GEO series
A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
GSE282122
Homo sapiens
Expression profiling by high throughput sequencing
216 samples
Submitted 2024/11/19
Platform GPL24676
Summary
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.
Published in
Thomas T, Friedrich M, Rich-Griffin C et al.
· Nature immunology 2024
· PMID 39438660
· doi:10.1038/s41590-024-01994-8
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE282122_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 216 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1179412 and SRA study SRP541799. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 216 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8636267 CID003352-2-reup
- GSM8636268 CID003353-1-reup
- GSM8636269 CID003354-1-reup
- GSM8636270 CID003355-1-reup
- GSM8636271 CID003356-1-reup
- GSM8636272 CID003357-1-reup
- GSM8636273 CID003359-1-reup
- GSM8636274 CID003360-1-reup
- GSM8636275 CID003361-1-reup
- GSM8636276 CID003362-1-reup
- GSM8636277 CID003363-1-reup
- GSM8636278 CID003364-1-reup
- GSM8636279 CID003365-1-reup
- GSM8636280 CID003366-1-reup
- GSM8636281 CID003367-2-reup
- GSM8636282 CID003368-1-reup
- GSM8636283 CID003369-1-reup
- GSM8636284 CID003370-1-reup
- GSM8636285 CID003371-2-reup
- GSM8636286 CID003372-1-reup
- GSM8636287 CID003373-1-reup
- GSM8636288 CID003374-1-reup
- GSM8636289 CID003375-1-reup
- GSM8636290 CID003376-1-reup
- GSM8636291 CID003377-1-reup
- GSM8636292 CID003378-1-reup
- GSM8636293 CID003379-1-reup
- GSM8636294 CID003380-1-reup
- GSM8636295 CID003381-1-reup
- GSM8636296 CID003382-1-reup
- GSM8636297 CID003383-1-reup
- GSM8636298 CID003384-1-reup
- GSM8636299 CID003385-1-reup
- GSM8636300 CID003386-1-reup
- GSM8636301 CID003665-1-reup
- GSM8636302 CID003666-1-reup
- GSM8636303 CID003667-1-reup
- GSM8636304 CID003669-1-reup
- GSM8636305 CID003670-1-reup
- GSM8636306 CID003671-1-reup
+ 176 more — browse all 216 samples with per-sample file links →
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