Clinical trial NCT05195502: Mapping the Human Colon Using Single Cell Sequencing
Official title: Cellular Composition of the Human Colon Using Single-cell RNA and Single-cell ATAC-sequencing.
Study type: OBSERVATIONAL
Overall status: UNKNOWN
Conditions: Diabetes
Large Bowel Cancer
Inflammatory Bowel Diseases
Lead sponsor: Bispebjerg Hospital
Sponsor class: OTHER
Collaborators: name: The Novo Nordisk Foundation Center for Basic Metabolic Research
First posted: 2022-01-19
Enrollment: 20
Sex: ALL
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Observational model: COHORT
Time perspective: PROSPECTIVE
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

Brief 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 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.

Eligibility criteria: 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

Primary outcomes:
measure: Profiling of open chromatin regions
timeFrame: 2 years
measure: Evaluation of metabolic profile
timeFrame: 2 years
Secondary outcomes:
measure: Colonic biofilm
timeFrame: 2 years
Other outcomes:
Locations:
city: Copenhagen
country: Denmark
facility: Bispebjerg University Hospital
Study officials:
affiliation: Bispebjerg Hospital
name: Jacob Antonsen, MD
role: PRINCIPAL_INVESTIGATOR
References:
citation: 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.
citation: Knight 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.
citation: Forgue-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.
citation: Costales-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.
citation: Buenrostro 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.