Regulation of gene expression in mouse germ cells upon exposure to tetrabutyltin

Tetrabutyltin is the starting material of the tributyltin and dibutyltin compounds. These tin compounds are starting materials for a wide range of organotin compounds used as stabilizers for PVC, biocides, fungicides, and anti-biofouling agents. It is commonly known that some of the environmental chemicals affect the human endocrine system. Since the 1970s, the harmful effects of endocrine disrupting chemical (EDC), Tetrabutyltin (TTBT) have been extensively studied. In the present study, we analyzed the effect of TTBT on gene regulation and expression of genes in mouse germ cells. Mouse germ cells were treated with TTBT for 3 and 24 hrs, and global gene expression was analyzed by using customized Agilent mouse arrays. We identified genes that were >2-fold differentially expressed in TTBT-treated cells than control cells (P<0.05) and analyzed their functions through Gene Ontology analysis. In a total number of 687 genes, there was differential expression between TTBT-treated and control cells. About 471 and 350 genes exhibited 2-fold (P<0.05) increased or decreased expression at 3 and 24 hrs, respectively. Additionally, in 134 genes, common and significant changes were observed in two-time series. Functional analysis of these genes showed that there were significant enrichments in some of the processes related to the reproduction such as, female gamete generation, homeostatic process, cell differentiation, response to chemical stress and reproductive process. In conclusion, the present study provides an insight on the effects of TTBT on mouse germ cells. Furthermore, it also increases our knowledge on the underlying molecular mechanisms on the adverse effects of organotin on the reproductive system.     

微小RNA在人髓母细胞瘤中的初步表达分析

目的检测人髓母细胞瘤(MB)与非肿瘤脑组织中微小RNA(miRNA)的表达差异情况,为进一步探讨miRNA参与MB发病的可能分子机制打下基础。方法选取经手术切除的MB组织标本及瘤旁正常小脑组织,分别提取总RNA和小分子RNA,在miRNA微阵列芯片中杂交检测,通过芯片扫描和数据分析,获得该病异常miRNAs表达谱。结果利用miRNA微阵列芯片技术筛选出9个MB的相关miRNAs,其中表达上调4个,表达下调5个。结论miRNA微阵列分析技术是一种快速、高效的研究生物信息的分子生物学技术;筛选出的差异表达miRNAs可能参与MB发病,为此病诊治提供了新的思路,值得进一步研究。     

Analysis of microRNA and gene expression profiling in triazole fungicide-treated HepG2 cell line

MicroRNA (miRNA) plays an important role in various diseases and in cellular and molecular responses to toxicants. In the present study, we investigated differential expression of miRNAs in response to three triazole fungicides (myclobutanil, propiconazole, and triadimefon). The human hepatoma cell line (HepG2) was treated with the above triazoles for 3 h or 48 h. miRNA-based microarray experiments were carried out using the Agilent human miRNA v13 array. At early exposure (3 h), six miRNAs were differentially expressed and at late exposure (48 h), three miRNAs were significantly expressed. Overall, this study provides an array of potential biomarkers for the above triazole fungicides. Furthermore, these miRNAs induced by triazoles could be the foundation for the development of a miRNA-based toxic biomarker library that can predict environmental toxicity.     

The role of microRNAs in cancer: diagnostic and prognostic biomarkers and targets of therapies

INTRODUCTION: miRNAs are noncoding RNAs that target specific mRNA with subsequent regulation of particular genes, implicated in various biological processes. In cancer, miRNAs could show a different expression from normal tissues. miRNAs have a role as oncogenes when they target tumor suppressor genes and similarly they are tumor suppressors when they target oncogenes. AREAS COVERED: In this review, areas covered include the role of miRNAs in cancer diagnosis, prognosis and research for achievement of therapeutic strategies implicating miRNAs in oncology. As biogenesis of miRNAs is fundamental to understand their usefulness, this has also been discussed. Both miRNA expression profiles in cancer tissues and miRNA levels in peripheral blood were studied for improvement in the management of cancer patients. EXPERT OPINION: miRNAs have the potential for better understanding of tumor biology, but could also provide clinical advancement in management and therapy of various malignancies. The possibility of miRNA detection in peripheral blood would allow an eager expansion of their application in various clinical settings for cancer. The applicability of miRNA expression profiles still needs to be defined.     

Comprehensive analysis of the effect of phytoestrogen, daidzein, on a testicular cell line, using mRNA and protein expression profile.

In this study, we examined the effects of exposure to phytoestrogen (daidzein), 17beta-estradiol (E2), diethylstilbestrol (DES) and staurosporin on the TM4 testicular cell line, using comprehensive analysis, such as cDNA microarray and two-dimension polyacrylamide gel electropholesis (2D-PAGE) analysis, and we demonstrated if these toxicogenomic analyses could classify the chemical compounds. First, RNA was extracted from TM4 cells that had been treated with daidzein (80 microM), DES, E2 (40 microM) and stauroporin (100 nM) for 30 min. We performed cDNA microarray analysis, and the expression ratio data thus obtained were then analyzed using hierarchical clustering. This hierarchical clustering showed that daidzein exposure induced a different effect on gene expression change from that of E2, DES and staurosporin. Next, protein extracted from TM4 cells also underwent cDNA microarray analysis for 3 h. We performed 2D-PAGE analysis, and the spot intensity ratio data thus obtained were analyzed using hierarchical clustering. As with cDNA microarray, the hierarchical clustering of protein spot ratios showed that daidzein exposure induced a different effect on gene expression change from that of the other substances. In conclusion, we have demonstrated for the first time that classification of these chemicals can be performed by clustering analysis, using data from cDNA microarray and 2D-PAGE analyses, and that exposure to daidzein induces effects different from those of E2, DES and staurosporin.     

The changes of miRNA expression in rat hippocampus following chronic lead exposure

miRNAs have been found to contribute to normal brain functions, nervous system diseases, as well as neurotoxicities induced by external agents. However, whether they are involved in lead-induced neurotoxicities is still not clear. To identify that, a lead-induced chronic neurotoxicity model of rats was built. Both miRNA microarray analysis and qRT-PCR were performed to determine the change of miRNA expression in hippocampus. Then 3 bioinformatics databases were used to analyze the relative target genes of these miRNA, which were further confirmed by qRT-PCR and Western blot. In the present study, lead exposure resulted in the changed expression of 7 miRNAs: miR-204, miR-211, miR-448, miR-449a, miR-34b, and miR-34c were greatly up-regulated while miR-494 was greatly down-regulated. Bioinformatics analysis results showed that the target genes of 6 up-regulated miRNAs were related to neural injury and neurodegeration, axon and synapse function, neural development and regeneration. Correspondingly, the expression levels of mature mRNAs and proteins of three target genes (Bcl-2, Itpr1, and Map2k1) were greatly repressed, verifying the results of bioinformatics analysis. Taken together, our results showed that the expression of several miRNAs reported to be associated with neurophysiological pathways and neurodegenerative diseases changed in rat hippocampus following chronic lead exposure. These miRNAs may play important roles in lead-induced neurotoxicity.     

神经母细胞瘤血浆外泌体差异表达miRNA靶基因预测及生物信息学分析

目的通过生物信息学分析筛选出神经母细胞瘤外周血血浆外泌体中差异表达miRNA,并对其靶基因功能进行分析预测。方法从高通量基因表达数据库下载数据集GSE128004,分析神经母细胞瘤血浆外泌体中miRNA的差异表达;通过miRTarBase数据库筛选差异表达miRNA的靶基因;进一步通过运用clusterProfiler进行靶基因的基因本体(GO)功能富集与京都基因与基因组百科全书数据库(KEGG)通路富集。结果经筛选发现,数据集GSE128004包含41个表达差异在2倍以上的血浆外泌体miRNA。靶基因预测显示,hsa-miR-199a-3p, hsa-miR-196b-5p, hsa-miR-127-3p, hsa-miR-410-3p和hsa-miR-487b-3p为靶基因最多的前5个差异表达miRNA。GO功能分析发现,这些靶基因大都在细胞运动正调节、细胞迁移正调节、血管生成等生物过程富集;在膜侧、细胞-基底连接、细胞-基底黏附连接、焦点黏连等细胞组成富集;在蛋白丝氨酸/苏氨酸激酶活性、蛋白异二聚体化活性、转录因子活性和RNA聚合酶Ⅱ核心启动子近端区序列特异性结合等分子功能富集。KEGG分析显示:这些差异表达miRNA的靶基因主要参与磷脂酰肌醇3激酶-蛋白激酶B信号通路、癌症相关miRNA、丝裂原活化蛋白激酶信号通路等通路富集。结论 hsa-miR-199a-3p, hsa-miR-127-3p和hsa-miR-410-3p可能作为神经母细胞瘤的潜在生物标志物或治疗靶标,进一步为该病的发病机制提供研究思路。     

Chir99021联合PD0325901对小鼠胚胎干细胞中miRNAs差异表达的影响

目的：通过研究Chir99021联合PD0325901对小鼠胚胎干细胞中miRNAs差异表达的影响,为揭示胚胎干细胞的自我更新和分化的机制提供更多线索。方法采用miRNA基因芯片技术检测Chir99021联合PD0325901处理组和PD0325901处理组miRNAs的表达谱差异。选取3倍以上及通过查文献与胚胎干细胞自我更新相关的1.5倍以上3倍以下的miRNAs,采用实时荧光定量PCR法验证,利用miRDB、Miranda两个数据库交叉预测差异表达的靶基因,并应用KEGG Pathway进行靶基因功能富集分析。结果与PD0325901单独处理相比,Chir99021联合PD0325901处理组有47种miRNAs上调1.5倍以上,75种miRNAs下调1.5倍以上;用实时荧光定量PCR验证差异表达的miRNAs,结果显示13个miRNAs与芯片结果相符。靶基因预测分析显示,miR-466a-5p、miR-466d-5p处于重要位置,Plcb1、Prkcb处于关键基因位置。结论 Chir99021可引起小鼠胚胎干细胞中的miRNAs差异表达,差异表达的miRNAs可能通过调控Plcb1、Prkcb基因而影响胚胎干细胞的自我更新。     

Long-term alteration of gene expression without morphological change in testis after neonatal exposure to genistein in mice: toxicogenomic analysis using cDNA microarray.

In this study, we carried out toxicogenomic analysis using in-house cDNA microarray to ascertain the long-term effects of neonatal exposure to genistein, also known as phytoestrogen, on testicular gene expression in mice. Male ICR mice, 1 day after birth, were exposed for 5 days to genistein (1000 microg/mouse/day) or diethylstilbestrol (DES) (50 microg/mouse/day), used as an example of a potent estrogen, and their testes were used when they were 12 weeks old. Since exposure to DES was been reported to induce morphological changes and alteration of gene expression in reproductive organs, DES was used as a positive control. Genistein-treated mice did not show any histological abnormalities or increased apoptotic cells in testes, but these abnormalities and increases were found in DES-treated mice. On the other hand, mRNA expression analysis using in-house cDNA microarray revealed that 2 down-regulated genes (GeneBank accession No. W49392 and AI430907) were detected in genistein-treated mouse testes. Moreover, real-time PCR analysis revealed that mRNAs of the W49392 gene, estrogen receptor alpha (ERalpha) and androgen receptor (AR), were down-regulated in the testes of both genistein-treated and DES-treated mice. In our present study using toxicogenomic analysis, long-term alteration in testicular mRNA expression, without morphological change in testes, was detected after neonatal treatment with genistein, indicating that the W49392 gene, in addition to ERalpha and AR, might be useful as a biological marker for predicting the effects of neonatal exposure to DES and genistein.     

Differential expression of microRNAs and their predicted targets in renal cells exposed to amphotericin B and its complex with copper (II) ions

MicroRNAs (miRNAs) have been reported to regulate essential biological processes, and their expression was shown to be affected by pathological processes and drug-induced toxicity. Amphotericin B (AmB) can cause liver and kidney injury, but a recently developed complex of AmB with copper (II) ions (AmB–Cu²⁺) exhibits a lower toxicity to human renal cells while retaining a high antifungal activity. The aim of our study was to assess AmB–Cu²⁺-induced changes in the miRNA profile of renal cells and examine which biological processes are significantly affected by AmB–Cu²⁺. We also aimed to predict whether differentially expressed miRNAs would influence observed changes in the mRNA profile. miRNA and mRNA profiles in normal human renal proximal tubule epithelial cells (RPTEC) treated with AmB–Cu²⁺ or AmB were appointed with the use of microarray technology. For differentially expressed mRNAs, the PANTHER overrepresentation binomial test was performed. miRNA target interactions (MTIs) were predicted using the miRTar tool. The mRNA profile was much more strongly affected than the miRNA profile, in both AmB–Cu²⁺- and AmB-treated cells. AmB–Cu²⁺ influenced both the miRNA and mRNA profiles much more strongly than AmB. The most affected biological processes were intracellular signal transduction (AmB–Cu²⁺) and signal transduction (AmB). Only a few interactions between differentiating miRNAs and mRNAs were found. Changes in the profiles of genes involved in signal transduction and intracellular signal transduction may not result from interactions with differentially expressed miRNAs. Changes in the miRNA profile suggest the possible influence of tested drugs on the regulation of fibrosis via a miRNA-dependent mechanism.     

Absence of mature microRNAs inactivates the response of gene expression to carcinogenesis induced by N‐ethyl‐N‐nitrosourea in mouse liver

This study aims to evaluate the role of microRNAs (miRNAs) in chemical tumorigenesis by evaluating genomic gene expression in miRNA knockout mice. Previous studies showed that mice without mature miRNAs due to hepatocyte‐specific Dicer1 knockout (KO) had a much higher liver tumor incidence than wild‐type mice. In this study, Dicer1 KO or the wild‐type mice were treated intraperitoneally with genotoxic carcinogen N‐ethyl‐N‐nitrosourea (ENU) at a single dose (150 mg kg^–1 that resulted in liver tumorigenesis) or the vehicle at 3 weeks of age. The animals were killed 2 weeks after treatment and the liver samples were collected for the gene expression study. Principal components analysis and hierarchical cluster analysis showed that gene expression was globally altered by the Dicer1 KO and ENU exposure. There were 5621, 3286 and 2565 differentially expressed genes for Dicer1 disruption, ENU treatment in wild‐type mice and ENU treatment in Dicer1 KO mice, respectively. Functional analysis of the differentially expressed genes suggests that the Dicer1 KO mouse liver lost their capability to suppress the carcinogenesis induced by ENU exposure in genomic level. In addition, the miRNA‐mediated BRCA1 and P53 signaling pathways were identified as the main pathways responsible for the tumorigenesis. We conclude that the mouse livers in the absence of mature miRNAs could not appropriately respond to carcinogenic insults from ENU treatment, indicating that miRNAs play a critical role in chemical carcinogenesis. Copyright © 2014 John Wiley & Sons, Ltd.