Inflammatory memory primes the intestine for enhanced regenerative potential

To assess whether Lgr5⁺ ISCs that persist after irradiation—and their progeny—undergo long-term transcriptomic and epigenetic alterations, we performed single-cell multiome sequencing (scRNA-seq and scATAC-seq) using the 10x Genomics Chromium platform.Moreover,to investigate whether this dedifferentiation process leads to lasting transcriptomic and epigenetic changes, we used Krt20CreERT2:Rosa26-tdTomato mice to specifically label villus epithelial cells.

In non-irradiated conditions, these cells are rapidly shed and lost. However, following irradiation, a subset of labeled cells dedifferentiates, migrates into the crypt compartment, and contributes to ISC regeneration. To characterize long-term molecular changes in these dedifferentiated cells and their progeny, we performed single-cell multiome sequencing (scRNA-seq and scATAC-seq) using the 10x Genomics Chromium platform.