Preserving the Microenvironment-Advances in Ex Vivo Colonic Tissue Culture for IBD Drug Discovery

Inflammatory bowel disease (IBD), encompassing ulcerative colitis and Crohn’s disease, is driven by complex and highly context-dependent biological processes. Despite decades of research, translation from preclinical discovery to clinical success in IBD remains challenging, in part because many experimental models fail to capture the complexity of human intestinal biology.¹ Increasingly, attention has shifted toward ex vivo colonic tissue culture systems, which preserve the native tissue microenvironment and offer a more predictive platform for drug discovery.

The Role of the Colonic Microenvironment in IBD

At the core of IBD pathology is disruption of the colonic microenvironment — a tightly regulated ecosystem composed of epithelial cells, immune populations, stromal components, and extracellular matrix.² These elements interact dynamically to regulate barrier function, immune tolerance, and inflammatory resolution. Dysregulation of these interactions contributes to chronic inflammation and tissue damage characteristic of IBD.³

Traditional in vitro models, such as immortalised cell lines or simplified co-cultures, isolate individual components of this system but cannot reproduce the spatial organisation, cellular diversity, or signalling networks present in intact human tissue. Animal models, while valuable for mechanistic exploration, often fail to reflect human-specific immune responses and disease heterogeneity, contributing to late-stage attrition in IBD drug development.⁴

Ex Vivo Colonic Tissue Culture as a Human-Relevant Model

Ex vivo colonic tissue culture addresses many of these limitations by maintaining intact human biopsies or surgical specimens under controlled laboratory conditions. Unlike organoid systems, which are typically epithelial-centric and lack immune and stromal compartments, ex vivo cultures preserve the full cellular architecture of the colon.⁵

Crypt structures, resident immune cells, extracellular matrix, and tissue polarity remain intact, enabling researchers to study drug responses within a physiologically relevant human context. This preservation of tissue architecture and cellular crosstalk is particularly critical in IBD, where immune–epithelial interactions drive both disease progression and therapeutic response.⁶

Advances in Culture Conditions and Tissue Viability

Recent technical advances have significantly improved the viability and functional stability of ex vivo colonic tissue cultures. Optimised culture media formulations now support the metabolic demands of multiple cell types simultaneously, reducing tissue stress and phenotypic drift over time.⁷

In parallel, refinements in oxygen control have enhanced physiological relevance. The colonic mucosa exists within steep oxygen gradients in vivo, which influence epithelial metabolism, immune activation, and microbial interactions. Replicating these conditions more accurately in culture has been shown to improve tissue responsiveness and extend viable culture windows.⁸

Structural Support and Preservation of Tissue Architecture

Mechanical and structural support has emerged as a critical factor in maintaining tissue integrity ex vivo. Advances in scaffold design and matrix support help prevent tissue contraction and degradation while preserving crypt architecture and epithelial polarity.

These physical cues are increasingly recognised as active regulators of cell behaviour, influencing cytokine secretion, barrier permeability, and inflammatory signalling. By stabilising the extracellular environment, ex vivo platforms allow drug effects to be assessed in a setting that closely mirrors the native colon.⁹

Retention of Immune Complexity

One of the most compelling advantages of ex vivo colonic tissue culture is the retention of endogenous immune populations. Resident T cells, macrophages, and other immune cells remain embedded within their native tissue context, enabling direct interrogation of inflammatory pathways and immunomodulatory drug effects.¹⁰

This is particularly valuable in IBD, where therapeutic efficacy often depends on modulating immune responses rather than achieving complete suppression of inflammation. Coupling ex vivo cultures with cytokine profiling, histological assessment, and molecular analyses provides a multidimensional view of tissue-level drug responses.

Applications in IBD Drug Discovery

From a drug discovery perspective, ex vivo colonic tissue culture systems offer advantages across multiple stages of development. In early discovery, they can be used to validate therapeutic targets within human disease-relevant pathways, reducing reliance on surrogate models.

During lead optimisation, candidate compounds can be ranked based on their ability to modulate inflammation, preserve epithelial barrier integrity, and avoid tissue toxicity in human colon tissue. When combined with transcriptomic or proteomic profiling, these systems also support the identification of biomarkers that may inform patient stratification strategies in clinical trials.¹¹

Current Limitations and Ongoing Innovation

Despite their promise, ex vivo colonic tissue culture systems are not without challenges. Throughput remains lower than that of cell-based assays, and inter-donor variability necessitates rigorous experimental design and careful statistical analysis. Standardisation of protocols and quality control of tissue samples are essential to maximise reproducibility and translational value.

Ongoing innovation continues to address these limitations, including integration with microfluidic platforms, advanced imaging techniques, and improved tissue preservation methods. These developments are expected to further enhance the robustness and scalability of ex vivo approaches.¹²

Conclusion

Preserving the colonic microenvironment through advanced ex vivo tissue culture is transforming how IBD is studied in preclinical research. By maintaining native tissue architecture, immune complexity, and extracellular context, these systems bridge a critical gap between reductionist in vitro models and the realities of human disease.

As methodologies continue to evolve, ex vivo colonic tissue culture is positioned to play an increasingly central role in IBD drug discovery, improving translational confidence and supporting the development of more effective therapies for patients living with IBD.

References: 

1. Seyhan, A.A. Lost in translation: the valley of death across preclinical and clinical divide – identification of problems and overcoming obstacles. transl med commun 4, 18 (2019). https://doi.org/10.1186/s41231-019-0050-7
2. Jang, J., Jeong, S. Inflammatory Bowel Disease: Pathophysiology, Treatment, and Disease Modeling. BioChip J 17, 403–430 (2023). https://doi.org/10.1007/s13206-023-00118-y
3. Hal, Chavan. “Understanding Immune Dysregulation: Causes, Effects, and Treatment Approaches.” Journal of Inflammatory Bowel Diseases & Disorders, Hilaris SRL, 30 Nov. 2024, www.hilarispublisher.com/open-access/understanding-immune-dysregulation-causes-effects-and-treatment-approaches-112399.html.
4. Chalak M, Hesaraki M, Mirbahari SN, Yeganeh M, Abdi S, Rajabi S, Hemmatzadeh F. Cell Immortality: In Vitro Effective Techniques to Achieve and Investigate Its Applications and Challenges. Life (Basel). 2024 Mar 21;14(3):417. doi: 10.3390/life14030417. PMID: 38541741; PMCID: PMC10971253.
5. Shakeri, R., Mirjalili, S.Z., Karakus, C.O. et al. Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We?. Stem Cell Rev and Rep (2026). https://doi.org/10.1007/s12015-025-11052-x
6. Ozcan, A., Vicanolo, T., Angeli, V. et al. Structural immunity: immune cells as architects of tissue barriers. Nat Rev Immunol (2025). https://doi.org/10.1038/s41577-025-01230-w
7. Challener, Cynthia A. “Addressing the Complexities of Media Formulation Development.” BioPharm International, 6 Feb. 2026, www.biopharminternational.com/view/addressing-the-complexities-of-media-formulation-development.
8. Yu, Jiaquin et al. Reconstructing physiological oxygen gradients reveals the role of hypoxia in colon epithelial organization. bioRxiv 2025.12.16.694730; doi: https://doi.org/10.64898/2025.12.16.694730
9. Elblová P, Lunova M, Dejneka A, Jirsa M, Lunov O. Impact of mechanical cues on key cell functions and cell-nanoparticle interactions. Discov Nano. 2024 Jun 22;19(1):106. doi: 10.1186/s11671-024-04052-2. PMID: 38907808; PMCID: PMC11193707.
10. Li, J., Xiao, C., Li, C. et al. Tissue-resident immune cells: from defining characteristics to roles in diseases. Sig Transduct Target Ther 10, 12 (2025). https://doi.org/10.1038/s41392-024-02050-5
11. “Advance Promising Drug Candidates with Lead Optimisation.” Medicines Discovery Catapult, 10 Sept. 2025, md.catapult.org.uk/drug-discovery/drug-discovery-process/lead-optimisation/.
12. Wang, XD., Ma, BY., Lai, SY. et al. High-throughput strategies for monoclonal antibody screening: advances and challenges. J Biol Eng 19, 41 (2025). https://doi.org/10.1186/s13036-025-00513-z