Study of Tissue Repair in Inflammatory Bowel Disease Exploiting Organoid Technology

Not Applicable

Not yet recruiting

• Conditions: Crohn Disease; Inflammatory Bowel Diseases (IBD); Ulcerative Colitis (Disorder)

• Registration Number: NCT06805890
• Lead Sponsor: Assistance Publique Hopitaux De Marseille

Brief Summary

Inflammatory Bowel Diseases (IBD) are chronic inflammations of the gastrointestinal tract. Regardless of the etiology, a common trait of IBD pathogenesis is the inflammatory damage inflicted on the intestinal mucosa and the loss of intestinal epithelial barrier integrity. Therefore, understanding the mechanisms that govern IEC's capacity to maintain barrier function and to orchestrate mucosal healing is considered a major goal in translational research. The investigators are interested in understanding how the inflammatory environment present in the intestinal mucosa, of IBD patients influences epithelial cells capacity to govern repair. The complexities of the cytokine and metabolic milieu present in IBD patients render the study of the contribution of each cytokine, metabolite, and intracellular pathway extremely complicated. Therefore, most of the processes that govern tissue regeneration are studied with the use of mouse models that recapitulate one or multiple features of IBD and allow for genetical modifications of the gene and pathway of interest. While mouse models are uniquely suited to study the complex crosstalk between the immune system, the microbiota, and the intestinal epithelia, they introduce the important problem of species-specific differences, which can hamper the translational value of mouse studies.

To overcome these shortcomings, the investigators propose to explore the influence of cytokines and metabolites in digestive organoids derived from patients and controls. Importantly, it was demonstrated that gene expression and innate immune responses are altered in primary organoids derived from patients with IBD, including altered ability to proliferate, respond to cytokines, metabolic capacity, and efficiently form organoids suggesting that major differences between patient's and control's epithelial cell biology can be faithfully replicated in this system.

Given these premises, the investigators propose the following objectives:

Primary objective:

The main objective of this study is to establish that patient's epithelial cells from inflamed mucosae have decreased ability to repair the intestinal mucosa, as compared to epithelial cells from non-inflamed regions in the same patient, or to control subject with no inflammatory digestive diseases.

The investigators will explore this question both deriving organoids from clinical samples and exposing them to pro inflammatory cytokines and metabolites in vitro, as well as by analyzing repair responses from the aforementioned clinical samples ex vivo.

Secondary objective

The secondary goals of this study are:

- To compare organoids derived from: epithelia in inflamed mucosa of IBD patients, epithelia in non-inflamed mucosa of IBD patients, and epithelia from the mucosa of non-IBD controls in their capacity to mount a repair response in response to inflammatory cytokines or luminal metabolites.

Namely the investigators will evaluate the following parameters:

* Their capacity to proliferate.

* Their ability to survive treatment with pro-inflammatory cytokines

* The activation of intracellular pathways associated with cell death.

* Their overall metabolic activity.

* The balance between stem and differentiated epithelial cell types.

* The transcriptional activation of protective pathways such as those associated with proliferation, migration, differentiation and cell survival.

* To evaluate hallmarks of tissue repair in biopsies derived from epithelia in inflamed mucosa of IBD patients, epithelia in non-inflamed mucosa of IBD patients, and epithelia from the mucosa of non-IBD controls, and to correlate them to the levels of inflammatory cytokines, luminal metabolites and overall disease severity. Namely the investigators will evaluate the following parameters:

* The abundance of proliferating cells.

* The activation of intracellular pathways associated with cell death and survival.

* Their overall metabolic activity.

* The balance between stem and differentiated epithelial cell types.

* The transcriptional activation of protective pathways such as those associated with proliferation, migration, differentiation and cell survival.

Detailed Description

Not available

Study Timeline

• Study First Submitted: 2025-01-28
• Study First Submitted QC: 2025-01-28
• Status Verified: 2025-02
• Study First Posted: 2025-02-03
• Last Update Submitted: 2025-02-21
• Last Update Posted: 2025-02-24
• Study Start: 2025-05-02
• Primary Completion: 2027-01-01
• Study Completion: 2027-01-01

Recruitment & Eligibility

• Status: NOT_YET_RECRUITING
• Sex: All
• Target Recruitment: 60

Inclusion Criteria

Not provided

Exclusion Criteria

Not provided

Study & Design

• Study Type: INTERVENTIONAL
• Study Design: PARALLEL

Primary Outcome Measures

Name	Time	Method
Repair status of IBD patient's epithelial cells from inflamed mucosae	From enrollmet to the end of following at 1 month	To establish that patient's epithelial cells from inflamed mucosae have decreased ability to repair the intestinal mucosa, as compared to epithelial cells from non-inflamed regions in the same patient, or to control subject with no inflammatory digestive diseases

Secondary Outcome Measures

Name	Time	Method
3. Explore the activation of molecular mechanisms identified in patient biopsies and correlate them with the inflammatory environment present in the patient's tissues	From enrollment to the end of following at 1 month	* Proliferation in FFPE biopsies and RNA from RNAlater fixed biopsies: Ki67 upregulation by immunohistochemistry (IHC), PCNA gene expression, Proliferation transcriptional signature by RNAseq etc...).; * Cell death by biochemical analysis of cell death pathways by Western Blot (WB) and IHC in flash frozen biopsies: relative quantification of biochemical activation of 1) apoptotic caspases; 2) pyroptosis effectors (GSDMs); 3) Necroptosis effectors (MLKL).; * Differentiation status of epithelial cells from DMSO conserved biopsies: staining of cell type markers by IHC, scRNAseq of dissociated epithelial cells.; * The metabolic landscape of epithelial cells in flash frozen biopsies: the metabolome of the cells.
Evaluate the molecular mechanism involved in the reduced capacity of epithelial cells of IBD patients to repair intestinal mucosa	From enrollment to the end of following at 1 month	Evaluation of: * The capacity epithelial cells of IBD patients to proliferate: ratio of Ki67+cells.; * The ability of epithelial cells of IBD patients to survive treatment with pro-inflammatory cytokines: ratio between live and dead organoids.; * The activation of intracellular pathways associated with cell death: relative quantification of biochemical activation of 1) apoptotic caspases,2) pyroptosis effectors (GSDMs),3) Necroptosis effectors (MLKL).; * The balance between stem and differentiated epithelial cell types: the relative gene expression of the stemness associated genes LGR5, OLFM4, and the hallmark genes of differentiated cell types AQP8, MUC2, LYZ1, CHGA).
Genetically determine the involvement of cell death and protective pathways that reduce repair capacity in patients.	From enrollment to the end of following at 1 month	After a genetically modify with CRISPR-CAS9 technology: * The capacity of modified epithelial cells of IBD patients to proliferate: ratio of Ki67+cells.; * The ability of modified epithelial cells of IBD patients to survive treatment with pro-inflammatory cytokines: ratio between live and dead organoids.; * The activation of intracellular pathways associated with cell death: relative quantification of biochemical activation of 1) apoptotic caspases,2) pyroptosis effectors (GSDMs),3) Necroptosis effectors (MLKL).; * The balance between stem and differentiated epithelial cell types: the relative gene expression of the stemness associated genes LGR5, OLFM4, and the hallmark genes of differentiated cell types AQP8, MUC2, LYZ1, CHGA).

Trial Locations

Locations (1)

Hord Hospital; 🇫🇷 Marseille, France