An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer

Cancer genomes contain many aberrant gene fusions-a few that drive disease and many more that are nonspecific passengers. We developed an algorithm (the concept signature or 'ConSig' score) that nominates biologically important fusions from high-throughput data by assessing their association with 'molecular concepts' characteristic of cancer genes, including molecular interactions, pathways and functional annotations. Copy number data supported candidate fusions and suggested a breakpoint principle for intragenic copy number aberrations in fusion partners. By analyzing lung cancer transcriptome sequencing and genomic data, we identified a novel R3HDM2-NFE2 fusion in the H1792 cell line. Lung tissue microarrays revealed 2 of 76 lung cancer patients with genomic rearrangement at the NFE2 locus, suggesting recurrence. Knockdown of NFE2 decreased proliferation and invasion of H1792 cells. Together, these results present a systematic analysis of gene fusions in cancer and describe key characteristics that assist in new fusion discovery.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling

During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated human platelets. We analyzed ten independent human samples and identified a total of 1507 unique proteins in platelets. This is the most comprehensive platelet proteome assembled to date and includes 190 membrane-associated and 262 phosphorylated proteins, which were identified via independent proteomic and phospho-proteomic profiling. We used this proteomic dataset to create a platelet protein-protein interaction (PPI) network and applied novel contextual information about the phosphorylation step to introduce limited directionality in the PPI graph. This newly developed contextual PPI network computationally recapitulated an integrin signaling pathway. Most importantly, our approach not only provided insights into the mechanism of integrin αIIbβ3 activation in resting platelets but also provides an improved model for analysis and discovery of PPI dynamics and signaling pathways in the future.

Predicting meiotic pathways in human fetal oogenesis

Gene function prediction has proven valuable in formulating testable hypotheses. It is particularly useful for exploring biological processes that are experimentally intractable, such as meiotic initiation and progression in the human fetal ovary. In this study, we developed the first functional gene network for the human fetal ovary, HFOnet, by probabilistically integrating multiple genomic features using a naïve Bayesian model. We demonstrated that this network could accurately recapture known functional connections between genes, as well as predict new connections. Our findings suggest that known meiosis-specific genes (i.e., with functions only in meiotic processes in the germ cells) make either no or a few functional connections but are highly clustered with neighbor genes. In contrast, known nonspecific meiotic genes (i.e., with functions in both meiotic and nonmeiotic processes in the germ cells and somatic cells) exhibit numerous connections but low clustering coefficients, indicating their role as central modulators of diverse pathways, including those in meiosis. We also predicted novel genes that may be involved in meiotic initiation and DNA repair. This global functional network provides a much-needed framework for exploring gene functions and pathway components in early human female meiosis that are difficult to tackle by traditional in vivo mammalian genetics.

Identification of functionally related genes using data mining and data integration: a breast cancer case study

Background

The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involved in regulating a cell, it is important to identify the set of genes to which it interacts with to determine cell function. In this context, the mining and the integration of a large amount of publicly available data, regarding the transcriptome and the proteome states of a cell, are a useful resource to complement biological research.

Results

We describe an approach for the identification of genes that interact with each other to regulate cell function. The strategy relies on the analysis of gene expression profile similarity, considering large datasets of expression data. During the similarity evaluation, the methodology determines the most significant subset of samples in which the evaluated genes are highly correlated. Hence, the strategy enables the exclusion of samples that are not relevant for each gene pair analysed. This feature is important when considering a large set of samples characterised by heterogeneous experimental conditions where different pools of biological processes can be active across the samples. The putative partners of the studied gene are then further characterised, analysing the distribution of the Gene Ontology terms and integrating the protein-protein interaction (PPI) data. The strategy was applied for the analysis of the functional relationships of a gene of known function, Pyruvate Kinase, and for the prediction of functional partners of the human transcription factor TBX3. In both cases the analysis was done on a dataset composed by breast primary tumour expression data derived from the literature. Integration and analysis of PPI data confirmed the prediction of the methodology, since the genes identified to be functionally related were associated to proteins close in the PPI network. Two genes among the predicted putative partners of TBX3 (GLI3 and GATA3) were confirmed by in vivo binding assays (crosslinking immunoprecipitation, X-ChIP) in which the putative DNA enhancer sequence sites of GATA3 and GLI3 were found to be bound by the Tbx3 protein.

Conclusion

The presented strategy is demonstrated to be an effective approach to identify genes that establish functional relationships. The methodology identifies and characterises genes with a similar expression profile, through data mining and integrating data from publicly available resources, to contribute to a better understanding of gene regulation and cell function. The prediction of the TBX3 target genes GLI3 and GATA3 was experimentally confirmed.

Empirical Bayes analysis of quantitative proteomics experiments

Background

Advances in mass spectrometry-based proteomics have enabled the incorporation of proteomic data into systems approaches to biology. However, development of analytical methods has lagged behind. Here we describe an empirical Bayes framework for quantitative proteomics data analysis. The method provides a statistical description of each experiment, including the number of proteins that differ in abundance between 2 samples, the experiment's statistical power to detect them, and the false-positive probability of each protein.

Methodology/Principal Findings

We analyzed 2 types of mass spectrometric experiments. First, we showed that the method identified the protein targets of small-molecules in affinity purification experiments with high precision. Second, we re-analyzed a mass spectrometric data set designed to identify proteins regulated by microRNAs. Our results were supported by sequence analysis of the 3′ UTR regions of predicted target genes, and we found that the previously reported conclusion that a large fraction of the proteome is regulated by microRNAs was not supported by our statistical analysis of the data.

Conclusions/Significance

Our results highlight the importance of rigorous statistical analysis of proteomic data, and the method described here provides a statistical framework to robustly and reliably interpret such data.

Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach

Screening and early identification of primary immunodeficiency disease (PID) genes is a major challenge for physicians. Many resources have catalogued molecular alterations in known PID genes along with their associated clinical and immunological phenotypes. However, these resources do not assist in identifying candidate PID genes. We have recently developed a platform designated Resource of Asian PDIs, which hosts information pertaining to molecular alterations, protein-protein interaction networks, mouse studies and microarray gene expression profiling of all known PID genes. Using this resource as a discovery tool, we describe the development of an algorithm for prediction of candidate PID genes. Using a support vector machine learning approach, we have predicted 1442 candidate PID genes using 69 binary features of 148 known PID genes and 3162 non-PID genes as a training data set. The power of this approach is illustrated by the fact that six of the predicted genes have recently been experimentally confirmed to be PID genes. The remaining genes in this predicted data set represent attractive candidates for testing in patients where the etiology cannot be ascribed to any of the known PID genes.

Oral magnesium supplementation reduces ambulatory blood pressure in patients with mild hypertension

BACKGROUND

Accumulating evidence implicates a role of Mg(2+) in the pathophysiology of essential hypertension. Previous studies evaluating the antihypertensive efficacy of Mg(2+) supplementation gave contradictory results. This study aimed to investigate the effect of oral Mg(2+) supplementation on 24-h blood pressure (BP) and intracellular ion status in patients with mild hypertension.

METHODS

A total of 48 patients with mild uncomplicated hypertension participated in the study. Among them, 24 subjects were assigned to 600 mg of pidolate Mg(2+) daily in addition to lifestyle recommendations for a 12-week period and another 24 age- and sex-matched controls were only given lifestyle recommendations. At baseline and study-end (12 weeks) ambulatory BP monitoring, determination of serum and intracellular ion levels, and 24-h urinary collections for determination of urinary Mg(2+) were performed in all study subjects.

RESULTS

In the Mg(2+) supplementation group, small but significant reductions in mean 24-h systolic and diastolic BP levels were observed, in contrast to control group (-5.6 +/- 2.7 vs. -1.3 +/- 2.4 mm Hg, P < 0.001 and -2.8 +/- 1.8 vs. -1 +/- 1.2 mm Hg, P = 0.002, respectively). These effects of Mg(2+) supplementation were consistent in both daytime and night-time periods. Serum Mg(2+) levels and urinary Mg(2+) excretion were significantly increased in the intervention group. Intracellular Mg(2+) and K(+) levels were also increased, while intracellular Ca(2+) and Na(+) levels were decreased in the intervention group. None of the intracellular ions were significantly changed in the control group.

CONCLUSION

This study suggests that oral Mg(2+) supplementation is associated with small but consistent ambulatory BP reduction in patients with mild hypertension.

The role of glutathione S- transferase M1 and T1 gene polymorphisms and oxidative stress-related parameters in Egyptian patients with essential hypertension

BACKGROUND

Essential hypertension is a complex, multifactorial, polygenic disease in which the underlying genetic components remain unknown. Glutathione S-transferase (GST) enzyme is involved in detoxification of reactive oxygen species. This study aimed to investigate GSTM1 and GSTT1 gene polymorphisms in Egyptian essential hypertensive patients and their relationship with oxidative stress-related parameters.

METHODS

The study included 40 newly-diagnosed, untreated, essential hypertensive patients and 40 normotensive subjects. Plasma levels of malondialdehyde (MDA), and nitrate/nitrite and erythrocyte reduced glutathione (GSH), activities of catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glutathione S-transferase (GST) were measured. Genotyping for GSTM1 and GSTT1 was performed.

RESULTS

The frequency of GSTM1+ve/GSTT1+ve in hypertensives (5%) was lower than in normotensives (37.5%).The frequency of GSTM1-ve/GSTT1-ve was elevated in hypertensives (35%) as compared to normotensives (7.5%). Plasma MDA was higher and nitrate/nitrite was lower in hypertensives than in normotensives. Erythrocyte GSH, activities of CAT, SOD, GSH-Px, and GST of hypertensives were lower than normotensives. Moreover, GST activity was lower in subjects with GSTM1-ve/GSTT1-ve than in those with GSTM1+ve/GSTT1+ve. In hypertensives, both systolic and diastolic blood pressures were negatively correlated with activities of CAT, GSH-Px, and GST.

CONCLUSIONS

GSTM1-ve/GSTT1-ve is a potential genetic factor to predict development of essential hypertension and permit early therapeutic intervention. The significant association between blood pressure and oxidative stress-related parameters indicates the pathogenic role of oxidative stress in hypertension. Antioxidants could be useful in the management of essential hypertension to prevent progressive deterioration and target organ damage however, further studies involving long-term clinical trials may help to assess the efficacy of these therapeutic agents.

Tyrosine phosphorylation of nuclear-membrane protein emerin by Src, Abl and other kinases

X-linked recessive Emery-Dreifuss muscular dystrophy (EDMD) is caused by loss of emerin, a nuclear-membrane protein with roles in nuclear architecture, gene regulation and signaling. Phosphoproteomic studies have identified 13 sites of tyrosine phosphorylation in emerin. We validated one study, confirming that emerin is hyper-tyrosine-phosphorylated in Her2-overexpressing cells. We discovered that non-receptor tyrosine kinases Src and Abl each phosphorylate emerin and a related protein, LAP2beta, directly. Src phosphorylated emerin specifically at Y59, Y74 and Y95; the corresponding triple Y-to-F (;FFF') mutation reduced tyrosine phosphorylation by approximately 70% in vitro and in vivo. Substitutions that removed a single hydroxyl moiety either decreased (Y19F, Y34, Y161F) or increased (Y4F) emerin binding to BAF in cells. Y19F, Y34F, Y161F and the FFF mutant also reduced recombinant emerin binding to BAF from HeLa lysates, demonstrating the involvement of both LEM-domain and distal phosphorylatable tyrosines in binding BAF. We conclude that emerin function is regulated by multiple tyrosine kinases, including Her2, Src and Abl, two of which (Her2, Src) regulate striated muscle. These findings suggest roles for emerin as a downstream effector and ;signal integrator' for tyrosine kinase signaling pathway(s) at the nuclear envelope.

Transcriptional network classifiers

Background

Gene interactions play a central role in transcriptional networks. Many studies have performed genome-wide expression analysis to reconstruct regulatory networks to investigate disease processes. Since biological processes are outcomes of regulatory gene interactions, this paper develops a system biology approach to infer function-dependent transcriptional networks modulating phenotypic traits, which serve as a classifier to identify tissue states. Due to gene interactions taken into account in the analysis, we can achieve higher classification accuracy than existing methods.

Results

Our system biology approach is carried out by the Bayesian networks framework. The algorithm consists of two steps: gene filtering by Bayes factor followed by collinearity elimination via network learning. We validate our approach with two clinical data. In the study of lung cancer subtypes discrimination, we obtain a 25-gene classifier from 111 training samples, and the test on 422 independent samples achieves 95% classification accuracy. In the study of thoracic aortic aneurysm (TAA) diagnosis, 61 samples determine a 34-gene classifier, whose diagnosis accuracy on 33 independent samples achieves 82%. The performance comparisons with three other popular methods, PCA/LDA, PAM, and Weighted Voting, confirm that our approach yields superior classification accuracy and a more compact signature.

Conclusions

The system biology approach presented in this paper is able to infer function-dependent transcriptional networks, which in turn can classify biological samples with high accuracy. The validation of our classifier using clinical data demonstrates the promising value of our proposed approach for disease diagnosis.

Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach

Deciphering interacting networks of the extracellular matrix is a major challenge. We describe an affinity purification and mass spectrometry strategy that has provided new insights into the molecular interactions of elastic fibers, essential extracellular assemblies that provide elastic recoil in dynamic tissues. Using cell culture models, we defined primary and secondary elastic fiber interaction networks by identifying molecular interactions with the elastic fiber molecules fibrillin-1, MAGP-1, fibulin-5, and lysyl oxidase. The sensitivity and validity of our method was confirmed by identification of known interactions with the bait proteins. Our study revealed novel extracellular protein interactions with elastic fiber molecules and delineated secondary interacting networks with fibronectin and heparan sulfate-associated molecules. This strategy is a novel approach to define the macromolecular interactions that sustain complex extracellular matrix assemblies and to gain insights into how they are integrated into their surrounding matrix.

PIAS proteins: pleiotropic interactors associated with SUMO

The interactions and functions of protein inhibitors of activated STAT (PIAS) proteins are not restricted to the signal transducers and activators of transcription (STATs), but PIAS1, -2, -3 and -4 interact with and regulate a variety of distinct proteins, especially transcription factors. Although the majority of PIAS-interacting proteins are prone to modification by small ubiquitin-related modifier (SUMO) proteins and the PIAS proteins have the capacity to promote the modification as RING-type SUMO ligases, they do not function solely as SUMO E3 ligases. Instead, their effects are often independent of their Siz/PIAS (SP)-RING finger, but dependent on their capability to noncovalently interact with SUMOs or DNA through their SUMO-interacting motif and scaffold attachment factor-A/B, acinus and PIAS domain, respectively. Here, we present an overview of the cellular regulation by PIAS proteins and propose that many of their functions are due to their capability to mediate and facilitate SUMO-linked protein assemblies.

Scaffolds: interaction platforms for cellular signalling circuits

Scaffold proteins influence cellular signalling by binding to multiple signalling enzymes, receptors or ion channels. Although normally devoid of catalytic activity, they have a big impact on controlling the flow of signalling information. By assembling signalling proteins into complexes, they play the part of signal processing hubs. As we learn more about the way signalling components are linked into natural signalling circuits, researchers are becoming interested in building non-natural signalling pathways to test our knowledge and/or to intentionally reprogram cellular behaviour. In this review, we discuss the role of scaffold proteins as efficient tools for assembling intracellular signalling complexes, both natural and artificial.

Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts

The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for drug development, in which therapeutic/toxicological profiles of candidate drugs can be checked computationally before costly clinical trials begin.

Prognostic value of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and TRAIL receptors in renal cell cancer

PURPOSE

The death ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its receptors (TRAIL-R) are involved in immune surveillance and tumor development. Here, we studied a possible association between the expression of TRAIL/TRAIL-Rs and the prognosis in patients with renal cell carcinomas (RCC).

EXPERIMENTAL DESIGN

A tissue microarray containing RCC tumor tissue samples and corresponding normal tissue samples from 838 patients was generated. Expression of TRAIL and TRAIL-Rs was examined by immunohistochemistry and the effect of TRAIL and TRAIL-R expression on disease-specific survival was assessed.

RESULTS

High TRAIL-R2 expression levels were associated with high-grade RCCs (P < 0.001) and correlated negatively with disease-specific survival (P = 0.01). Similarly, high TRAIL expression was associated with a shorter disease-specific survival (P = 0.01). In contrast, low TRAIL-R4 expression was associated with high-stage RCCs (P < 0.001) as well as with the incidence of distant metastasis (P = 0.03) and correlated negatively with disease-specific survival (P = 0.02). In patients without distant metastasis, multivariate Cox regression analyses revealed that TRAIL-R2 and TRAIL are independent prognostic factors for cancer-specific survival (in addition to tumor extent, regional lymph node metastasis, grade of malignancy, and type of surgery).

CONCLUSION

High TRAIL-R2, high TRAIL, and low TRAIL-R4 expression levels are associated with a worse disease-specific survival in patients with RCCs. Therefore, the assessment of TRAIL/TRAIL-R expression offers valuable prognostic information that could be used to select patients for adjuvant therapy studies. Moreover, our findings are of relevance for a potential experimental therapeutic administration of TRAIL-R agonists in patients with RCCs.

Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling

c-Src non-receptor tyrosine kinase is an important component of the platelet-derived growth factor (PDGF) receptor signaling pathway. c-Src has been shown to mediate the mitogenic response to PDGF in fibroblasts. However, the exact components of PDGF receptor signaling pathway mediated by c-Src remain unclear. Here, we used stable isotope labeling with amino acids in cell culture (SILAC) coupled with mass spectrometry to identify Src-family kinase substrates involved in PDGF signaling. Using SILAC, we were able to detect changes in tyrosine phosphorylation patterns of 43 potential c-Src kinase substrates in PDGF receptor signaling. This included 23 known c-Src kinase substrates, of which 16 proteins have known roles in PDGF signaling while the remaining 7 proteins have not previously been implicated in PDGF receptor signaling. Importantly, our analysis also led to identification of 20 novel Src-family kinase substrates, of which 5 proteins were previously reported as PDGF receptor signaling pathway intermediates while the remaining 15 proteins represent novel signaling intermediates in PDGF receptor signaling. In validation experiments, we demonstrated that PDGF indeed induced the phosphorylation of a subset of candidate Src-family kinase substrates - Calpain 2, Eps15 and Trim28 - in a c-Src-dependent fashion.

DASMI: exchanging, annotating and assessing molecular interaction data

MOTIVATION

Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.

RESULTS

We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.

AVAILABILITY

The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.

DASMIweb: online integration, analysis and assessment of distributed protein interaction data

In recent years, we have witnessed a substantial increase of the amount of available protein interaction data. However, most data are currently not readily accessible to the biologist at a single site, but scattered over multiple online repositories. Therefore, we have developed the DASMIweb server that affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein and domain interactions simultaneously, it serves as an important starting point for interactome studies and assists the user in finding publicly accessible interaction data with minimal effort. The pool of queried resources is fully configurable and supports the inclusion of own interaction data or confidence scores. In particular, DASMIweb integrates confidence measures like functional similarity scores to assess individual interactions. The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at http://www.dasmiweb.de.

Recent advances in neuroblastoma

PURPOSE OF REVIEW

Although there have been recent advances with multimodal therapy, treatment of neuroblastoma remains a clinical challenge. Despite the identification of several genetic features, there has not been a significant increase in 5-year survival in the last decade. This review will highlight the current operative strategies along with new research developments aimed at improving survival.

RECENT FINDINGS

The goal of surgical intervention in the early stages of neuroblastoma is complete curative resection. In advanced-stage disease, tissue biopsy for staging is the initial goal. In recent years, minimally invasive surgery (MIS) is considered in carefully selected patients. Recent advances in neuroblastoma research have focused on tyrosine kinase inhibition, differentiation, pathway inhibition, and immunotherapy. Several of these targets have shown promising results in vivo and are currently under investigation for potential clinical trials.

SUMMARY

New information on the importance of cell signaling and the targeting of specific genes of interest are providing key insights into neuroblastoma. Only through the discovery of novel treatment strategies made available through the advancement of research will neuroblastoma be survivable for patients with advanced-stage disease.

MedlineRanker: flexible ranking of biomedical literature

The biomedical literature is represented by millions of abstracts available in the Medline database. These abstracts can be queried with the PubMed interface, which provides a keyword-based Boolean search engine. This approach shows limitations in the retrieval of abstracts related to very specific topics, as it is difficult for a non-expert user to find all of the most relevant keywords related to a biomedical topic. Additionally, when searching for more general topics, the same approach may return hundreds of unranked references. To address these issues, text mining tools have been developed to help scientists focus on relevant abstracts. We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker.

Customized treatment in non-small-cell lung cancer based on EGFR mutations and BRCA1 mRNA expression

BACKGROUND

Median survival is 10 months and 2-year survival is 20% in metastatic non-small-cell lung cancer (NSCLC) treated with platinum-based chemotherapy. A small fraction of non-squamous cell lung cancers harbor EGFR mutations, with improved outcome to gefitinib and erlotinib. Experimental evidence suggests that BRCA1 overexpression enhances sensitivity to docetaxel and resistance to cisplatin. RAP80 and Abraxas are interacting proteins that form complexes with BRCA1 and could modulate the effect of BRCA1. In order to further examine the effect of EGFR mutations and BRCA1 mRNA levels on outcome in advanced NSCLC, we performed a prospective non-randomized phase II clinical trial, testing the hypothesis that customized therapy would confer improved outcome over non-customized therapy. In an exploratory analysis, we also examined the effect of RAP80 and Abraxas mRNA levels.

METHODOLOGY/PRINCIPAL FINDINGS

We treated 123 metastatic non-squamous cell lung carcinoma patients using a customized approach. RNA and DNA were isolated from microdissected specimens from paraffin-embedded tumor tissue. Patients with EGFR mutations received erlotinib, and those without EGFR mutations received chemotherapy with or without cisplatin based on their BRCA1 mRNA levels: low, cisplatin plus gemcitabine; intermediate, cisplatin plus docetaxel; high, docetaxel alone. An exploratory analysis examined RAP80 and Abraxas expression. Median survival exceeded 28 months for 12 patients with EGFR mutations, and was 11 months for 38 patients with low BRCA1, 9 months for 40 patients with intermediate BRCA1, and 11 months for 33 patients with high BRCA1. Two-year survival was 73.3%, 41.2%, 15.6% and 0%, respectively. Median survival was influenced by RAP80 expression in the three BRCA1 groups. For example, for patients with both low BRCA1 and low RAP80, median survival exceeded 26 months. RAP80 was a significant factor for survival in patients treated according to BRCA1 levels (hazard ratio, 1.3 [95% CI, 1-1.7]; P = 0.05).

CONCLUSIONS/SIGNIFICANCE

Chemotherapy customized according to BRCA1 expression levels is associated with excellent median and 2-year survival for some subsets of NSCLC patients , and RAP80 could play a crucial modulating effect on this model of customized chemotherapy.

TRIAL REGISTRATION

(ClinicalTrials.gov) NCT00883480.

Nuclear transport factors in neuronal function

Active nucleocytoplasmic transport of macromolecules requires soluble transport carriers of the importin/karyopherin superfamily. Although the nuclear transport machinery is essential in all eukaryotic cells, neurons must also mobilise importins and associated proteins to overcome unique spatiotemporal challenges. These include switches in importin alpha subtype expression during neuronal differentiation, localized axonal synthesis of importin beta1 to coordinate a retrograde injury signaling complex on axonal dynein, and trafficking of regulatory and signaling molecules from synaptic terminals to cell bodies. Targeting of RNAs encoding critical components of the importins complex and the Ran system to axons allows sophisticated local regulation of the system for mobilization upon need. Finally, a number of importin family members have been associated with mental or neurodegenerative diseases. The extended roles recently discovered for importins in the nervous system might also be relevant in non-neuronal cells, and the localized modes of importin regulation in neurons offer new avenues to interrogate their cytoplasmic functions.

NASCENT: an automatic protein interaction network generation tool for non-model organisms

Large quantity of reliable protein interaction data are available for model organisms in public depositories (e.g., MINT, DIP, HPRD, INTERACT). Most data correspond to experiments with the proteins of Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli and Mus musculus. For other important organisms the data availability is poor or non-existent. Here we present NASCENT, a completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein interaction network modeling through gene-name mapping, and outputs the resulting network in graphical form and also in computer-readable graph-forms, directly applicable by popular network modeling software.

POINeT: protein interactome with sub-network analysis and hub prioritization

BACKGROUND

Protein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools.

RESULTS

We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3) to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles.

CONCLUSION

The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to selected tissues can be revealed. The straightforward interface of POINeT makes PPI search and analysis just a few clicks away. The modular design permits further functional enhancement without hampering the simplicity. POINeT is available at (http://poinet.bioinformatics.tw/).

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions

SUMMARY

MatrixDB (http://matrixdb.ibcp.fr) is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. It takes into account the full interaction repertoire of the extracellular matrix involving full-length molecules, fragments and multimers. The current version of MatrixDB contains 1972 interactions corresponding to 4412 experiments and involving 259 extracellular biomolecules.

AVAILABILITY

MatrixDB is freely available at http://matrixdb.ibcp.fr

Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology

Although high-throughput technologies used in biology have resulted in the accumulation of vast amounts of data in the literature, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Databases have assumed a crucial role in assimilating and storing information that could enable future discoveries. To this end, our group has developed two resources - Human Protein Reference Database (HPRD) and Human Proteinpedia - that provide integrated information pertaining to human proteins. These databases contain information on a number of features of proteins that have been discovered using various experimental methods. Human Proteinpedia was developed as a portal for community participation to annotate and share proteomic data using HPRD as the scaffold. It allows proteomic investigators to even share unpublished data and provides an effective medium for data sharing. As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, classical genetics, and chemical genetics in understanding the relationships among genome, gene functions, and living systems.

Dysregulation of vascular TRPM7 and annexin-1 is associated with endothelial dysfunction in inherited hypomagnesemia

Inadequate magnesium intake and hypomagnesemia may contribute to chronic diseases, such as hypertension. The novel magnesium transporter TRPM7 is a critical regulator of magnesium homeostasis in vascular cells, but its role in pathophysiology is unclear. In a model of hypomagnesemia, we examined microvascular structure and function, TRPM7 expression, and vascular inflammatory status using inbred mice selected for normal-high intracellular magnesium levels or low intracellular magnesium levels (MgLs). Blood pressure was significantly increased in MgLs compared with normal-high intracellular magnesium levels. Pressurized myography of mesenteric resistance arteries showed that MgLs had significantly impaired endothelial function together with decreased plasma nitrate levels and endothelial NO synthase expression when compared with normal-high intracellular magnesium levels. Significant differences in vascular structure were also evident in both mesenteric arteries and aortas from MgLs. Aortas from MgLs had increased medial cross-sectional areas, whereas mesenteric arteries from MgLs had increased lumen diameters with increased medial cross-sectional areas, indicating outward hypertrophic remodeling. Expression of the magnesium transporter TRPM7 was significantly elevated in the vasculature of MgLs, whereas expression of a TRPM7 downstream target, the anti-inflammatory molecule annexin-1, was reduced. MgLs had increased expression of vascular cell adhesion molecule-1 and plasminogen activator inhibitor-1, indicating vascular inflammation. Taken together, these data demonstrate that the inherited magnesium status of MgLs and normal-high intracellular magnesium levels mice affects magnesium transporter expression, endothelial function, vascular structure, and inflammation. Our findings suggest a potential regulatory role for TRPM7 signaling in the maintenance of vascular integrity. Alterations in magnesium status and/or TRPM7 signaling may contribute to vascular injury in conditions associated with hypomagnesemia.

Predictors of survival of advanced renal cell carcinoma: long-term results from Southwest Oncology Group Trial S8949

PURPOSE

S8949 demonstrated improved overall survival for debulking nephrectomy in interferon treated patients with advanced renal cell carcinoma. We present an updated analysis of S8949, now with a median followup of 9 years. We explored clinical predictors of overall survival.

MATERIALS AND METHODS

Univariate and multivariate Cox regression analysis was performed to evaluate the impact of clinical variables potentially influencing survival.

RESULTS

Of 246 patients 241 were eligible and randomized to interferon with or without nephrectomy. Patients randomized to nephrectomy continued to have improved overall survival (HR 0.74, 95% CI 0.57-0.96, p = 0.022). Multivariate analysis showed that performance status 1 vs 0 (HR 1.95, p <0.0001), high alkaline phosphatase (HR 1.5, p = 0.002) and lung metastasis only (HR 0.73, p = 0.028) were overall survival predictors. There was no evidence of an interaction of performance status, measurable disease or lung metastases with nephrectomy (each p >0.30). In a patient subset that survived at least 90 days after randomization early progressive disease within 90 days was prognostic of overall survival in a multivariate model (HR 2.1, p <0.0001), as was performance status (HR 1.7, p = 0.0006).

CONCLUSIONS

Nephrectomy prolonged long-term overall survival in this updated analysis, supporting its role as standard therapy in patients with advanced renal cell carcinoma. A nephrectomy benefit was seen across all prespecified patient subsets. Early progressive disease and performance status were strong predictors of overall survival. These results support efforts to identify biomarkers of renal cell carcinoma resistance to treatment and early progressive disease to facilitate rational patient selection for systemic therapy.

Decoy receptor 3 is a prognostic factor in renal cell cancer

BACKGROUND

Decoy receptor 3 (DcR3) is a soluble protein that binds to and inactivates the death ligand CD95L. Here, we studied a possible association between DcR3 expression and prognosis in patients with renal cell carcinomas (RCCs).

METHODS

A tissue microarray containing RCC tumor tissue samples and corresponding normal tissue samples was generated. Decoy receptor 3 expression in tumors of 560 patients was examined by immunohistochemistry. The effect of DcR3 expression on disease-specific survival and progression-free survival was assessed using univariate analysis and multivariate Cox regression analysis. Decoy receptor 3 serum levels were determined by ELISA.

FINDINGS

High DcR3 expression was associated with high-grade (P = .005) and high-stage (P = .048) RCCs. The incidence of distant metastasis (P = .03) and lymph node metastasis (P = .002) was significantly higher in the group with high DcR3 expression. Decoy receptor 3 expression correlated negatively with disease-specific survival (P < .001) and progression-free survival (P < .001) in univariate analyses. A multivariate Cox regression analysis retained DcR3 expression as an independent prognostic factor that outperformed the Karnofsky performance status. In patients with high-stage RCCs expressing DcR3, the 2-year survival probability was 25%, whereas in patients with DcR3-negative tumors, the survival probability was 65% (P < .001). Moreover, DcR3 serum levels were significantly higher in patients with high-stage localized disease (P = .007) and metastatic disease (P = .001).

INTERPRETATION

DcR3 expression is an independent prognostic factor of RCC progression and mortality. Therefore, the assessment of DcR3 expression levels offers valuable prognostic information that could be used to select patients for adjuvant therapy studies.

Effects of serum homocysteine and adiponectin levels on platelet aggregation in untreated patients with essential hypertension

The aim of the present study is to determine and correlate adiponectin, homocysteine, nitric oxide, and ADP-induced platelet aggregation levels in untreated patients with essential hypertension and healthy individuals. A total of 36 individuals, 23 untreated patients with essential hypertension and 13 healthy individuals, were included in the scope of this study. Enzyme-linked immunosorbent assay (ELISA) was used to determine the serum adiponectin and TNF-alpha levels. The levels of serum homocysteine were measured by using competitive chemiluminescent enzyme immunoassay. Serum concentrations of hsCRP were measured by the Nephelometer. Plasma nitrite, nitrate, and total nitric oxide (NOx) levels were determined by colorimetric method. Homocysteine and hsCRP levels in patients with essential hypertension were found to be significantly higher than those in the control group (P = 0.02, P = 0.001, respectively). The average platelet aggregation levels in patient group were higher than control group, but there were no statistically significant differences between them (P > 0.05). In addition, in patients with essential hypertension adiponectin and nitrite levels are significantly lower than control group (P < 0.001, P = 0.045, respectively). We have also found significant correlations between nitrite-platelet aggregation amplitude, nitrite-platelet aggregation slope, nitrite-adiponectin, homocysteine-platelet aggregation amplitude, and sistolic blood pressure-platelet aggregation amplitude levels (r = -0.844; P < 0.001, r = -0.680; P = 0.011, r = 0.454; P = 0.05, r = 0.414; P = 0.05, r = 0.442; P = 0.035, respectively). Increased homocysteine and decreased adiponectin serum levels in patients with essential hypertension correlate well with changes in ADP-induced conventional platelet aggregation. This association may potentially contribute to future thrombus formation and higher risks for cardiovascular events in hypertensive patients.

Oxidative stress in prehypertension: rationale for antioxidant clinical trials

Prehypertension has been recently described as an independent category of blood pressure. Mounting evidence suggests that blood pressure in the prehypertensive range is associated with an increased risk of developing hypertension and cardiovascular disease. Several reports have assigned a critical role for oxidative stress in these disease processes. This review focuses on the clinical and experimental studies done in prehypertension and hypertension within the context of oxidative stress. This article also provides insights into why diverse therapeutic interventions, which have in common the ability to reduce oxidative stress, can impede or delay the onset of hypertension in prehypertension subjects.

Gender specific association of endothelial nitric oxide synthase gene (Glu298Asp) polymorphism with essential hypertension in a south Indian population

BACKGROUND

Endothelial derived nitric oxide (NO) plays a major role in blood pressure regulation. The role of missense variant eNOS-Glu298Asp has been demonstrated by many studies with conflicting results. Our objective was to investigate the association of eNOS gene polymorphism with essential hypertension in a south Indian population.

METHODS

We carried out a case control study in 438 hypertensive patients and 444 healthy control subjects in a homogenous population. Genotyping was done by PCR-RFLP method. Multiple logistic regression analysis was used to detect the association between genotype and hypertension.

RESULTS

The homozygous variant genotype Asp298Asp was significantly associated with hypertension (odds ratio 2.4; 95% CI, 1.23-5.0, p<0.01). Gender specific analysis showed both the heterozygous (odds ratio, 2.0; 95% CI, 1.3-2.9, p<0.01) and homozygous variants (odds ratio, 7.9; 95% CI, 2.0-4.1, p<0.001) were positively associated with hypertension in females. The variant allele Asp was higher in female hypertensives when compared to male hypertensive cases (22% vs. 16%).

CONCLUSION

The eNOS gene polymorphism is a candidate gene for hypertension and the association to be gender specific with respect to females in a south Indian Tamilian population.

Targeting reactive oxygen species in hypertension

Oxidative stress plays an important role in the pathogenesis of hypertension. A number of sources of reactive oxygen species have been identified including NADPH oxidase, endothelial NO synthase, and xanthine oxidase. Inhibitors of these systems reduce blood pressure in experimental models. Targeted overexpression of antioxidant systems and interference with expression of oxidant systems has also been successfully used in animal models of hypertension. It is expected that these strategies will eventually be translated to human disease, but currently, the specificity and toxicity of such measures are not yet fulfilling quality criteria for treatment of humans. In the meantime, presumably nontoxic measures, such as administration of antioxidant vitamins, are the only available treatments for oxidative stress in humans. In this review, we discuss strategies to target oxidative stress both in experimental models and in humans. We also discuss how patients could be selected who particularly benefit from antioxidant treatment. In clinical practice, diagnostic procedures beyond measurement of blood pressure will be necessary to predict the response to antioxidants; these procedures will include measurement of antioxidant status and detailed assessment of vascular structure and function.

Plasma matrix metalloproteinase-7 as a metastatic marker and survival predictor in patients with renal cell carcinomas

We evaluated the clinical usefulness of plasma matrix metalloproteinase-7 (MMP-7) as a diagnostic and prognostic biomarker in patients with renal cell carcinoma (RCC). MMP-7 was quantified in plasma of 50 healthy subjects and 97 RCC patients using a Fluorokine MultiAnalyte Profiling assay. RCC patients were stratified into the following groups: without metastases (N0M0; n = 39), with lymph nodes (N1M0; n = 13), and with distant metastases (M1; n = 45). Diagnostic performance of MMP-7 was analyzed by the receiver operating characteristics (ROC) curve. Kaplan-Meier analysis and the Cox regression model were used to estimate the impact of MMP-7 on the cancer-specific survival outcome of RCC patients. MMP-7 was significantly higher in both metastatic groups N1M0 and M1 (medians, 3.82 and 3.34 microg/L) compared to N0M0 group or controls (medians, 1.85 and 1.64 microg/L; all P < 0.001). In ROC analysis, the area under the ROC curve of MMP-7 was 0.80 in the detection of metastases in RCC (P < 0.0001). In the Kaplan-Meier analysis, patients with MMP-7 above the 95th percentile of controls showed less favorable survival rates compared to those with normal MMP-7 (log-rank test, 15.7; P < 0.0001). High MMP-7 was associated with cancer-related mortality estimated by univariate Cox regression (risk ratio, 4.34, 95% CI, 1.12-10.6; P = 0.032). The multivariate Cox regression model determined MMP-7 (risk ratio, 2.70, 95% CI, 1.39-5.24; P = 0.003) and metastases (risk ratio, 5.81, 95% CI, 2.77-12.2; P < 0.0001) as independent determinants of cancer-related survival outcomes. In conclusion, increased plasma MMP-7 could be related to metastatic disease and poor prognosis in patients with RCC.

Relationship between oxidative stress and essential hypertension

This study investigated the association of blood pressure with blood oxidative stress-related parameters in normotensive and hypertensive subjects. A cross-sectional design was applied to 31 hypertensive patients and 35 healthy normotensive subjects. All subjects were men between the ages of 35 and 60 years. Exclusion criteria were obesity, dyslipidemia, diabetes mellitus, smoking and current use of any medication. All patients underwent 24-h ambulatory blood pressure monitoring and sampling of blood and urine. Antioxidant enzymes activity, reduced/oxidized glutathione ratio (GSH/GSSG), and lipid peroxidation (malondialdehyde) were determined in erythrocytes. Parameters measured in the plasma of test subjects were plasma antioxidant status, lipid peroxidation (8-isoprostane), plasma vitamin C and E, and the blood pressure modulators renin, aldosterone, endothelin-1 and homocysteine. Daytime systolic and diastolic blood pressures of hypertensives were negatively correlated with plasma antioxidant capacity (r=-0.46, p<0.009 and r=-0.48, p<0.007), plasma vitamin C levels (r=-0.53, p<0.003 and r=-0.44, p<0.02), erythrocyte activity of antioxidant enzymes, and erythrocyte GSH/GSSG ratio, with hypertensives showing higher levels of oxidative stress. Blood pressures showed a positive correlation with both plasma and urine 8-isoprostane. Neither plasma vitamin E nor the assessed blood pressure modulator levels showed significant differences between the groups or correlation with blood pressures. These findings demonstrate a strong association between blood pressure and some oxidative stress-related parameters and suggest a possible role of oxidative stress in the pathophysiology of essential hypertension.

Diagnostic and prognostic molecular markers in renal cell carcinoma

PURPOSE

We reviewed the contemporary literature on molecular biomarkers in renal cell carcinoma and their prognostic significance.

MATERIALS AND METHODS

Articles published during 1981 to 2007 in English on renal cell carcinoma were surveyed using the MEDLINE/PubMed database. The subject headings included were genetics, biomarkers, prognosis and risk models of renal cell carcinoma. We present a synthesis of currently known renal cell carcinoma biomarkers at various stages of development and their clinical significance, and prognostic nomograms incorporating biomarkers.

RESULTS

The beneficiary role of biomarkers in renal cell carcinoma is challenged by the relatively low prevalence of the disease. Even if a biomarker for renal cell carcinoma had 100% sensitivity and 99.4% specificity, the positive predictive value of the marker in men older than 65 years would be only 10%. Several biomarkers are being investigated in renal cell carcinoma, of which many relate to pathogenic molecular changes that are currently therapeutic targets. Carbonic anhydrase IX is a von Hippel-Lindau mediated enzyme that is expressed in most renal cell carcinoma cases. High (greater than 85%) expression of this marker indicates favorable prognosis and may predict the response to interleukin-2 therapy. B7-H1 expression in renal cell carcinoma cells/lymphocytes may indicate worse survival, possibly through impaired host antitumor immunity. Prognostic nomograms incorporating clinical variables and molecular markers to refine the prediction of treatment outcomes are in active development and await prospective clinical validation.

CONCLUSIONS

Several renal cell carcinoma molecular markers appear promising to refine the prognosis and prediction of localized, advanced or metastatic renal cell carcinoma. Currently carbonic anhydrase IX is the best studied and promising marker. Prospective, multicenter clinical validation aimed at the practical clinical usefulness of renal cell carcinoma biomarkers is warranted.

Transient receptor potential melastatin 6 and 7 channels, magnesium transport, and vascular biology: implications in hypertension

Magnesium, an essential intracellular cation, is critically involved in many biochemical reactions involved in the regulation of vascular tone and integrity. Decreased magnesium concentration has been implicated in altered vascular reactivity, endothelial dysfunction, vascular inflammation, and structural remodeling, processes important in vascular changes and target organ damage associated with hypertension. Until recently, very little was known about mechanisms regulating cellular magnesium homeostasis, and processes controlling transmembrane magnesium transport had been demonstrated only at the functional level. Two cation channels of the transient receptor potential melastatin (TRPM) cation channel family have now been identified as magnesium transporters, TRPM6 and TRPM7. These unique proteins, termed chanzymes because they possess a channel and a kinase domain, are differentially expressed, with TRPM6 being found primarily in epithelial cells and TRPM7 occurring ubiquitously. Vascular TRPM7 is modulated by vasoactive agents, pressure, stretch, and osmotic changes and may be a novel mechanotransducer. In addition to its magnesium transporter function, TRPM7 has been implicated as a signaling kinase involved in vascular smooth muscle cell growth, apoptosis, adhesion, contraction, cytoskeletal organization, and migration, important processes involved in vascular remodeling associated with hypertension and other vascular diseases. Emerging evidence suggests that vascular TRPM7 function may be altered in hypertension. This review discusses the importance of magnesium in vascular biology and implications in hypertension and highlights the transport systems, particularly TRPM6 and TRPM7, which may play a role in the control of vascular magnesium homeostasis. Since the recent identification and characterization of Mg2+-selective transporters, there has been enormous interest in the field. However, there is still a paucity of information, and much research is needed to clarify the exact mechanisms of magnesium regulation in the cardiovascular system and the implications of aberrant transmembrane magnesium transport in the pathogenesis of hypertension and other vascular diseases.

Wnt antagonist family genes as biomarkers for diagnosis, staging, and prognosis of renal cell carcinoma using tumor and serum DNA

PURPOSE

We hypothesized that combined methylation analysis of Wnt antagonist genes could serve as a panel of biomarkers for diagnosis, staging, and prognosis in renal cell carcinoma (RCC).

EXPERIMENTAL DESIGN

Samples (n = 62) of RCC and corresponding normal renal tissue (NRT) were analyzed using methylation-specific PCR for methylation of six Wnt antagonist genes (sFRP-1, sFRP-2, sFRP-4, sFRP-5, Wif-1, and Dkk-3). To increase the sensitivity/specificity of RCC detection, the methylation score (M score) for multigene methylation analysis was developed. Receiver operator characteristic curve analysis was used to determine the optimal sensitivity/specificity of the M score. In addition, the M score was compared with the clinicopathologic outcome. Thirty-three serum DNA samples were also used to investigate the methylation status of Wnt antagonist genes.

RESULTS

The methylation levels of all Wnt antagonists were significantly higher in RCC than in NRT. In multivariate regression analysis, the methylation level of sFRP-1 was a significant independent predictor of RCC, whereas for sFRP-2 and sFRP-4 there was a trend toward significance as independent predictors. The M score of Wnt antagonist genes was significantly higher in RCC than in NRT. Overall, the M score had a sensitivity of 79.0% and a specificity of 75.8% (area under the curve, 0.808) as a diagnostic biomarker. In addition, the M score could significantly distinguish grade, pT category, M category, and overall survival of RCC patients. The M score was independent of age and gender in predicting overall survival by the Cox proportional hazards model. In RCC patients, 72.7% of the methylation-specific PCR results had identical methylation in samples of tumor and serum DNA. No serum DNA in normal controls showed aberrant methylation of the Wnt antagonist genes. In addition, the methylation status of Wnt antagonist genes in serum DNA was significantly correlated with tumor grade and stage.

CONCLUSIONS

This is the first report showing that M score analysis of Wnt antagonist genes can serve as an excellent epigenetic biomarker panel for detection, staging, and prognosis of RCC using serum DNA.

Quercetin reduces blood pressure in hypertensive subjects

Epidemiological studies report that quercetin, an antioxidant flavonol found in apples, berries, and onions, is associated with reduced risk of coronary heart disease and stroke. Quercetin supplementation also reduces blood pressure in hypertensive rodents. The efficacy of quercetin supplementation to lower blood pressure in hypertensive humans has never been evaluated. We tested the hypothesis that quercetin supplementation reduces blood pressure in hypertensive patients. We then determined whether the antihypertensive effect of quercetin is associated with reductions in systemic oxidant stress. Men and women with prehypertension (n = 19) and stage 1 hypertension (n = 22) were enrolled in a randomized, double-blind, placebo-controlled, crossover study to test the efficacy of 730 mg quercetin/d for 28 d vs. placebo. Blood pressure (mm Hg, systolic/diastolic) at enrollment was 137 +/- 2/86 +/- 1 in prehypertensives and 148 +/- 2/96 +/- 1 in stage 1 hypertensive subjects. Blood pressure was not altered in prehypertensive patients after quercetin supplementation. In contrast, reductions in (P < 0.01) systolic (-7 +/- 2 mm Hg), diastolic (-5 +/- 2 mm Hg), and mean arterial pressures (-5 +/- 2 mm Hg) were observed in stage 1 hypertensive patients after quercetin treatment. However, indices of oxidant stress measured in the plasma and urine were not affected by quercetin. These data are the first to our knowledge to show that quercetin supplementation reduces blood pressure in hypertensive subjects. Contrary to animal-based studies, there was no quercetin-evoked reduction in systemic markers of oxidative stress.

Factors that regulate embryonic gustatory development

Numerous molecular factors orchestrate the development of the peripheral taste system. The unique anatomy/function of the taste system makes this system ideal for understanding the mechanisms by which these factors function; yet the taste system is underutilized for this role. This review focuses on some of the many factors that are known to regulate gustatory development, and discusses a few topics where more work is needed. Some attention is given to factors that regulate epibranchial placode formation, since gustatory neurons are thought to be primarily derived from this region. Epibranchial placodes appear to arise from a pan-placodal region and a number of regulatory factors control the differentiation of individual placodes. Gustatory neuron differentiation is regulated by a series of transcription factors and perhaps bone morphongenic proteins (BMP). As neurons differentiate, they also proliferate such that their numbers exceed those in the adult, and this is followed by developmental death. Some of these cell-cycling events are regulated by neurotrophins. After gustatory neurons become post-mitotic, axon outgrowth occurs. Axons are guided by multiple chemoattractive and chemorepulsive factors, including semaphorins, to the tongue epithelium. Brain derived neurotrophic factor (BDNF), functions as a targeting factor in the final stages of axon guidance and is required for gustatory axons to find and innervate taste epithelium. Numerous factors are involved in the development of gustatory papillae including Sox-2, Sonic hedge hog and Wnt-β-catenin signaling. It is likely that just as many factors regulate taste bud differentiation; however, these factors have not yet been identified. Studies examining the molecular factors that regulate terminal field formation in the nucleus of the solitary tract are also lacking. However, it is possible that some of the factors that regulate geniculate ganglion development, outgrowth, guidance and targeting of peripheral axons may have the same functions in the gustatory CNS.