McCormick Genomic and Proteomics Center, The George Washington University, Washington, District of Columbia, USA.
PLoS One. 2013 Aug 12;8(8):e66585. doi: 10.1371/journal.pone.0066585. eCollection 2013.
P21-activated kinase 1 (PAK1), a serine/threonine protein kinase, modulates many cellular processes by phosphorylating its downstream substrates. In addition to its role in the cytoplasm, PAK1 also affects gene transcription due to its nuclear localization and association with chromatin. It is now recognized that PAK1 kinase activity and its nuclear translocation are rapidly stimulated by ionizing radiation (IR), and that PAK1 activation is a component of the DNA damage response. Owing to the role of PAK1 in the cell survival, its association with the chromatin, and now, stimulation by ionizing radiation, we hypothesize that PAK1 may be contributing to modulation of genes with roles in cellular processes that might be important in the DNA damage response. The purpose of this study was to identify new PAK1 targets in response to ionizing radiation with putative role in the DNA damage response. We examined the effect of IR on the gene expression patterns in the murine embryonic fibroblasts with or without Pak1 using microarray technology. Differentially expressed transcripts were identified using Gene Spring GX 10.0.2. Pathway, network, functional analyses and gene family classification were carried out using Kyoto Encyclopedia of Genes and Genomes (KEGG), Ingenuity Pathway, Gene Ontology and PANTHER respectively. Selective targets of PAK1 were validated by RT-qPCR. For the first time, we provide a genome-wide analysis of PAK1 and identify its targets with potential roles in the DNA damage response. Gene Ontology analysis identified genes in the IR-stimulated cells that were involved in cell cycle arrest and cell death. Pathway analysis revealed p53 pathway being most influenced by IR responsive, PAK1 targets. Gene family of transcription factors was over represented and gene networks involved in DNA replication, repair and cellular signaling were identified. In brief, this study identifies novel PAK1 dependent IR responsive genes which reveal new aspects of PAK1 biology.
P21 激活激酶 1（PAK1）是一种丝氨酸/苏氨酸蛋白激酶，通过磷酸化其下游底物来调节许多细胞过程。除了在细胞质中的作用外，PAK1 还由于其核定位和与染色质的关联而影响基因转录。现在已经认识到，PAK1 激酶活性及其核易位被电离辐射（IR）迅速刺激，并且 PAK1 的激活是 DNA 损伤反应的组成部分。由于 PAK1 在细胞存活中的作用、其与染色质的关联以及现在被电离辐射刺激，我们假设 PAK1 可能有助于调节与细胞过程相关的基因，这些基因在 DNA 损伤反应中可能很重要。本研究的目的是鉴定新的 PAK1 靶标，以响应可能在 DNA 损伤反应中起作用的电离辐射。我们使用微阵列技术检查了用或不用 Pak1 的鼠胚胎成纤维细胞中 IR 对基因表达模式的影响。使用 GeneSpring GX 10.0.2 识别差异表达的转录本。使用京都基因与基因组百科全书（KEGG）、Ingenuity 通路、基因本体论和 PANTHER 分别进行通路、网络、功能分析和基因家族分类。通过 RT-qPCR 验证了 PAK1 的选择性靶标。我们首次提供了 PAK1 的全基因组分析，并确定了其在 DNA 损伤反应中具有潜在作用的靶标。基因本体论分析确定了 IR 刺激细胞中涉及细胞周期停滞和细胞死亡的基因。通路分析显示，p53 通路受 IR 反应性、PAK1 靶标影响最大。转录因子基因家族过度表达，并确定了涉及 DNA 复制、修复和细胞信号转导的基因网络。简而言之，本研究鉴定了新的 PAK1 依赖性 IR 反应基因，揭示了 PAK1 生物学的新方面。
