Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death [RNA-Seq III]

The expression of transcription factor brachyury (TBXT) is normally restricted to embryonic development and its silencing after mesoderm development is epigenetically regulated. In chordoma, a rare tumour of notochordal differentiation, TBXT acts as a putative oncogene, and we hypothesised that its expression could be contolled through epigenetic inhibition. Screening of five chordoma cell lines revealed that inhibitors of the histone 3 lysine 27 demethylases KDM6A (UTX) and KDM6B (Jmjd3) reduce TBXT expression and lead to cell death, findings validated in primary patient-derived culture systems. Pharmacological inhibition was phenocopied by genetic inactivation of KDM4/B using CRISPR/Cas9. Transcriptional profiles in response to a novel KDM6A/B inhibitor, KDOBA67, revealed downregulation of critical genes and transcription factor networks for chordoma survival pathways, characterised by paired and homeobox genes, whereas upregulated pathways are dominated by stress, cell cycle and pro-apoptotic response pathways. This study supports previous data showing that the function of TBXT is essential for maintaining notochord cell fate and function and provides further evidence that TBXT is an oncogenic driver in chordoma. The data suggest that TBXT can potentially be targeted therapeutically by modulating epigenetic control mechanisms such as H3K27 demethylases. Examination of gene expression differences in 3 chordoma cell lines in the presence of DMSO or KDOBA67

转录因子brachyury（TBXT）的表达通常仅局限于胚胎发育过程，其在中胚层发育后的沉默受表观遗传调控。在脊索瘤——一种罕见的脊索分化源性肿瘤中，TBXT作为潜在癌基因发挥作用，我们据此假设可通过表观遗传抑制手段调控其表达。对5株脊索瘤细胞系的筛选显示，组蛋白3赖氨酸27去甲基化酶KDM6A（UTX）与KDM6B（Jmjd3）的抑制剂可降低TBXT的表达并诱导细胞死亡，该结论在患者来源原代培养体系中得到验证。通过CRISPR/Cas9对KDM4/B进行基因失活，可重现药物抑制的表型。针对新型KDM6A/B抑制剂KDOBA67的转录谱分析显示，脊索瘤存活通路的关键基因与转录因子网络出现下调，其特征为配对盒基因与同源盒基因的表达变化；而上调通路则以应激、细胞周期与促凋亡应答通路为主。本研究佐证了此前关于TBXT功能对维持脊索细胞命运与功能至关重要的结论，并进一步证明TBXT是脊索瘤的致癌驱动因子。研究数据表明，可通过调控H3K27去甲基化酶等表观遗传调控机制，实现对TBXT的治疗性靶向干预。本研究还分析了3株脊索瘤细胞系在经二甲基亚砜（DMSO）或KDOBA67处理后的基因表达差异。