Different mutant RUNX1 oncoprotein classes program alternate haematopoietic differentiation trajectories [ChIP-seq2]. Different mutant RUNX1 oncoprotein classes program alternate haematopoietic differentiation trajectories [ChIP-seq2]

Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend on the class of RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique diseases has been well studied but the genomic basis of their differential action is unknown. To address this question we compared integrated phenotypic, transcriptomic and genomic data from cells expressing four types of RUNX1 oncoproteins in an inducible fashion during blood development from embryonic stem cells. We show that each class of RUNX1 mutation rapidly deregulates endogenous RUNX1 function by different mechanisms, leading to specific alterations in developmentally controlled transcription factor binding and chromatin programming. The result are distinct perturbations in the trajectories of gene regulatory network changes underlying blood cell development that are consistent with the nature of the final disease phenotype. The development of novel treatments for RUNX1-driven diseases will therefore require consideration beyond RUNX1 haploinsufficiency. Overall design: ChIP-Seq targeting GATA1 and PU1 in mouse hematopietic progenitor cells expressing a doxycyclin inducible Runx1 oncoprotein construct. Samples include cells with and without doxycycline treatment.

造血主调控因子RUNX1的突变可引发急性髓系白血病、家族性血小板障碍及其他血液系统恶性肿瘤，此类疾病的表型与预后取决于RUNX1突变的类别。目前针对这些致癌蛋白的生化特性及其诱发独特疾病的能力已有充分研究，但它们差异化作用的基因组基础仍未明确。
为解决这一科学问题，我们对胚胎干细胞向造血发育过程中可诱导表达四种RUNX1致癌蛋白的细胞的整合表型组、转录组及基因组数据进行了对比分析。研究表明，每一类RUNX1突变均可通过不同机制快速失调内源性RUNX1的功能，导致发育调控的转录因子结合与染色质编程发生特异性改变。其结果是调控血细胞发育的基因调控网络的动态变化轨迹出现显著扰动，这与最终疾病表型的特征相符。因此，针对RUNX1驱动型疾病的新型治疗策略，所需考量的范围不应仅局限于RUNX1单倍体剂量不足。
整体实验设计：在表达多西环素诱导型Runx1致癌蛋白构建体的小鼠造血祖细胞中，针对GATA1与PU.1开展染色质免疫沉淀测序（ChIP-Seq）。实验样本涵盖经多西环素处理与未处理的两组细胞。