Differential 5-FU responses of crypt-derived organoids embedded in collagen versus Matrigel, and their transcriptomic comparison with villus-derived organoids

We compared the effects of 5-fluorouracil (5-FU) on gene expression profiles of mouse crypt-derived intestinal organoids embedded in either Matrigel (MG) or collagen type I (COL). Distinct sets of genes were upregulated in COL-embedded organoids following 5-FU treatment, suggesting that collagen-based ECM uniquely modulates inflammatory and DNA-damage responses. We further compared COL-embedded crypt-derived organoids with COL-embedded villus-derived organoids (V-organoids) and found that their transcriptional profiles were highly similar. These results indicate that collagen embedding promotes the emergence of revival stem cell–like signatures regardless of the cellular origin of the organoids.