In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single-cell transcriptome analysis of tumors and matched non-cancerous tissues of twelve colorectal cancer patients. We defined patient-overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non-genetic cancer cell heterogeneity and re-routing of trajectories as a response to targeted therapy.

中文翻译：

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丝裂原激活的蛋白激酶活性驱动结直肠癌的细胞轨迹

在结直肠癌中，致癌突变将分层组织且稳态的上皮转变为缺乏可见组织的侵袭性癌组织。我们试图通过对 12 名结直肠癌患者的肿瘤和匹配的非癌组织进行单细胞转录组分析来定义结直肠癌细胞的转录状态和控制其发育的信号。我们定义了患者总体结直肠癌细胞簇，其特征是致癌信号通路（例如丝裂原激活蛋白激酶）和致癌特征（例如复制应激）的差异活性。RNA代谢标记和患者来源类器官中RNA速度的评估揭示了沿着丝裂原激活的蛋白激酶活性梯度组织的结直肠癌细胞的发育轨迹。这与沿着分级 Wnt 活性发育的正常结肠类器官细胞形成对比。癌症类器官中 EGFR-BRAF-MEK 的实验靶向影响了取决于预测性 KRAS/BRAF 突变的信号传导和基因表达，并诱导细胞可塑性超越默认的发育轨迹。我们的结果强调定向癌细胞发育是非遗传性癌细胞异质性的驱动因素，并且作为对靶向治疗的反应而重新调整轨迹。