A KRAS variant is a biomarker of poor outcome, platinum chemotherapy resistance and a potential target for therapy in ovarian cancer

Germ-line variants in the 3′ untranslated region (3′UTR) of cancer genes disrupting microRNA (miRNA) regulation have recently been associated with cancer risk. A variant in the 3′UTR of the KRAS oncogene, referred to as the KRAS-variant, is associated with both cancer risk and altered tumor biology. Here we test the hypothesis that the KRAS-variant can act as a biomarker of outcome in epithelial ovarian cancer (EOC), and investigate the cause of altered outcome in KRAS-variant positive EOC patients. As this variant appears to be associated with tumor biology, we additionally test the hypothesis that this variant can be directly targeted to impact cell survival.

EOC patients with complete clinical data were genotyped for the KRAS-variant and analyzed for outcome (n=536), response to neoadjuvant chemotherapy (n=125), and platinum resistance (n=306). Outcome was separately analyzed for women with known BRCA mutations (n=79). Gene expression was analyzed on a subset of tumors with available tissue. Cell lines were employed to confirm altered sensitivity to chemotherapy with the KRAS-variant. The KRAS-variant was directly targeted through siRNA/miRNA oligonucleotides in cell lines and survival was measured.

Post-menopausal EOC patients with the KRAS-variant were significantly more likely to die of ovarian cancer by multivariate analysis (HR=1.67, 95% CI=1.09–2.57, p=0.019, n=279). Possibly explaining this finding, EOC patients with the KRAS-variant were significantly more likely to be platinum resistant (OR=3.18, CI=1.31–7.72, p=0.0106, n=291). Additionally, direct targeting of the KRAS-variant led to a significant reduction in EOC cell growth and survival in vitro.

These findings confirm the importance of the KRAS-variant in EOC, and indicate that the KRAS-variant is a biomarker of poor outcome in EOC likely due to platinum resistance. In addition, this work supports the hypothesis that these tumors have continued dependence on such 3′UTR lesions, and that direct targeting may be a viable future treatment approach.

Characterization and Safety of Uniform Particle Size NovaSil Clay as a Potential Aflatoxin Enterosorbent

NovaSil (NS) clay, a common anti-caking agent in animal feeds, has been shown to adsorb aflatoxins and diminish their bioavailability in multiple animal models. The safety of long-term dietary exposure to NS has also been demonstrated in a 6-month sub-chronic study in rats and in a 3-month intervention in humans highly exposed to aflatoxins. Uniform particle size NovaSil (UPSN) is a refined material derived from parent NS; it contains lower levels of dioxins/furans, and has been selected for a more consistent uniform particle size. Nevertheless, the efficacy and potential safety/toxicity of UPSN for long term-use has not yet been determined. In this research, 4-week-old male and female Sprague Dawley rats were fed rations free of clay (control) and containing UPSN at low dose (0.25%) and high dose (2%) for 13 weeks. AFB(1) sorption characteristics remained the same for both clays. When compared to the control, total body weight gain was unaffected in either sex at the doses tested. No UPSN-dependent differences in relative organ weights or gross appearance were observed. Isolated differences between UPSN groups and the control were observed for some biochemical parameters and selected vitamins and minerals. None of these differences were dose-dependent, and all parameters fell between ranges reported as normal for rats less than 6 month old. The Na/K ratio, Na and vitamin E concentrations were the only parameters that were increased in both males and females in the low dose and high dose UPSN groups. Serum Zn levels in males from the 2% UPSN treatment were lower compared to the control. Serum K levels were lower in the males of UPSN groups than in the control. However, neither Na/K ratio, K, nor Zn values were dose dependent and fell outside ranges reported as normal. These results suggest that dietary inclusion of UPSN at levels as high as 2% (w/w) does not result in overt toxicity. Nevertheless, further research on the effects of clays on Na, Zn, K and vitamin E is warranted.

The embryo rescue derived intergeneric hybrid between chrysanthemum and Ajania przewalskii shows enhanced cold tolerance

Five intergeneric hybrids between the chrysanthemum cultivar 'Zhongshanjingui' (as female) and Ajania przewalskii (as male) were obtained with the help of embryo culture. While 'Zhongshanjingui' bears a standard anemone type flower and A. przewalskii a non-anemone type one, the inflorescence type of the hybrids varied. The diameter of the hybrids' flowers was intermediate between those of the parents. The chromosome number of the hybrids was 2n = 45, of which GISH analysis was able to establish that 27 were inherited from 'Zhongshanjingui' and the other 18 from A. przewalskii. A combination of various assays was used to show that the cold tolerance of the hybrids was equivalent to that of the highly tolerant A. przewalskii parent. Enhanced cold tolerance was correlated with an increase in free proline and a decrease in malondialdehyde content.

The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut-brain communication

BACKGROUND

The probiotic Bifidobacterium longum NCC3001 normalizes anxiety-like behavior and hippocampal brain derived neurotrophic factor (BDNF) in mice with infectious colitis. Using a model of chemical colitis we test whether the anxiolytic effect of B. longum involves vagal integrity, and changes in neural cell function. Methods  Mice received dextran sodium sulfate (DSS, 3%) in drinking water during three 1-week cycles. Bifidobacterium longum or placebo were gavaged daily during the last cycle. Some mice underwent subdiaphragmatic vagotomy. Behavior was assessed by step-down test, inflammation by myeloperoxidase (MPO) activity and histology. BDNF mRNA was measured in neuroblastoma SH-SY5Y cells after incubation with sera from B. longum- or placebo-treated mice. The effect of B. longum on myenteric neuron excitability was measured using intracellular microelectrodes.

KEY RESULTS

Chronic colitis was associated with anxiety-like behavior, which was absent in previously vagotomized mice. B. longum normalized behavior but had no effect on MPO activity or histological scores. Its anxiolytic effect was absent in mice with established anxiety that were vagotomized before the third DSS cycle. B. longum metabolites did not affect BDNF mRNA expression in SH-SY5Y cells but decreased excitability of enteric neurons.

CONCLUSIONS & INFERENCES

In this colitis model, anxiety-like behavior is vagally mediated. The anxiolytic effect of B. longum requires vagal integrity but does not involve gut immuno-modulation or production of BDNF by neuronal cells. As B. longum decreases excitability of enteric neurons, it may signal to the central nervous system by activating vagal pathways at the level of the enteric nervous system.

Impact of luteolin on the production of alpha-toxin by Staphylococcus aureus

AIMS

To investigate the influence of subinhibitory concentrations of luteolin on the production of α-toxin in Staphylococcus aureus.

METHODS AND RESULTS

The minimal inhibitory concentrations (MICs) were determined using a broth microdilution method, and the MICs of luteolin against the tested Staph. aureus strains ranged from 16 to 64 μg ml(-1). Haemolysis, Western blot and real-time reverse transcription (RT)-PCR assays were used to evaluate the effect of luteolin on Staph. aureusα-toxin secretion and on the level of gene expression, respectively. The data indicated that subinhibitory concentrations of luteolin dose dependently decreased the production of α-toxin in both meticillin-sensitive Staph. aureus (MSSA) and meticillin-resistant Staph. aureus (MRSA). Furthermore, the transcriptional levels of agr (accessory gene regulator) in Staph. aureus were also inhibited by luteolin.

CONCLUSIONS

Luteolin decreases the production and/or secretion of α-toxin in Staph. aureus; the reduced production may be dependent, in part, upon the luteolin-induced inhibition of the agr locus.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings indicate that luteolin may be used as a basis for the development of antimicrobial agents aimed at bacterial virulence factors.

High prevalence of bla(CTX-M) extended-spectrum β-lactamase genes in Escherichia coli isolates from pets and emergence of CTX-M-64 in China

As a cause of community-acquired infections, extended-spectrum β-lactamase (ESBL)-producing Escherichia coli constitute an emerging public-health concern. Few data on the molecular epidemiology of ESBL-producing E. coli isolates from pets are available in China. Detection and characterization of ESBL genes (bla(CTX-M), bla(SHV) and bla(TEM)) was conducted among 240 E. coli isolates recovered from healthy and sick pets in South China from 2007 to 2008. The clonal relatedness of ESBL-producing E. coli isolates was assessed by pulsed field gel electrophoresis. ESBL-encoding genes were identified in 97 (40.4%) of the 240 isolates and 96 (40.0%) of them harbored CTX-M. The most common CTX-M types were CTX-M-14 (n = 45) and CTX-M-55 (n = 24). The recently reported CTX-M-64 was identified in three isolates. Isolates producing CTX-M-27, -15, -65, -24, -3 and -9 were also identified. Ten isolates carried two or three CTX-M types, with the combination of CTX-M-14 and CTX-M-55 being the most frequent (n = 6). ISEcp1 was identified in the upstream region of 93 out of the 107 bla(CTX-M) genes (86.9%). The sequence of the spacer region (45 bp) between ISEcp1 and the start codon of all bla(CTX-M-55) genes (except four) was identical to that of bla(CTX-M-64). No major clonal relatedness was observed among these CTX-M producers. It is suggested that the horizontal transfer of bla(CTX-M) genes, mediated by mobile elements, contributes to their dissemination among E. coli isolates from pets. Our finding of high prevalence of ESBL in E. coli of companion animal origin illustrates the importance of molecular surveillance in tracking CTX-M-producing E. coli strains in pets.

Chrysanthemum leaf epidermal surface morphology and antioxidant and defense enzyme activity in response to aphid infestation

Artificial aphid infestation experiments on the three chrysanthemum cultivars 'Keiun', 'Han6' and 'Jinba' showed that the three cultivars vary markedly in their resistance. Of the three cultivars, the most resistant ('Keiun') produced the longest, highest and densest trichomes, the largest and fullest gland cells, and the most wax on the lower leaf epidermis. Superoxide dismutase (EC 1.15.1.1), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), polyphenol oxidase activity (EC 1.14.18.1) and phenylalanine ammonia lyase (EC 4.3.1.5) were enhanced by aphid herbivory. In the two more resistant cultivars ('Keiun' and 'Han6'), the activity of superoxide dismutase and ascorbate peroxidase enzymes rapidly increased following infestation, and their levels remained high from seventy-two to one hundred and sixty-eight hours after inoculation. We suggest that these two antioxidant enzymes contribute to aphid resistance of these chrysanthemum cultivars. All three cultivars showed quick responses to aphid infestation by increasing polyphenol oxidase and phenylalanine ammonia lyase activities during the early period after inoculation. Activities of these two defense enzymes were higher in the two resistant cultivars after 72h after inoculation, suggesting involvement of these two enzymes in aphid resistance.

The I/D polymorphism of angiotensin-converting enzyme gene and asthma risk: a meta-analysis

BACKGROUND

  The insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) gene has been implicated in susceptibility to asthma, but a large number of studies have reported inconclusive results. The aim of this study is to investigate the association between the I/D polymorphism of ACE gene and asthma risk by meta-analysis.

METHODS

  We searched Medline (Ovid), Pubmed, CNKI, Wanfang, and Weipu database, covering all papers until March 12, 2010. Statistical analysis was performed by using the software revman 4.2 (The Cochrane Collaboration, http://www.cochrane.org) and stata 10.0 (StataCorp, College Station, TX, USA, http://www.stata.com).

RESULTS

  A total of 1946 cases and 2152 controls in 18 case-control studies were included in this meta-analysis. The results indicated that the DD homozygote carriers had a 59% increased risk of asthma, when compared with the homozygotes II and heterozygote DI [odds ratio (OR)=1.59, 95% confidence interval (CI): 1.16-2.18]. In the subgroup analysis by ethnicity, significant elevated risks were associated with DD homozygote carriers in Asians (OR=2.02 and 95% CI: 1.29-3.16 for DD vs DI+II) but not in Caucasians (OR=1.14 and 95% CI: 0.76-1.72 for DD vs DI+II). In the subgroup analysis by age, significant elevated risks were associated with DD homozygote carriers in children (OR=2.44 and 95% CI: 1.36-4.38 for DD vs II+DI) but not in adults (OR=1.54 and 95% CI: 0.94-2.51 for DD vs II+DI).

CONCLUSIONS

  This meta-analysis suggested that the I/D polymorphism of ACE gene would be a risk factor of asthma. To further evaluate gene-to-gene and gene-to-environment interactions between polymorphisms of ACE gene and asthma risk, more studies with large groups of patients are required.

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.

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.

A new pandemic influenza A(H1N1) genetic variant predominated in the winter 2010 influenza season in Australia, New Zealand and Singapore

Pandemic H1N1 influenza virus is of global health concern and is currently the predominant influenza virus subtype circulating in the southern hemisphere 2010 winter. The virus has changed little since it emerged in 2009, however, in this report we describe several genetically distinct changes in the pandemic H1N1 influenza virus. These variants were first detected in Singapore in early 2010 and have subsequently spread through Australia and New Zealand. At this stage, these signature changes in the haemagglutinin and neuraminidase proteins have not resulted in significant antigenic changes which might make the current vaccine less effective, but such adaptive mutations should be carefully monitored as the northern hemisphere approaches its winter influenza season.