ECM Signatures Reveal Quiescent Stem Cell Diversity in the Colonic Niche

Abstract

Colonic stem cells have a key role in the continuous regeneration of a healthy intestinal epithelium. Despite considerable advances in single-cell omics technologies, the transcriptional heterogeneity of rare cell types such as colonic stem cells, as well as their functional states and niche-specific behaviors, remain poorly characterised. In this study, we leverage a meta-analysis of scRNA-seq and spatial transcriptomic datasets to comprehensively map the heterogeneity of colonic stem cells. We identify multiple, previously underappreciated stem cell states, including distinct quiescent subtypes marked by CDKN1A (P21), CDKN1B (P27), and CDKN1C (P57), proliferative populations defined by MKI67 (Ki67) and LRIG1, and a lineage-committed intermediate subpopulation expressing MUC2. Strikingly, we find that these states can be robustly identified solely by their extracellular matrix (ECM) gene expression signatures, revealing ECM composition as a critical determinant of stem cell identity. Notably, LAMA1 expression is highly specific to the P57+ quiescent population, linking laminin-mediated microenvironments to the active maintenance of deep quiescence, consistent with our recent findings associating LAMA1 with quiescent cell survival. By applying these ECM gene signatures, we delineate discrete "micro-niches" of quiescent stem cells in healthy tissue and provide evidence that analogous states persist in the colorectal cancer (CRC) environment. Extending our approach to an unrelated tissue, the pancreas, we detect parallel quiescent cell subtypes, illustrating the broader applicability of ECM-based signatures. Taken together, our findings redefine the concept of stem cell heterogeneity in the colon, establish ECM-driven gene signatures as a powerful tool for characterizing stem cell states, and offer new perspectives on the niche-dependent regulation of both healthy and cancerous stem cell populations.