Pilot study to validate scRNA sequencing and CyTOF analysis in intestinal biopsies from patients with inflammatory bowel disease

Crohn*s disease (CD) and ulcerative colitis (UC) are chronic idiopathic
diseases affecting the gastrointestinal tract. Unless highly effective
therapies, the majority of patients experience disease progression that leads
to tissue damaging and complications affecting patient*s quality of life,
morbidity and mortality. Where ulcerative colitis is characterized by extensive
and progressive inflammation of the colon, Crohn*s disease is known to affect
the entire gastrointestinal tract. More than 30 % of patients with CD encounter
complications such as fibrotic stenosis or fistulas in their life.
Because CD en UC involves many different pathological pathways (inflammatory,
microbial and tissue remodelling mechanisms) we aim to investigate the
mechanism of action of the different treatment modalities and biomarkers that
will allow stratification to a more targeted approach.
In this pilot study we will assess whether intestinal mucosal biopsies from
rectum and colon are suitable to conduct future research with single cell RNA
sequencing (scRNAseq) and CyTOF (cytometry by time-of-flight, i.e. mass
cytometry). Most experience with scRNAseq and CyTOF has been performed with
peripheral blood mononuclear cells (PBMC) obtained from blood. It is not known
how many biopsies must be obtained with endoscopy to harvest enough viable
cells to perform the analysis to obtain new biomarkers. Therefore, a pilot
study is needed to assess the quantity of viable cells obtained by biopsies
during colonoscopy to ensure future study protocols can be formed.

In this pilot study we will validate intestinal mucosa biopsies for usage in
scRNA sequencing and CyTOF analysis for future research in patients with CD and
UC. Key in this validation is the number of viable cells in mucosal biopsies
and the number of inflammation related cells (CD45 +ve). Some biopsies will be
taken from inflamed mucosa to account for the supposed higher cell count in
inflamed tissue than in healthy tissue.

Cross-sectional study to acquire data for future research at the Amsterdam UMC,
not meant to be published. We will collect 5 biopsies from rectal and/or
colonic mucosa in addition to clinically required biopsies during standardized
follow-up colonoscopies. These *fresh* biopsies will be analysed by FACS (i.e.
flowcytometry), CyTOF and scRNAseq to assess cell count, viable cell count and
CD45 +ve and CD45 -ve cell count and perform proof of principle analysis on
single cell proteomic and transcriptomic analysis. To account for potential
altering variables we ask the patients to collect additional serum and a stool
sample to their clinically indicated blood and stool collection. Clinical data
will be collected as far as disease entity, progression, location and current
and past treatment.

Endoscopic biopsies taken during colonoscopy include a minimal risk of
complication, mainly bleeding or perforation (< 1: 10.000). In case
complication occurs, endoscopic treatment (hemostasis/clipping) is effective in
most cases during the same session. Rarely, hospital admission with/without a
second endoscopy or surgical intervention, antibiotic therapy and/or blood
transfusion can be required. Peripheral blood is sampled with a negligible risk
and low burden.
Patients participating in this pilot study undergo additional biopsies to
clinically required biopsies, we do not expect this to be a significant extra
burden.