Atz Mary, Walsh David, Cartagena Preston, Li Jun, Evans Simon, Choudary Prabhakara, Overman Kevin, Stein Richard, Tomita Hiro, Potkin Steven, Myers Rick, Watson Stanley J, Jones E G, Akil Huda, Bunney William E, Vawter Marquis P
Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, CA, USA.
J Neurosci Methods. 2007 Jul 30;163(2):295-309. doi: 10.1016/j.jneumeth.2007.03.022. Epub 2007 Apr 8.
Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.
死后脑组织的基因表达谱是理解神经精神疾病的重要资源。质量协变量对基因表达研究的分析和结果的影响是重要问题。本文探讨了可能影响两个脑区基因表达的关键变量。确定了基因表达谱研究中的四大类质量指标（临床、组织、RNA和微阵列质量）。这些质量控制指标显著相关，然而一个质量变量并不能解释微阵列基因表达的总方差。数据表明，濒死因素和低pH值与两个脑区提取RNA的完整性降低相关。这三个参数还调节了线粒体相关基因改变的显著性。所有转录本的平均F比率汇总表明，AffyRNAdeg程序中的RNA降解比所有其他质量因素导致的变异更高。综上所述，这些发现证实了先前的研究，即包括RNA完整性、濒死因素和pH值在内的质量参数与死后脑基因表达谱的差异有关。在事后分析中，可以用这些质量参数评估单个候选基因，以帮助加强与精神疾病的相关性。我们发现，临床、组织、RNA和微阵列质量都是人类死后研究中基因表达结果的收集、研究设计、分析和解释中有用的变量。
