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

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differentially regulated in colon cancers and in their model organoids and respond differentially to radiation therapy (unpublished).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.