer. Although the mechanism of formation of most of these translocations is still unclear, in the second part we discuss the recent advances in this area of research.     

On the replication of genetic associations: timing can be everything!

The failure of researchers to replicate genetic-association findings is most commonly attributed to insufficient statistical power, population stratification, or various forms of between-study heterogeneity or environmental influences.(1) Here, we illustrate another potential cause for nonreplications that has so far not received much attention in the literature. We illustrate that the strength of a genetic effect can vary by age, causing "age-varying associations." If not taken into account during the design and the analysis of a study, age-varying genetic associations can cause nonreplication. By using the 100K SNP scan of the Framingham Heart Study, we identified an age-varying association between a SNP in ROBO1 and obesity and hypothesized an age-gene interaction. This finding was followed up in eight independent samples comprising 13,584 individuals. The association was replicated in five of the eight studies, showing an age-dependent relationship (one-sided combined p = 3.92 x 10(-9), combined p value from pediatric cohorts = 2.21 x 10(-8), combined p value from adult cohorts = 0.00422). Furthermore, this study illustrates that it is difficult for cross-sectional study designs to detect age-varying associations. If the specifics of age- or time-varying genetic effects are not considered in the selection of both the follow-up samples and in the statistical analysis, important genetic associations may be missed.     

Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE

Alzheimer's disease (AD) is a genetically complex and heterogeneous disorder. To date four genes have been established to either cause early-onset autosomal-dominant AD (APP, PSEN1, and PSEN2(1-4)) or to increase susceptibility for late-onset AD (APOE5). However, the heritability of late-onset AD is as high as 80%, (6) and much of the phenotypic variance remains unexplained to date. We performed a genome-wide association (GWA) analysis using 484,522 single-nucleotide polymorphisms (SNPs) on a large (1,376 samples from 410 families) sample of AD families of self-reported European descent. We identified five SNPs showing either significant or marginally significant genome-wide association with a multivariate phenotype combining affection status and onset age. One of these signals (p = 5.7 x 10(-14)) was elicited by SNP rs4420638 and probably reflects APOE-epsilon4, which maps 11 kb proximal (r2 = 0.78). The other four signals were tested in three additional independent AD family samples composed of nearly 2700 individuals from almost 900 families. Two of these SNPs showed significant association in the replication samples (combined p values 0.007 and 0.00002). The SNP (rs11159647, on chromosome 14q31) with the strongest association signal also showed evidence of association with the same allele in GWA data generated in an independent sample of approximately 1,400 AD cases and controls (p = 0.04). Although the precise identity of the underlying locus(i) remains elusive, our study provides compelling evidence for the existence of at least one previously undescribed AD gene that, like APOE-epsilon4, primarily acts as a modifier of onset age.     

Heavy metals modify costs of reproduction and clonal growth in the stoloniferous herb Potentilla anserina

We examined costs of sexual reproduction and clonal propagation, and their consequences for resource allocation in the clonal stoloniferous herb, Potentilla anserina, a typical pioneer species in disturbed areas. We used heavy-metal treatment in soil to create unfavourable growing conditions, because costs of reproduction are more likely to be expressed when resources are limited. We also studied whether heavy metals affect the plasticity of clonal growth form that enables the plants to avoid poor growing conditions. Ramets collected from field were grown in a greenhouse under the heavy-metal treatment consisting of a control and two levels of heavy-metals added in soil. Clonal propagation was costly in terms of total biomass of flowering ramets. Also the costs of sexual reproduction were detected in flowering ramets. Contrary to our predictions, the costs of flower production were visible in the control but not in the heavy-metal contaminated plants. Only the flowering ramets were able to produce longer stolons under heavy-metal stress, but the stolon biomass was not affected by heavy metals. Results indicate that clonal propagation and sexual reproduction may be costly for P. anserina. However, the costs are modified by heavy-metal contamination.Co-ordinating editor: J. Tuomi     

Intraclonal variation in defence substances and palatability: a study on Carex and lemmings

Clonal sedges consist of integrated ramets at different development stages. Many of these sedges are important food for herbivores, yet differences in herbivore preferences and defence allocation between ramet development stages have not previously been evaluated. In this study we investigated intraclonal ramet variation in level of plant defence and nutrient compounds and intraclonal ramet preferences by lemmings ( Lemmus trimucronatus ) in field samples of a rhizomatous sedge ( Carex stans ). Plant defence was measured as the level of proteinase inhibitor activity (PIA) and the ratio of PIA to soluble plant proteins (SPP), whereas plant nutrients were measured as the level of soluble plant sugars (SPS) and SPP. Flowering ramets generally had a higher content of defence compared to vegetative ramets, which is consistent with the optimal defence theory predicting that defence compounds are allocated to the ramet stage of the highest fitness value. Compared to vegetative ramets, the flowering ramets had a lower content of SPP and a higher content of SPS. The lemmings showed preference differences between the ramet development stages, and to a large extent the ramet content of defence compounds and nutrient compounds covaried with these preferences in the predicted way. This study shows that defence allocation between ramet development stages of the clonal sedge Carex conforms to predictions of the optimal defence theory.     

The importance of hardening and winter temperature for growth in mountain birch populations

Seedlings of five mountain birch populations (Betula pubescens Ehrh. ssp. czerepanovii) from Fennoscandia and Iceland were raised and grown at natural daylengths at Tromsø, Norway (69°N) and different temperatures during late summer and fall season, followed by winter temperature treatment at ambient and +4 °C above ambient temperatures at Bergen, Norway (60°N). The experiment took place during two seasons (2000/01 and 2001/02). The following summer shoot and biomass growth were reduced as a result of winter warming and subsequent premature dehardening in early flushing provenances and treatments. Biomass increased in plants grown at low hardening temperature when compared with high temperature treatment. As a conclusion, increased winter temperatures would tend to increase the risk of spring frost damage and reduce growth in birch seedlings, because the differences between the frost hardening and ambient temperatures are decreasing, and because the time from budbreak to dehardening is shortened. The results are discussed in relation to simultaneous experiments with frost hardiness in the same populations and treatments.     

Pollen modelling, palaeoecology and archaeology: virtualisation and/or visualisation of the past?

Recent developments in pollen modelling and landscape reconstruction have the potential to have a profound impact on our understanding of landscape change related to human activity. Initial findings have already revealed the weaknesses of a number of key assumptions previously made about pollen–landscape relationships. Close interrelationships exist between landscape reconstruction based on pollen analysis and archaeology, and model-based developments raise a range of pertinent issues for both disciplines. These include the way in which past vegetation patterning is conceptualised (the patch vs. the matrix), the nature of the underlying physical environment in vegetation placement, the development of hypothesis-led approaches and the scale of landscapes under consideration. This paper discusses these issues, and also raises questions concerning the meaning of landscape. It may be erroneous to term pollen-based reconstructions as landscapes given the heavily charged meaning of the word as understood by companion and end user disciplines.     

LKB1 in endothelial cells is required for angiogenesis and TGFbeta-mediated vascular smooth muscle cell recruitment

Inactivation of the tumor suppressor kinase Lkb1 in mice leads to vascular defects and midgestational lethality at embryonic day 9-11 (E9-E11). Here, we have used conditional targeting to investigate the defects underlying the Lkb1(-/-) phenotype. Endothelium-restricted deletion of Lkb1 led to embryonic death at E12.5 with a loss of vascular smooth muscle cells (vSMCs) and vascular disruption. Transforming growth factor beta (TGFbeta) pathway activity was reduced in Lkb1-deficient endothelial cells (ECs), and TGFbeta signaling from Lkb1(-/-) ECs to adjacent mesenchyme was defective, noted as reduced SMAD2 phosphorylation. The addition of TGFbeta to mutant yolk sac explants rescued the loss of vSMCs, as evidenced by smooth muscle alpha actin (SMA) expression. These results reveal an essential function for endothelial Lkb1 in TGFbeta-mediated vSMC recruitment during angiogenesis.     

Optimisation of supercritical fluid extraction of indole alkaloids from Catharanthus roseus using experimental design methodology--comparison with other extraction techniques

Response surface modelling, using MODDE 6 software for Design of Experiments and Optimisation, was applied to optimise supercritical fluid extraction (SFE) conditions for the extraction of indole alkaloids from the dried leaves of Catharanthus roseus. The effects of pressure (200-400 bar), temperature (40-80 degrees C), modifier concentration (2.2-6.6 vol%) and dynamic extraction time (20-60 min) on the yield of alkaloids were evaluated. The extracts were analysed by high-performance liquid chromatography and the analytes were identified using ion trap-electrospray ionisation-mass spectrometry. The method was linear for alkaloid concentration in the range 0.18-31 microg/mL. The limits of detection and quantification for catharanthine, vindoline, vinblastine and vincristine were 0.2, 0.15, 0.1 and 0.08 microg/mL and 2.7, 2.0, 1.3 and 1.1 microg/g, respectively. The dry weight content of major alkaloids in the plants were compared using different extraction methods, i.e. SFE, Soxhlet extraction, solid-liquid extraction with sonication and hot water extraction at various temperatures. The extraction techniques were also compared in terms of reproducibility, selectivity and analyte recoveries. Relative standard deviations for the major alkaloids varied from 4.1 to 17.5% in different extraction methods. The best recoveries (100%) for catharanthine were obtained by SFE at 250 bar and 80 degrees C using 6.6 vol% methanol as modifier for 40 min, for vindoline by Soxhlet extraction using dichloromethane in a reflux for 16 h, and for 3',4'-anhydrovinblastine by solid-liquid extraction using a solution of 0.5 m sulphuric acid and methanol (3:1 v/v) in an ultrasonic bath for 3 h.     

Identification of the human cytochrome P450 enzymes involved in the in vitro biotransformation of lynestrenol and norethindrone

This study examined the cytochrome P450 (CYP) enzyme selectivity of in vitro bioactivation of lynestrenol to norethindrone and the further metabolism of norethindrone. Screening with well-established chemical inhibitors showed that the formation of norethindrone was potently inhibited by CYP3A4 inhibitor ketoconazole (IC(50)=0.02 microM) and with CYP2C9 inhibitor sulphaphenazole (IC(50)=2.13 microM); the further biotransformation of norethindrone was strongly inhibited by ketoconazole (IC(50)=0.09 microM). Fluconazole modestly inhibited both lynestrenol bioactivation and norethindrone biotransformation. Lynestrenol bioactivation was mainly catalysed by recombinant human CYP2C9, CYP2C19 and CYP3A4; rCYP3A4 was responsible for the hydroxylation of norethindrone. A significant correlation was observed between norethindrone formation and tolbutamide hydroxylation, a CYP2C9-selective activity (r=0.63; p=0.01). Norethindrone hydroxylation correlated significantly with model reactions of CYP2C19 and CYP3A4. The greatest immunoinhibition of lynestrenol bioactivation was seen in incubations with CYP2C-Ab. The CYP3A4-Ab reduced norethindrone hydroxylation by 96%. Both lynestrenol and norethindrone were weak inhibitors of CYP2C9 (IC(50) of 32 microM and 46 microM for tolbutamide hydroxylation, respectively). In conclusion, CYP2C9, CYP2C19 and CYP3A4 are the primary cytochromes in the bioactivation of lynestrenol in vitro, while CYP3A4 catalyses the further metabolism of norethindrone.