Tissue-specific and circulatory immune signatures of mucosal inflammation in Crohn’s disease
Bibliographic record
Abstract
Abstract Crohn’s disease (CD) is a heterogeneous disease characterized by chronic inflammation of the gastrointestinal tract driven by an aberrant immune response. To understand the immune mechanisms underlying mucosal inflammation, we performed single-cell RNA sequencing on paired terminal ileum biopsies and blood samples from 125 CD patients. Our findings reveal that the transcriptional profiles of immune cells are primarily shaped by the local tissue microenvironment, with mucosal immune cells undergoing profound inflammation-associated changes, while circulating immune cells largely fail to reflect these signatures. However, a subset of circulating T cells with a tissue-resident memory-like phenotype retained transcriptional hallmarks of mucosal inflammation, mirroring their ileal counterparts with enrichment in cytokine pathways, including interferon gamma and TNF receptor signaling. Altogether, our single-cell atlas provides a high-resolution resource for dissecting the mucosal and circulatory immune landscape of CD and its link to mucosal inflammation.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".