Proteomics profiling identify CAPS as a potential predictive marker of tamoxifen resistance in estrogen receptor positive breast cancer

Background

Despite the success of tamoxifen since its introduction, about one-third of patients with estrogen (ER) and/or progesterone receptor (PgR) - positive breast cancer (BC) do not benefit from therapy. Here, we aim to identify molecular mechanisms and protein biomarkers involved in tamoxifen resistance.

Results

Using iTRAQ and Immobilized pH gradient-isoelectric focusing (IPG-IEF) mass spectrometry based proteomics we compared tumors from 12 patients with early relapses (<2 years) and 12 responsive to therapy (relapse-free > 7 years). A panel of 13 proteins (TCEAL4, AZGP1, S100A10, ALDH6A1, AHNAK, FBP1, S100A4, HSP90AB1, PDXK, GFPT1, RAB21, MX1, CAPS) from the 3101 identified proteins, potentially separate relapse from non-relapse BC patients. The proteins in the panel are involved in processes such as calcium (Ca²⁺) signaling, metabolism, epithelial mesenchymal transition (EMT), metastasis and invasion. Validation of the highest expressed proteins in the relapse group identify high tumor levels of CAPS as predictive of tamoxifen response in a patient cohort receiving tamoxifen as only adjuvant therapy.

Conclusions

This data implicate CAPS in tamoxifen resistance and as a potential predictive marker.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9080-y) contains supplementary material, which is available to authorized users.     

Optic Disc - Fovea Angle: The Beijing Eye Study 2011

Purpose

To determine the optic disc-fovea angle (defined as angle between the horizontal and the line between the optic disc center and the fovea) and to assess its relationships with ocular and systemic parameters.

Methods

The population-based cross-sectional Beijing Eye Study 2011 included 3468 individuals. A detailed ophthalmic examination was carried out. Using fundus photographs, we measured the disc-fovea angle.

Results

Readable fundus photographs were available for 6043 eyes of 3052 (88.0%) individuals with a mean age of 63.6±9.3 years (range: 50–91 years) and a mean axial length of 23.2±1.0 mm (range: 18.96–28.87 mm). Mean disc-fovea angle was 7.76 ± 3.63° (median: 7.65°; range: -6.3° to 28.9°). The mean inter-eye difference was 4.01 ± 2.94° (median: 3.49°; range: 0.00–22.3°). In multivariate analysis, larger disc-fovea angle was associated (regression coefficient r²: 0.08) with older age (P = 0.009; standardized regression coefficient beta: 0.05), thinner RNFL in the nasal superior sector (P<0.001; beta: -0.17), superior sector (P<0.001; beta: -0.10) and temporal superior sector (P<0.001; beta: -0.11) and thicker RNFL in the inferior sector (P<001; beta: 0.13), nasal inferior sector (P<001; beta: 0.13) and nasal sector (P = 0.007; beta: 0.06), higher prevalence of retinal vein occlusion (P = 0.02; beta: 0.04), and with larger cylindrical refractive error (P = 0.04; beta: 0.04).

Conclusions

The optic disc-fovea angle markedly influences the regional distribution of the RNFL thickness pattern. The disc-fovea angle may routinely be taken into account in the morphological glaucoma diagnosis and in the assessment of structure-function relationship in optic nerve diseases. Future studies may address potential associations between a larger disc-fovea angle and retinal vein occlusions and between the disc-fovea angle and the neuroretinal rim shape.     

Comparison of Extended-Spectrum β-Lactamase (ESBL) CTX-M Genotypes in Franklin Gulls from Canada and Chile

Migratory birds have been suggested to contribute to long-distance dispersal of antimicrobial resistant bacteria, but tests of this hypothesis are lacking. In this study we determined resistance profiles and genotypes of ESBL-producing bacteria in randomly selected Escherichia coli from Franklin´s gulls (Leucophaeus pipixcan) at breeding sites in Canada and compared with similar data from the gulls'' wintering grounds in Chile. Resistant E. coli phenotypes were common, most notably to ampicillin (30.1%) and cefadroxil (15.1%). Furthermore, 17.0% of the gulls in Canada carried ESBL producing bacteria, which is higher than reported from human datasets from the same country. However, compared to gulls sampled in Chile (30.1%) the prevalence of ESBL was much lower. The dominant ESBL variants in Canada were bla _CTX-M-14 and bla _CTX-M-15 and differed in proportions to the data from Chile. We hypothesize that the observed differences in ESBL variants are more likely linked to recent exposure to bacteria from anthropogenic sources, suggesting high local dissemination of resistant bacteria both at breeding and non-breeding times rather than a significant trans-hemispheric exchange through migrating birds.     

Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders

Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n = 396 patients and n = 659 controls). We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4%) patients and in 16 of 1,090 (1.5%) controls (P = 0.004, OR = 2.37, 95% CI = 1.23–4.70). In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P = 0.0013). Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11–q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the “multiple hit model” for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD.     

Optimization of pH,Temperature and Inoculum Ratio for the Production of β‐D‐Galactosidase by Kluyveromyces marxianus Using a Lactose‐free Medium

The pH, temperature and inoculum ratio for the production of β‐galactosidase by Kluyveromyces marxianus CDB 002 were optimized using sugar‐cane molasses (100 g/l) in a lactose‐free medium. The temperature optimum was evaluated in the range from 28–37 °C. Lactase production was initiated after substrate consumption indicating a reversible enzyme inhibition or catabolic repression. The specific enzyme activity after 45 h was between 456.3 U/g cell mass (37 °C) and 733.3 U/g (34 °C), whereas the highest volumetric activity was obtained at 30 °C: 21.8 U/ml. This is generally consistent with results from other authors that used whey as a carbon source. Ethanol as a by‐product reached its maximum concentration after 10–14 h (31.1–40.5 g/l), but was completely consumed afterwards. A pH of 5.5 without further control gave the best production rate for lactase (484.4 U/l × h). In this process, the pH was stable during cell growth at 5.5 and then went up to pH 7.2 after 45 h. At a fixed pH of 5.5 or 6.5, the production rates achieved 313.3 U/l × h and 233.3 U/ l × h, respectively. These results differed from those of other authors, who suggested a fixed pH at 7.0 using whey as a carbon source. There were no significant differences between inoculum ratios of 1% [v/v] and 10% [v/v] so that 1% is the preferable ratio as it is cheaper. Yeast extract (10 g/l) and peptone (20 g/l) were used as the vitamin and nitrogen source, respectively, for the studies of temperature and pH. These were substituted by corn steep liquor (100 g/l) for inoculum ratio experiments. Production of lactase using sugar cane molasses in a lactose‐free medium gave better enzyme productivity rates than obtained by other authors using whey. The optimum conditions for β‐galactosidase synthesis were a temperature of 30–34 °C and an inoculum ratio of 1% [v/v], an initial pH of 5.5 without any further control or a control of 5.5 during cell growth. Then the pH was raised up to 7.     

Biodegradation and appearance of plastic treated solid wood

The biodegradation of plastics and wood with different susceptibility to fungal attack have in this study been compared in order to show the biodegradability in relation to the properties of plastic and solid wood. Wood blocks of Scots pine and English Oak were treated with biodegradable aliphatic polyester, polycaprolactone, and a non-biodegradable aromatic thermoplastic, polystyrene. The plastics were applied to the wood samples dissolved in an organic solvent and thereafter the treated wood samples were exposed to brown rot decay (Postia placenta) in an agar plate test for 8 weeks. The polycaprolactone treatments did not result in wood protection, whereas polystyrene treatments provided a protection from fungal attack. Both plastics are transparent and after treatment the solid wood blocks retained their natural wood appearance with a somewhat darker shinier surface.

Scientific relevance

Usually commercial wood-plastic composites are made using wood derived lignocellulose-fibers melt-blended in a screw extruder with a plastic matrix, and then the resulting material is mainly a plastic (in terms of properties and appearance) which contain some lignocellulose. We have instead used solid wood to which we have added transparent plastics, which preserve the unique and precious esthetic value of natural wood. This study describes the biodegradation of two (a more and a less resistant) wood species in combination with a biodegradable and a non-biodegradable plastic. The purpose was to study any synergetic effect in the biodegradation property between solid wood and plastic since there is a socio-environmental desire to use biodegradable plastics of renewable raw material for e.g. composite material. We show that both the wood and the plastic influence the biodegradation, for example by using an easily degraded European wood specie in combination with a biodegradable plastic (polycarolactone) no protection of the wood is obtained, whereas a relative small amount recalcitrant plastic (polystyrene) can somewhat protect both Scots pine and Oak wood without significantly compromising their appearance.     

Patenting of university and non-university public research organisations in Germany: evidence from patent applications for medical research results

Background

Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations.

Methods/Principal Findings

We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47%) of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable.

Conclusions

We search, process and analyse patent applications from publicly accessible databases. Internationally mounting evidence questions the viability of policies to increase commercial exploitation of publicly funded research results. To evaluate the outcome of research policies a transparent evidence base for public debate is needed in Germany.     

Djinga cheekii sp. nov. (Podostemaceae) from Cameroon

A new species is added to the monotypic African genus Djinga. Djinga cheekii Ghogue, Huber & Rutish. (Podostemaceae) is described as a new species from Cameroon (Littoral Province) and its morphological affinities and conservation status are assessed. The main distinguishing characters are: stamens 2 (not 1 as in D. felicis), flower buds inside spathella strongly inclined (not only slightly inclined as in D. felicis), and stems lacking or only up to 6 mm long (not up to > 6 cm as in D. felicis). A molecular analysis revealed that D. cheekii is sister to D. felicis, and both together are sister to Ledermanniella linearifolia and L. pusilla which show completely inverted flower buds inside the spathella, as typical for the large and still artificial genus Ledermanniella.     

Ultrastructural analysis reveals striking differences of intercellular contact lengths in bovine embryos produced in vivo, in vitro and by somatic cell nuclear transfer

Cellular coherence and communication, thus cell-to-cell contact is an indispensable premise to sustain the formation of complex, multi-cellular organisms. We have analyzed intercellular contact lengths in NT-cloned bovine embryos compared to the in vivo or in vitro produced counterparts. Therefore, ultrastructural analysis was carried out by transmission electron microscopy (TEM) at the 8-cell and blastocyst stage of development. To obtain embryos generated in vivo, oviducts of superovulated cows were flushed 3 days after insemination, subsequent to slaughter. Standard in vitro maturation (IVM) and -fertilization (IVF) were utilized to obtain in vitro embryos. Cloned embryos by somatic nuclear transfer were produced by the handmade cloning (HMC) procedure. The points of apposition/focal contact points (CPs) between the blastomeres were of the shortest order in cloned embryos (236 +/- 135 nm) and of highest order in the in vivo produced embryos (2,085 +/- 1,540 nm), although no significant differences regarding the blastomere sizes in the various groups of 8-cell embryos could be established. In summary, the CP lengths in case of in vitro and in vivo 8-cell embryos were, on an average, five or nine times longer, respectively, than in the case of the cloned embryos. These differences of CP lengths vanished in embryos reaching the blastocyst stage of embryonic development in all the three groups of embryos. The observed differences of intercellular contact length at distinct stages of embryonic development could be responsible for differences in intercellular communication between the blastomeres at the beginning of cellular differentiation. These may be one reason for the lower developmental competence of cloned (NT) embryos.     

The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry

We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein modifications. The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. The Mass Distance Fingerprint is calculated from high accuracy measured peptide masses. For the data sets used in this study, known mass differences are detected at electron mass accuracy or better. The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifications. Both modified and unmodified peptides have to be present in the sample to be detected. The method can be used for automated detection of chemical/post-translational modifications, quality control of experiments and labeling approaches, and to control the modification settings of protein identification tools. The algorithm is implemented as a web application and is distributed as open source software.