Crohn DiseaseORGANOIDSNCT06805890
Study of Tissue Repair in Inflammatory Bowel Disease Exploiting Organoid Technology
A study testing Colonoscopy - IBD inflamed tissue, Surgical resection - IBD inflamed mucous membrane and Colonoscopy - biopsies in healthy tissue in people with Crohn Disease and Inflammatory Bowel Diseases (IBD), run by Assistance Publique Hopitaux De Marseille at 1 site in France.
Trial 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. Read more about this study
- Who is it for?
- Ages 18 years and older
- Conditions the study is for
- Crohn Disease, Inflammatory Bowel Diseases (IBD), Ulcerative Colitis (Disorder)
- What is being tested?
- Colonoscopy - IBD inflamed tissue, Surgical resection - IBD inflamed mucous membrane and Colonoscopy - biopsies in healthy tissue
- Type of treatment
- Surgery or procedure
- Could I receive a placebo?
- Yes, some participants may receive a placebo
- How many people
- 60 participants
- Where
- 1 siteFrance
- Study dates
- 24 Jul 2025to 24 Mar 2027
- Phase
- Interventional
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 years and older
- All sexes
- No healthy volunteers
- Adult, Older adult
For IBD group the inclusion criteria will be:
- Patients of either sex aged 18 years or older
- Patient that have read the information form and signed consent
- Patient covered with health insurance
- Patients with Crohn's Disease or ulcerative colitis in accordance with accepted clinical, endoscopic, histological and/or radiologic criteria, regardless of the level, severity of the disease or duration of disease progression.
- Patients with colonic involvement of Crohn's disease or ulcerative colitis
- Patients undergoing a screening colonoscopy in the context of IBD disease follow-up OR undergoing intestinal resection for IBD disease aggravation
For control group the inclusion criteria will be:
- Patients of either sex aged 18 years or older
- Patient that have read the information form and signed consent
- Patient covered with health insurance
- Patients undergoing a screening colonoscopy in the context of a family history of colonic neoplasia, follow-up of colonic polyps or functional intestinal disorders OR undergoing intestinal resection for intestinal neoplasia, occlusive syndrome or colostomy
The non-inclusion criteria for IBD group will be:
- Contraindication to the anaesthetic or colonoscopy procedure
- Patients without colonic involvement of Crohn's disease or ulcerative colitis
- Patients of Adults without legal capacity
- Patients in Health and Social Establishments
- Persons in emergency situations
- Persons deprived of their liberty
- Non-affiliated to a social security scheme
- Absence or refusal of the informed consent
The non-inclusion criteria for control group will be:
- IBD disease revealed during colonoscopy or gastrointestinal resection
- Patient suffering from Immune-Mediated Inflammatory Diseases (IMIDs)
- Contraindication to the anaesthetic or colonoscopy procedure
- Patients of Adults without legal capacity
- Patients in Health and Social Establishments
- Persons in emergency situations
- Persons deprived of their liberty
- Non-affiliated to a social security scheme
- Absence or refusal of the informed consent
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
France1 site, 1 recruiting
- Recruiting
Nord Hospital
Marseille, 13915
Lucas GUILLO, 0491335817 ext. +33, promotion.interne@ap-hm.fr
About this study
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.
Read more
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.
- Being tested
- Colonoscopy - IBD inflamed tissue, Surgical resection - IBD inflamed mucous membrane, Colonoscopy - biopsies in healthy tissue, Surgical resection - healthy mucous membrane
- Medical subject headings
- Crohn Disease, Inflammatory Bowel Diseases, Colitis, Ulcerative
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Colonoscopy - IBD inflamed tissueProcedure or surgery
Collection of 10 colonic biopsies in IBD inflamed tissue
Surgical resection - IBD inflamed mucous membraneProcedure or surgery
Collection of a portion of IBD inflamed mucous membrane
Colonoscopy - biopsies in healthy tissueProcedure or surgery
Collection of 10 colonic biopsies in healthy tissue
Surgical resection - healthy mucous membraneProcedure or surgery
Collection of a portion of healthy mucous membrane
| Study group | Role | What they receive |
|---|---|---|
| Control group | Sham comparator | Patients of either sex aged 18 years or older and undergoing a screening colonoscopy in the context of a family history of colonic neoplasia, follow-up of colonic polyps or functional intestinal disorders OR undergoing intestinal resection for intestinal neoplasia, occlusive syndrome or colostomy Receives: Procedure: Colonoscopy - biopsies in healthy tissue; Procedure: Surgical resection - healthy mucous membrane |
| IBD group | Experimental | Patients of either sex aged 18 years or older with Crohn's Disease or ulcerative colitis in accordance with accepted clinical, endoscopic, histological and/or radiologic criteria, regardless of the level, severity of the disease or duration of disease progression or patients undergoing a screening colonoscopy in the context of IBD disease follow-up OR undergoing intestinal resection for IBD disease aggravation Receives: Procedure: Colonoscopy - IBD inflamed tissue; Procedure: Surgical resection - IBD inflamed mucous membrane; Procedure: Surgical resection - healthy mucous membrane |
What is being measured
The primary outcome is the main question the study is designed to answer.
Repair status of IBD patient's epithelial cells from inflamed mucosae
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
Measured: From enrollmet to the end of following at 1 month
Secondary outcomes (3)
Evaluate the molecular mechanism involved in the reduced capacity of epithelial cells of IBD patients to repair intestinal mucosa
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).
Measured: From enrollment to the end of following at 1 month
Genetically determine the involvement of cell death and protective pathways that reduce repair capacity in patients.
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).
Measured: From enrollment to the end of following at 1 month
3. Explore the activation of molecular mechanisms identified in patient biopsies and correlate them with the inflammatory environment present in the patient's tissues
- 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.
Measured: From enrollment to the end of following at 1 month
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted3 Feb 2025
- Study start24 Jul 2025
- Primary completion24 Mar 2027 (estimated)
- Study completion24 Mar 2027 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Crohn DiseaseStudies of the same condition, open and under way.
- More trials run by Assistance Publique Hopitaux De MarseilleThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase N/A
- Primary purpose
- Basic science
- Allocation
- Non-randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Enrolment
- 60 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Assistance Publique Hopitaux De Marseille
- Sponsor type
- University, hospital or other
- Responsible party
- Sponsor
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT06805890
- Sponsor's protocol ID
- RCAPHM24_0062
- Other IDs
- 2024-A00510-47
- Acronym
- ORGANOIDS
- Status last verified
- Sep 2026
- First submitted
- 28 Jan 2025
- Last updated
- 21 Sep 2026
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No
Study at a glance
From the registry record, last updated by the sponsor on 21 Sep 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Study of Tissue Repair in Inflammatory Bowel Disease Exploiting Organoid Technology
- ClinicalTrials.gov ID
- NCT06805890
- Acronym / sponsor ID
- ORGANOIDS / RCAPHM24_0062
- Study type
- Interventional
- Recruitment status
- Recruiting
- Enrolment
- 60 participants (estimated)
- Lead sponsor
- Assistance Publique Hopitaux De MarseilleUniversity, hospital or other
- Study start
- 24 Jul 2025 (actual)
- Primary completion
- 24 Mar 2027 (estimated)
- Study completion
- 24 Mar 2027 (estimated)
- First posted
- 3 Feb 2025 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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.
Study design
- Primary purpose
- Basic science
- Allocation
- Non-randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Number of arms
- 2
| Arm | Type | Receives |
|---|---|---|
| Control group | Sham comparator | Procedure: Colonoscopy - biopsies in healthy tissue, Procedure: Surgical resection - healthy mucous membranePatients of either sex aged 18 years or older and undergoing a screening colonoscopy in the context of a family history of colonic neoplasia, follow-up of colonic polyps or functional intestinal disorders OR undergoing intestinal resection for intestinal neoplasia, occlusive syndrome or colostomy |
| IBD group | Experimental | Procedure: Colonoscopy - IBD inflamed tissue, Procedure: Surgical resection - IBD inflamed mucous membrane, Procedure: Surgical resection - healthy mucous membranePatients of either sex aged 18 years or older with Crohn's Disease or ulcerative colitis in accordance with accepted clinical, endoscopic, histological and/or radiologic criteria, regardless of the level, severity of the disease or duration of disease progression or patients undergoing a screening colonoscopy in the context of IBD disease follow-up OR undergoing intestinal resection for IBD disease aggravation |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Colonoscopy - IBD inflamed tissueCollection of 10 colonic biopsies in IBD inflamed tissue | Procedure or surgery | IBD group |
| Surgical resection - IBD inflamed mucous membraneCollection of a portion of IBD inflamed mucous membrane | Procedure or surgery | IBD group |
| Colonoscopy - biopsies in healthy tissueCollection of 10 colonic biopsies in healthy tissue | Procedure or surgery | Control group |
| Surgical resection - healthy mucous membraneCollection of a portion of healthy mucous membrane | Procedure or surgery | Control group, IBD group |
Primary outcome
Repair status of IBD patient's epithelial cells from inflamed mucosae
Time frame: 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
3 secondary outcomes
Evaluate the molecular mechanism involved in the reduced capacity of epithelial cells of IBD patients to repair intestinal mucosa
Time frame: From enrollment to the end of following at 1 month
Genetically determine the involvement of cell death and protective pathways that reduce repair capacity in patients.
Time frame: From enrollment to the end of following at 1 month
3. Explore the activation of molecular mechanisms identified in patient biopsies and correlate them with the inflammatory environment present in the patient's tissues
Time frame: From enrollment to the end of following at 1 month
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 21 Sep 2026.
- Individual participant dataSharing planned: No
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing Colonoscopy - IBD inflamed tissue, Surgical resection - IBD inflamed mucous membrane and Colonoscopy - biopsies in healthy tissue in people with Crohn Disease and Inflammatory Bowel Diseases (IBD), run by Assistance Publique Hopitaux De Marseille at 1 site in France.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: looking for participants now, as of the sponsor's last update on 21 Sep 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in France. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. Some participants in this study may receive a placebo. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Lucas GUILLO (0491335817 ext. +33, promotion.interne@ap-hm.fr), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Repair status of IBD patient's epithelial cells from inflamed mucosae (time frame: From enrollmet to the end of following at 1 month). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 21 Sep 2026.