Konu Ozlen, Xu Xiaoyuan, Ma Jennie Z, Kane Justin, Wang Ju, Shi Shirley J, Li Ming D
Program in Genomics and Bioinformatics on Drug Addiction, Department of Psychiatry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, Mail Code 7792, San Antonio, TX 78229-3900, USA.
Brain Res Mol Brain Res. 2004 Feb 5;121(1-2):102-13. doi: 10.1016/j.molbrainres.2003.11.012.
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+)) 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.
维持细胞内稳态对于细胞信号传导以及细胞生长和分裂的适当调节至关重要。在本研究中，我们报告了一种聚焦于细胞内稳态相关基因的通路微阵列的开发及质量评估。由于已知尼古丁对细胞内钙稳态具有高度调节作用，因此我们测试了这种聚焦于稳态通路的微阵列在检测经1 mM尼古丁处理48小时的PC - 12细胞相对于未处理的对照细胞的基因表达方面的适用性。我们首先详细描述了该聚焦阵列的基因和通路内容，然后使用一种稳健回归程序评估阵列质量，该程序允许排除不可靠的测量值，同时减少假阳性的数量。结果，本研究中使用的阵列重复测量之间的平均相关系数（对照与尼古丁处理，每组三个样本）从0.974±0.017提高到了0.995±0.002。此外，我们发现尼古丁影响了PC - 12细胞中AKT/PKB信号通路的各种结构和信号成分以及蛋白质合成和降解过程。由于细胞内钙浓度（[Ca(2 +)]i）的调节和磷脂酰肌醇信号传导在各种生物学过程如神经递质释放和包括肿瘤形成在内的组织发病机制中很重要，我们预计这种聚焦于稳态通路的微阵列在滥用药物和多种环境刺激（如饥饿和氧化应激）的比较研究中可能可用于识别独特的基因表达谱。
