Expression and therapeutic targeting of dopamine receptor-1 (D1R) in breast cancer

Patients with advanced breast cancer often fail to respond to treatment, creating a need to develop novel biomarkers and effective therapeutics. Dopamine (DA) is a catecholamine that binds to five G protein-coupled receptors. We discovered expression of DA type-1 receptors (D1Rs) in breast cancer, thereby identifying these receptors as novel therapeutic targets in this disease. Strong to moderate immunoreactive D1R expression was found in 30% of 751 primary breast carcinomas, and was associated with larger tumors, higher tumor grades, node metastasis and shorter patient survival. DA and D1R agonists, signaling through the cGMP/protein kinase G (PKG) pathway, suppressed cell viability, inhibited invasion and induced apoptosis in multiple breast cancer cell lines. Fenoldopam, a peripheral D1R agonist that does not penetrate the brain, dramatically suppressed tumor growth in two mouse models with D1R-expressing xenografts by increasing both necrosis and apoptosis. D1R-expressing primary tumors and metastases in mice were detected by fluorescence imaging. In conclusion, D1R overexpression is associated with advanced breast cancer and poor prognosis. Activation of the D1R/cGMP/PKG pathway induces apoptosis in vitro and causes tumor shrinkage in vivo. Fenoldopam, which is FDA (Food and Drug Administration) approved to treat renal hypertension, could be repurposed as a novel therapeutic agent for patients with D1R-expressing tumors.

Preparation of vesicular stomatitis virus pseudotype with Chikungunya virus envelope protein

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes Chikungunya fever (CHIKF) in millions of people mainly in developing countries. CHIKF is characterized by high fever, fatigue, headache, nausea, vomiting, rash, myalgia and severe arthralgia. To date, there is no specific treatment and no licensed vaccine against CHIKV infection. In this study, we developed a safe, efficient and easy neutralization assay of CHIKV based on vesicular stomatitis virus (VSV) pseudotype with CHIKV envelope protein and the green fluorescent protein (GFP) or luciferase as reporter gene, which could be used under a reduced safety level. The VSV pseudotype can be applied to the epidemic survey by measuring the expression of GFP or luciferase activity in infected cells. This system can also be used to study the mechanisms of virus entry.

Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing

Although many quality control (QC) methods have been developed to improve the quality of single-nucleotide variants (SNVs) in SNV-calling, QC methods for use subsequent to single-nucleotide polymorphism-calling have not been reported. We developed five QC metrics to improve the quality of SNVs using the whole-genome-sequencing data of a monozygotic twin pair from the Korean Personal Genome Project. The QC metrics improved both repeatability between the monozygotic twin pair and reproducibility between SNV-calling pipelines. We demonstrated the QC metrics improve reproducibility of SNVs derived from not only whole-genome-sequencing data but also whole-exome-sequencing data. The QC metrics are calculated based on the reference genome used in the alignment without accessing the raw and intermediate data or knowing the SNV-calling details. Therefore, the QC metrics can be easily adopted in downstream association analysis.

Cost implications of the use of basal insulin glargine in people with early dysglycemia: the ORIGIN trial

AIMS

The cost implications of the Outcome Reduction with an Initial Glargine Intervention (ORIGIN) trial were evaluated using a prespecified analysis plan.

METHODS

Purchasing power parity-adjusted country-specific costs were applied to consumed healthcare resources by participants from each country. Subgroup analyses were conducted on subgroups based on baseline metabolic status and diabetes duration.

RESULTS

The total undiscounted cost per participant in the insulin glargine arm was $13,491 ($13,080 to $14,254) versus $11,189 ($10,568 to $12,147) for standard care, an increase of $2303 ($1370 to $3235; p < 0.0001); the discounted increase was $2099 ($1276 to $2923; P < 0.0001). The greater number of mainly generic oral anti-diabetic agents in the standard group partially offset the higher cost of basal insulin glargine. As the trial progressed and the standard group required more anti-diabetic medications, the annual cost difference decreased, reaching $68 (-$160 to $295) in the last year. The subgroup whose baseline diabetes duration was ≥ 6 years achieved cost-savings during the trial.

CONCLUSIONS

From a global perspective basal insulin glargine use in ORIGIN incurred greater costs than standard care using older generic drugs. Nevertheless, the cost difference fell with time such that the intervention was cost-neutral by the last year.

DNA methylation of membrane-bound tyrosine phosphatase genes in acute lymphoblastic leukaemia

Aberrant DNA promoter methylation with associated gene silencing is a common epigenetic abnormality in acute lymphoblastic leukaemia (ALL) and is associated with poor survival. We have identified a family of transmembrane tyrosine phosphatase proteins as targets of hypermethylation in ALL and high-grade B cell lymphoma and demonstrated that this abnormal methylation correlates with transcript expression. PTPRG was methylated in 63% of ALL samples, PTPRK in 47%, PTPRM in 64% and PTPRO in 54% of cases, with most ALL samples containing methylation at multiple phosphatase loci. PTPRK promoter methylation was associated with a decreased overall survival in the cohort. Restoration of PTPRK transcript levels in leukaemia cells, where phosphatase transcript was silenced, reduced cell proliferation, inhibited colony formation and increased sensitivity to cytotoxic chemotherapy. These biological changes were associated with a reduction in levels of phosphorylated Erk1/2, Akt, STAT3 and STAT5 suggesting functional phosphatase activity after transcript re-expression. Methylation of the phosphatase promoters was reversible with decitabine and a histone deacetylase inhibitor, suggesting that PTPRK-mediated cell signalling pathways may be targeted with epigenetic therapies in lymphoid malignancy.

Exploring the FDA adverse event reporting system to generate hypotheses for monitoring of disease characteristics

The US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) is a database for postmarketing drug safety monitoring and influences changes in FDA safety guidance documents such as drug labels. The number of cases in the FAERS has rapidly increased with the improvement of submission methods and data standards and thus has become an important resource for regulatory science. Although the FAERS has been predominantly used for safety signal detection, this study explored its utility for disease characteristics.

European guidelines for quality assurance in colorectal cancer screening and diagnosis: overview and introduction to the full supplement publication

Population-based screening for early detection and treatment of colorectal cancer (CRC) and precursor lesions, using evidence-based methods, can be effective in populations with a significant burden of the disease provided the services are of high quality. Multidisciplinary, evidence-based guidelines for quality assurance in CRC screening and diagnosis have been developed by experts in a project co-financed by the European Union. The 450-page guidelines were published in book format by the European Commission in 2010.  They include 10 chapters and over 250 recommendations, individually graded according to the strength of the recommendation and the supporting evidence. Adoption of the recommendations can improve and maintain the quality and effectiveness of an entire screening process, including identification and invitation of the target population, diagnosis and management of the disease and appropriate surveillance in people with detected lesions. To make the principles, recommendations and standards in the guidelines known to a wider professional and scientific community and to facilitate their use in the scientific literature, the original content is presented in journal format in an open-access Supplement of Endoscopy. The editors have prepared the present overview to inform readers of the comprehensive scope and content of the guidelines.

Bending sensor based on intermodal interference properties of two-dimensional waveguide array fiber

We propose a highly sensitive bending sensor based on the intermodal interference properties of a strongly coupled two-dimentional waveguide array fiber (WAF). The interference resonance peaks formed by the SMF-WAF-SMF Mach-Zehnder interferometer are intrinsically the result of interference between the LP(01)-like supermode and other higher order supermodes, displaying supernormal sensitivity to bending in a wide curvature range. The bending sensitivity of the intermodal MZI is a quadratic function of curvature, and the resonance wavelength shift is up to 100 nm within a curvature range 0-10 m(-1). The fabrication reveals briefness, and temperature response shows little impact on the bend sensing precision. The high bending sensitivity and wide sensing range can make this device a candidate for bending discrimination and measurement in widespread areas.

Associations between metabolic syndrome and its components and alcohol drinking

AIMS

The relationship between alcohol drinking and metabolic syndrome (MetS) and its components are not fully confirmed, we examined relationship between alcohol drinking and MetS and its components.

METHODS

2,538 Mongolian people aged 20 or more were included in this study. The data for demographic characteristics, lifestyle factors, family history of hypertension, blood pressure (BP) measurements and physical examination were obtained, and fasting plasma glucose (FPG) and lipids examined for all participants. Associations between MetS and its components and alcohol drinking were analyzed with Logistic regression.

RESULTS

The risks of MetS associated with alcohol drinking and various drinking volume were not significant after adjustment for other variables. Alcohol drinking was significantly and positively associated with high BP and high TG, the multivariate adjusted OR (95% CI) of high BP and high TG for drinking were 1.399(1.109, 1.764) and 2.464(1.866, 3.252), respectively, compared with no drinking. However, drinking was inversely associated with low HDL-C, the multivariate adjusted OR (95% CI) of low HDL-C was 0.597(0.479, 0.745) for alcohol drinking compared with no drinking.

CONCLUSIONS

Alcohol drinking was significantly and positively associated with high BP and high TG, while alcohol drinking inversely associated with low HDL-C.

Value of CYP3A5 genotyping on determining initial dosages of tacrolimus for Chinese renal transplant recipients

Optimal blood levels of tacrolimus in transplant recipients are critically important to preserve the allograft. Suboptimal doses of the immunosuppressant can result in allograft toxicity or rejection. In the present study, we determined CYP3A5 genotypes of patients and analyzed their medical documents in 2 successive periods. In the first period, a fixed initial dosage of 0.1 mg/kg was prescribed daily for 28 patients regardless of their CYP3A5 genotype. In the second period, CYP3A5 genotyping was performed with polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing. The frequency distribution of CYP3A5 genotypes was 47.4% (38/78) for *1/*3, 2.6% (2/78) for *1/*1, and 50% (39/78) for *3/*3. The patients with *1/*3 had shown significantly lower tacrolimus blood levels than those with the *3/*3 when the initial dose of 0.10 mg/kg was given for 2 weeks postoperatively. In the second period, initial dosages were selected according to individuals' CYP3A5 genotypes, 0.08 mg/kg/d for recipients with CYP3A5 *3/*3 and 0.15 mg/kg/d for recipients with *1/*3. Adjustment of the initial dosage of tacrolimus was documented to improve the proportion of patients achieving target drug blood levels in the early postoperative stage: from 46.7% to 81.8% of the *1/*3 group and from 46.2% to 73.1% of the *3/*3 group on the third day. In conclusion, CYP3A5 polymorphism plays an important role in influencing tacrolimus blood levels. Initial tacrolimus dosage selection based on CYP3A5 genotyping can improve drug blood levels in the early stage following renal transplantation.

Electron localization and magnetism in SrRuO3 with non-magnetic cation substitution

The destruction of the ferromagnetism of alloyed SrRuO(3) can be caused by electron localization at the substitution sites. Among all the non-magnetic cations that enter the B site, Zr(4+) is the least disruptive to conductivity and ferromagnetism. This is because Zr(4+) does not cause any charge disorder, and its empty d electron states which are poorly matched in energy with the Ru t(2g)(4) states cause the least resonance scattering of Ru's d electrons. Conducting Sr(Ru, Zr)O(3) may be used as an electrode for perovskite-based thin film devices, while its insulating counterpart provides unprecedented magnetoresistance, seldom seen in other non-manganite and non-cobaltite perovskites.

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine.

Genomic indicators in the blood predict drug-induced liver injury

Genomic biomarkers for the detection of drug-induced liver injury (DILI) from blood are urgently needed for monitoring drug safety. We used a unique data set as part of the Food and Drug Administration led MicroArray Quality Control Phase-II (MAQC-II) project consisting of gene expression data from the two tissues (blood and liver) to test cross-tissue predictability of genomic indicators to a form of chemically induced liver injury. We then use the genomic indicators from the blood as biomarkers for prediction of acetaminophen-induced liver injury and show that the cross-tissue predictability of a response to the pharmaceutical agent (accuracy as high as 92.1%) is better than, or at least comparable to, that of non-therapeutic compounds. We provide a database of gene expression for the highly informative predictors, which brings biological context to the possible mechanisms involved in DILI. Pathway-based predictors were associated with inflammation, angiogenesis, Toll-like receptor signaling, apoptosis, and mitochondrial damage. The results show for the first time and support the hypothesis that genomic indicators in the blood can serve as potential diagnostic biomarkers predictive of DILI.

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

Batch effects are the systematic non-biological differences between batches (groups) of samples in microarray experiments due to various causes such as differences in sample preparation and hybridization protocols. Previous work focused mainly on the development of methods for effective batch effects removal. However, their impact on cross-batch prediction performance, which is one of the most important goals in microarray-based applications, has not been addressed. This paper uses a broad selection of data sets from the Microarray Quality Control Phase II (MAQC-II) effort, generated on three microarray platforms with different causes of batch effects to assess the efficacy of their removal. Two data sets from cross-tissue and cross-platform experiments are also included. Of the 120 cases studied using Support vector machines (SVM) and K nearest neighbors (KNN) as classifiers and Matthews correlation coefficient (MCC) as performance metric, we find that Ratio-G, Ratio-A, EJLR, mean-centering and standardization methods perform better or equivalent to no batch effect removal in 89, 85, 83, 79 and 75% of the cases, respectively, suggesting that the application of these methods is generally advisable and ratio-based methods are preferred.

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results.

Effects of bone morphogenetic protein-2 on proliferation and angiogenesis in oral squamous cell carcinoma

Experimental data and limited patient experience suggest that rhBMP-2 can be used to regenerate bone in acquired segmental defects of the mandible. Most of these defects are caused by resection of oral squamous cell carcinoma (OSCC) and the biologic effects of rhBMP-2 on these carcinoma cells are unknown. The objective of this study was to determine whether rhBMP-2 produces adverse effects on proliferation and angiogenesis in OSCC, two biologic processes critical to tumor formation. In vitro studies included treating OSCC cells with rhBMP-2 or an adenoviral vector containing the cDNA for BMP-2. In vivo studies involved co-transplantation of OSCC cells with bone marrow stromal cells genetically modified to over express BMP-2, to mimic a clinically relevant scenario for regenerating bone using cell-based therapy in a wound containing microscopic residual disease. Proliferation, as measured by a MTT assay in vitro and tumor growth in vivo was not affected by treatment with BMP-2. Angiogenesis, measured by secretion of the proangiogenic molecules VEGF and IL-8 in vitro and microvessel density in vivo, was not affected. Exposure of OSCC cells to BMP-2 does not stimulate proliferation or angiogenesis. Further studies are needed before using rhBMP-2 for bone tissue engineering in oral cancer-related defects.