Lei Chen

The intestinal epithelium exhibits a remarkable capacity for regeneration following injury, yet the spatial and temporal dynamics of the damage-repair cycle remain incompletely understood. We present a spatial transcriptomics atlas of ionizing radiation-induced injury and repair in the mouse jejunum, capturing mRNA from 16,921 genes across approximately 26 million bins at 2-µm resolution in 23 biological samples spanning six days post-irradiation. Analysis reveals transcriptional patterns and niche signals undetectable by bulk or single-cell approaches, including spatially restricted interferon-target gene activation, an altered differentiation trajectory in the lower villus during early repair, two transcriptionally distinct crypt regenerative cell populations, and global transcriptional upregulation consistent with hypertranscription as a hallmark of intestinal regeneration, with evidence for hypertranscription extending to human Crohn’s disease. In this work, we provide a spatiotemporal atlas of mouse intestinal regeneration at subcellular 2-µm resolution that will inform future therapeutic strategies for inflammatory bowel diseases and gastrointestinal pathologies arising from injury or cancer therapy.

The intestinal epithelium is a highly regenerative tissue organized along the crypt–villus axis, where spatially compartmentalized gene expression governs stem cell renewal, proliferation, and differentiation. Super-enhancers (SEs) are large clusters of regulatory elements densely bound by transcription factors (TFs) and cofactors that drive high-level expression of genes controlling cell identity and fate, yet their roles in intestinal epithelial identity and differentiation remain unclear. Here, we generate a spatiotemporal map of SEs in the small intestine, identifying compartment-specific SEs that define crypt and villus programs. Using mouse genetic models, we identify CDX2, HNF4, and SMAD4 as core TFs orchestrating SE-driven transcriptional networks essential for epithelial differentiation. CDX2 is required for SE integrity, and its loss causes widespread SE collapse and silencing of intestinal identity genes. We further demonstrate SE remodeling during colorectal cancer, in which HNF4 and SMAD4 function as SE-associated tumor suppressors that restrain oncogenic enhancer programs. Together, our findings establish SEs as central regulators of intestinal architecture, epithelial fidelity, and tumor progression.

Wnt-mediated tissue transformation is more pronounced in the small intestine and is associated with activation of regenerative pathways

Modification of Epiregulin levels in mesenchyme or enteroids does not impact growth or viability of either control or β-cateninGOF enteroids

Decreased levels of CDX2 enhances the fetal state via YAP activation

Reprogramming of Pdgfra+ fibroblasts in β-cateninGOF mice

Pdgfra cells are responsive to TGFB1 that acts as a strong inducer of fetal and regenerative genes in the epithelium

Increased expression of both pro-regenerative and Wnt signaling antagonists occur in Pdgfra-lo cells exposed to oncogenic epithelium