Single cells and spatial RNA profiling reveal that inflammatory fibroblasts arise from Edil3 stromal cells in the colon after irradiation.

Patients with cancer who are treated for tumors located in the abdominopelvic region may develop radiation proctitis. This condition is characterized by severe mucosal inflammation that can significantly impair quality of life. In the colon, it's now established that the stroma orchestrates epithelial, endothelial, and immune cell homeostasis and plays a pivotal role following an injury. A more comprehensive understanding of the underlying mechanisms responsible for digestive mucosa injury and regeneration processes would enable therapeutic targets to be identified for limiting or even treating digestive lesions caused by radiotherapy. In this work, single-cell RNA sequencing was combined with spatial transcriptomics (ST) for an in-depth characterization of colonic stromal cells, highlighting their heterogeneity, their specific functions and interactions in homeostasis, and changes they undergo following localized colon irradiation. The present study identifies the Edil3 marker, (EGF-like repeats and discoidin domains 3), that distinguishes the most abundant stromal population, alongside the previously characterized trophocytes and telocytes. We propose the term "mesitocytes", from the ancient Greek "mesítês" ("intermediary"), for this stromal subtype, in accordance with both their position along the crypt axis and their role in the BMP/Wnt gradient. After irradiation, we demonstrate the deregulation of the stromal compartment, with an increase of genes involved in immune response, angiogenesis, and regenerative epithelial process. Specifically in the ulcerated area, Edil3 mesitocytes and telocytes are no longer detected by ST. Instead, inflammation-associated fibroblasts (IAFs) emerge, characterized by a distinct transcriptomic signature, including Ereg, Igfbp5, Il11 and C3. This feature is substantiated by analysis of human transcriptomic data which underscores the significance of our findings. Cell fate analysis further clarifies the origins of IAFs, identifying Edil3 mesitocytes as their main source. Furthermore, we observe that IAFs cooperate with endothelial cells, and we also demonstrate IAF-specific molecules involvement in epithelial disruption and endothelial activation, suggesting their key role in disease progression.