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

Study Overview
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Brief Summary
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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.

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

Conditions
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Crohn Disease

Intervention / Treatment
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* Other: Sample Collection


Participation Criteria
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Eligibility Criteria
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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

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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Accepts Healthy Volunteers

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Crohn's Disease<br>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<br>* Tissue biopsies will be performed at the time of colonoscopy along with blood and stool sample collection.<br>|
| Control<br>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<br>* Tissue biopsies will be performed at the time of colonoscopy along with blood and stool sample collection.<br>|
| Cooperative Human Tissue Network<br>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?
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Primary Outcome Measures

| Outcome Measure | Measure Description | 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 |