Mapping the Human Colon Using Single Cell Sequencing (COLATA)

June 10, 2026 updated by: Jacob Antonsen, Bispebjerg Hospital

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.

Study Overview

Status

Completed

Conditions

Intervention / Treatment

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 Type

Observational

Enrollment (Actual)

40

Contacts and Locations

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

Study Locations

  • Denmark
      • Copenhagen, Denmark, 2720
        • Bispebjerg University Hospital

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

18 years and older (Adult, Older Adult)

Accepts Healthy Volunteers

N/A

Sampling Method

Non-Probability Sample

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

Description

Inclusion Criteria:

  • 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.

Exclusion Criteria:

  • 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

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
Intervention / Treatment
Screening colonoscopy patients
Patients referred for out-patient colonoscopy in the Danish Colorectal Screening program
Diagnostic test: Biopsy
Participants included in the study, will have additional biopsies performed during their colonoscopy

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
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
2 years
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
2 years

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Colonic biofilm
Time Frame: 2 years
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
2 years

Collaborators and Investigators

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

Sponsor

Bispebjerg Hospital

Collaborators

The Novo Nordisk Foundation Center for Basic Metabolic Research

Investigators

  • Principal Investigator: Jacob Antonsen, MD, Bispebjerg Hospital

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)

July 1, 2022

Primary Completion (Actual)

December 31, 2022

Study Completion (Actual)

June 1, 2024

Study Registration Dates

First Submitted

January 7, 2022

First Submitted That Met QC Criteria

January 7, 2022

First Posted (Actual)

January 19, 2022

Study Record Updates

Last Update Posted (Actual)

June 12, 2026

Last Update Submitted That Met QC Criteria

June 10, 2026

Last Verified

June 1, 2026

More Information

Terms related to this study

Additional Relevant MeSH Terms

Other Study ID Numbers

  • COLKEND01

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

IPD Plan Description

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.

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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