Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells.

Abstract

Maintenance of cellular homeostasis is integral to appropriate regulation of cellular signaling and cell growth and division. In this study, we report the development and quality assessment of a pathway-focused microarray comprising genes involved in cellular homeostasis. Since nicotine is known to have highly modulatory effects on the intracellular calcium homeostasis, we therefore tested the applicability of the homeostatic pathway-focused microarray on the gene expression in PC-12 cells treated with 1 mM nicotine for 48 h relative to the untreated control cells. We first provided a detailed description of the focused array with respect to its gene and pathway content and then assessed the array quality using a robust regression procedure that allows for the exclusion of unreliable measurements while decreasing the number of false positives. As a result, the mean correlation coefficient between duplicate measurements of the arrays used in this study (control vs. nicotine treatment, three samples each) has increased from 0.974+/-0.017 to 0.995+/-0.002. Furthermore, we found that nicotine affected various structural and signaling components of the AKT/PKB signaling pathway and protein synthesis and degradation processes in PC-12 cells. Since modulation of intracellular calcium concentrations ([Ca(2+)](i)) and phosphatidylinositol signaling are important in various biological processes such as neurotransmitter release and tissue pathogenesis including tumor formation, we expect that the homeostatic pathway-focused microarray potentially can be used for the identification of unique gene expression profiles in comparative studies of drugs of abuse and diverse environmental stimuli, such as starvation and oxidative stress.

• Authors: Ozlen Konu, Xiaoyuan Xu, Jennie Z Ma, Justin Kane, Ju Wang, Shirley J Shi, Ming D Li
• Journal: Brain research. Molecular brain research (Brain Res Mol Brain Res) Vol. 121 Issue 1-2 Pg. 102-13 (Feb 05 2004) ISSN: 0169-328X [Print] Netherlands
• PMID: 14969741 (Publication Type: Comparative Study, Journal Article, Research Support, U.S. Gov't, P.H.S.)

Chemical References

• Nicotinic Agonists
• RNA, Messenger
• Nicotine

Topics

• Animals
• Cluster Analysis
• Gene Expression (drug effects)
• Gene Expression Profiling (methods)
• Homeostasis (genetics)
• Models, Neurological
• Nicotine (pharmacology)
• Nicotinic Agonists (pharmacology)
• Oligonucleotide Array Sequence Analysis (methods)
• PC12 Cells
• RNA, Messenger (biosynthesis)
• Rats
• Regression Analysis
• Reproducibility of Results
• Reverse Transcriptase Polymerase Chain Reaction (methods)
• Sequence Analysis, DNA (methods)
• Signal Transduction (drug effects, genetics)