Epigenetic Drifts during Long-Term Intestinal Organoid Culture

Area of Science:

• Stem cell biology
• Epigenetics
• Genomics

Background:

• Organoids mimic tissue structure and function, making them valuable for studying aging and tissue maintenance.
• Long-term organoid culture can lead to alterations in growth patterns and kinetics.
• Epigenetic drift is a potential cause for these observed changes.

Purpose of the Study:

• To investigate epigenetic changes, specifically histone tri-methylation at H3K4me3 and H3K27me3, and transcriptome profiles in long-term organoid cultures.
• To compare organoids from mismatch repair (MMR)-deficient and control mice.
• To understand the impact of long-term culture on organoid epigenomes and transcriptional landscapes.

Main Methods:

• Culturing intestinal organoids from MMR-deficient and control mice for 3 and 20 weeks.
• Analyzing histone tri-methylation (H3K4me3, H3K27me3) patterns.
• Profiling transcriptomes and comparing them with tissue of origin data.
• Utilizing a mathematical model to explain observed epigenetic changes.

Main Results:

• Organoids exhibited profound epigenetic changes during long-term culture, beyond short-term adaptations.
• Key changes included H3K4me3 recruitment to new genes and H3K27me3 loss from bivalent genes, indicating epigenetic gene activation.
• Long-term culture induced broad transcriptional changes related to maturation and metabolic adaptation.
• MMR-deficient organoids showed a disturbed adaptation process, leading to endoplasmic reticulum stress and Wnt pathway activation.

Conclusions:

• Long-term organoid culture induces significant epigenetic reprogramming and transcriptional alterations.
• These changes reflect a maturation and metabolic adaptation process that can be disrupted in genetically modified organoids.
• Epigenetic drift in organoids is linked to DNA demethylation, which may be impaired under conditions of disturbed metabolic adaptation.