Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants
Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants
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DOI：
10.1016/j.aquatox.2008.07.020
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发表时间：
2008-11-11
影响因子：
4.5
通讯作者：
Chipman, J. K.
中科院分区：
文献类型：
--
作者：
Falciani, F.;Diab, A. M.;Chipman, J. K.
基因组技术通过了解对污染物暴露作出反应的功能途径，提供了对生物体健康状况进行更全面评估的机会。我们为欧洲比目鱼Platichthys flesus （EU-GENIPOL项目）开发了一个13000个克隆的cDNA毒理基因组芯片。我们的目的是根据其肝脏基因表达谱，利用生物信息学方法区分来自北欧六个不同污染状况采样点的比目鱼的来源。为了确定哪些基因表达差异可能与污染物影响有关，我们完成了比目鱼与选定毒物的补充实验室暴露，并确定了相关的基因表达谱。利用多元变量选择与统计建模程序（GALGO）相结合，我们可以预测地理位置，但准确性仅限于特定地点。有效预测分类成员的基因组合的搜索空间非常大，然而，通过结合来自急性实验室暴露于单个化学物质的特征来限制搜索空间，实现了所有不同环境位点的非常准确的分类模型。最后的模型利用了16个克隆的表达谱，并通过包含这些基因的qPCR阵列进行验证，正确地为在独立采样中从三个位点获得的鱼分配了原产地。这些数据表明，用这些阵列获得的基因表达指纹主要归因于不同地点化学污染物响应的差异，表明它们在环境影响评价中的潜在效用。(c) 2008 Elsevier B.V.版权所有
Genomic technologies offer opportunities to gain a more global assessment of the health status of an organism through an understanding of the functional pathways that are responding to pollutant exposure. We have developed a 13,000 clone cDNA toxicogenomics microarray for Platichthys flesus, the European flounder (EU-GENIPOL Project). We aimed to distinguish the origins of flounder taken from six sampling sites of different pollution status in Northern Europe according to their hepatic gene expression profile using bioinformatic approaches. To determine which gene expression differences may relate to pollutant impact, we have completed complementary laboratory exposures of flounder to selected toxicants and determined the associated gene expression profiles. Using multivariate variable selection coupled with a statistical modelling procedure (GALGO) we can predict geographical site but the accuracy is limited to specific sites. The search space for a combination of genes that effectively predicts class membership is very large, however, by combining the signatures derived from acute laboratory exposure to individual chemicals to limit the search space, a very accurate model for classification of all the different environmental sites was achieved. The final model utilised the expression profiles of 16 clones and validation with a qPCR array comprising these genes correctly assigned the site of origin for fish obtained from three of the sites in an independent sampling. These data would imply that the gene expression fingerprints obtained with these arrays are primarily attributable to variations in chemical pollutant responses at the different sites, indicating their potential utility in environmental impact assessment. (c) 2008 Elsevier B.V. All rights reserved.