Diagnostic and Prognostic Value of SHOX2 and SEPT9 DNA Methylation and Cytology in Benign,Paramalignant and Malignant Pleural Effusions

Pleural effusions (PE) are a common clinical problem. The discrimination between benign (BPE), malignant (MPE) and paramalignant (PPE) pleural effusions is highly important to ensure appropriate patient treatment. Today, cytology is the gold standard for diagnosing malignant pleural effusions. However, its sensitivity is limited due to the sometimes low abundance of tumor cells and the challenging assessment of cell morphology in cytological samples. This study aimed to develop and validate a diagnostic test, which allows for the highly specific detection of malignant cells in pleural effusions based on the DNA methylation biomarkers SHOX2 and SEPT9. A quantitative real-time PCR assay was developed which enabled the accurate and sensitive detection of SHOX2 and SEPT9 in PEs. Cytological and DNA methylation analyses were conducted in a case control study comprised of PEs from 114 patients (58 cases, 56 controls). Cytological analysis as well as SHOX2 and SEPT9 methylation resulted in 100% specificity. 21% of the cases were cytologically positive and 26% were SHOX2 or SEPT9 methylation positive. The combined analysis of cytology and DNA methylation resulted in an increase of 71% positively classified PEs from cancer patients as compared to cytological analysis alone. The absolute sensitivity of cytology and DNA methylation was not determinable due to the lack of an appropriate gold standard diagnostic for distinguishing between MPEs and PPEs. Therefore, it was unclear which PEs from cancer patients were malignant (containing tumor cells) and which PEs were paramalignant and resulted from benign conditions in cancer patients, respectively. Furthermore, DNA methylation analysis in PEs allowed the prognosis of the overall survival in cancer patients (Kaplan-Meier analysis, log rank test, p = 0.02 (SHOX2), p = 0.02 (SEPT9)). The developed test may be used as a diagnostic and prognostic adjunct to existing clinical and cytopathological investigations in patients with PEs of unclear etiology.     

Decavanadate displaces inositol 1,4,5-trisphosphate (IP3) from its receptor and inhibits IP3 induced Ca release in permeabilized pancreatic acinar cells

Inositol 1,4,5-trisphosphate (IP₃) induced Ca²⁺ release in digitonin permeabilized rat pancreatic acinar cells is specifically inhibited by decavanadate. The Ca²⁺ release induced with 0.18 μM IP₃ is half maximally inhibited with approximately 5 μM decavanadate. Complete inhibition is achieved with around 20 μM decavanadate. Removal of decavanadate from the permeabilized cells fully restores sensitivity towards IP₃, indicating the reversibility of the inhibition. Oligovanadate, which inhibits ATP dependent Ca²⁺ uptake into intracellular stores, does not influence IP₃ induced Ca²⁺ release. In order to reveal the mechanism underlying the effects of the different vanadate species, binding of IP₃ to the same cellular preparations was investigated. We found that binding of IP₃ to a high affinity receptor site (K_d approx. 1.2 nM) could be abolished by decavanadate but not by oligovanadate. With 0.5 μM decavanadate, IP₃ binding was half maximally inhibited. A similar potency of decavanadate was also found with adrenal cortex microsomes which bind IP₃ with the same affinity (K_d approx. 1.4 nM) as permeabilized pancreatic acinar cells. Labelled IP₃ was displaced from these subcellular membranes with similar kinetics by unlabelled IP₃ and decavanadate. The data suggest that the inhibitory action of decavanadate on IP₃ induced Ca²⁺ release is a consequence of its effect on binding of IP₃ to its receptor.     

Biophysical investigations of the dose-effect relationship in chromosome aberrations of human lymphocytes caused by Thorotrast deposits

Summary Thorotrast is a X-ray contrast medium which has been used in the ears 1930–1950. It is hardly ever eliminated from the body and is stored in the organs of the reticulohistiocytic system (RHS). Since Thorotrast contains all radionuclides of the thorium decay chain, the effect of internal irradiation by these radionuclides can be investigated in the so called Thorotrast patients. It is the purpose of this study to determine the radiation dose absorbed by the lymphocytes of the peripheral blood of these persons, and to correlate it with their chromosome aberration rate.Part I of the paper describes the physical aspects of dose evaluation. The chromosome aberration rates of Thorotrast patients were subjected to a repeated statistical test. They show a logarithmic normal distribution at a mean value of about seven dicentric chromosomes per 100 cells. The corresponding dose has to be determined. The method for evaluating size and distribution of Thorotrast conglomerates in the examined tissue is demonstrated, and the function and resolution power of the applied texture analysing system (TAS) is described. Size-distributions of Thorotrast conglomerates of lymph nodes from the neck, the lung and from the lower aorta (bifurcatio) are given.In the lymphatic system more than 90% of the absorbed dose in tissue is due to-particles. The computation method of calculating the self-absorption of-particles in the conglomerates and of calculating the annual doses in the lymph nodes is described. The values lie between 135 and 1200 rad/year. The contribution to irradiation from outside the lymphatic system can be neglected. The method of dose determination is discussed and compared with microdosimetric methods. With these methods, the dose of a lymphocyte caused by one hit of an-particle lies between 80 and 920 rad. An energy dissipation does not take place and the total energy emitted acts on the lymphocytes thus inducing chromosome aberrations.Dedicated to Professor Dr. Hermann Muth, Homburg (Saar), on the occasion of his 65th birthday     

Binding of Escherichia coli hemolysin and activation of the target cells is not receptor-dependent

Production of a single cysteine substitution mutant, S177C, allowed Escherichia coli hemolysin (HlyA) to be radioactively labeled with tritiated N-ethylmaleimide without affecting biological activity. It thus became possible to study the binding characteristics of HlyA as well as of toxin mutants in which one or both acylation sites were deleted. All toxins bound to erythrocytes and granulocytes in a nonsaturable manner. Only wild-type toxin and the lytic monoacylated mutant stimulated production of superoxide anions in granulocytes. An oxidative burst coincided with elevation of intracellular Ca(2+), which was likely because of passive influx of Ca(2+) through the toxin pores. Competition experiments showed that binding to the cells was receptor-independent, and preloading of cells with a nonlytic HlyA mutant did not abrogate the respiratory burst provoked by a subsequent application of wild-type HlyA. In contrast to a previous report, expression or activation of the beta(2) integrin lymphocyte function-associated antigen-1 did not affect binding of HlyA. We conclude that HlyA binds nonspecifically to target cells and a receptor is involved neither in causing hemolysis nor in triggering cellular reactions.     

Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.     

DNA damage response curtails detrimental replication stress and chromosomal instability induced by the dietary carcinogen PhIP

PhIP is an abundant heterocyclic aromatic amine (HCA) and important dietary carcinogen. Following metabolic activation, PhIP causes bulky DNA lesions at the C8-position of guanine. Although C8-PhIP-dG adducts are mutagenic, their interference with the DNA replication machinery and the elicited DNA damage response (DDR) have not yet been studied. Here, we analyzed PhIP-triggered replicative stress and elucidated the role of the apical DDR kinases ATR, ATM and DNA-PK_cs in the cellular defense response. First, we demonstrate that PhIP induced C8-PhIP-dG adducts and DNA strand breaks. This stimulated ATR-CHK1 signaling, phosphorylation of histone 2AX and the formation of RPA foci. In proliferating cells, PhIP treatment increased the frequency of stalled replication forks and reduced fork speed. Inhibition of ATR in the presence of PhIP-induced DNA damage strongly promoted the formation of DNA double-strand breaks, activation of the ATM-CHK2 pathway and hyperphosphorylation of RPA. The abrogation of ATR signaling potentiated the cell death response and enhanced chromosomal aberrations after PhIP treatment, while ATM and DNA-PK inhibition had only marginal effects. These results strongly support the notion that ATR plays a key role in the defense against cancer formation induced by PhIP and related HCAs.     

Heparin: role in protein purification and substitution with animal-component free material

Heparin is a highly sulfated polysaccharide which belongs to the family of glycosaminoglycans. It is involved in various important biological activities. The major biological purpose is the inhibition of the coagulation cascade to maintain the blood flow in the vasculature. These properties are employed in several therapeutic drugs. Heparin’s activities are associated with its interaction to various proteins. To date, the structural heparin-protein interactions are not completely understood. This review gives a general overview of specific patterns and functional groups which are involved in the heparin-protein binding. An understanding of the heparin-protein interactions at the molecular level is not only advantageous in the therapeutic application but also in biotechnological application of heparin for downstreaming. This review focuses on the heparin affinity chromatography. Diverse recombinant proteins can be successfully purified by this method. While effective, it is disadvantageous that heparin is an animal-derived material. Animal-based components carry the risk of contamination. Therefore, they are liable to strict quality controls and the validation of effective good manufacturing practice (GMP) implementation. Hence, adequate alternatives to animal-derived components are needed. This review examines strategies to avoid these disadvantages. Thereby, alternatives for the provision of heparin such as chemical synthesized heparin, chemoenzymatic heparin, and bioengineered heparin are discussed. Moreover, the usage of other chromatographic systems mimetic the heparin effect is reviewed.