A microarray study of MPP-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
ABSTRACT This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear.
In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 muM MPP+ treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+ treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+ treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures.
Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.
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ABSTRACT: Abstract The MCBIOS 2004 conference brought together regional researchers and students in biology, computer science and bioinformatics on October 7th-9th 2004 to present their latest work. This editorial describes the conference itself and introduces the twelve peer-reviewed manuscripts accepted for publication in the Proceedings of the MCBIOS 2004 Conference. These manuscripts included new methods for analysis of high-throughput gene expression experiments, EST clustering, analysis of mass spectrometry data and genomic analysisBMC Bioinformatics 07/2005; 6(Suppl 2). DOI:10.1186/1471-2105-6-S2-S1 · 2.67 Impact Factor
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ABSTRACT: Demand for high quality gene expression data has driven the development of revolutionary microarray technologies. The quality of the data is affected by the performance of the microarray platform as well as how the nucleic acid targets are prepared. The most common method for target nucleic acid preparation includes in vitro transcription amplification of the sample RNA. Although this method requires a small amount of starting material and is reported to have high reproducibility, there are also technical disadvantages such as amplification bias and the long, laborious protocol. Using RNA derived from human brain, breast and colon, we demonstrate that a non-amplification method, which was previously shown to be inferior, could be transformed to a highly quantitative method with a dynamic range of five orders of magnitude. Furthermore, the correlation coefficient calculated by comparing microarray assays using non-amplified samples with qRT-PCR assays was approximately 0.9, a value much higher than when samples were prepared using amplification methods. Our results were also compared with data from various microarray platforms studied in the MicroArray Quality Control (MAQC) project. In combination with micro-columnar 3D-Gene™ microarray, this non-amplification method is applicable to a variety of genetic analyses, including biomarker screening and diagnostic tests for cancer.PLoS ONE 02/2012; 7(2):e31397. DOI:10.1371/journal.pone.0031397 · 3.53 Impact Factor
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ABSTRACT: The present study was performed to investigate the possible protective effects of green tea polyphenols against ultraviolet (UV)-C light irradiation-induced cell death in the cultured rat cortical neurons. We found that UV-C light irradiation induced marked cell death tested by 3-(4,5-Dimethylthiazole-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) and TdT-mediated biotin-dUTP nicked-end labeling (TUNEL) assay. Protective effects of green tea polyphenols on UV-C light irradiation-induced apoptosis in cortical neurons were demonstrated by testing the content of Bax, which is involved in cell death. The expression of active Bax in cultured rat cortical neurons was inhibited significantly by green tea polyphenols compared to UV irradiation group tested by the immunoprecipitation assay and Western blot assay. However, there were no significant changes in the contents of total Bax after treatment with green tea polyphenols in UV-C light-irradiated rat cortical neurons. Our results demonstrated that the green tea polyphenols inhibited the active Bax expression, suggesting a neuroprotective effect of green tea polyphenols against the UV-C light irradiation-induced injury on cortical neurons.Neuroscience Letters 10/2008; DOI:10.1016/j.neulet.2008.08.029 · 2.06 Impact Factor