Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer

Abstract

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.

Oncogenic signalling is coupled to colorectal cancer cell differentiation state

“…Antagonistic Wnt and MAPK activity has recently been shown to limit anti-MAPK therapy efficiency in CRC. 14,38 Our data extend this antagonistic model to activities of the APC and KRAS driver mutations during CRC progression. Additional loss of TGF-βand BMP signal transducer SMAD4 reversed the KRAS effect in our data.…”

“…5a). 13,14 We therefore cultured the lines in the presence or absence of Wnt and/or EGF (Fig. 3a), and observed similar effects on the distribution of cells across a pseudo-differentiation axis defined by EphB2 (Fig.…”

“…The following organoid lines were used in this study: Normal colon organoids, established from human intraoperative material (Charité ethics committee approval #EA4/015/13), isogenic normal and CRISPR-modified human colon organoids (Drost et al 2015 11 ), human colon organoid lines OT227, OT302 (Schütte et al 2017 13 ) and P009T, P013T (Uhlitz et al 2021 14 ).…”

Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis

“…4f ), implying a common pathogenic mechanism during the normal-adenoma transition. We further validated the recurrence of the adenoma precursor cell population using data from GSE166555, 36 which consisted of patient-matched tumor and adjacent normal tissue from 12 untreated patients with CRC. We clustered adjacent normal tissue-derived epithelial cells by unsupervised graph-based clustering (Supplementary Fig.…”

Recent advances in targeted drug delivery systems for resistant colorectal cancer

“…Thus such finding can contribute to better treatment design [ 157 ]. Likewise, single cell analysis of normal colon and CRC tissue reveled WNT-independent MAPK activity in CRC as a key driver of tumor cell plasticity [ 158 ]. Furthermore, as CRC display a high degree of tumor heterogeneity, recent single-cell RNA sequencing analysis revealed heterogeneity in gene regulatory networks and identified CRC critical regulators such as transcription factor ERG [ 159 ].…”