NQO1 609C > T polymorphism interaction with tobacco smoking and alcohol drinking increases colorectal cancer risk in a Chinese population

Background

NAD (P)H:quinone oxidoreductase (NQO1) catalyzes the activation of some environmental procarcinogens present in tobacco smoke or the diet. We conducted a hospital-based case–control study to evaluate the potential association between NQO1 609C > T polymorphisms and colorectal cancer risk in a Chinese population.

Methods

The study population comprised 672 histologically confirmed colorectal cancer patients and 672 frequency-matched control subjects without cancer or systemic illness. We used PCR restriction fragment length polymorphism-based methods for genotyping analyses and unconditional logistic regression model for statistical evaluations.

Results

The risk of colorectal cancer increased with the level of smoking and decreased with the consumption of tea, fresh fruits, and vegetables. In addition, we found that the NQO1 609 CT and TT genotypes were associated with an increased risk of colorectal cancer (CT: adjusted OR = 2.02, 95% CI = 1.55–2.57; TT: adjusted OR = 2.51, 95% CI = 1.82–3.47), compared with the CC genotype. Moreover, NQO1 609C > T appeared to have a multiplicative joint effect with both tobacco smoking and alcoholic drinking (P for multiplicative interactions were 0.0001 and 0.013, respectively) on colorectal cancer risk.

Conclusion

Our findings suggest that the NQO1 609C > T polymorphism plays an important role in the development of colorectal cancer in the Chinese population, which is strengthened by alcohol drinking or tobacco smoking.     

No association of functional variant in pri-miR-218 and risk of congenital heart disease in a Chinese population

Background

MiR-218 plays an important role in heart development in zebrafish. pri-miR-218 rs11134527 variant is associated with cervical cancer carcinogenesis. Therefore, we hypothesized that single nucleotide polymorphism (SNPs) in pri-miR-218 might influence susceptibility to sporadic congenital heart disease (CHD).

Methods and results

We conducted a case–control study of CHD in a Chinese population to test our hypothesis by sequencing and genotyping pri-miR-218 in 1116 CHD cases and 1219 non-CHD controls. We identified one SNP rs11134527 located in pri-miR-218 sequence. Logistic regression analyses showed that there was no significant association in genotype and allele frequencies of pri-miR-218 rs11134527 A/G polymorphism between CHD cases in overall or various subtypes and the control group. However, real-time PCR analysis showed that rs11134527 allele G significantly increased mature miR-218 expression. In vitro binding assays further revealed that the rs11134527 variant affects miR-218-mediated regulation of Robo1.

Conclusions

This is the first study to investigate the relationship between miR-218 and CHD cases. Our results demonstrate that the functional variant rs11134527 in pri-miR-218 has no major role in genetic susceptibility to sporadic CHD, at least in the population studied here.     

Prognostic value of epidermal growth factor receptor in patients with gastric cancer: A meta-analysis

Background

The epidermal growth factor receptor (EGFR) plays important roles in the development of gastric cancer. This study aims to analyze the prognostic value of EGFR in patients with gastric cancer.

Methods

A meta-analysis is performed by searching Cochrane Library, PubMed, EMBASE and Science Direct databases from Jan 1970 to May 2013. Data are extracted from studies evaluating the survival of gastric cancer patients with either positive or negative EGFR expression. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) are calculated.

Results

Totally 1600 cases of gastric cancer patients from five studies are subjected to final analysis. The HR of post-operational survival of patients with positive EGFR expression is 1.16 (95% CI: 0.94–1.43) as compared with those with negative expression, indicating that positive EGFR expression does not significantly predict the poor survival of gastric cancer.

Conclusions

EGFR expression is not an independent predictor for the survival of gastric cancer patients.     

Consistency of seasonal patterns of insect succession on pig cadavers at Yeongdo Island in Busan,Korea

Cadaver insects cause dead bodies to break down in ecological processes. Still, the knowledge has been accumulated slowly about the structure and role of the insect assemblages attending to death scenes. This study analysed the successional patterns of insects on pig cadavers in the spring, summer, and autumn from 2016 to 2019 at Yeongdo Island, Busan, South Korea. A sum of 71 insect species belonging to four orders and 21 families were sampled. Predominant insects were largely Diptera and Coleoptera. The majority of the flies were the calliphorids as Chrysomya pinguis (Walker) and Lucilia porphyrina (Walker). The most common beetles were Creophilus maxillosus (L.), Omosita japonica (Reitter), and Staphylinidae sp. regardless of seasons. Occurrence matrices were made from the successional patterns of insect species during 42 sampling intervals in the spring, 38 sampling intervals in the summer, and 26 sampling intervals in the autumn. Permutation analyses of the occurrence matrices showed that the patterns of succession were similar between spring 2016 and 2017 (P = 0.019), between summer 2016 and 2017 (P = 0.003), and between autumn 2016 and 2019 (P = 0.002). The result shows that there are clear patterns in succession between seasons, and provides the reference data to presume the death time, at least in the southeast part of South Korea.     

Application of phylogenetic networks in evolutionary studies

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.     

Association of TGF-β1 − 509 C/T, 29 C/T and 788 C/T gene polymorphisms with chronic periodontitis: A case–control study

The aim of this study was to investigate the possible association between TGF-β1 − 509 C/T (rs1800469), 29 C/T (Prol10Leu, rs1800470) and 788 C/T (Thr263Ile, rs1800472) gene polymorphisms and chronic periodontitis (CP) in a sample of Iranian population. This case–control study was conducted on 100 CP patients and 100 healthy unrelated, age-, sex-, and ethnicity-matched. Genotyping was performed by tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) technique. Our findings showed that there was a significant difference between the groups regarding TGF-β1 29 C/T (rs1800470) polymorphism (χ2 = 23.23, P < 0.0001). The CT and TT genotypes increased the risk of CP in comparison with the CC genotype (OR = 4.42, 95% CI = 2.16–9.06, P < 0.001 and OR = 5.84, 95% CI = 2.32–14.71, P < 0.001, respectively). The T allele increased the risk of CP (OR = 2.50, 95% CI = 1.66–3.74, P < 0.001) in comparison with C allele. No significant association was found among the groups regarding − 509 C/T and 788 C/T variants of TGF-β1 gene. This study shows that TGF-β1 29 C/T polymorphism, but not − 509 C/T and 788 C/T polymorphisms, may contribute to the development of CP in a sample of Iranian population. Further studies with larger sample sizes and different ethnicities are needed to validate our findings.     

Permutation‐based inference for the AUC: A unified approach for continuous and discontinuous data

We investigate rank‐based studentized permutation methods for the nonparametric Behrens–Fisher problem, that is, inference methods for the area under the ROC curve. We hereby prove that the studentized permutation distribution of the Brunner‐Munzel rank statistic is asymptotically standard normal, even under the alternative. Thus, incidentally providing the hitherto missing theoretical foundation for the Neubert and Brunner studentized permutation test. In particular, we do not only show its consistency, but also that confidence intervals for the underlying treatment effects can be computed by inverting this permutation test. In addition, we derive permutation‐based range‐preserving confidence intervals. Extensive simulation studies show that the permutation‐based confidence intervals appear to maintain the preassigned coverage probability quite accurately (even for rather small sample sizes). For a convenient application of the proposed methods, a freely available software package for the statistical software R has been developed. A real data example illustrates the application.     

Improved error bounds for genetic distances from DNA sequences

The genetic distance between two DNA sequences may be measured by the average number of nucleotide substitutions per position that has occurred since the two sequences diverged from a common ancestor. Estimates of this quantity can be derived from Markov models for the substitution process, while the variances are estimated using the delta method and confidence intervals calculated assuming normality. However, when the sampling distribution of the estimator deviates from normality, such intervals will not be accurate. For simple one-parameter models of nucleotide substitution, we propose a transformation of normal confidence intervals, which yields an almost exact approximation to the true confidence intervals of the distance estimators. To calculate confidence intervals for more complicated models, we propose the saddlepoint approximation. A simulation study shows that the saddlepoint-derived confidence intervals are a real improvement over existing methods.     

Time-course analysis of the phenols in cucumber mosaic virus-resistant, -tolerant and -susceptible tomato genotypes

In this study, changes in quantity and quality of phenolic compounds were compared in cucumber mosaic virus (CMV)-inoculated and -un-inoculated plants of nine resistant, tolerant, susceptible and highly susceptible genotypes at three different time intervals. Total phenolic contents and the number of phenolic compounds were generally increased in CMV-inoculated plants. Maximum per cent increase in total phenolic contents over un-inoculated controls was observed as 77.55% in resistant genotype TMS-1, 84.17% in tolerant genotype L06238 and 82.88% in resistant genotype L02223 after 10, 20 and 30 days of inoculation, respectively. Thin layer chromatography of inoculated and un-inoculated plants indicates that in most of the tested genotypes, the number of phenolic compounds varied from cultivar to cultivar and within the same cultivar, depending upon the status of plants and growth stages. However, the trend of increase in quantity and quality of phenolic compounds in the tested units was not constant to draw a meaningful conclusion.