DiabetesCOLATANCT05195502
Mapping the Human Colon Using Single Cell Sequencing
An observational study of Diabetes and Large Bowel Cancer, run by Bispebjerg Hospital at 1 site in Denmark.
Trial summary
The overall purpose of this study is to describe the cellular composition of the human colon and its gene expression using scRNAseq and scATACseq methods. This will potentially provide is with a detailed map of the colon aiding our understanding of how diseases of the colon develop as well as the colons influence on… Read more about this study
- Who is it for?
- Ages 18 years and older
- Conditions the study is for
- Diabetes, Large Bowel Cancer, Inflammatory Bowel Diseases
- What is being tested?
- Biopsy
- How many people
- 40 participants
- Where
- 1 siteDenmark
- Study dates
- 1 Jul 2022to 1 Jun 2024
- Phase
- Observational
- Are there results?
- None posted in the registry
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
- Adult, Older adult
Study population: Citizens aged 50 to 74 are invited to partake in screening for bowel cancer every second year. Patients who accept referral based on a positive fecal immunochemical test, will be invited to participate in this study
Who may be able to join
- Patients referred for out-patient colonoscopy as a result of positive hemoccult.
- Patients able to read and understand danish.
- Patients able to give informed consent.
- Patients of Scandinavian ethnicity.
Who cannot join
- Previous large bowel resections
- Suspicion pre or intraoperatively of benign or malignant disease of the colon
- Known inflammatory bowel disease.
- Immuno-modulation treatment
- Chemotherapy.
- Daily smoking
- > 21 weekly units of alcohol
- < 18 years of age
Trial locations and contacts
1 site in 1 country.
About this study
Official title: Cellular Composition of the Human Colon Using Single-cell RNA and Single-cell ATAC-sequencing.
The overall purpose of this study is to describe the cellular composition of the human colon and its gene expression using scRNAseq and scATACseq methods. This will potentially provide is with a detailed map of the colon aiding our understanding of how diseases of the colon develop as well as the colons influence on systemic diseases such as type II diabetes.
Read the detailed description
The human colon is composed of four distinct histological layers: Serosa, muscularis externa, submucosa, and mucosa. The inner mucosal surface is composed of columnar epithelium and glandular tissue containing crypts of Lieberkühn and secretory goblet cells, lamina propria and muscularis mucosa. Several distinct cell types have been discovered in varying degree in the colon for example enteroendocrine cells and M-cells.
The cellular composition, patterns of gene expression and upstream regulatory pathways of the human colon varies across different anatomical location. This is evident in the anatomical bias in benign and malignant colorectal diseases. For example, the distal colon has a higher incidens of ulcerative colitis, diverticulitis, and chromosomal instability cancer whereas in the proximal colon ischemic colitis, collagenous colitis and microsatellite instability-induced cancer are predominant.
Currently there are no studies describing baseline data for genome-wide coding, methylation or gene expression related to specific anatomic locations in the human colon.
By using scRNAseq and scATACseq (Single-cell Assay of Transposase Accessible Chromatin sequencing) we will be able to map open regions in the cell's DNA and RNA, thus providing us with a unique "map" of the cells in the colon as well is their gene expression. ScATACseq visualizes open regions in the chromatin, generating "peaks" which can then be used to map DNA motifs, such as transcription factor binding sites. With the emergence of scATACseq, chromatin accessibility is in combination with gene expression data an extremely useful resource to study cell type specific regulatory DNA interactions. To further study the immunological aspects of the colon, we will extract immune cells from the colon. Lastly, full blood will be extracted to better analyze metabolic risk factors in relation to the colon's metabolic cellular regulation.
The overall purpose of this study is to describe the cellular composition of the human colon and its gene expression using scRNAseq and scATACseq methods. This will potentially provide is with a detailed map of the colon aiding our understanding of how diseases of the colon develop as well as the colons influence on systemic diseases such as type II diabetes.
- Conditions
- Diabetes, Large Bowel Cancer, Inflammatory Bowel Diseases
- Being tested
- Biopsy
- Medical subject headings
- Diabetes Mellitus, Colonic Neoplasms, Inflammatory Bowel Diseases
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
BiopsyDiagnostic test
Participants included in the study, will have additional biopsies performed during their colonoscopy
| Study group | Role | What they receive |
|---|---|---|
| Screening colonoscopy patients | Patients referred for out-patient colonoscopy in the Danish Colorectal Screening program Receives: Diagnostic Test: Biopsy |
What is being measured
The primary outcome is the main question the study is designed to answer.
Profiling of open chromatin regions
Mapping of cell types, including rare cell types, using profiling of open chromatin regions. (ATAC-seq) in mucosal biopsies from the large bowel
Measured: 2 years
Evaluation of metabolic profile
Using bioimpedance, insulin and glucose measurements and CHiP-seq we will determine patient phenotype and epigenetics to evaluate their metabolic risk-profile and correlate this to cell types in the large bowel
Measured: 2 years
Secondary outcomes (1)
Colonic biofilm
By sequencing bacterial DNA in our samples, we will evaluate the mucosa-associated microbiome of the large bowel. This will be correlated to the two primary outcome measures
Measured: 2 years
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted19 Jan 2022
- Study start1 Jul 2022
- Primary completion31 Dec 2022
- Study completion1 Jun 2024
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (5)Papers the sponsor has linked to this study.
- Other trials for DiabetesStudies of the same condition, open and under way.
- 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
- Observational
- Observational model
- Cohort
- Time perspective
- Prospective
- Enrolment
- 40 participants (actual)
Sponsor and investigators
- Lead sponsor
- Bispebjerg Hospital
- Sponsor type
- University, hospital or other
- Collaborators
- The Novo Nordisk Foundation Center for Basic Metabolic Research
- Responsible party
- Principal investigator, Jacob Antonsen, Bispebjerg Hospital
- Investigators
- Jacob Antonsen, MD, Principal investigator, Bispebjerg Hospital
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT05195502
- Sponsor's protocol ID
- COLKEND01
- Acronym
- COLATA
- Status last verified
- Jun 2026
- First submitted
- 7 Jan 2022
- Last updated
- 12 Jun 2026
- Results posted
- No
- Data monitoring committee
- Yes
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No: Data in this study is based on biological samples and data from patient registry. These data are protected by the Danish Act on Processing of Personal Data and can be accessed through application to and approval from the Danish Data Protection Agency and the Danish Health Data Authority \[https://sundhedsda tastyrelsen.dk/da/forskerservice/ansog-om-data\] where the purpose and the feasibility of the intended analysis should be accounted for.
Publications
Kaz AM, Wong CJ, Dzieciatkowski S, Luo Y, Schoen RE, Grady WM. Patterns of DNA methylation in the normal colon vary by anatomical location, gender, and age. Epigenetics. 2014 Apr;9(4):492-502. doi: 10.4161/epi.27650. Epub 2014 Jan 10.
PubMed 24413027Knight JM, Kim E, Ivanov I, Davidson LA, Goldsby JS, Hullar MA, Randolph TW, Kaz AM, Levy L, Lampe JW, Chapkin RS. Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue. Physiol Genomics. 2016 Sep 1;48(9):651-9. doi: 10.1152/physiolgenomics.00023.2016. Epub 2016 Jul 8.
PubMed 27401218Forgue-Lafitte ME, Fabiani B, Levy PP, Maurin N, Flejou JF, Bara J. Abnormal expression of M1/MUC5AC mucin in distal colon of patients with diverticulitis, ulcerative colitis and cancer. Int J Cancer. 2007 Oct 1;121(7):1543-9. doi: 10.1002/ijc.22865.
PubMed 17565737Costales-Carrera A, Fernandez-Barral A, Bustamante-Madrid P, Dominguez O, Guerra-Pastrian L, Cantero R, Del Peso L, Burgos A, Barbachano A, Munoz A. Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue. Cancers (Basel). 2020 Aug 15;12(8):2302. doi: 10.3390/cancers12082302.
PubMed 32824266Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-21.29.9. doi: 10.1002/0471142727.mb2129s109.
PubMed 25559105
Study at a glance
From the registry record, last updated by the sponsor on 12 Jun 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Cellular Composition of the Human Colon Using Single-cell RNA and Single-cell ATAC-sequencing.
- ClinicalTrials.gov ID
- NCT05195502
- Acronym / sponsor ID
- COLATA / COLKEND01
- Conditions
- Diabetes, Large Bowel Cancer, Inflammatory Bowel Diseases
- Study type
- Observational
- Recruitment status
- Completed
- Enrolment
- 40 participants (actual)
- Lead sponsor
- Bispebjerg HospitalUniversity, hospital or other
- Collaborators
- The Novo Nordisk Foundation Center for Basic Metabolic Research
- Study start
- 1 Jul 2022 (actual)
- Primary completion
- 31 Dec 2022 (actual)
- Study completion
- 1 Jun 2024 (actual)
- First posted
- 19 Jan 2022 (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.
The overall purpose of this study is to describe the cellular composition of the human colon and its gene expression using scRNAseq and scATACseq methods. This will potentially provide is with a detailed map of the colon aiding our understanding of how diseases of the colon develop as well as the colons influence on systemic diseases such as type II diabetes.
Detailed description
The human colon is composed of four distinct histological layers: Serosa, muscularis externa, submucosa, and mucosa. The inner mucosal surface is composed of columnar epithelium and glandular tissue containing crypts of Lieberkühn and secretory goblet cells, lamina propria and muscularis mucosa. Several distinct cell types have been discovered in varying degree in the colon for example enteroendocrine cells and M-cells.
The cellular composition, patterns of gene expression and upstream regulatory pathways of the human colon varies across different anatomical location. This is evident in the anatomical bias in benign and malignant colorectal diseases. For example, the distal colon has a higher incidens of ulcerative colitis, diverticulitis, and chromosomal instability cancer whereas in the proximal colon ischemic colitis, collagenous colitis and microsatellite instability-induced cancer are predominant.
Currently there are no studies describing baseline data for genome-wide coding, methylation or gene expression related to specific anatomic locations in the human colon.
By using scRNAseq and scATACseq (Single-cell Assay of Transposase Accessible Chromatin sequencing) we will be able to map open regions in the cell's DNA and RNA, thus providing us with a unique "map" of the cells in the colon as well is their gene expression. ScATACseq visualizes open regions in the chromatin, generating "peaks" which can then be used to map DNA motifs, such as transcription factor binding sites. With the emergence of scATACseq, chromatin accessibility is in combination with gene expression data an extremely useful resource to study cell type specific regulatory DNA interactions. To further study the immunological aspects of the colon, we will extract immune cells from the colon. Lastly, full blood will be extracted to better analyze metabolic risk factors in relation to the colon's metabolic cellular regulation.
The overall purpose of this study is to describe the cellular composition of the human colon and its gene expression using scRNAseq and scATACseq methods. This will potentially provide is with a detailed map of the colon aiding our understanding of how diseases of the colon develop as well as the colons influence on systemic diseases such as type II diabetes.
Study design
- Observational model
- Cohort
- Time perspective
- Prospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Screening colonoscopy patients | – | Diagnostic Test: BiopsyPatients referred for out-patient colonoscopy in the Danish Colorectal Screening program |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Age groups
- Adult, Older adult
- Study population
- Citizens aged 50 to 74 are invited to partake in screening for bowel cancer every second year. Patients who accept referral based on a positive fecal immunochemical test, will be invited to participate in this study
Key inclusion criteria (4 listed)
- Patients referred for out-patient colonoscopy as a result of positive hemoccult.
- Patients able to read and understand danish.
- Patients able to give informed consent.
- Patients of Scandinavian ethnicity.
Key exclusion criteria (8 listed)
- Previous large bowel resections
- Suspicion pre or intraoperatively of benign or malignant disease of the colon
- Known inflammatory bowel disease.
- Immuno-modulation treatment
- Chemotherapy.
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 |
|---|---|---|
| BiopsyParticipants included in the study, will have additional biopsies performed during their colonoscopy | Diagnostic test | Screening colonoscopy patients |
Primary outcome
Profiling of open chromatin regions
Time frame: 2 years
Mapping of cell types, including rare cell types, using profiling of open chromatin regions. (ATAC-seq) in mucosal biopsies from the large bowel
Evaluation of metabolic profile
Time frame: 2 years
Using bioimpedance, insulin and glucose measurements and CHiP-seq we will determine patient phenotype and epigenetics to evaluate their metabolic risk-profile and correlate this to cell types in the large bowel
1 secondary outcome
Colonic biofilm
Time frame: 2 years
Results and safety
The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 12 Jun 2026.
- Background: PubMed 24413027Kaz AM, Wong CJ, Dzieciatkowski S, Luo Y, Schoen RE, Grady WM. Patterns of DNA methylation in the normal colon vary by anatomical location, gender, and age. Epigenetics. 2014 Apr;9(4):492-502. doi: 10.4161/epi.27650. Epub 2014 Jan 10.
- Background: PubMed 27401218Knight JM, Kim E, Ivanov I, Davidson LA, Goldsby JS, Hullar MA, Randolph TW, Kaz AM, Levy L, Lampe JW, Chapkin RS. Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue. Physiol Genomics. 2016 Sep 1;48(9):651-9. doi: 10.1152/physiolgenomics.00023.2016. Epub 2016 Jul 8.
- Background: PubMed 17565737Forgue-Lafitte ME, Fabiani B, Levy PP, Maurin N, Flejou JF, Bara J. Abnormal expression of M1/MUC5AC mucin in distal colon of patients with diverticulitis, ulcerative colitis and cancer. Int J Cancer. 2007 Oct 1;121(7):1543-9. doi: 10.1002/ijc.22865.
- Background: PubMed 32824266Costales-Carrera A, Fernandez-Barral A, Bustamante-Madrid P, Dominguez O, Guerra-Pastrian L, Cantero R, Del Peso L, Burgos A, Barbachano A, Munoz A. Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue. Cancers (Basel). 2020 Aug 15;12(8):2302. doi: 10.3390/cancers12082302.
- Background: PubMed 25559105Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-21.29.9. doi: 10.1002/0471142727.mb2129s109.
- Individual participant dataSharing planned: No. Data in this study is based on biological samples and data from patient registry. These data are protected by the Danish Act on Processing of Personal Data and can be accessed through application to and approval from the Danish Data Protection Agency and the Danish Health Data Authority [https://sundhedsda tastyrelsen.dk/da/forskerservice/ansog-om-data] where the purpose and the feasibility of the intended analysis should be accounted for.
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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. This study is not recruiting at the moment.
Jacob Antonsen, MD principal investigator
Bispebjerg Hospital
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Diabetes and Large Bowel Cancer, run by Bispebjerg Hospital at 1 site in Denmark.
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 4 inclusion and 8 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: finished, as of the sponsor's last update on 12 Jun 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 Denmark. 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?
The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Profiling of open chromatin regions (time frame: 2 years). 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 NCT05195502, 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 12 Jun 2026; AzTrials last refreshed its copy on 29 Oct 2026.