Comprehensive expression analyses of neural cell type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes.. Rattus norvegicus

We performed microarray profiling of miRNA expression across the four principal cell types of the central nervous system: neurons, astrocytes, oligodendrocytes and microglia, isolated from rat cortex. Our microarray results showed that the four cell types differ extensively in their miRNA expression. Over one third of the 351 miRNAs examined had higher than 5-fold differences in expression between two of the four cell types. As expected, cell types of common developmental origin differed least in their miRNA expression profiles (astrocytes and oligodendrocytes), while neurons and microglia showed more unique miRNA expression profiles. 63 miRNAs showed cell type specific enrichment (39 miRNAs) or depletion (24 miRNAs) when comparing the four cell types using criteria of a minimum 5-fold difference in expression in one cell type compared to the average expression in the other three and minimum 2-fold change compared to each of the other three types individually and a false positive rate (FDR) p value lower than 0.01. When comparing only neurons, astrocytes and oligodendrocytes 115 miRNAs were specifically enriched (89 miRNAs) or depleted (36 miRNAs) in one cell type. Overall design: Genome-wide profiling comparing miRNA expression between mature neurons, astrocytes, oligodendrocytes and microglia. Three to four biological replicates per cell type were analyzed.

本研究针对从大鼠皮层分离得到的中枢神经系统四类主要细胞类型——神经元（neurons）、星形胶质细胞（astrocytes）、少突胶质细胞（oligodendrocytes）以及小胶质细胞（microglia）——开展了微小RNA（microRNA, miRNA）表达的基因芯片谱分析（microarray profiling）。芯片分析结果显示，四类细胞的miRNA表达模式存在显著差异。在所检测的351个miRNA中，超过三分之一的miRNA在四类细胞中的任意两类间表达差异倍数达到5倍以上。正如预期，发育起源相近的细胞类型间miRNA表达谱差异最小（如星形胶质细胞与少突胶质细胞），而神经元与小胶质细胞则呈现更为独特的miRNA表达谱。通过以下标准对四类细胞进行比较分析后，共鉴定出63个具有细胞类型特异性富集（39个）或缺失（24个）的miRNA：目标细胞类型相较于其余三类细胞的平均表达量差异倍数不低于5倍，相较于其余三类细胞中的每一类单独比较时表达变化倍数不低于2倍，且假阳性率（false discovery rate, FDR）对应的p值小于0.01。当仅比较神经元、星形胶质细胞与少突胶质细胞三类时，共鉴定出115个在某一细胞类型中特异性富集（89个）或缺失（36个）的miRNA。
实验整体设计：对成熟神经元、星形胶质细胞、少突胶质细胞与小胶质细胞的miRNA表达开展全基因组范围的表达谱比较分析；每类细胞设置3至4个生物学重复样本用于后续分析。