Combinatorial Single Cell Strategies for a Crohn's Disease Gut Cell Atlas

Inflammatory bowel disease (IBD), consisting of two major forms, Crohn's disease (CD) and ulcerative colitis, affects more than 1.6 million people in the United States alone. Despite current therapies, remission only occurs in approximately half of patients. The goal of study is to map single-cell spatial relationships across the spectrum of ileum/ascending colon from healthy control patients to uninvolved/quiescent and involved/active CD patients and assess for relationships between single-cell data and patient clinical data.

The investigators will utilize endoscopic mucosal biopsies and surgical resection specimens with rapid transfer of fresh tissue to the single-cell preparation for RNA-sequencing and use of tissues for RNA-fluorescence in situ hybridization and multiplex immunofluorescence. Along with machine learning image analysis and bioinformatics, this will generate a robust/detailed single-cell gut cell atlas (GCA) of ileo-colonic CD at all disease activities versus normal tissues. The study will also compare the results of endoscopic mucosal biopsies to those obtained from full thickness surgical specimens by utilizing the Cooperative Human Tissue Network (CHTN).

The investigators anticipate the GCA data will provide new insights into disease pathogenesis, leading to new therapeutic targets.

Study Overview

• Status: Active, not recruiting
• Conditions: Crohn Disease
• Intervention / Treatment: Other: Sample Collection

• Study Type: Observational
• Enrollment (Actual): 178

Contacts and Locations

Study Locations

• United States
  • Tennessee
    • Nashville, Tennessee, United States, 37232
      • Vanderbilt University Medical Center

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years and older (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes

• Sampling Method: Non-Probability Sample

Study Population

Patients undergoing standard of care colonoscopy procedure at Vanderbilt University Medical Center (VUMC) and/or receiving care at the VUMC Inflammatory Bowel Disease Clinic.

Description

Inclusion criteria:

• Provision of consent form
• Male or female greater than or equal to 18 years old
• Healthy volunteers without IBD undergoing colonoscopy for colorectal cancer screening or patients with a diagnosis of Crohn's disease (CD) confirmed by endoscopy or radiology assessment undergoing colonoscopy for clinical care

Exclusion criteria:

• Pregnancy
• Coagulopathy or bleeding disorder
• Renal or hepatic impairment
• History of organ transplantation

Study Plan

How is the study designed?

Number of groups / cohorts

3

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Crohn's Disease; This group consists of patients with a diagnosis of Crohn's disease undergoing colonoscopy for clinical care. Samples including tissue biopsy, blood and stool will be collected one time. In addition, patient information that may include questionnaires and medical record review will be collected.	Other: Sample Collection; Tissue biopsies will be performed at the time of colonoscopy along with blood and stool sample collection.
Control; This group will include patients undergoing screening colonoscopy as part of standard of care. Samples including tissue biopsy, blood and stool will be collected one time. In addition, patient information that may include questionnaires and medical record review will be collected.	Other: Sample Collection; Tissue biopsies will be performed at the time of colonoscopy along with blood and stool sample collection.
Cooperative Human Tissue Network; This group will consist of non-IBD patients and Crohn's disease patients participating in the Cooperative Human Tissue Network (CHTN). The CHTN will be utilized to obtain surgical specimens from these patients. The patients will be screened and consented via the CHTN protocol. No additional samples in the form of blood or stool will be collected. Associated clinical data will be collected through medical record review.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Time Frame
The change in cellular composition (i.e., percentage of cell types) between Crohn's disease and control patients as assessed by single-cell RNA sequencing analysis, RNA-fluorescence in situ hybridization, and multiplex immunofluorescence.	36 months

Collaborators and Investigators

• Sponsor: Vanderbilt University Medical Center
• Collaborators: The Leona M. and Harry B. Helmsley Charitable Trust
• Investigators: Principal Investigator: Lori A Coburn, MD, Vanderbilt University Medical Center; Study Director: Keith T Wilson, MD, Vanderbilt University Medical Center

Study record dates

Study Major Dates

• Study Start (Actual): December 17, 2019
• Primary Completion (Estimated): February 1, 2027
• Study Completion (Estimated): February 1, 2027

Study Registration Dates

• First Submitted: September 27, 2019
• First Submitted That Met QC Criteria: October 1, 2019
• First Posted (Actual): October 3, 2019

Study Record Updates

• Last Update Posted (Estimated): November 4, 2025
• Last Update Submitted That Met QC Criteria: October 31, 2025
• Last Verified: October 1, 2025

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Intestinal Diseases; Digestive System Diseases; Gastrointestinal Diseases; Gastroenteritis; Inflammatory Bowel Diseases; Crohn Disease; Investigative Techniques; Clinical Laboratory Techniques; Diagnostic Techniques and Procedures; Diagnosis; Specimen Handling
• Other Study ID Numbers: 191738

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: YES
• IPD Plan Description: The investigators agree to the timely release and sharing of information to be no later than the acceptance for publication of the main findings from the final data set. Investigators are also committed to ensuring that all data are free of identifiers that would permit linkage to individual research participants as well as variables that could lead to deductive disclosure of the identity of individual subjects.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No