Molecular and Chromatin Accessibility Programs Underlying Epithelial Injury and Impaired Regeneration in Neonatal...

Area of Science:

• Gastroenterology
• Developmental Biology
• Epigenetics

Background:

• Neonatal necrotizing enterocolitis (NEC) is a life-threatening condition characterized by intestinal injury and impaired epithelial repair.
• Understanding the molecular mechanisms behind defective epithelial regeneration in NEC is crucial for developing effective therapies.

Purpose of the Study:

• To comprehensively map epithelial injury in a neonatal mouse model of NEC using an integrated multi-omics approach.
• To identify key regulators of intestinal stem cell (ISC) function and epithelial regeneration in the context of NEC.

Main Methods:

• Utilized a neonatal mouse model of NEC induced by formula feeding, hypoxia, and lipopolysaccharide.
• Applied integrated multi-omics: bulk RNA sequencing, single-nucleus RNA sequencing (snRNA-seq), single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), and multiplexed error-robust fluorescence in situ hybridization (MERFISH).
• Conducted in vitro and in vivo experiments to assess NEC phenotypes, intestinal morphology, and organoid formation.

Main Results:

• Observed significant changes in epithelial cell composition, transcriptional networks, and chromatin accessibility in NEC.
• Identified a reduction in intestinal stem cells (ISCs) and transit-amplifying cells, alongside disrupted WNT signaling and stem cell maintenance genes.
• Revealed the epigenetic regulator Ezh2 as critical for LGR5+ ISC identity and homeostasis; its knockdown exacerbated inflammation and reduced stemness.

Conclusions:

• This study provides a multi-omics atlas of epithelial injury in experimental NEC, highlighting novel mechanisms of ISC failure.
• Ezh2 is identified as a key regulator of LGR5+ ISC identity and regeneration.
• Targeting Ezh2 and WNT signaling presents a promising therapeutic strategy to restore epithelial integrity in NEC.