%0 Journal Article %T Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. %A Uhlitz F %A Bischoff P %A Peidli S %A Sieber A %A Trinks A %A Lüthen M %A Obermayer B %A Blanc E %A Ruchiy Y %A Sell T %A Mamlouk S %A Arsie R %A Wei TT %A Klotz-Noack K %A Schwarz RF %A Sawitzki B %A Kamphues C %A Beule D %A Landthaler M %A Sers C %A Horst D %A Blüthgen N %A Morkel M %J EMBO Mol Med %V 13 %N 10 %D 10 2021 7 %M 34409732 %F 14.26 %R 10.15252/emmm.202114123 %X 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.