Using fuzzy association rule mining in cancer classification

The classification of the cancer tumors based on gene expression profiles has been extensively studied in numbers of studies. A wide variety of cancer datasets have been implemented by the various methods of gene selection and classification to identify the behavior of the genes in tumors and find the relationships between them and outcome of diseases. Interpretability of the model, which is developed by fuzzy rules and linguistic variables in this study, has been rarely considered. In addition, creating a fuzzy classifier with high performance in classification that uses a subset of significant genes which have been selected by different types of gene selection methods is another goal of this study. A new algorithm has been developed to identify the fuzzy rules and significant genes based on fuzzy association rule mining. At first, different subset of genes which have been selected by different methods, were used to generate primary fuzzy classifiers separately and then proposed algorithm was implemented to mix the genes which have been associated in the primary classifiers and generate a new classifier. The results show that fuzzy classifier can classify the tumors with high performance while presenting the relationships between the genes by linguistic variables.     

DNA microarray technology reveals similar gene expression patterns in rats with vitamin a deficiency and chemically induced colitis

Previous studies suggest that vitamin A deficiency may induce or intensify inflammatory changes in the rat gastrointestinal system. The present study was designed to compare the expression profiles of rat models of vitamin A deficiency and induced colitis. cDNA-microarray technology was used to determine the genes involved in the inflammatory processes in the two models. mRNA was extracted from colons of rats that were vitamin A deficient, vitamin A supplemented (control), or had 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis, reverse-transcribed into fluorescence-labeled cDNA and hybridized onto microarrays containing a duplicate set of 1152 cDNAs, derived mainly from the colon carcinoma cell line Caco-2. Differential gene expression was detected in vitamin A deficiency and in TNBS-induced colitis vs. control. beta-Actin, translation initiation factor A4 and translation elongation factor 1, ornithine decarboxylase (ODC) and keratin 19 were markedly down-regulated, whereas spermidine/spermine N1-acetyltransferase (SSAT) and polyubiquitin (UbC) were up-regulated in both vitamin A-deficient rats and those with TNBS-induced colitis. The strong association between the differential gene expression in the two animal models, compared with the control, suggests that deficiency of vitamin A causes inflammatory changes in the rat colon that are similar to processes occurring in colitis. Further investigation is required to elucidate the importance of each of the regulated genes to the pathology of colitis and vitamin A inadequacy.     

Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis.     

Identification of putative gene based markers of renal toxicity

This study, designed and conducted as part of the International Life Sciences Institute working group on the Application of Genomics and Proteomics, examined the changes in the expression profile of genes associated with the administration of three different nephrotoxicants--cisplatin, gentamicin, and puromycin--to assess the usefulness of microarrays in the understanding of mechanism(s) of nephrotoxicity. Male Sprague-Dawley rats were treated with daily doses of puromycin (5-20 mg/kg/day for 21 days), gentamicin (2-240 mg/kg/day for 7 days), or a single dose of cisplatin (0.1-5 mg/kg). Groups of rats were sacrificed at various times after administration of these compounds for standard clinical chemistry, urine analysis, and histological evaluation of the kidney. RNA was extracted from the kidney for microarray analysis. Principal component analysis and gene expression-based clustering of compound effects confirmed sample separation based on dose, time, and degree of renal toxicity. In addition, analysis of the profile components revealed some novel changes in the expression of genes that appeared to be associated with injury in specific portions of the nephron and reflected the mechanism of action of these various nephrotoxicants. For example, although puromycin is thought to specifically promote injury of the podocytes in the glomerulus, the changes in gene expression after chronic exposure of this compound suggested a pattern similar to the known proximal tubular nephrotoxicants cisplatin and gentamicin; this prediction was confirmed histologically. We conclude that renal gene expression profiling coupled with analysis of classical end points affords promising opportunities to reveal potential new mechanistic markers of renal toxicity.     

Gene expression analysis of the pro-oestrous-stage rat uterus reveals neuroligin 2 as a novel steroid-regulated gene

In the present study, differential gene expression in the uteri of ovariectomised (OVX) and pro-oestrous rats (OVX v. pro-oestrus pair) was investigated using cDNA expression array analysis. Differential uterine gene expression in OVX rats and progesterone (P(4))-injected OVX rats (OVX v. OVX + P(4) pair) was also examined. The uterine gene expression profiles of these two sets of animals were also compared for the effects of P(4) treatment. RNA samples were extracted from uterine tissues and reverse transcribed in the presence of [alpha(32)P]-dATP. Membrane sets of rat arrays were hybridised with cDNA probe sets. Northern blot analysis was used to validate the relative gene expression patterns obtained from the cDNA array. Of the 1176 cDNAs examined, 23 genes showed significant (>two-fold) changes in expression in the OVX v. pro-oestrus pair. Twenty of these genes were upregulated during pro-oestrus compared with their expression in the OVX rat uterus. In the OVX v. OVX + P(4) pair, 22 genes showed significant (>two-fold) changes in gene expression. Twenty of these genes were upregulated in the OVX + P(4) animals. The genes for nuclear factor I-XI, afadin, neuroligin 2, semaphorin Z, calpain 4, cyclase-associated protein homologue, thymosin beta-4X and p8 were significantly upregulated in the uteri of the pro-oestrus and OVX + P(4) rats of both experimental pairs compared with the OVX rat uteri. These genes appear to be under the control of P(4). One of the most interesting findings of the present study is the unexpected and marked expression of the neuroligin 2 gene in the rat uterus. This gene is expressed at high levels in the central nervous system and acts as a nerve cell adhesion factor. According to Northern blot analysis, neuroligin 2 gene expression was higher during the pro-oestrus and metoestrus stages than during the oestrus and dioestrus stages of the oestrous cycle. In addition, neuroligin 2 mRNA levels were increased by both 17beta-oestradiol (E(2)) and P(4), although P(4) administration upregulated gene expression to a greater extent than injection of E(2). These results indicate that neuroligin 2 gene expression in the rat uterus is under the control of both E(2) and P(4), which are secreted periodically during the oestrous cycle.     

染矽尘大鼠毒理效应相关差异基因表达谱的研究

目的 研究染矽尘大鼠毒理效应相关差异基因表达谱.方法 应用气管暴露法对雄性Wistar大鼠进行二氧化硅(50 mg/ml)染尘,对照组大鼠气管内灌注1ml灭菌生理盐水.染尘后第14天处死大鼠,取肺组织.应用Illumina激光共聚焦光纤微珠基因芯片技术,研究大鼠肺组织差异基因表达谱,采用因注释、富集数据库(the database for annotation,visualization and integrated discovery,DAVID)生物信息学分析工具,对差异基因的基因功能和生物学通路进行富集统计学分析.结果 检测出的有效基因共22107个,筛选出染矽尘组与对照组的差异基因共1567个,其中上调基因为765个,下调基因为802个.与毒理效应相关的差异基因有461个,其中上调基因为285个,下调的有176个.Real-time PCR实验验证了血红素加氧酶(HMOX1)、过氧化物歧化酶(SOD2)基因上调的趋势和基因芯片结果是一致的.结论 二氧化硅粉尘诱导的大鼠肺组织纤维化中起毒理效应的大量相关基因上调或下调,二氧化硅所致的肺纤维化可能存在复杂的基因网络调控系统,其中,毒理机制是肺纤维化发生发展过程中的重要一环.     

基因组学技术初步分析甲基汞神经毒性功能基因

目的探讨甲基汞神经毒性差异表达基因功能。方法利用基因芯片筛选大鼠暴露体重剂量为0·5mg/Kg的氯化甲基汞后脑中的差异表达基因,并利用基因组学技术分析其功能。结果基因表达谱中差异表达基因共有303条,其中上调基因为170条,下调基因为133条。发生显著性改变的功能基因主要涉及到①免疫应答及解毒作用;②遗传信息传递与表达;③细胞信号传导;④神经传导;⑤细胞增殖与分化;⑥细胞凋亡;⑦其它未知功能等7组。在暴露组样本中,脑中有关细胞信号传导和神经传导功能基因发生了特别显著的差异表达。结论甲基汞通过对信号传导过程的影响,发挥其神经毒性的作用。     

Prediction of toxicant-specific gene expression signatures after chemotherapeutic treatment of breast cell lines

Global gene expression profiling has demonstrated that the predominant cellular response to a range of toxicants is a general stress response. This stereotyped environmental stress response commonly includes repression of protein synthesis and cell-cycle-regulated genes and induction of DNA damage and oxidative stress-responsive genes. Our laboratory recently characterized the general stress response of breast cell lines derived from basal-like and luminal epithelium after treatment with doxorubicin (DOX) or 5-fluorouracil (5FU) and showed that each cell type has a distinct response. However, we expected that some of the expression changes induced by DOX and 5FU would be unique to each compound and might reflect the underlying mechanisms of action of these agents. Therefore, we employed supervised analyses (significance analysis of microarrays) to identify genes that showed differential expression between DOX-treated and 5FU-treated cell lines. We then used cross-validation analyses and identified genes that afforded high predictive accuracy in classifying samples into the two treatment classes. To test whether these gene lists had good predictive accuracy in an independent data set, we treated our panel of cell lines with etoposide, a compound mechanistically similar to DOX. We demonstrated that using expression patterns of 100 genes we were able to obtain 100% predictive accuracy in classifying the etoposide samples as being more similar in expression to DOX-treated than to 5FU-treated samples. These analyses also showed that toxicant-specific gene expression patterns, similar to general stress responses, vary according to cell type.     

A Dirichlet process mixture model for clustering longitudinal gene expression data

Subgroup identification (clustering) is an important problem in biomedical research. Gene expression profiles are commonly utilized to define subgroups. Longitudinal gene expression profiles might provide additional information on disease progression than what is captured by baseline profiles alone. Therefore, subgroup identification could be more accurate and effective with the aid of longitudinal gene expression data. However, existing statistical methods are unable to fully utilize these data for patient clustering. In this article, we introduce a novel clustering method in the Bayesian setting based on longitudinal gene expression profiles. This method, called BClustLonG, adopts a linear mixed‐effects framework to model the trajectory of genes over time, while clustering is jointly conducted based on the regression coefficients obtained from all genes. In order to account for the correlations among genes and alleviate the high dimensionality challenges, we adopt a factor analysis model for the regression coefficients. The Dirichlet process prior distribution is utilized for the means of the regression coefficients to induce clustering. Through extensive simulation studies, we show that BClustLonG has improved performance over other clustering methods. When applied to a dataset of severely injured (burn or trauma) patients, our model is able to identify interesting subgroups. Copyright © 2017 John Wiley & Sons, Ltd.     

Chronic Intermittent Sucrose Consumption Facilitates the Ability to Discriminate Opioid Receptor Blockade with Naltrexone in Rats

The opioid antagonist naltrexone (NTX) decreases intake of preferred diets in rats at very low doses relative to doses needed to decrease intake of “bland” laboratory chow. In the absence of an opioid agonist, NTX is not discriminable using operant techniques. In the current study, we found that rats given intermittent access to a 25% sucrose solution learned to discriminate between various naltrexone doses and saline. None of the rats given only water learned to discriminate between naltrexone and saline. When access to the sucrose solution was discontinued for 14 days, the rats lost the ability to discriminate between NTX and saline. We also studied the changes of c-Fos IR in selected brain regions in rats treated with saline versus NTX that were drinking water or 25% sucrose. An injection of NTX or saline resulted in a significant drug, diet, and interaction effect in various brain regions associated with feeding behavior, particularly the amygdala, accumbens, and hypothalamic sites. Thus, we found that ingestion of a sucrose solution results in the ability of rats to reliably discriminate naltrexone administration. In addition, sucrose and naltrexone altered c-Fos IR in an interactive fashion in brain regions known to be involved in ingestion behavior.     

1-溴丙烷引发雄性大鼠性腺基因表达谱的变化

目的研究1-溴丙烷(1-BP)诱发大鼠性腺基因表达谱的变化,探索1-BP雄性生殖毒性相关的mRNA改变。方法雄性F344/NSIc大鼠12只,随机分为2组,分别吸入新鲜空气或5030mg/m31-BP8h。染毒后16h处死大鼠取出睾丸,运用大鼠性腺cDNA微阵列和real-timePCR方法测定1-BP染毒后性腺相关基因表达谱的变化。结果在大鼠性腺芯片5087个cDNA微点阵中,有62个基因被1-BP显著下调,3个基因显著上调。其中包括性激素合成相关基因细胞色素P450芳香化酶(CYP19a),谷胱苷肽S-转移酶(GSTT1),肌酸激酶(Ckb),髓鞘和淋巴细胞蛋白(Mal)和S100的钙结合蛋白(S100a4)。归类分析结果显示绝大多数变化的基因与蛋白质/脂类代谢相关,其次与应激防御反应相关。实时定量PCR证实了1-BP可引起CYP19a、S100a4、GSTT1和Mal的下调。结论急性高剂量染毒1-BP可引起睾丸组织CYP19a、S100a4、GSTT1、Mal等基因的下调,提示其可能通过内分泌干扰和氧化应激效应而导致雄性生殖毒性。     

Environmental impact on vascular development predicted by high-throughput screening

Background: Understanding health risks to embryonic development from exposure to environmental chemicals is a significant challenge given the diverse chemical landscape and paucity of data for most of these compounds. High-throughput screening (HTS) in the U.S. Environmental Protection Agency (EPA) ToxCast™ project provides vast data on an expanding chemical library currently consisting of > 1,000 unique compounds across > 500 in vitro assays in phase I (complete) and Phase II (under way). This public data set can be used to evaluate concentration-dependent effects on many diverse biological targets and build predictive models of prototypical toxicity pathways that can aid decision making for assessments of human developmental health and disease.Objective: We mined the ToxCast phase I data set to identify signatures for potential chemical disruption of blood vessel formation and remodeling.Methods: ToxCast phase I screened 309 chemicals using 467 HTS assays across nine assay technology platforms. The assays measured direct interactions between chemicals and molecular targets (receptors, enzymes), as well as downstream effects on reporter gene activity or cellular consequences. We ranked the chemicals according to individual vascular bioactivity score and visualized the ranking using ToxPi (Toxicological Priority Index) profiles.Results: Targets in inflammatory chemokine signaling, the vascular endothelial growth factor pathway, and the plasminogen-activating system were strongly perturbed by some chemicals, and we found positive correlations with developmental effects from the U.S. EPA ToxRefDB (Toxicological Reference Database) in vivo database containing prenatal rat and rabbit guideline studies. We observed distinctly different correlative patterns for chemicals with effects in rabbits versus rats, despite derivation of in vitro signatures based on human cells and cell-free biochemical targets, implying conservation but potentially differential contributions of developmental pathways among species. Follow-up analysis with antiangiogenic thalidomide analogs and additional in vitro vascular targets showed in vitro activity consistent with the most active environmental chemicals tested here.Conclusions: We predicted that blood vessel development is a target for environmental chemicals acting as putative vascular disruptor compounds (pVDCs) and identified potential species differences in sensitive vascular developmental pathways.     

内皮抑素在子宫内膜异位大鼠模型致低妊娠功能的治疗作用

目的:建立大鼠子宫内膜异位(EMT)模型,观察内异症所致低妊娠状态,并探讨内皮抑素(恩度)的治疗作用。方法:自体移植术建立SD大鼠EMT模型,造模成功后随机分为模型组、达那唑组、恩度组,8只行假手术。术后4周开始用药,用药14天,各组随机选半数大鼠处死,取血清检测FSH、LH、E2、P,取异位灶切片观察组织大体情况,免疫组化检测VEGF表达。余下鼠雌雄合笼观察妊娠状态。结果:32只大鼠造模,成功28只,假手术组、达那唑组、恩度组VEGF表达低于模型组(P<0.05),血清FSH、LH、E2、P水平前3组与模型组比较差异有统计学意义(P<0.05),模型组处于低妊娠状态,恩度组与达那唑组受孕情况比较差异有统计学意义(P<0.05)。结论:SD大鼠子宫内膜异位症模型建立成模率高,能模拟内异症所致低妊娠状态,恩度对内异症所致低妊娠功能有一定的治疗作用,且不良反应小。     

Keratinocyte growth factor (KGF) gene therapy mediated by an attenuated form of Salmonella typhimurium ameliorates radiation induced pulmonary injury in rats

The aim of this study is to investigate the effect of KGF (Keratinocyte growth factor) gene therapy mediated by the attenuated Salmonella typhimurium Ty21a on radiation-induced pulmonary injury in rats model. Sprague-Dawley rats were divided into three groups: TPK group (treated with TPK strain, attenuated Salmonella typhimurium Ty21a-recombined human KGF gene); TP group (treated with TP strain, attenuated Salmonella typhimurium Ty21a-recombined blank plasmid); and Saline group (treated with saline). After intraperitoneal administration for 48 h, the thoraxes of the rats were exposed to X-ray (20 Gy), and the rats were administered again two weeks after radiation. On the 3rd, 5th, 7th, 14th and 28th day after radiation, the rats were sacrificed and lung tissues were harvested. Histological analysis was performed, MDA contents and SOD activity were detected, mRNA levels of KGF, TGF-β, SP-A and SP-C were measured by Real-time RT-PCR, and their concentrations in the BALF were quantified with ELISA. Administration of TPK strain improved the pathological changes of the lung on the 28th day. In the TPK group, KGF effectively expressed since the 3rd day, MDA contents decreased and SOD activity increased significantly, on the 7th day and 14th day respectively. SP-A and SP-C expression elevated, whereas TGF-β expression was inhibited in the TPK group. These results suggest that this novel gene therapy of KGF could ameliorate radiation-induced pulmonary injury in rats, and may be a promising therapy for the treatment of radiative pulmonary injury.     

Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions.

The objective of this study was to determine if there are innate differences in gene expression in selected CNS regions between inbred alcohol-preferring (iP) and -non-preferring (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU), and hippocampus (HIPP) of alcohol-na?ve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Using Linear Modeling for Microarray Analysis with a false discovery rate threshold of 0.1, there were 16 genes with differential expression in the ACB, 54 in the AMYG, 8 in the FC, 24 in the CPU, and 21 in the HIPP. When examining the main effect of strain across regions, 296 genes were differentially expressed. Although the relatively small number of genes found significant within individual regions precluded a powerful analysis for over-represented Gene Ontology categories, the much larger list resulting from the main effect of strain analysis produced 17 over-represented categories (P < .05), including axon guidance, gliogenesis, negative regulation of programmed cell death, regulation of programmed cell death, regulation of synapse structure function, and transmission of nerve impulse. Co-citation analysis and graphing of significant genes revealed a network involved in the neuropeptide Y (NPY) transmitter system. Correlation of all significant genes with those located within previously established rat alcohol QTLs revealed that of the total of 313 significant genes, 71 are located within such QTLs. The many regional and overall gene expression differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats.     

Extracts of Phyllostachys pubescens Leaves Represses Human Steroid 5-Alpha Reductase Type 2 Promoter Activity in BHP-1 Cells and Ameliorates Testosterone-Induced Benign Prostatic Hyperplasia in Rat Model

Benign prostatic hyperplasia (BPH) is the most common symptomatic abnormality of the human prostate characterized by uncontrolled proliferation of the prostate gland. In this study, we investigated the effect of bamboo, Phyllostachys pubescens, leaves extract (PPE) on human 5α-reductase type 2 (SRD5A2) gene promoter activity in human prostate cell lines and the protective effect of PPE on a testosterone-induced BPH rat model. PPE repressed human SRD5A2 promoter activity and its mRNA expression. The rats treated with PPE for 4 weeks showed a significantly attenuated prostate weight compared to vehicle control. PPE-treated rats also showed reduced serum dihydrotestosterone, testosterone, prostate-specific antigen, and SRD5A2 levels by testosterone injection. Quantitative real-time polymerase chain reaction showed that PPE treatment significantly decreased mRNA expression of SRD5A2, androgen receptor (AR), proliferating cell nuclear antigen (PCNA), and fibroblast growth factor 2 compared with the vehicle-treated, testosterone-injected rats in the prostate. Furthermore, PPE treatment showed reduced AR, PCNA, and tumor necrosis factor alpha expression in the prostate via immunohistofluorescence staining. In conclusion, oral administration of PPE prevented and inhibited the development and progression of enlarged prostate lesions in testosterone-induced animal models through various anti-proliferative and anti-inflammatory pharmacological effects and induced suppression of SRD5A2 gene expression.     

三氯乙烯染毒SD大鼠肝脏的基因表达图谱

目的分析三氯乙烯(TCE)染毒多次后SD大鼠肝脏的基因表达图谱,为研究机体多次接触TCE其肝脏所产生的分子毒理学反应特性提供线索。方法SD大鼠背部皮内注射体积分数为15%的TCE,每7d1次。分别于第5和第7次染毒后24h收集大鼠的肝脏组织,提取总RNA,用Affymetrix的大鼠U34毒理基因芯片分析其基因表达谱。结果大鼠染毒TCE5次及7次24h肝脏中的Gadd45a、Myc和Mel基因及与固醇类、脂类代谢合成相关的基因或电子传递相关的P450家族基因显著性上调表达,而部分P450家族和热胁迫基因则下调表达。结论本文首次报道了SD大鼠多次接触TCE后肝脏组织的基因表达图谱。