Promoter regulation heterogeneity and stratification of colorectal cancer organoids - complex disease

发育中的肿瘤由克隆亚群的混合物组成，含有导致不同转录组特征的不同突变模式。在这方面，它们与发育中的胚胎不同，后者也具有谱系特异性转录组的特征。这些混合的癌症形成干细胞群体的致瘤潜力是由达尔文选择驱动的，允许高水平的可塑性，使肿瘤逃避治疗。肿瘤的克隆结构分析与转录组学分析和数学建模一起可以帮助对肿瘤进行分层，并解决异质性对肿瘤形成的个体发育和治疗抗性的贡献的重要性。我们假设，了解由类器官建模的肿瘤的转录组异质性将允许有意义的分层，这最终将导致改进的生物标志物和干预策略设计。定义肿瘤进展的重要信号通路之一是mTOR通路，据报道其在各种肿瘤中上调，因此已成为有吸引力的治疗靶点[1][2]。最近，Beggs实验室发现mTOR通路在结肠癌及其模型类器官中受到差异调节，并且对放射治疗有差异反应（未发表）。mTOR途径响应营养和代谢应激，并被生长因子激活，从而通过专门的转录启动子调节翻译途径。这种活性的标志是非经典转录起始途径的上调[3]。了解肿瘤细胞接收和整合这些影响其生长和代谢的信号的机制对于开发靶向良好的治疗至关重要。Mueller实验室最近通过启动子基因组学技术（CAGE-测序）显示，代表mTOR信号传导靶标的转录起始机制（TOP启动子）在开发中的使用比先前报道的广泛得多（Nepal等人，MS在制备中）。在这个项目中，与肿瘤进展相关的转录机制将被分析为他们以前的工作与发展过程中的时空异质性的类比，并将用于分层结肠癌类器官模型。

Developing tumours are composed of a mixture of clonal subpopulations, containing distinct patterns of mutations leading to distinct transcriptome features. In this respect they are not akin to developing embryos, which are also characterized by lineage-specific transcriptomes. The tumourigenic potential of these mixed populations of cancer forming stem cells is driven by Darwinian selection permitting a high level plasticity, allowing the tumour to evade treatment. Clonal architecture analysis of a tumour together with transcriptomic analysis and mathematical modeling can help in stratifying tumors and to address the significance of heterogeneity in contribution to the ontogeny and treatment resistance of tumour formation. We hypothesize that understanding the transcriptome heterogeneity of tumors modeled by organoids will allow meaningful stratification, which will eventually lead to improved biomarkers and intervention strategy designs. One of the important signaling pathways, which define tumour progression is the mTOR pathway, which has been reported to be upregulated in various tumors and as a result has become an appealing therapeutic target [1] [2]. Recently, the Beggs laboratory found that mTOR pathway, is differentially regulated in colon cancers and in their model organoids and respond differentially to radiation therapy (unpublished). The mTOR pathway responds to nutrient and metabolic stress is and is activated by growth factors and thus regulates translation pathways via a specialized transcriptional promoter. A hallmarks of this activity is the upregulation of a non-canonical transcription initiation pathway [3]. An understanding of the mechanisms by which tumour cells receive and integrate these signals, that influence their growth and metabolism, is essential to developing a well-targeted therapy. The Mueller lab has recently shown by promoter genomics technology (CAGE-sequencing) that the transcription initiation mechanisms (TOP promoters) representative for mTOR signaling targets are far more pervasively used in development than previously reported (Nepal et al., ms in preperation). In this project, transcription mechanisms associated with tumor progression will be analysed to the analogy of their previous work with spatio-temporal heterogeneity during development and will be used to stratify colon cancer organoid models.