Histomolecular Profiling in Small-Bowel Diseases (Deep Bowel)

April 24, 2026 updated by: Juha Taavela, Tampere University Hospital

Histological and Molecular Profiling in the Diagnostics and Treatment of Small-Bowel Diseases - A Prospective Cohort Study (The DeepBowel Study)

This prospective cohort study aims to establish reliable histological reference values for normal small-bowel mucosa, improve histological diagnostic quality in celiac disease, and develop an advanced molecular profile for disease diagnosis and treatment response evaluation. The study will collect duodenal biopsies from three groups: healthy controls undergoing clinically indicated gastroscopy, patients referred for primary celiac disease diagnostics, and patients with small-bowel mucosal injury unresponsive to a gluten-free diet. Patients will undergo routine clinical assessment via standard pathology review of diagnostic biopsies. Biopsies will be analyzed using digital morphometry, AI-based image analysis, RNA sequencing (transcriptomics), and intestinal organoid cultures.

Study Overview

Status

Recruiting

Conditions

Detailed Description

Celiac disease is a chronic autoimmune condition affecting approximately 2.4% of the Finnish population. Despite advances in diagnostics, histological assessment of duodenal biopsies remains the gold standard for diagnosis in most cases. However, histological evaluation is subject to inter-observer variability, with a 10% diagnostic error rate reported in international multicenter studies.

This study will:

  1. Establish reliable digital morphometric reference values (villus-to-crypt ratio) for normal small-bowel mucosa using digitized biopsy slides and AI/machine-learning-based analysis tools;
  2. Investigate molecular pathways underlying celiac disease progression and treatment response through RNA sequencing (RNA-Seq transcriptomics) of biopsies from celiac disease patients and healthy controls, with a reference comparison to a drug-trial dataset;
  3. Model disease progression and refractory small-bowel injury using intestinal organoid cultures derived from biopsies of celiac patients, refractory patients, and healthy controls.

Research biopsy samples will be processed at the Tampere University Celiac Disease Research Center under pseudonymization. Statistical analyses will be done in collaboration with the study statistician. All data will be stored for 15 years following study completion.

Study Type

Observational

Enrollment (Estimated)

300

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Locations

  • Finland
      • Tampere, Finland, 33720
        • Recruiting
        • Hatanpää Specialist Medical Care
        • Contact:
      • Tampere, Finland, 33720
        • Recruiting
        • Tampere University Hospital (Tays)
        • Contact:
      • Valkeakoski, Finland, 33720
        • Recruiting
        • Valkeakoski Regional Hospital
        • Contact:

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Adult
  • Older Adult

Accepts Healthy Volunteers

Yes

Sampling Method

Non-Probability Sample

Study Population

Healthy, seropositive patients and refractory to treatment

Description

Inclusion Criteria:

  • Age ≥ 18 years
  • Clinically indicated upper gastrointestinal endoscopy (gastroscopy)
  • Written informed consent obtained prior to procedure
  • For Group 1 (Healthy Controls): Negative celiac disease antibodies (anti-transglutaminase and/or anti-endomysium); no suspected celiac
  • For Group 2 (Celiac Diagnostics): Referred for primary celiac disease diagnostics requiring duodenal biopsy
  • For Group 3 (Refractory Injury): Confirmed small-bowel mucosal injury not responsive to a gluten-free diet

Exclusion Criteria:

  • For Group 1 (Healthy Controls): Other small-bowel diseases causing mucosal injury, including Crohn's disease and small-bowel ulcers
  • Inability to provide written informed consent
  • Refusal to participate

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

Cohorts and Interventions

Group / Cohort
Group 1 - Healthy Controls (n = 130)
Adults ≥18 years undergoing clinically indicated gastroscopy (e.g., reflux symptoms) with no suspicion of celiac disease and negative celiac antibodies (anti-transglutaminase and/or anti-endomysium).
Group 2 - Celiac Disease Diagnostic Group (n = 130)
Adults referred for primary celiac disease diagnostics requiring duodenal biopsy, in accordance with standard care guidelines.
Group 3 - Refractory Small-Bowel Injury Group (n = 40)
Adults with small-bowel mucosal injury (villous atrophy) that does not respond to a gluten-free diet, referred for endoscopy to exclude ongoing histological damage.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Villus-to-crypt ratio
Time Frame: Research biopsy obtained at time of endoscopy; digital morphometry performed through study completion (up to December 31, 2025)
Villus-to-crypt ratio in normal duodenal mucosa established by digital morphometry
Research biopsy obtained at time of endoscopy; digital morphometry performed through study completion (up to December 31, 2025)
Transcriptomic
Time Frame: Research biopsy obtained at time of endoscopy; RNA-Seq analysis performed through study completion (up to December 31, 2025)
Transcriptomic (RNA-Seq) profile of duodenal mucosa in celiac disease patients and healthy controls
Research biopsy obtained at time of endoscopy; RNA-Seq analysis performed through study completion (up to December 31, 2025)

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
AI/machine-learning-based image analysis
Time Frame: Throughout study period up to December 31, 2035
Development and validation of an AI/machine-learning-based image analysis tool for grading small-bowel mucosal damage
Throughout study period up to December 31, 2035
Organoid culture models of celiac
Time Frame: Throughout study period up to December 31, 2035
Organoid culture models of celiac and refractory small-bowel epithelial inflammatory responses at the cellular and molecular level
Throughout study period up to December 31, 2035
Comparison of transcriptomic profiles
Time Frame: Throughout study period up to December 31, 2035
Comparison of transcriptomic profiles between this cohort and the reference drug-trial dataset
Throughout study period up to December 31, 2035

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Tampere University Hospital

Collaborators

Tampere University

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

November 1, 2025

Primary Completion (Estimated)

December 31, 2035

Study Completion (Estimated)

December 31, 2035

Study Registration Dates

First Submitted

April 20, 2026

First Submitted That Met QC Criteria

April 24, 2026

First Posted (Actual)

April 29, 2026

Study Record Updates

Last Update Posted (Actual)

April 29, 2026

Last Update Submitted That Met QC Criteria

April 24, 2026

Last Verified

April 1, 2026

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • R25009

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

IPD Plan Description

Individual participant data will not be shared. Data contains sensitive health information protected under EU GDPR and Finnish data protection legislation. Aggregate and anonymized results will be published in peer-reviewed journals.

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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