Spatially Resolved IBD: Spatial Transcriptomics of Inflammatory Bowel Disease (IBD)

The goal of this retrospective observational study is to obtain the spatial resolution of the entire intestinal fibrotic process through the technology STOmics Stereoseq. For this study we will use surgical specimens from 8 UC e 8 CD previously collected for the already approved project, IBD Biobank, and stored at -80° C.

Study Overview

• Status: Not yet recruiting
• Conditions: Patients With Histologically Confirmed CD Undergoing Intestinal Resection According to Standard of Care Due to Complicating Disease; Patients With Histologically Confirmed UC Undergoing Intestinal Resection According to Standard of Care Due to Complicating Disease
• Intervention / Treatment: Other: transcriptomic analysis

Detailed Description

This is a monocentric observational study in which we will use the biological material from surgery carried out for normal clinical practice, and already stored at -80°C.

This project has as purpose:

1. To unravel the changes in the intestine leading to complications in CD and UC patients. In particular, we aim to identify the cell populations, their spatial organization, interactions, and specific transcriptional shifts, leading the progression from healthy tissue to inflamed and from inflamed to fibrotic tissue. We will be interested in producing a profile of Spatial transcriptomics of all areas of the surgical specimen.
2. To compare the spatial organization and differential gene expression of tissue

• Study Type: Observational
• Enrollment (Estimated): 16

Contacts and Locations

Study Locations

• Italy
  • Milan, Italy
    • IRCCS Ospedale San Raffaele
  • Milano, Italy, 20132
    • IRCCS Ospedale San Raffaele

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: N/A

• Sampling Method: Probability Sample

Study Population

Retrospective observational study involving patients with Crohn's disease (CD) (n=8) and patients with ulcerative colitis (UC)(n=8) who had undergone surgery according to the standard of care. We will use the biological material from surgery carried out for normal clinical practice, and already stored at -80°C for IBD Biobank project. The retrospective referral period of time goes from July 2022 until July 2023.

Description

Inclusion Criteria:

• adult patient (age ≥18 years), both male and female patients with histologically confirmed CD and UC undergoing intestinal resection according to standard of care due to complicating disease, regardless of their current or past medical treatment;
• patients that have signed the IBD Biobank informed consent and consented to the use of their own biological material in future study or pertaining to the same field of investigation.

Exclusion Criteria:

• - patients with unconfirmed both UC and CD diagnoses;
• patients with superimposed dysplasia or cancer diagnosis and resections for which post- operative endoscopic assessment of recurrence is not feasible;
• patients who have not signed the IBD Biobank informed consent.

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
patients with histologically confirmed CD; patients with histologically confirmed CD undergoing intestinal resection	Other: transcriptomic analysis; to use their biological samples from UC and CD patients, already stored at -80°C for transcriptomic analysis through STOmics Stereoseq
patients with histologically confirmed UC; patients with histologically confirmed UC undergoing intestinal resection	Other: transcriptomic analysis; to use their biological samples from UC and CD patients, already stored at -80°C for transcriptomic analysis through STOmics Stereoseq

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Profile of Spatial transcriptomics of all areas of the surgical specimen from UC and CD patients	to perform a transcriptomic analysis of the entire surgical specimen will be embedded in OCT block. To overcome any failures in the OCT embedding, we will cut serial sections and stain them to evaluate the presence of all intestinal regions of interest, and then choose the adjacent one for the spatial analysis. Moreover, we will evaluate by histological assessment whether one single piece of surgical specimen will encompass not inflamed, inflamed (in case of UC) and also fibrotic areas (in case of CD)	1 year

Collaborators and Investigators

• Sponsor: IRCCS San Raffaele
• Collaborators: BGI, China

Study record dates

Study Major Dates

• Study Start (Estimated): August 1, 2024
• Primary Completion (Estimated): February 1, 2025
• Study Completion (Estimated): August 1, 2025

Study Registration Dates

• First Submitted: June 26, 2024
• First Submitted That Met QC Criteria: July 1, 2024
• First Posted (Actual): July 3, 2024

Study Record Updates

• Last Update Posted (Actual): July 3, 2024
• Last Update Submitted That Met QC Criteria: July 1, 2024
• Last Verified: June 1, 2024

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Digestive System Diseases; Gastrointestinal Diseases; Gastroenteritis; Intestinal Diseases; Inflammatory Bowel Diseases
• Other Study ID Numbers: STOmics

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

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