Integrative multi-omics analysis of intestinal organoid differentiation

Area of Science:

• Gastroenterology and Hepatology
• Molecular Biology
• Developmental Biology

Background:

• Intestinal organoids are valuable in vitro models for studying epithelial homeostasis and cell differentiation.
• Understanding the molecular drivers of adult intestinal stem cell differentiation is crucial for regenerative medicine and disease research.

Purpose of the Study:

• To comprehensively investigate the molecular mechanisms governing gene expression during mouse intestinal stem cell differentiation using a multi-omics approach.
• To identify key regulatory elements and transcription factors involved in enterocyte lineage specification.

Main Methods:

• Application of a multi-omics framework (transcriptomics, proteomics, epigenomics) on mouse intestinal organoids.
• Analysis of stem cell-enriched and stem cell-depleted organoid populations.
• Integration of absolute mRNA and protein copy numbers to assess gene expression regulation.

Main Results:

• A global rewiring of the transcriptome and proteome was observed between intestinal stem cells and differentiating enterocytes.
• The majority of dynamic protein expression changes were transcriptionally driven.
• Post-transcriptional regulation was identified through integrated mRNA and protein copy number analysis.
• Epigenetic profiling revealed numerous cell-type-specific regulatory elements, highlighting Hnf4g as a critical transcription factor for enterocyte differentiation.

Conclusions:

• Integrative systems biology approaches provide a holistic view of gene expression regulation during cell differentiation.
• Multiple layers of regulation, including transcriptional and post-transcriptional control, govern intestinal stem cell differentiation.
• Hnf4g plays a significant role in driving enterocyte lineage specification and plasticity in the mouse small intestine.