Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer [RNA-seq]

The Epithelial-to-Mesenchymal Transition (EMT) is a dynamic cellular program that is frequently used by cancer cells to increase migratory and invasive cell characteristics. It is a key contributor to both heterogeneity and chemo-resistance and metastasis in many solid tumors, including triple negative breast cancer. In particular, the intermediate or hybrid EMT state has increased tumor initiating and stem-like properties. Here, we have identified multiple distinct EMT states derived from the human breast cell line, SUM149PT, including three unique intermediate states, possessing distinct migratory, tumor initiating, and metastatic qualities. We have used this model to interrogate the epigenetic landscape of these distinct EMT states in a multi-omics approach, identifying and RUNX2 as relevant in regulating the intermediate state, as well as to develop a novel multiplexed staining approach to evaluate E-M heterogeneity (EMH) and overall EMT score in orthotopic tumors as well as patient tumor samples. This model reveals insights into the complex EMT spectrum of cell states, the networks that control them, and how EMT plasticity contributes to tumor heterogeneity in breast cancer. Overall design: Single-end RNA-sequencing of three replicates per cell line (7). No treatments

上皮间质转化（Epithelial-to-Mesenchymal Transition, EMT）是一类动态细胞程序，癌细胞常借助该程序增强自身的迁移与侵袭能力。它是包括三阴性乳腺癌（triple negative breast cancer）在内的多种实体瘤中，肿瘤异质性、化疗耐药与肿瘤转移的关键驱动因素。其中，中间型（混合型）EMT状态具有更强的肿瘤起始能力与干细胞样特性。本研究从人乳腺细胞系SUM149PT中鉴定出多种不同的EMT状态，包含三种独特的中间型状态，这些状态具备迥异的迁移、肿瘤起始与转移特性。我们利用该模型通过多组学方法解析了这些不同EMT状态的表观遗传景观，确定RUNX2在调控中间型EMT状态中发挥相关作用；同时开发了一种新型多重染色方法，用于评估原位肿瘤及患者肿瘤样本中的上皮间质异质性（EMT heterogeneity, EMH）与整体EMT评分。本模型为解析细胞状态的复杂EMT谱系、调控这些状态的分子网络，以及EMT可塑性如何促进乳腺癌肿瘤异质性提供了新的研究视角。整体实验设计：每个细胞系设置3次生物学重复，开展单端RNA测序（Single-end RNA-sequencing），共7组样本，未施加任何处理措施。