HOXC9-induced neuronal differentiation in human neuroblastoma BE(2)-C cells [Gene expression profiling]

Cell differentiation is an essential process of normal development by which a stem cell or progenitor cell becomes a post-mitotic, specialized cell with unique morphology and function. Also, it has long been recognized that differentiation is associated with a marked reduction in DNA damage response at the global level. The molecular basis for the coordination between cell cycle exit, acquirement of specialized structure and function, and attenuation of DNA damage response during differentiation is not well understood. We have conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program in human neuroblastoma cells. Gene expression profiling reveals that HOXC9-induced differentiation is associated with transcriptional regulation of 2,395 genes, which is characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping demonstrates that HOXC9 occupies 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and DNA damage response. These findings suggest that HOXC9 directly activates and represses the transcription of distinct sets of genes to coordinate the cellular events characteristic of neuronal differentiation. Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of BE(2)-C/Tet-Off/Myc-HOXC9 cells cultured in the presence or absence of doxycycline for 6 days.

细胞分化（Cell differentiation）是正常发育的核心过程，指干细胞（stem cell）或祖细胞（progenitor cell）转化为具备独特形态与功能的有丝分裂后（post-mitotic）特化细胞的生命进程。此外，学界长期以来已公认，细胞分化在全局水平上与DNA损伤应答（DNA damage response）的显著下调密切相关。但目前，细胞分化过程中细胞周期退出、特化结构与功能获得，以及DNA损伤应答减弱之间的协同调控分子机制仍未被充分阐明。本研究针对人神经母细胞瘤细胞中HOXC9诱导的神经元分化程序开展了全基因组分析。基因表达谱分析结果显示，HOXC9诱导的细胞分化与2395个基因的转录调控密切相关，其特征为神经元相关基因的全局上调，以及细胞周期与DNA修复相关基因的下调。值得注意的是，全基因组定位实验表明，HOXC9可结合上述40%的差异调控基因，其中包含大量参与神经元分化、细胞周期进程及DNA损伤应答的基因。上述研究结果提示，HOXC9可通过直接激活或抑制不同基因集的转录，协同调控神经元分化特有的细胞生物学事件。本研究按照试剂盒说明书，对分别在添加或不添加多西环素（doxycycline）的培养基中培养6天的BE(2)-C/Tet-Off/Myc-HOXC9细胞所提取的三份独立总RNA样本，开展了Affymetrix基因芯片（Affymetrix microarray）实验。