Therapeutic Potential of Human Intestinal Organoids in Tissue Repair Approaches in Inflammatory Bowel Diseases

Abstract

Inflammatory bowel diseases (IBDs) are chronic immune-mediated conditions characterized by significant gut tissue damage due to uncontrolled inflammation. Anti-inflammatory treatments have improved, but there are no current prorepair approaches. Organoids have developed into a powerful experimental platform to study mechanisms of human diseases. Here, we specifically focus on its role as a direct tissue repair modality in IBD. We discuss the scientific rationale for this, recent parallel advances in scientific technologies (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9 and metabolic programming), and in addition, the clinical IBD context in which this therapeutic approach is tractable. Finally, we review the translational roadmap for the application of organoids and the need for this as a novel direction in IBD.

Keywords: CD; IBD; UC; organoids; repair; stem cells.

Figure 1.

Structure of the intestinal epithelium. The intestinal epithelium is organized into units that consist of crypts and—in the small bowel—protrusions called villi. At the base of the intestinal crypt lies the stem cell compartment, where LGR5 intestinal stem cells (ISCs) divide and replicate, whereas +4 stem cells act as reserve stem cells. As ISCs divide, they advance along the crypt villus axis, first entering the transit-amplifying zone before differentiating into the specialized, terminally differentiated cells of the epithelium (eg, goblet, tuft, and enteroendocrine cells). Finally, at the tip cells undergo anoikis and shed into the lumen.

Figure 2.

Overview of the causes of epithelial barrier dysfunction in inflammatory bowel disease (IBD). Genome-wide association studies and microarray studies of IBD patients have identified multiple risk loci in key epithelial genes (eg, HNF4a, CDH1, REG4). Furthermore, alterations in expression of key junctional proteins increase permeability and susceptibility to IBD. Specific alterations in function of epithelial cell subtypes are seen in IBD, for example a reduction in goblet cell abundance and the corresponding reduced mucus barrier layer seen in ulcerative colitis and Paneth cell aberrations in Crohn’s disease. Finally, metabolic and mitochondrial injury—of which DNA and mitochondrial encoding genes are frequently the most downregulated in active IBD—can lead to energy deficient states that reduce the epithelial barrier’s ability to regenerate after injury. DAMP, damage-associated molecular pattern; ER, endoplasmic reticulum.

Figure 3.

Human intestinal organoid culture. During routine endoscopy, 2 to 4 biopsies are sampled and stored on ice. Crypts are then liberated after incubation in EDTA solution for 60 minutes. During in vitro expansion, HIOs are maintained in a growth media that enforces a stem cell state. The expanded growth medium is modified by withdrawing growth factors and adding components that facilitate differentiation, as evidenced by increasing thickness, granularity, budding, and accumulation of intraluminal debris (scale bar = 250 µm).

Figure 4.

Timeline highlighting advances in organoid technology and transplantation. The first studies predated discovery of specialized media that drive intestinal stem cell (ISC) growth and expansion, instead digesting tissue whole and transplanting onto denuded animal intestine. Subsequent advances leveraged the discovery of the canonical WNT pathway and its influence on LGR5 stem cell in vitro culture. More recent studies have explored animal and later human intestinal organoids to heal damaged animal intestine and the restoration in normal physiology that this can generate. DSS, dextran sulfate sodium.

Figure 5.

Proposed application of human intestinal organoid (HIO) therapy. First, HIOs are isolated from patient via endoscopic sampling for subsequent autologous application. HIOs are expanded in vitro to generate a healthy pool of organoids. Once sufficient quantities have been achieved, HIOs are transplanted endoscopically. Specific clinical situations for which HIO application may be utilized include restoration of epithelial barrier as rescue therapy for medically refractory inflammatory bowel disease (IBD), fibrosing Crohn’s disease phenotypes, and early postoperative recurrence. Future in vitro culture therapy may include correction of aberrant metabolic phenotypes with mitochondrial therapy or targeted genetic therapy for specific pathogenic mutations. CRISPR, clustered regularly interspaced short palindromic repeats; mtROS, mitochondrial reactive oxygen species.