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Celiac DiseaseDeep BowelNCT07556328

Histomolecular Profiling in Small-Bowel Diseases

An observational study of Celiac Disease and Small Bowel Disease, run by Tampere University Hospital at 3 sites in Finland.

Recruiting

Looking for participants now. Contact the study team or a site below to ask about taking part.

Sites and contacts
Official record
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Trial summary

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. Read more about this study

Who is it for?
Ages 18 years and olderHealthy volunteers can take part
How many people
300 participants
Where
3 sitesFinland
Study dates
1 Nov 2025to 31 Dec 2035
How long will I take part?
12 Months
Phase
Observational
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
  • Healthy volunteers accepted
  • Adult, Older adult

Study population: Healthy, seropositive patients and refractory to treatment

Who may be able to join

  • 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

Who cannot join

  • 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

Trial locations and contacts

3 sites in 1 country. Contact the study team or a site near you to ask about taking part.

Juha Taavela contact

+358443400330

juha.taavela@tuni.fi

Finland3 sites, 3 recruiting

  • Hatanpää Specialist Medical Care

    Tampere, 33720

    Juha Taavela, +358443400330, juha.taavela@tuni.fi

    Recruiting

  • Tampere University Hospital (Tays)

    Tampere, 33720

    Juha Taavela, +358443400330, juha.taavela@tuni.fi

    Recruiting

  • Valkeakoski Regional Hospital

    Valkeakoski, 33720

    Juha Taavela, +358443400330, juha.taavela@otuni.fi

    Recruiting

Other trials in Finland

About this study

Official title: 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.

Read the 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.

Keywords
celiac disease, duodenal biopsy, histology, digital morphometry, artificial intelligence, RNA sequencing, transcriptomics, organoids, small bowel, villous atrophy, molecular profiling, machine learning
Medical subject headings
Celiac Disease

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

Study groups in NCT07556328
Study groupRoleWhat they receive
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 being measured

The primary outcome is the main question the study is designed to answer.

  1. Villus-to-crypt ratio

    Villus-to-crypt ratio in normal duodenal mucosa established by digital morphometry

    Measured: Research biopsy obtained at time of endoscopy; digital morphometry performed through study completion (up to December 31, 2025)

  2. Transcriptomic

    Transcriptomic (RNA-Seq) profile of duodenal mucosa in celiac disease patients and healthy controls

    Measured: Research biopsy obtained at time of endoscopy; RNA-Seq analysis performed through study completion (up to December 31, 2025)

Secondary outcomes (3)

  1. AI/machine-learning-based image analysis

    Development and validation of an AI/machine-learning-based image analysis tool for grading small-bowel mucosal damage

    Measured: Throughout study period up to December 31, 2035

  2. Organoid culture models of celiac

    Organoid culture models of celiac and refractory small-bowel epithelial inflammatory responses at the cellular and molecular level

    Measured: Throughout study period up to December 31, 2035

  3. Comparison of transcriptomic profiles

    Comparison of transcriptomic profiles between this cohort and the reference drug-trial dataset

    Measured: Throughout study period up to December 31, 2035

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted29 Apr 2026
  2. Study start1 Nov 2025
  3. Primary completion31 Dec 2035 (estimated)
  4. Study completion31 Dec 2035 (estimated)

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Observational
Observational model
Cohort
Time perspective
Prospective
Enrolment
300 participants (estimated)
Target duration
12 Months
IDs, dates and publications
ClinicalTrials.gov ID
NCT07556328
Sponsor's protocol ID
R25009
Acronym
Deep Bowel
Status last verified
Apr 2026
First submitted
20 Apr 2026
Last updated
29 Apr 2026
Results posted
No
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
No: 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.

Publications

  • Schuppan D, Maki M, Lundin KEA, Isola J, Friesing-Sosnik T, Taavela J, Popp A, Koskenpato J, Langhorst J, Hovde O, Lahdeaho ML, Fusco S, Schumann M, Torok HP, Kupcinskas J, Zopf Y, Lohse AW, Scheinin M, Kull K, Biedermann L, Byrnes V, Stallmach A, Jahnsen J, Zeitz J, Mohrbacher R, Greinwald R; CEC-3 Trial Group. A Randomized Trial of a Transglutaminase 2 Inhibitor for Celiac Disease. N Engl J Med. 2021 Jul 1;385(1):35-45. doi: 10.1056/NEJMoa2032441.

    PubMed 34192430

  • Taavela J, Viiri K, Popp A, Oittinen M, Dotsenko V, Peraaho M, Staff S, Sarin J, Leon F, Maki M, Isola J. Histological, immunohistochemical and mRNA gene expression responses in coeliac disease patients challenged with gluten using PAXgene fixed paraffin-embedded duodenal biopsies. BMC Gastroenterol. 2019 Nov 15;19(1):189. doi: 10.1186/s12876-019-1089-7.

    PubMed 31730447

  • Taavela J, Viiri K, Valimaki A, Sarin J, Salonoja K, Maki M, Isola J. Apolipoprotein A4 Defines the Villus-Crypt Border in Duodenal Specimens for Celiac Disease Morphometry. Front Immunol. 2021 Jul 29;12:713854. doi: 10.3389/fimmu.2021.713854. eCollection 2021.

    PubMed 34394117

  • Risnes LF, Reims HM, Doyle RM, Qiao SW, Sollid LM, Lundin KEA, Christophersen A. Gluten-Free Diet Induces Rapid Changes in Phenotype and Survival Properties of Gluten-Specific T Cells in Celiac Disease. Gastroenterology. 2024 Jul;167(2):250-263. doi: 10.1053/j.gastro.2024.03.027. Epub 2024 Mar 28.

    PubMed 38552723

  • Dotsenko V, Oittinen M, Taavela J, Popp A, Peraaho M, Staff S, Sarin J, Leon F, Isola J, Maki M, Viiri K. Genome-Wide Transcriptomic Analysis of Intestinal Mucosa in Celiac Disease Patients on a Gluten-Free Diet and Postgluten Challenge. Cell Mol Gastroenterol Hepatol. 2021;11(1):13-32. doi: 10.1016/j.jcmgh.2020.07.010. Epub 2020 Jul 31.

    PubMed 32745639

Questions about this trial

What is this clinical trial studying?

An observational study of Celiac Disease and Small Bowel Disease, run by Tampere University Hospital at 3 sites in Finland.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 6 inclusion and 3 exclusion criteria. 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 29 Apr 2026. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 3 sites in Finland. 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. 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 Juha Taavela (+358443400330, juha.taavela@tuni.fi), or a site near the patient. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

Villus-to-crypt ratio (time frame: Research biopsy obtained at time of endoscopy; digital morphometry performed through study completion (up to December 31, 2025)). The study lists 2 primary outcomes in all. It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT07556328, which also lists 5 linked publications.

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 29 Apr 2026.

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