Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project

Quantitative structure-activity relationship (QSAR) models are powerful in silico tools for predicting the mutagenicity of unstable compounds, impurities and metabolites that are difficult to examine using the Ames test. Ideally, Ames/QSAR models for regulatory use should demonstrate high sensitivity, low false-negative rate and wide coverage of chemical space. To promote superior model development, the Division of Genetics and Mutagenesis, National Institute of Health Sciences, Japan (DGM/NIHS), conducted the Second Ames/QSAR International Challenge Project (2020-2022) as a successor to the First Project (2014-2017), with 21 teams from 11 countries participating. The DGM/NIHS provided a curated training dataset of approximately 12,000 chemicals and a trial dataset of approximately 1,600 chemicals, and each participating team predicted the Ames mutagenicity of each trial chemical using various Ames/QSAR models. The DGM/NIHS then provided the Ames test results for trial chemicals to assist in model improvement. Although overall model performance on the Second Project was not superior to that on the First, models from the eight teams participating in both projects achieved higher sensitivity than models from teams participating in only the Second Project. Thus, these evaluations have facilitated the development of QSAR models.

Robotic versus laparoscopic left colectomy with complete mesocolic excision for left-sided colon cancer: a multicentre study with propensity score matching analysis

BACKGROUND

Robotic surgery for right-sided colon and rectal cancer has rapidly increased; however, there is limited evidence in the literature of advantages of robotic left colectomy (RLC) for left-sided colon cancer. The purpose of this study was to compare the outcomes of RLC versus laparoscopic left colectomy (LLC) with complete mesocolic excision (CME) for left-sided colon cancer.

METHODS

Patients who had RLC or LLC with CME for left-sided colon cancer at 5 hospitals in China between January 2014 and April 2022 were included. A one-to-one propensity score matched analysis was performed to decrease confounding. The primary outcome was postoperative complications occurring within 30 days of surgery. Secondary outcomes were disease-free survival, overall survival and the number of harvested lymph nodes.

RESULTS

A total of 292 patients (187 males; median age 61.0 [20.0-85.0] years) were eligible for this study, and propensity score matching yielded 102 patients in each group. The clinical-pathological characteristics were well-matched between groups. The two groups did not differ in estimated blood loss, conversion to open rate, time to first flatus, reoperation rate, or postoperative length of hospital stay (p > 0.05). RLC was associated with a longer operation time (192.9 ± 53.2 vs. 168.9 ± 52.8 minutes, p=0.001). The incidence of postoperative complications did not differ between the RLC and LLC groups (18.6% vs. 17.6%, p = 0.856). The total number of lymph nodes harvested in the RLC group was higher than that in the LLC group (15.7 ± 8.3 vs. 12.1 ± 5.9, p< 0.001). There were no significant differences in 3-year and 5-year overall survival or 3-year and 5-year disease-free survival.

CONCLUSIONS

Compared to laparoscopic surgery, RLC with CME for left-sided colon cancer was found to be associated with higher numbers of lymph nodes harvested and similar postoperative complications and long-term survival outcomes.

Angular dependence of spin-flop transition in triangular lattice antiferromagnet Cu2(OH)3Br

We report angular dependence of spin-flop transition in triangular lattice antiferromagnet Cu₂(OH)₃Br by angle-dependent magnetization and ESR measurements. The results show that the antiferromagnetic easy magnetization axis is the diagonal direction (θ= 45°) of theac^*plane, i.e., the orientation of Cu1 spins based on the magnetic structure (2020Phys. Rev. Lett.125037204), whereas the spin-flop axis is thebaxis. A phenomenological model is proposed to describe the angle-dependent spin-flop transitions. Based on this model, Cu1 spins are sensitive to external magnetic field, while Cu2 spins are robust against to the field, showing partial decoupling. The model is expected to be used in other uniaxial antiferromagnets with a more general easy axis and complex spin-flop transitions.

Combined transabdominal-transanal surgical approach for iatrogenic rectovaginal fistula: two case reports

Rectovaginal fistula (RVF) is a type of anastomotic leakage that may occur after low anterior resection for rectal cancer. The repair of RVF can be challenging because of the scar tissue stenosis and incomplete obstruction. Two patients presented in our department with vaginal faecal discharge almost 7 months after the radical resection of rectal cancer. On vaginal examination, titanium nails related to the rectal surgery were found in the vaginal wall. The patients were diagnosed with RVF. Considering that RVF positions in the patients were high and might adhere to the pelvic tissue, a combined transabdominal-transanal resection and vaginal repair surgery was performed. About 3 months after surgery, both patients underwent colonic closure surgery, with consequent good recovery. A combined transabdominal-transanal approach may provide distinct advantages in surgical repair of difficult cases of RVF.

Combined transabdominal-transanal surgical approach for iatrogenic rectovaginal fistula: two case reports

Rectovaginal fistula (RVF) is a type of anastomotic leakage that may occur after low anterior resection for rectal cancer. The repair of RVF can be challenging because of the scar tissue stenosis and incomplete obstruction. Two patients presented in our department with vaginal faecal discharge almost 7 months after the radical resection of rectal cancer. On vaginal examination, titanium nails related to the rectal surgery were found in the vaginal wall. The patients were diagnosed with RVF. Considering that RVF positions in the patients were high and might adhere to the pelvic tissue, a combined transabdominal-transanal resection and vaginal repair surgery was performed. About 3 months after surgery, both patients underwent colonic closure surgery, with consequent good recovery. A combined transabdominal-transanal approach may provide distinct advantages in surgical repair of difficult cases of RVF.

LncRNA CASC11 promotes the development of lung cancer through targeting microRNA-302/CDK1 axis

OBJECTIVE

To elucidate whether long non-coding RNA cancer susceptibility candidate 11 (lncRNA CASC11) could participate in the development of lung cancer through targeting microRNA-302/CDK1 axis.

PATIENTS AND METHODS

Expression levels of CASC11, microRNA-302 and CDK1 in lung cancer tissues and paracancerous tissues were determined by quantitative real-time polymerase chain reaction (qRT-PCR). CASC11 expression in lung cancer cell lines was also determined. The regulatory effect of CASC11 on proliferative potential of lung cancer cells was accessed by cell counting kit-8 (CCK-8) and colony formation assay. The binding condition between microRNA-302 to CASC11 and CDK1 was evaluated by dual-luciferase reporter gene assay. CDK1 expression in lung cancer cells with CASC11 or microRNA-302 knockdown was detected by Western blot. The proliferation of lung cancer cells was determined after transfection of microRNA-302 inhibitor or co-transfection of microRNA-302 inhibitor and si-CASC11.

RESULTS

CASC11 and CDK1 were highly expressed, whereas microRNA-302 was lowly expressed in lung cancer tissues. Identically, CASC11 was highly expressed in lung cancer cell lines (A547, H157 and SPC-A-1) than controls as well. CASC11 knockdown attenuated proliferative capacity of lung cancer cells. The opposite trend was observed by microRNA-302 knockdown. Dual-luciferase reporter gene assay verified that CASC11 could bind to microRNA-302 and microRNA-302 could bind to CDK1. CDK1 expression in lung cancer cells was negatively regulated by CASC11. MicroRNA-302 knockdown reversed the inhibitory effect of CASC11 on CDK1 expression. The proliferation of lung cancer cells co-transfected with microRNA-302 inhibitor and si-CASC11 decreased compared with those transfected with microRNA-302 inhibitor.

CONCLUSIONS

High expression of CASC11 promotes the development of lung cancer through upregulating CDK1 expression by binding to microRNA-302.

Value of contrast-enhanced ultrasound in the diagnosis of breast US-BI-RADS 3 and 4 lesions with calcifications

AIM

To evaluate the diagnostic performance of contrast-enhanced ultrasound (CEUS) for Breast Imaging-Reporting and Data System for Ultrasound (US-BI-RADS) 3 and 4 lesions with calcifications.

MATERIALS AND METHODS

A retrospective study of 168 breast lesions with calcifications detected on both mammography and conventional ultrasonography (US) in 152 patients were categorised as US-BI-RADS 3-4 at US between June 2009 and June 2018. CEUS scores were obtained based on a CEUS five-point scoring system. The combination of US-BI-RADS and CEUS scores created the Rerated BI-RADS (referred to as CEUS-BI-RADS). All results were compared with the histological findings. The diagnostic performances of US and CEUS-BI-RADS were compared.

RESULTS

The diagnostic sensitivity, specificity, and accuracy of US were 81.8% (95% confidence interval [CI]: 71.6%, 92%), 85% (95% CI: 78.4%, 91.5%), and 83.9% (95% CI: 78.4%, 89.5%), respectively, while those for CEUS-BI-RADS were 98.2% (95% CI: 94.7%, 100%), 90.3% (95% CI: 84.8%, 95.7%), and 92.9% (95% CI: 89%, 96.8%), respectively. The diagnostic sensitivity and accuracy values of CEUS-BI-RADS greatly improved compared with those of US (p=0.003 and p=0.004, respectively). The areas under the receiver operating characteristic (ROC) curves for US and CEUS-BI-RADS were 0.888 (95% CI: 0.840, 0.936) and 0.963 (95% CI: 0.936, 0.989), respectively. The diagnostic efficacy of CEUS-BI-RADS was significantly higher than that of US alone (p=0.004).

CONCLUSION

CEUS-BI-RADS significantly improves the diagnostic accuracy for breast US-BI-RADS 3 and 4 lesions with calcifications compared with US.

Long noncoding RNA CRNDE promotes proliferation, migration and invasion in prostate cancer through miR-101/Rap1A

Prostate cancer (Pca) is the second frequent malignancy in men. Long noncoding RNAs (lncRNAs) have been reported to play essential roles in the progression of cancers, including Pca. LncRNA colorectal neoplasia differentially expressed (CRNDE) has been found to affect tumorigenesis in many cancers. However, the exact role and mechanism of CRNDE in Pca remain poorly understood. 64 Pca patients were recruited in this study. PC3 and 22RV1 cells were used in vitro experiments. The expressions of CRNDE, microRNA-101 (miR-101), and Ras-related protein 1A (Rap1A) were detected in vivo and in vitro by quantitative real-time polymerase chain reaction and western blot, respectively. Cell proliferation, apoptosis, migration, and invasion were investigated through cell counting kit-8, flow cytometry, and Transwell assays, respectively. The interaction between miR-101 and CRNDE or Rap1A was explored by bioinformatics analysis and luciferase reporter assay. High expression of CRNDE was shown in Pca tissues and cells and predicted poor outcomes of patients. Overexpression of CRNDE promoted cell proliferation, migration, and invasion but decreased apoptosis in Pca cells, while its knockdown showed an opposite effect. CRNDE was a decoy of miR-101 and its effect on Pca progression was reversed by miR-101. Rap1A was identified as a target of miR-101 and it attenuated the effect of miR-101 on Pca development. Moreover, the Rap1A protein level was positively regulated by CRNDE, which was weakened by miR-101. CRNDE contributed to cell proliferation, migration, and invasion by regulating the miR-101/Rap1A axis in Pca, providing a novel strategy for Pca treatment.

Possible magnetic correlation above the ferromagnetic phase transition temperature in Cr2Ge2Te6

Cr₂Ge₂Te₆ has recently emerged as a new two-dimensional ferromagnetic semiconductor (2DFMS) that is promising for spintronic applications. The origin of the ferromagnetism is a debatable point. In this study, ac/dc susceptibility and electronic spin resonance (ESR) measurements are performed to explore the origin of the ferromagnetism in Cr₂Ge₂Te₆. Through the ac susceptibility scaling, the critical temperature T_C = 62.84 K and δ = 5.24 from the critical isotherm, γ + β = 1.78 from the temperature dependence of the crossover line and γ = 1.43 from the temperature dependence of the susceptibility along the same line. Unlike Cr₂Si₂Te₆ whose magnetism can be well described by the 2D-Ising model, Cr₂Ge₂Te₆ cannot be simply described by a single theory model. Meanwhile, the origin of the abnormal critical behavior has been explored and it may be related to the presence of the possible magnetic correlation around the high temperature T* ∼ 160 K, which is confirmed by different probing measurements. The magnetic correlation at high temperature accompanied by the strong magnetic-crystalline anisotropy at low temperature plays an important role in the origin of the abnormal ferromagnetism in Cr₂Ge₂Te₆. Our results may supply a typical reference to investigate the abnormal ferromagnetism of 2DFMSs.

Review article: therapeutic bile acids and the risks for hepatotoxicity

BACKGROUND

Bile acids play important roles in cholesterol metabolism and signal through farnesoid X receptor and G protein-coupled receptors. Given their importance in liver biology, bile acid therapy enables therapeutic applications beyond the treatment of cholestatic liver disease. However, predicting hepatotoxicity of bile acids in humans is obscured due to inconsistent extrapolations of animal data to humans.

AIM

To review the evidence that could explain discordant bile acids hepatotoxicity observed in humans and animals.

METHOD

Literature search was conducted in PubMed using keywords "bile acid," "transporter," "hepatotoxicity," "clinical study," "animal study," "species difference," "mechanism," "genetic disorder." Relevant articles were selected for review.

RESULTS

Clinically significant hepatotoxicity was reported in response to certain bile acids, namely chenodeoxycholic acid, which was given a boxed warning for potential hepatotoxicity. The chemical structure, specifically the number and orientation of hydroxyl groups, significantly affects their hydrophobicity, an important factor in bile acid toxicity. Experimental studies show that hydrophobic bile acids can lead to liver injury through various mechanisms, such as death receptor signalling, mitochondrial dysfunction and inflammation. Although animal studies play a central role in investigating bile acid safety, there are considerable differences in bile acid composition, metabolism and hepatobiliary disposition across species. This does not allow appropriate safety inference, especially for predicting hepatotoxicity in humans. Exploring evidences stemming from inborn errors, genetic models of disease and toxicology studies further improves an understanding of bile acid hepatotoxicity.

CONCLUSION

Species differences should be considered in the development of bile acid related therapeutics. Although the mechanism of bile acid hepatotoxicity is still not fully understood, continued mechanistic studies will deepen our understanding.

Downregulation of PCK2 remodels tricarboxylic acid cycle in tumor-repopulating cells of melanoma

For cancer cells to proliferate, a balance must be built between biomass-forming, glucose-metabolized intermediates and ATP production. How intrinsic glucose carbon flow regulates this balance remains unclear. Here we show that mitochondrial phosphoenolpyruvate carboxykinase (PCK2), the hub molecule linking tricarboxylic acid (TCA) cycle, glycolysis and gluconeogenesis by conversion of mitochondrial oxaloacetate (OAA) to phosphoenolpyruvate, regulates glucose carbon flow direction in stem-like cells that repopulate tumors (tumor-repopulating cells (TRCs)). PCK2 downregulation accelerated biosynthesis and transportation of citrate from mitochondria to the cytosol, leading to cytosolic glucose carbon flow via OAA-malate-pyruvate and acetyl-CoA-fatty acid pathways in TRCs. On the other hand, downregulating PCK2 hindered fumarate carbon flows in TCA cycle, leading to attenuated oxidative phosphorylation. In pathological terms, PCK2 overexpression slowed TRC growth in vitro and impeded tumorigenesis in vivo. Overall, our work unveiled unexpected glucose carbon flows of TRCs in melanoma that have implications for targeting metabolic aspects of melanoma.

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.

Toluene diisocyanate enhances human bronchial epithelial cells' permeability partly through the vascular endothelial growth factor pathway

BACKGROUND

Toluene diisocyanate (TDI) is a recognized chemical asthmogen; yet, the mechanisms of its toxicity have not been elucidated.

OBJECTIVE

To investigate the influence of TDI on the permeability of human bronchial epithelial cell (HBE; HBE135-E6E7) monolayers in vitro, and the expression of vascular endothelial growth factor (VEGF) in these cells.

METHODS

TDI-human serum albumin (HSA) conjugates were prepared by a modification of Son's method. Fluorescein isothiocyanate-labelled dextran and transmission electron microscopy were used to evaluate the effects of TDI-HSA on HBE135-E6E7 permeability. RT-PCR and ELISA were used to evaluate VEGF gene expression and protein release from HBE135-E6E7 cells stimulated by TDI-HSA. A VEGF-neutralizing antibody was used in monolayer permeability experiments to determine the role of the VEGF pathway in this process.

RESULTS

TDI-HSA significantly increased the permeability coefficients of HBE135-E6E7 monolayers (P<0.01). TDI-HSA treatment significantly increased the expression of VEGF165 and VEGF189 genes (P<0.01). ELISA showed that TDI significantly induces VEGF release from HBE135-E6E7 cells. Cells treated with TDI-HSA and VEGF-neutralizing antibody had significantly lower permeability coefficients than cells treated with TDI-HSA only (P<0.01), but still significantly higher than control cells (P<0.01). Cells treated with TDI-HSA had fewer tight junctions (TJs) than control and HSA-treated cells, and addition of the anti-VEGF antibody did not restore the original number of TJs.

CONCLUSION

TDI increases the permeability of HBE cell monolayers, partly through a VEGF-mediated pathway. This suggests the importance of VEGF in TDI-induced pulmonary diseases, but shows that other pathways may be involved in the pathogenic process.

In vitro and in vivo anti-leukemia activity of CHR-2845, a cell-targeted HDAC inhibitor for use in monocytic leukemia

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Background: Histone deacetylase inhibitors alter gene expression and induce apoptosis in a wide range of cancer cells including those derived from human leukemias. CHR-2845 is a novel hydroxamic acid derivative histone deacetylase inhibitor (HDACi) which is a selective substrate for the intracellular carboxylesterase hCE-1, whose expression is restricted to cells of the monocyte- macrophage lineage. Methods: We studied the in vitro and in vivo anti-leukemia activity of CHR-2845 using cell proliferation assay, annexin V binding assay, cell cycle analysis, western blot and in vitro primary leukemia cell culture. Results: Both U937 and THP1 cells express high levels of hCE-1 whereas the myeloid cell line, HL60, does not. In comparison to vorinostat, CHR-2845 showed increased anti-proliferative potency (IC50) against monocytic cell lines (THP1, 30 nM vs 700 nM and U937, 30 nM vs 475 nM), compared to a myeloid cell line (HL60, 700nM vs 470 nM). In a broad panel of leukemic cell lines, the potency of CHR-2845 over vorinostat correlated completely with hCE-1 expression. In monocytic cell lines, CHR-2845 induced more apoptosis than vorinostat (THP1: 45±5% vs 11±1% and U937: 23±14% vs 6±1%), as measured by flow cytometry using Annexin V. Biochemical assessment of histone H3 and H4 protein acetylation by Western blot also indicateed that CHR-2845 is at least 10 times more potent than vorinostat in monocytic cell lines but not in HL-60 cells. This increase in histone acetylation was associated with increased phosphohistone H2AX, indicating formation of double-strand DNA breaks induced by this compound. These data for CHR-2845 and vorinostat on apoptosis and histone acetylation in THP1 and U937 versus HL60 cells, confirmed the selectivity of this novel compound for cells of the monocytic lineage. We also studied the anti-leukemia activity of CHR-2845 in primary leukemia cells from 8 patients with acute or chronic myelomonocytic leukemia. CHR-2845 decreased proliferation and induced apoptosis more than an equivalent dose of vorinostat in some of the patients we studied. Conclusions: These results indicated that CHR-2845 has potential to be efficacious in the treatment of patients with monocytic leukemia.

[Table: see text]

Treatment and outcomes of elderly versus younger patients with advanced NSCLC at Mayo Clinic Arizona (MCA)

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Background: Non-small cell lung cancer (NSCLC) is predominantly a disease of the elderly. Most patients (pts) present with incurable advanced disease, but chemotherapy for good performance status (PS) pts improves quality and quantity of life. Despite good PS, many elderly pts with metastatic NSCLC do not receive chemotherapy. This study compared treatment, outcomes, and survival in elderly vs younger pts with stage IV NSCLC. Methods: All analytic MCA Cancer Registry pts with stage IV NSCLC from 1998–2007 were retrospectively reviewed for type of therapy and outcome. Pts were analyzed by age: <75 vs ≥75 years old. Categorical variables were compared using chi-squared tests and survival was compared by Cox regression. Results: 344 pts with stage IV NSCLC were identified. 234 (68%) pts were <75 years old, and 110 pts (32%) were ≥75 years old. Median survival for all pts was 7 months. Among 302 pts with treatment data available, 60.8% of pts <75 years old received some form of systemic therapy (chemotherapy/targeted therapy) compared to only 32% of pts ≥ 75 years old (p <0.0001). Among pts with PS 0–1, pts <75 years old more frequently received systemic therapy than elderly patients (88.5% vs 32.1%, p<0.0001); whereas a difference was not evident in pts with PS 2–4 (34.1% vs 41.7%, p=0.49). Median survival in the <75 age group was 7 months vs. 3.4 months in the ≥75 age group (p=0.048). In the <75 age group, median survival was 12 months in pts who received chemotherapy vs. 2 months in the other or no treatment group (p<0.0001). In the elderly group, median survival was 10 months in the chemotherapy group vs. 2 months in the pts who received other or no treatment (p=0.0003). Thus, the median survival was significantly improved among the pts who received systemic therapy independent of age. Statistical significance persisted when stratifying by PS. Conclusions: Pts with stage IV NSCLC have improved survival with systemic therapy independent of age. Our results confirm that despite an improvement in survival similar to younger pts, elderly patients with metastatic NSCLC are often undertreated. Prospective trials should be designed to include metastatic NSCLC patients without age discrimination

No significant financial relationships to disclose.

The prevalence of lymphogranuloma venereum infection in men who have sex with men: results of a multicentre case finding study

Objective:

To determine the prevalence of lymphogranuloma venereum (LGV) and non-LGV associated serovars of urethral and rectal Chlamydia trachomatis (CT) infection in men who have sex with men (MSM).

Design:

Multicentre cross-sectional survey.

Setting:

Four genitourinary medicine clinics in the United Kingdom from 2006–7.

Subjects:

4825 urethral and 6778 rectal samples from consecutive MSM attending for sexual health screening.

Methods:

Urethral swabs or urine and rectal swabs were tested for CT using standard nucleic acid amplification tests. Chlamydia-positive specimens were sent to the reference laboratory for serovar determination.

Main outcome:

Positivity for both LGV and non-LGV associated CT serovars; proportion of cases that were symptomatic.

Results:

The positivity (with 95% confidence intervals) in rectal samples was 6.06% (5.51% to 6.66%) for non-LGV CT and 0.90% (0.69% to 1.16%) for LGV; for urethral samples 3.21% (2.74% to 3.76%) for non-LGV CT and 0.04% (0.01% to 0.16%) for LGV. The majority of LGV was symptomatic (95% of rectal, one of two urethral cases); non-LGV chlamydia was mostly symptomatic in the urethra (68%) but not in the rectum (16%).

Conclusions:

Chlamydial infections are common in MSM attending for sexual health screening, and the majority are non-LGV associated serovars. We did not identify a large reservoir of asymptomatic LGV in the rectum or urethra. Testing for chlamydia from the rectum and urethra should be included for MSM requesting a sexual health screen, but serovar-typing is not indicated in the absence of symptoms. We have yet to identify the source of most cases of LGV in the UK.