Identification of the tumour transition states occurring during EMT [RNA-seq]

EMT in cancer has been associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However,direct in vivo evidence supporting this possibility is still lacking. By screening a large panel of cell surface markers, we identified the existence of multiple tumour subpopulations associated with different EMT stages from epithelial to completely mesenchymal states passing through intermediate hybrid states in skin and mammary primary tumours. Although all EMT subpopulations presented similar tumour propagating cell capacity, they displayed different , invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes defined by RNA-seq and ATAC-seq identified the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulateEMT transition states. Overall design: RNA sequencing on the different intermediate states of EMT肿瘤中的上皮间质转化（Epithelial-Mesenchymal Transition，EMT）与肿瘤干细胞性、肿瘤转移及治疗抵抗密切相关。近期有研究提出，EMT并非单纯的二元过程，而是通过多种不同中间状态逐步完成的。然而目前仍缺乏支持该假说的直接体内实验证据。本研究通过筛选大量细胞表面标志物，在皮肤和乳腺原发性肿瘤中鉴定出多个肿瘤亚群，这些亚群对应从上皮状态、中间混合表型状态至完全间质状态的不同EMT阶段。尽管所有EMT相关亚群均具备相似的肿瘤增殖传代能力，但其侵袭性与转移潜能存在显著差异。研究团队通过RNA测序（RNA-seq）与转座酶可及性染色质测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）解析了这些亚群的转录组与表观基因组特征，明确了调控不同EMT转化状态的潜在基因调控网络、转录因子及信号通路。最终研究发现，上述肿瘤亚群定位于不同的肿瘤生态位（niche）中，这些生态位可差异化调控EMT转化状态。整体实验设计：针对不同EMT中间状态的样本开展RNA测序。