Recent molecular classifications of colorectal cancer (CRC) based on global gene expression profiles have defined subtypes displaying resistance to therapy and poor prognosis. Upon evaluation of these classification systems, we discovered that their predictive power arises from genes expressed by stromal cells rather than epithelial tumor cells. Bioinformatic and immunohistochemical analyses identify stromal markers that associate robustly with disease relapse across the various classifications. Functional studies indicate that cancer-associated fibroblasts (CAFs) increase the frequency of tumor-initiating cells, an effect that is dramatically enhanced by transforming growth factor (TGF)-β signaling. Likewise, we find that all poor-prognosis CRC subtypes share a gene program induced by TGF-β in tumor stromal cells. Using patient-derived tumor organoids and xenografts, we show that the use of TGF-β signaling inhibitors to block the cross-talk between cancer cells and the microenvironment halts disease progression.

Colorectal cancers (CRCs) are composed of an amalgam of cells with distinct genotypes and phenotypes. Here we reveal a previously unappreciated heterogeneity in the biosynthetic capacities of CRC cells. We discover that the majority of ribosomal DNA transcription and protein synthesis in CRCs occur in a limited subset of tumor cells that localize in defined niches. The rest of the tumor cells undergo an irreversible loss of their biosynthetic capacities as a consequence of differentiation. Cancer cells within the biosynthetic domains are characterized by elevated levels of the RNA Polymerase 1 subunit A -POLR1A. Genetic ablation of POLR1A-high cell population imposes an irreversible growth arrest to CRCs. We show that elevated biosynthesis defines stemness in both LGR5+ and LGR5-tumor cells. Therefore, a common architecture in CRC is a simple cell hierarchy based on the differential capacity to transcribe ribosomal DNA and synthesize proteins.

The standard of care for advanced colorectal cancer (CRC) includes treatment with chemotherapeutic drugs that target the cell proliferation machinery 1 . In CRC patients with overt metastases, chemotherapy initially halts tumor growth but, almost inevitably, disease progresses after some cycles of treatment. Adjuvant chemotherapy is also administered to eliminate minimal residual disease, yet it only diminishes the risk of relapse by 10-25% 2 . Previous studies have shown that patient-derived organoids predict responses to chemotherapy 3-6 . Therefore, we used them as models to investigate the mechanisms behind the limited benefit of these treatments. Whereas CRC organoids expand from highly proliferative Lgr5+ tumor cells, we discovered that lack of optimal stem cell growth conditions specifies a latent Lgr5+ cell population. These cells expressed the gene Mex3a, were largely insensitive to chemotherapy and regenerated the organoid culture after treatment. In mouse models of metastatic latency, Mex3a+ cells contributed marginally to metastatic outgrowth. However, after chemotherapy treatment, Mex3a+ cells produced large cell clones that regenerated metastatic disease. Using lineage-tracing analysis combined with single cell profiling, we showed that drug-tolerant persister Mex3a+ cells downregulate the WNT/Lgr5+ stem cell program immediately after chemotherapy and adopt a transient regenerative state

Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced GI injury. Through single-cell RNA-sequencing of the irradiated mouse intestine, we find that p53 target genes are specifically enriched in stem cells of the regenerating epithelium, including revival stem cells that promote animal survival after GI damage. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce revival stem cells. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells that is controlled by an Mdm2-mediated negative feedback loop. These results suggest that p53 suppresses severe radiation-indued GI injury by promoting intestinal epithelial cell reprogramming.