Centre for Genomic Regulation (CRG), Barcelona, Spain.
BMC Genomics. 2013 Jun 1;14:371. doi: 10.1186/1471-2164-14-371.
Epidermal Growth Factor (EGF) plays an important function in the regulation of cell growth, proliferation, and differentiation by binding to its receptor (EGFR) and providing cancer cells with increased survival responsiveness. Signal transduction carried out by EGF has been extensively studied at both transcriptional and post-transcriptional levels. Little is known about the involvement of microRNAs (miRNAs) in the EGF signaling pathway. miRNAs have emerged as major players in the complex networks of gene regulation, and cancer miRNA expression studies have evidenced a direct involvement of miRNAs in cancer progression.
In this study, we have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by reverse transcription quantitative PCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomiRs) among regulated miRNAs.
We propose that the use of global genomic miRNA cross-validation derived from high throughput technologies can be used to generate more reliable datasets inferring more robust networks of co-regulated predicted miRNA target genes.
表皮生长因子（EGF）通过与其受体（EGFR）结合，为癌细胞提供更高的生存反应能力，从而在细胞生长、增殖和分化的调节中发挥重要作用。EGF 的信号转导在转录和转录后水平都得到了广泛的研究。然而，miRNAs（microRNAs）在 EGF 信号通路中的作用知之甚少。miRNAs 已成为基因调控复杂网络中的主要调控因子，癌症 miRNA 表达研究表明，miRNAs 直接参与了癌症的进展。
在这项研究中，我们使用综合的高内涵分析方法来鉴定与 HeLa 细胞中 EGF 信号相关的特定 miRNAs，作为癌症相关功能的潜在介导物。我们使用微阵列和深度测序技术，以获得 EGF miRNA 转录组的全局视图，并进行了稳健的实验交叉验证。通过应用基于 Rankprod 检验的程序，我们确定了一组可靠的 EGF 调节 miRNAs。通过逆转录定量 PCR 验证调节 miRNAs 后，我们从预测的靶基因中获得了蛋白质网络和生物学功能，以深入了解 miRNAs 在 EGF 处理细胞中的潜在作用。此外，我们还分析了由于参考序列（isomiRs）而导致的编辑引起的调节 miRNAs 中的序列异质性。
我们提出，使用高通量技术衍生的全局基因组 miRNA 交叉验证，可以生成更可靠的数据集，推断出更稳健的共调节预测 miRNA 靶基因网络。
