TI epithelial
Download from source ↗Dataset overview
The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon.
Abstract
Crohn's disease (CD) is a chronic gastrointestinal disease that is increasing in prevalence worldwide. CD is multifactorial, involving the complex interplay of genetic, immune, and environmental factors, necessitating a system-level understanding of its etiology. To characterize cell-type-specific transcriptional heterogeneity in active CD, we profiled 720,633 cells from the terminal ileum and colon of 71 donors with varying inflammation status. Our integrated datasets revealed organ- and compartment-specific responses to acute and chronic inflammation; most immune changes were in cell composition, whereas transcriptional changes dominated among epithelial and stromal cells. These changes correlated with endoscopic inflammation, but small and large intestines exhibited distinct responses, which were particularly apparent when focusing on IBD risk genes. Finally, we mapped markers of disease-associated myofibroblast activation and identified CHMP1A, TBX3, and RNF168 as regulators of fibrotic complications. Altogether, our results provide a roadmap for understanding cell-type- and organ-specific differences in CD and potential directions for therapeutic development.
doi:10.1016/j.immuni.2023.01.002 ↗ PMID 36720220 ↗ PMC9957882 ↗
Study facts
- Organism
- Homo sapiens
- Platform
- 10x Genomics
- Age group
- —
- Disease groups
- —
- Anatomical sites
- epithelium of small intestine, ileal epithelium, ileum, ileum lamina propria, lamina propria of small intestine, small intestine
Data availability
- Raw counts
- Processed matrix
File types
H5AD
Files and samples
Strengths & limitations for reuse
Strengths
- Raw counts are advertised
- Processed matrices are advertised
- Cell metadata are advertised
- Participant counts are documented
Extraction evidence & provenance
Each extracted field is shown with the source excerpt and location used to resolve it.
Assay
| Field | Value | Evidence |
|---|---|---|
assay.assay_type |
10x 3' v2 from source |
assay=10x 3' v2 Section |
assay.library_chemistry |
10x 3' v2 and 10x 3' v3 from source |
"assay": [{"label": "10x 3' v2", "ontology_term_id": "EFO:0009899"}, {"label": "10x 3' v3", "ontology_term_id": "EFO:0009922"}] Section |
assay.platform |
10x Genomics |
"assay": [{"label": "10x 3' v2", "ontology_term_id": "EFO:0009899"}, {"label": "10x 3' v3", "ontology_term_id": "EFO:0009922"}] Section |
assay.sequencing_type |
scrna_seq from source |
sequencing_type=scrna_seq Section |
Cohort
| Field | Value | Evidence |
|---|---|---|
cohort.total_participants |
42 computed |
"donor_id": ["105446", "127643", "178961", "158108", "180749", "110216", "199129", "152638", "158160", "101694", "102141", "157844", "180844", "130064", "139892", "182231", "191305", "127693", "134300", "104152", "115208", "104689", "166301", "148824", "183146", "174364", "109389", "158891", "105598", "192985", "172428", "148519", "176196", "134764", "195045", "165697", "128346", "168051", "189696 Section |
Data_Assets
| Field | Value | Evidence |
|---|---|---|
data_assets.cell_metadata |
True from source |
CELLxGENE dataset exposes cell metadata Section |
data_assets.open_access |
True from source |
public CELLxGENE dataset Section |
data_assets.processed_matrix |
True from source |
CELLxGENE dataset exposes H5AD Section |
data_assets.raw_counts |
True from source |
"raw_data_location": "raw.X" Section |
Specimens
| Field | Value | Evidence |
|---|---|---|
specimens.anatomical_sites |
['epithelium of small intestine', 'ileal epithelium', 'ileum', 'ileum lamina propria', 'lamina propria of small intestine', 'small intestine'] from source |
tissues=epithelium of small intestine, ileal epithelium, ileum, ileum lamina propria, lamina propria of small intestine, small intestine Section |
specimens.number_of_cells |
154136 from source |
cell_count=154136 Section |