Single-cell atlas of niche factor responses in human intestinal organoids

Introduction

Epithelial regeneration in inflammatory bowel disease (IBD) is governed by complex interactions between intestinal epithelial cells and their surrounding microenvironment. The mechanism by which this occurs is poorly understood, and the influence of these nice-derived factors on epithelial repair in a state of inflammatory bowel disease (IBD) is largely uncharacterised. To address this, the authors developed a human colonic organoid injury model that mimics inflammatory conditions and systematically profiled epithelial responses to a range of secreted niche factors.

The study used multiplexed single-cell RNA sequencing to generate a comprehensive “dictionary” of epithelial responses to 79 ligands, across different cell types and injury contexts. This atlas has identified cell-type-specific signalling pathways, revealed relationships between poorly characterised ligands, and linked organoid-derived transcriptional programs to human IBD tissue. These findings provide a global framework for understanding epithelial regeneration pathways and highlight the utility of human organoid platforms for translational discovery in intestinal inflammation.

Main Points

• The authors developed human colonic organoid injury models using inflammatory cytokines, irradiation and DSS exposure to mimic the epithelial damage associated with IBD.
• These injury models reproduced key transcriptional and functional features of inflamed intestinal epithelium, including apoptosis, barrier disruption and altered metabolic signalling.
• A panel of 79 secreted niche ligands was selected from human intestinal datasets and applied to inflamed organoids.
• Donor-pooled, multiplexed, single-cell RNA sequencing enabled high-throughput profiling of epithelial responses across stem, transit-amplifying and differentiated cell populations
• Ligand-induced responses clustered into signalling families, revealing shared transcriptional programs and pathway-specific effects.
• Responses were highly context-dependent, with distinct signalling outputs observed between homeostatic and injured epithelial states.
• Several niche factors altered epithelial cell composition, influencing stem cell maintenance, goblet cell differentiation and colonocyte maturation.
• Gene program analysis identified pathways linked to inflammation, metabolism, repair and differentiation, that were selectively activated by individual ligands.
• A subset of ligands induced transcriptional programs linked to remission-associated goblet cell signatures in IBD.
• Mapping organoid-derived gene signatures onto human single-cell and spatial IBD datasets confirmed translational relevance.
• Comparative analysis revealed functional differences within ligand families, suggesting differential receptor usage and downstream pathway activation.
• The resulting dataset provides a reference framework linking niche-derived signals to epithelial repair and inflammatory responses.

Conclusion

This study establishes a comprehensive atlas of epithelial responses to microenvironmental niche factors during inflammatory injury. By combining human intestinal organoid modelling with multiplexed single-cell transcriptomics, the authors defined cell-type-specific signalling pathways governing epithelial repair, differentiation and inflammation. Importantly, these responses mapped directly to human IBD tissue, supporting the translational relevance of organoid-based discovery platforms. The resulting “dictionary” provides a powerful resource for identifying regenerative signalling pathways and therapeutic targets. These findings further highlight the value of human intestinal organoids as scalable systems for modelling epithelial-microenvironment interactions and for prioritising candidate pathways for translational development in inflammatory bowel disease.

EPISTEM SERVICES

Epistem can support studies investigating epithelial repair and niche signalling using clinically relevant intestinal organoid and in vivo platforms. Our capabilities include multi-species (including human) organoids, inflammatory injury modelling, and multiplex screening.

The team also have decades experience modelling IBD and radiation injury / regeneration. Models of both acute and chronic IBD are available. Key cell populations can be isolated for phenotyping by immuno-labelling techniques and/or short-term culture and functional assays.

A range of analytical platforms are available, including live imaging, barrier function assessments, histology/IHC and quantitative image analysis, flow cytometry, luminex-based multiplex analysis of cytokines and chemokines and gene expression analysis (PCR, NGS and RNAscope).

All of our models are supported by bioinformatics analysis, including differential expression and pathway analysis. We also offer biomarker signature discovery and analysis using our proprietary software in clinical and preclinical samples.

Together, these integrated services enable translation of microenvironment-driven epithelial biology into biomarker discovery, target identification and preclinical therapeutic development for IBD.