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. To define differences in cellular composition between the normal colon and colorectal cancer, and to map potential cellular interactions between tumor cells and their microenvironment, we profiled transcriptomes of >50,000 single cells from tumors and matched normal tissues of eight colorectal cancer patients. We find that tumor formation is accompanied by changes in epithelial, immune and stromal cell compartments in all patients. In the epithelium, we identify a continuum of five tumor-specific stem cell and progenitor-like populations, and persistent multilineage differentiation. We find multiple stromal and immune cell types to be consistently expanded in tumor compared to the normal colon, including cancer-associated fibroblasts, pericytes, monocytes, macrophages and a subset of T cells. We identify epithelial tumor cells and cancer-associated fibroblasts as relevant for assigning colorectal cancer consensus molecular subtypes. Our survey of growth factors in the tumor microenvironment identifies cell types responsible for increased paracrine EGFR, MET and TGF-β signaling in tumor tissue compared to the normal colon.We show that matched colorectal cancer organoids retain cell type heterogeneity, allowing to define a distinct differentiation trajectory encompassing stem and progenitor-like tumor cells. In summary, our single-cell analyses provide insights into cell types and signals shaping colorectal cancer cell plasticity.

LSD1 promotes secretory cell specification to driveBRAFmutant colorectal cancer

“…Our finding that BRAF mutant CRC cell lines maintain high levels of EEC progenitors suggests the cell lines may provide suitable models for the study of secretory cells in progenitor states. When comparing our scRNA-seq data from HT29 and H508 cell lines to a normal human colon sample, multiple of the clearly defined cell types seen in the colon sample appeared in a more undifferentiated or transcriptionally altered state in the CRC cell lines, consistent with other studies of CRC tumors at single-cell resolution (Uhlitz et al, 2020). However, distinct cell types such as goblet cells and putative early EECs appeared well-defined and with clearly conserved markers in both the normal colon and CRC cell lines.…”

“…Aggressive subtypes of NETs include those with goblet cell differentiation (goblet cell carcinoids) (McGory et al, 2005), and poorly differentiated NETs (PDNETs) (Basturk et al, 2014). While distinct from mucinous tumors, goblet cell carcinoids are pathologically more similar to adenocarcinomas of the large intestine than to other NET subtypes (van Eeden et al, 2007), which may contribute to their under-characterization in the large intestine due to the difficulty in differentiating them from canonical adenocarcinomas. However, recent pathological studies have begun to identify tumors similar to goblet cell carcinoids in the large intestine (Inoue et al, 2020) (Abdalla et al, 2020), indicating that mixed secretory lineage CRCs form at some previously unappreciated frequency.…”

Angiocrine Regulation of Epithelial Barrier Integrity in Inflammatory Bowel Disease

“…The latter indicated that angiocrine activities in the colon may trigger the course of diseases in a microenvironment–dependent manner. A recent single cell RNAseq approach of intestinal cells and subsequent bioinformatics interaction analyses supported the molecular interaction between endothelial cells and epithelial cells in the colon ( 121 ).…”

Maintaining and escaping feedback control in hierarchically organised tissue: a case study of the intestinal epithelium

“…An interesting avenue for future research lies in comparing healthy with tumoural intestinal tissue to clarify, whether one indeed observes similar cellular subpopulations and differen-tiation gradients. Recent research indeed suggests this [49,50]. Tracking the numbers of different cell types over time during development and after perturbations could therefore be expected to yield data for validating and parametrising the presented model.…”