非酒精性脂肪性肝炎大鼠TLR4基因及其甲基化水平的相关性研究

目的 观察非酒精性脂肪性肝炎（NASH）大鼠肝脏中Toll样受体4（TLR4）基因的表达及其甲基化水平的 变化,并探讨两者在NASH发病中的相关性。方法 将20只大鼠采用随机数字表法分为正常组与模型组,每组10 只。正常组与模型组大鼠分别饲喂普通饲料和高脂高糖饲料,于24周后处死。测量大鼠体质量及肝质量,并取各组 大鼠血清及肝脏组织,于低温保存。通过病理染色观察肝细胞的形态变化、脂肪变性及炎性细胞浸润程度。采用酶 联免疫吸附测定（ELISA）法检测血清中丙氨酸转氨酶（ALT）、天冬氨酸转氨酶（AST）、三酰甘油（TG）及总胆固醇 （TC）水平;采用免疫组织化学染色法检测肝脏CD68蛋白的表达;采用蛋白免疫印迹法检测肝脏TLR4蛋白的表达; 实时荧光定量PCR检测肝脏TLR4基因mRNA的表达;亚硫酸氢测序PCR（BSP）检测肝脏TLR4基因甲基化水平。结 果 与正常组相比,模型组肝细胞体积增大,出现大量脂肪空泡,炎性细胞浸润明显;肝指数升高,血清中ALT、AST、 TC及TG明显升高（P＜0.01）;CD68蛋白的表达含量明显升高;TLR4蛋白、mRNA表达明显升高（P＜0.01）;甲基化水 平降低（P＜0.01）。TLR4的甲基化水平与其mRNA相对含量的表达呈负相关（P＜0.01）。结论 NASH模型大鼠肝 脏TLR4基因的表达与其甲基化水平呈负相关,TLR4基因甲基化水平的降低在NASH发病因素中发挥重要作用。     

Defining in vivo dose-response curves for kidney DNA adduct formation of aristolochic acid I in rat,mouse and human by an in vitro and physiologically based kinetic modeling approach

Aristolochic acid I (AAI) is a well-known genotoxic kidney carcinogen. Metabolic conversion of AAI into the DNA-reactive aristolactam-nitrenium ion is involved in the mode of action of tumor formation. This study aims to predict in vivo AAI-DNA adduct formation in the kidney of rat, mouse and human by translating the in vitro concentration-response curves for AAI-DNA adduct formation to the in vivo situation using physiologically based kinetic (PBK) modeling-based reverse dosimetry. DNA adduct formation in kidney proximal tubular LLC-PK1 cells exposed to AAI was quantified by liquid chromatography-electrospray ionization-tandem mass spectrometry. Subsequently, the in vitro concentration-response curves were converted to predicted in vivo dose-response curves in rat, mouse and human kidney using PBK models. Results obtained revealed a dose-dependent increase in AAI-DNA adduct formation in the rat, mouse and human kidney and the predicted DNA adduct levels were generally within an order of magnitude compared with values reported in the literature. It is concluded that the combined in vitro PBK modeling approach provides a novel way to define in vivo dose-response curves for kidney DNA adduct formation in rat, mouse and human and contributes to the reduction, refinement and replacement of animal testing.     

Histone demethylase JHDM2A regulates H3K9 dimethylation in response to arsenic-induced DNA damage and repair in normal human liver cells

Long-term arsenic exposure is a worldwide public health problem that causes serious harm to human health. The liver is the main target organ of arsenic toxicity; arsenic induces disruption of the DNA damage repair pathway, but its mechanisms remain unclear. In recent years, studies have found that epigenetic mechanisms play an important role in arsenic-induced lesions. In this study, we conducted experiments in vitro using normal human liver cells (L-02) to explore the mechanism by which the histone demethylase JHDM2A regulates H3K9 dimethylation (me2) in response to arsenic-induced DNA damage. Our results indicated that arsenic exposure upregulated the expression of JHDM2A, downregulated global H3K9me2 modification levels, increased the H3K9me2 levels at the promoters of base excision repair (BER) genes (N-methylpurine-DNA glycosylase [MPG], XRCC1 and poly(ADP-ribose)polymerase 1) and inhibited their expression levels, causing DNA damage in cells. In addition, we studied the effects of overexpression and inhibition of JHDM2A and found that JHDM2A can participate in the molecular mechanism of arsenic-induced DNA damage via the BER pathway, which may not be involved in the BER process because H3K9me2 levels at the promoter region of the BER genes were unchanged following JHDM2A interference. These results suggest a potential mechanism by which JHDM2A can regulate the MPG and XRCC1 genes in the process of responding to DNA damage induced by arsenic exposure and can participate in the process of DNA damage repair, which provides a scientific basis for understanding the epigenetic mechanisms and treatments for endemic arsenic poisoning.     

New nanodrug design for cancer therapy: Its synthesis,formulation, in vitro and in silico evaluations

The aim of this study was to develop a novel nanosize drug candidate for cancer therapy. For this purpose, (S)-methyl 2-[(7-hydroxy-2-oxo-4-phenyl-2H-chromen-8-yl)methyleneamino]-3-(1H-indol-3-yl)propanoate (ND3) was synthesized by the condensation reaction of 8-formyl-7-hydroxy-4-phenylcoumarin with l -tryptophan methyl ester. Its controlled release formulation was prepared and characterized by different spectroscopic and imaging methods. The cytotoxic effects of ND3 and its controlled release formulation were evaluated against MCF-7 and A549 cancer cell lines, and it was found that both of them have a toxic effect on cancer cells. For drug design and process development, the molecular docking analysis technique helps to clarify the effects of some DNA-targeted anticancer drugs to determine the interaction mechanisms of these drugs on DNA in a shorter time and at a lower cost. By using the molecular docking analysis and DNA binding assays, the interaction between the synthesized compound and DNA was elucidated and non-binding interactions were also determined. To predict the pharmacokinetics, and thereby accelerate drug discovery, the absorption, distribution, metabolism, excretion and toxicity values of the synthesized compound were determined by in silico methods.     

Discrimination of haplotype in mitochondrial DNA mixtures using LNA-mediated PCR clamping

Locked nucleic acid (LNA) has been widely used for various genetic analyses, and has many benefits, in terms of the specificity or sensitivity of amplification, because LNA-containing primers/probes form more stable duplexes with template DNA than probes lacking LNA. Here, we developed a new method for discriminating HV1 haplotypes from mitochondrial DNA (mtDNA) mixtures by applying PCR clamping using LNA. PCR clamping is based on the selective inhibition of amplification using LNA-containing probes, which can discriminate single-nucleotide differences. Before designing probes, we selected 171 sequences with single-nucleotide variations from the HV1 region, and evaluated the specificity of LNA-containing probes for them by predicting Tm values. The differences of Tm between mismatched and exactly matched probe–template duplexes depended markedly on the type of LNA nucleotides for discriminating single-nucleotide differences, and the cytosine LNA nucleotide at the site of variations in the probes was most effective to discriminate these differences. For mixture analysis, each probe targeted one or two variations (16209C, 16217C, 16257A/16261T, 16297C/16298C, 16304C, 16362C, or 16362T) that are particularly common in the Japanese population, and seven designed probes completely inhibited the amplification of exactly matched templates. We prepared mixed samples by mixing DNA from two individuals at a ratio of 1:9, 1:4, 1:1, 4:1, or 9:1, and then performed Sanger sequencing analysis after PCR clamping with each probe. Our method distinguished each haplotype at lower ratios from two-person mixtures, and enabled sensitive detection at 12 pg of total DNA including 600 copies of mtDNA. Moreover, we analyzed three-person mixtures with representative sequences, and detected the minor haplotype of one individual present at a rate of 10% by adding two selected probes. The ability to discriminate haplotypes in mixed samples by using LNA-mediated PCR clamping indicates the potential value of mtDNA analysis in criminal investigations.     

Development and comprehensive evaluation of a noninvasive prenatal paternity testing method through a scaled trial

PurposeTo eliminate the miscarriage risks caused by traditional invasive sampling methods, we develop a noninvasive prenatal paternity testing (NIPPT) method and evaluate its efficiency, reliability and sensitivity based on a scaled trial.MethodsWe use maternal cell-free DNA and massive parallel sequencing to obtain NIPPT genotypes for parents and fetuses based on quality-controlled genome-wide single nucleotide polymorphisms (SNPs). In a preliminary testing, data from 14 pregnant women and 7 negative controls are used for setting threshold of fetal genotyping in reference to postpartum children. After that, those from 349 cases with pregnancies of 6–35 gestational weeks (GW) and 9 negative controls from non-pregnant women who have fertility experience previously are in-depth evaluated.ResultsIn all cases, the biological fathers have been successfully identified from unrelated with a combined paternity index (CPI) of 3.58 × 10¹⁸ – 1.46 × 10¹⁶⁵ for the cases versus 1.52 × 10⁻²² – 2.30 × 10^-839 for the controls. For negative controls, fetal SNPs originating from previous pregnancies could not be detected. Our NIPPT results completely aligned with the invasive prenatal test results using PCR-CE STR methods.ConclusionNIPPT can be applied to determine paternity accurately from 6 weeks after conception until birth and may serve as an alternative prenatal paternity test advantageous to the currently-used methods.     

Assessment of the transfer,persistence, prevalence and recovery of DNA traces from clothing: An inter-laboratory study on worn upper garments

Among the various items recovered from crime scenes or persons involved in a crime event, clothing items are commonly encountered and submitted for forensic DNA sampling. Depending on the case circumstances and the activity-of-interest, sampling of the garment may concentrate on collecting DNA from the wearer, or from one or more offenders who have allegedly contacted the item and/or wearer. Relative to the targeted DNA, background DNA already residing on the item from previous contacts, or transferred during or after the crime event, may also be collected during sampling and observed in the resultant DNA profile. Given our limited understanding of how, and from where, background DNA is derived on clothing, research on the transfer, persistence, prevalence, and recovery (TPPR) of DNA traces from upper garments was conducted by four laboratories. Samples were collected from several areas of two garments, each worn on separate working or non-working days and individually owned by four individuals from each of the four laboratories, and processed from DNA extraction through to profiling. Questionnaires documented activities relating to the garment prior to and during wearing, and reference profiles were obtained from the wearer and their close associates identified in the questionnaire. Among the 448 profiles generated, variation in the DNA quantity, composition of the profiles, and inclusion/exclusion of the wearer and their close associates was observed among the collaborating laboratories, participants, garments worn on different occasions, and garment areas sampled.     

DNAxs/DNAStatistX: Development and validation of a software suite for the data management and probabilistic interpretation of DNA profiles

The data management, interpretation and comparison of sets of DNA profiles can be complex, time-consuming and error-prone when performed manually. This, combined with the growing numbers of genetic markers in forensic identification systems calls for expert systems that can automatically compare genotyping results within (large) sets of DNA profiles and assist in profile interpretation. To that aim, we developed a user-friendly software program or DNA eXpert System that is denoted DNAxs. This software includes features to view, infer and match autosomal short tandem repeat profiles with connectivity to up and downstream software programs. Furthermore, DNAxs has imbedded the ‘DNAStatistX’ module, a statistical library that contains a probabilistic algorithm to calculate likelihood ratios (LRs). This algorithm is largely based on the source code of the quantitative probabilistic genotyping system EuroForMix [1]. The statistical library, DNAStatistX, supports parallel computing which can be delegated to a computer cluster and enables automated queuing of requested LR calculations. DNAStatistX is written in Java and is accessible separately or via DNAxs. Using true and non-contributors to DNA profiles with up to four contributors, the DNAStatistX accuracy and precision were assessed by comparing the DNAStatistX results to those of EuroForMix. Results were the same up to rare differences that could be attributed to the different optimizers used in both software programs. Implementation of dye specific detection thresholds resulted in larger likelihood values and thus a better explanation of the data used in this study. Furthermore, processing time, robustness of DNAStatistX results and the circumstances under which model validations failed were examined. Finally, guidelines for application of the software are shared as an example. The DNAxs software is future-proof as it applies a modular approach by which novel functionalities can be incorporated.