Customized PCR-array analysis informed by gene-chip microarray and biological hypothesis reveals pathways involved in lung inflammatory response to titanium dioxide in pregnancy.
Customized PCR-array analysis informed by gene-chip microarray and biological hypothesis reveals pathways involved in lung inflammatory response to titanium dioxide in pregnancy.
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基因 - 芯片微阵列和生物学假设告知的定制PCR阵列分析揭示了妊娠中对肺二氧化钛的肺部炎症反应涉及的途径。
DOI：
10.1080/15287390903566641
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
Fedulov AV
中科院分区：
文献类型：
--
作者：
Lamoureux DP;Kobzik L;Fedulov AV
基因芯片结果的验证是基因组学研究中的一个挑战。成功使用定制设计的96孔聚合酶链反应（PCR）阵列研究环境二氧化钛（TiO 2）颗粒对妊娠小鼠肺部的意外炎症效应，在对照小鼠中未见类似结果。在我们的方法中，候选基因的定制PCR阵列的选择是由先前的基因芯片微阵列分析。结果表明，妊娠小鼠肺中的基因多次上调，但对照组小鼠的肺中的基因未上调。定制的PCR阵列是一种灵活的工具，它提供了将“盲”全基因组扫描与假设驱动的方法相结合的能力，通过包括由微阵列阳性鉴定的用于验证的“候选”基因和在基因组数据中未能发现的生物学相关的“嫌疑人”。与传统的逐基因qPCR或制造商预设的途径试剂盒相比，该技术提供了一种具有成本效益且节省时间的分析方法，并允许产生强且易于检测的信号。具有确认的差异表达的基因进一步用于途径分析，并表明参与几种生物学相关途径，包括树突状细胞中的过敏介质信号传导。最后，建立了一个分析网络，为进一步的机理研究提供信息。这项工作的双重目的是证明新型定制PCR阵列是一种方便的方法来验证微阵列结果，并通过PCR阵列与途径分析获得有关TiO 2诱导的炎症的生物学重要数据，这为支持未来的实验研究提供了可行的假设。
Validation of gene-chip microarray results is one of the challenges in genomic studies. The successful use of a custom-designed 96-well polymerase chain reaction (PCR) array to study the unexpected inflammatory effect of environmental titanium dioxide (TiO2) particles on the lungs of pregnant mice, with similar results not seen in control mice, is reported. In our approach, selection of candidate genes for the custom PCR array was informed by prior gene-chip microarray profiling. Results demonstrated multiple upregulation of genes in the lungs of pregnant but not control mice produced by TiO2 exposure. Customized PCR array is a flexible tool that offers the ability to combine the “blind” genome-wide scan with a hypothesis-driven approach, by including both the “candidate” genes for validation positively identified by the microarray and biologically relevant “suspects” that failed to be found in the genomic data. Compared to conventional gene-by-gene qPCR or manufacturer-preset pathway kits, this technique provides a cost-effective and time-saving method of analysis and allows for a strong, easily detectable signal. Genes with confirmed differential expression were further used for pathway analysis and indicated involvement in several biologically relevant pathways including allergy mediator signaling in dendritic cells. Finally, an analytical network was created that will inform further mechanistic studies. The dual purpose of the work was to demonstrate that the novel custom PCR array is a convenient approach to validate the microarray results, and to obtain biologically significant data on TiO2-induced inflammation by following the PCR array with pathway analysis, which provided feasible hypotheses to support future experimental studies.
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DOI：
10.1080/15287390701738509
发表时间：
2008-01-01
影响因子：
2.6
作者：
Gwinn, Maureen R.;Weston, Ainsley
通讯作者：
Weston, Ainsley
影响因子：
4.1
作者：
Rajeevan, MS;Vernon, SD;Unger, ER
通讯作者：
Unger, ER
影响因子：
6.4
作者：
McIlroy, A;Caron, G;Jeannin, P
通讯作者：
Jeannin, P
影响因子：
5
作者：
Drumm, K;Schindler, H;Kienast, K
通讯作者：
Kienast, K
影响因子：
8.3
作者：
Shinyashiki, Masaru;Eiguren-Fernandez, Arantza;Cho, Arthur K.
通讯作者：
Cho, Arthur K.