Randall Division of Cell and Molecular Biophysics, New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK.
J Pathol. 2012 Nov;228(3):274-85. doi: 10.1002/path.4082. Epub 2012 Sep 26.
Chordoma is a rare malignant tumour of bone, the molecular marker of which is the expression of the transcription factor, brachyury. Having recently demonstrated that silencing brachyury induces growth arrest in a chordoma cell line, we now seek to identify its downstream target genes. Here we use an integrated functional genomics approach involving shRNA-mediated brachyury knockdown, gene expression microarray, ChIP-seq experiments, and bioinformatics analysis to achieve this goal. We confirm that the T-box binding motif of human brachyury is identical to that found in mouse, Xenopus, and zebrafish development, and that brachyury acts primarily as an activator of transcription. Using human chordoma samples for validation purposes, we show that brachyury binds 99 direct targets and indirectly influences the expression of 64 other genes, thereby acting as a master regulator of an elaborate oncogenic transcriptional network encompassing diverse signalling pathways including components of the cell cycle, and extracellular matrix components. Given the wide repertoire of its active binding and the relative specific localization of brachyury to the tumour cells, we propose that an RNA interference-based gene therapy approach is a plausible therapeutic avenue worthy of investigation.
软骨肉瘤是一种罕见的骨恶性肿瘤，其分子标志物是转录因子 brachyury 的表达。我们最近证明，沉默 brachyury 会诱导软骨肉瘤细胞系生长停滞，现在我们试图确定其下游靶基因。在这里，我们使用了一种整合的功能基因组学方法，包括 shRNA 介导的 brachyury 敲低、基因表达微阵列、ChIP-seq 实验和生物信息学分析来实现这一目标。我们证实，人类 brachyury 的 T 盒结合基序与在小鼠、非洲爪蟾和斑马鱼发育中发现的基序相同，并且 brachyury 主要作为转录激活剂发挥作用。使用人软骨肉瘤样本进行验证，我们表明 brachyury 结合 99 个直接靶标，并间接地影响 64 个其他基因的表达，从而作为一个复杂致癌转录网络的主调控因子，该网络包括细胞周期的组成部分和细胞外基质成分等多种信号通路。鉴于其活性结合的广泛谱和 brachyury 相对特异性地定位于肿瘤细胞，我们提出基于 RNA 干扰的基因治疗方法是一种值得研究的合理治疗途径。
