A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling.
A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling.
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DOI：
10.1371/journal.pone.0178302
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Seligmann BE
中科院分区：
文献类型：
--
作者：
Yeakley JM;Shepard PJ;Goyena DE;VanSteenhouse HC;McComb JD;Seligmann BE
使用基因表达特征来对化合物进行分类，识别功效或毒性，并区分接近的类似物依赖于识别调节基因的方法的敏感性。我们使用了一种新颖的基于连接的靶向全转录组表达分析方法TempO-Seq®，以确定以前未报道的化合物响应基因是否可以被鉴定并纳入广泛但特定的化合物特征。TempO-Seq对20,629个靶标具有99.6%的特异性、单细胞敏感性和与RNA-Seq测量的折叠差异的良好相关性（R2 = 0.9）。与许多表达分析不同，TempO-Seq不需要RNA纯化，cDNA合成或捕获目标RNA，并且缺乏3 '端偏置。为了研究TempO-Seq检测识别显著调节的化合物反应基因的敏感性，我们从使用组蛋白去乙酰化酶抑制剂Trichostatin A （TSA）处理的MCF-7细胞中获得了全转录组图谱，并鉴定了9000多个差异表达基因。MCF-7细胞的TSA谱在连通性图谱（cMAP）数据库中与HL-60和PC-3细胞的TSA谱重叠，表明它们具有独立于基线基因表达的共同TSA特异性表达谱。从cMAP中提取了43个基因细胞无关的TSA特征，并在TempO-Seq MCF-7数据中得到证实。cMAP数据库中先前未报道的对TSA敏感的其他基因也被确定。经TSA处理的5种细胞类型共发现1136个差异表达基因，其中包括785个先前未报道的TSA应答基因。我们得出的结论是，TSA诱导了一个特定的表达特征，该特征在广泛不同的细胞类型中是一致的，该特征包含以前与TSA反应无关的基因，TempO-Seq提供了定义这种化合物特异性、细胞无关的表达变化所需的敏感差异表达检测。
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3′ end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.