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.
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
40
Participants included in the study, will have additional biopsies performed during their colonoscopy
Bispebjerg University Hospital
Copenhagen, Denmark
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
Time frame: 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
Time frame: 2 years
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
Time frame: 2 years
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