Biofabrication of primary patient tissue-derived inflammatory bowel disease (IBD) model by organoid three-dimensional culture

Background: Inflammatory bowel disease is a chronic gastrointestinal disorder characterized by relapsing inflammation, disruption of the epithelial barrier, and dysregulated immune responses, leading to substantial morbidity. Conventional in vitro cell cultures and animal models often fail to reproduce the cellular heterogeneity, tissue architecture, and patient-specific features of the disease, limiting mechanistic understanding and therapeutic development. This study aimed to develop and characterize a patient-derived three-dimensional organoid model that closely recapitulates the structural, functional, and molecular hallmarks of the disease. Colonic biopsies from inflamed and non-inflamed regions of patients were embedded in alginate–gelatin scaffolds to generate organoids that maintain physiological tissue architecture and long-term viability. Results: Organoids from non-inflamed tissue maintained uniform spherical morphology with well-defined crypt-like domains, whereas organoids derived from inflamed tissue exhibited irregular architecture, disrupted epithelial junctions, and delayed recovery after passage. Scanning electron microscopy confirmed epithelial discontinuities and surface microfold irregularities in inflamed organoids. Functional viability assessments demonstrated an average survival rate of 71.0% at day 21. Gene expression analysis revealed significant downregulation of the intestinal stem cell marker LGR5 in inflamed organoids compared to controls (0.43 ± 0.05 vs. 1.03 ± 0.06, p = 0.0002), along with marked upregulation of inflammatory chemokines CXCL8 (3.65 ± 0.37, p = 0.0003), CCL2 (2.71 ± 0.17, p = 0.0001), and CXCL10 (4.28 ± 0.15, p < 0.0001). Conclusions: This patient-derived three-dimensional organoid system accurately models disease-associated structural deterioration, impaired regenerative capacity, and inflammatory signaling, providing a physiologically relevant and reproducible platform for mechanistic studies. The model enables high-throughput drug screening, evaluation of patient-specific therapeutic responses, and development of personalized interventions. By bridging the gap between conventional in vitro and in vivo systems, this organoid platform represents a significant advance in tissue engineering and translational gastrointestinal research, facilitating precise investigation of disease pathophysiology and accelerating the development of effective therapies for chronic inflammatory disorders.