NBDC Research ID: hum0454.v1
SUMMARY
Aims: Crohn's disease is one of inflammatory bowel diseases with unknown etiology, however dysfunction of lymphatic vessels has been reported to be associated with its etiology. Whereas, epithelioid cell granuloma is often found in lymphatic vessel and it is suggested that granulomas in lymphatic vessels are responsible for the impaired lymphatic flow in Crohn's disease. As described above, granulomas in lymphatic vessels are important immunological structures in the pathogenesis of Crohn's disease, but little is known about its characteristics. In this study, we will clarify the characteristics of intra- and extra- lymphatic granulomas and examine the correlation between intra- and extra- lymphatic granulomas and clinicopathological findings of Crohn's disease. We analyzed changes in the immune response in Crohn's disease after administering biologics as well.
Methods: Formalin-fixed paraffin-embedded specimens (FFPE) was thin sliced with 5 µm thickness and mounted on slides for Xenium analysis, 4 cases per slide. 50 custom molecules were added to the 377 molecules in the multi tissue panel for Xenium analysis.
Participants/Materials: FFPE of Crohn's disease surgery cases, 10 cases. As controls, 6 cases of FFPE from ulcerative colitis, cytomegalovirus enteritis, and cancer were used.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000697 | Xenium In Situ Gene Expression | Controlled-access (Type I) | 2024/12/16 |
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MOLECULAR DATA
| Participants/Materials |
Crohn's disease (ICD10: K509): 10 cases 8 cases without strong preoperative treatment such as steroids or biological agents 2 cases receiving TNFα inhibitors ulcerative colitis: 4 cases cytomegalovirus enteritis: 1 case cancer: 1 case |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 427 genes (multi tissue panel: 377 genes, custom: 50 genes） |
| Platform | 10x Genomics [Xenium Analyzer] |
| Source | surgical sections (FFPE) |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) | Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software | xenium-1.7.1.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000830 |
| Total Data Volume | 182.8 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Makoto Kodama
Affiliation: Department of Pathology, Tokyo Yamate Medical Center
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Transformative Research Areas | Platform for Advanced Genome Sciences | 22H04925 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Tertiary lymphoid structure as a therapeutic target of Crohn’s disease: modulation by TNFα blockade | doi:10.1101/2024.11.23.625032 | JGAD000830 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
