GSE217352

A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

265 case / 0 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Summary

Surgical resection in severe Crohn's disease is a common consequence of therapeutic failure. We identified 2 severe CD subtypes: one similar to non-IBD subjects, the other exhibited a mucosal-like gene signature, altered T-cell subsets, severity features and decreased pro-inflammatory expression post-surgery. These findings may identify targets for CD subtype-specific therapeutic and biomarker development.

Overall design

CD3+ T-cells were purified from paired blood and mucosa from 100 CD and 17 non-inflammatory bowel disease (IBD) subjects requiring surgery. Longitudinal samples (n=49) were collected 4-13 months postoperatively. Expression profiles were generated by RNA-Seq. Transcriptional Risk Scores (TRS), T-cell subset deconvolution, gene pathway and kinase analyses were performed.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
265 GSM samples
Primary source
recount3

Planned trusted source for processed count availability.

No match found
Expression Atlas

Planned source for curated expression experiment links.

No match found
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

1 linked publication 1 DOI

Primary publication

  1. A blood-based transcriptomic signature stratifies severe Crohn's disease and defines potentially targetable therapeutic pathways. Frontiers in gastroenterology (Lausanne, Switzerland), 2023
Available

Metadata Quality Components

Analysis Readiness

Not ready
55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

Study design is model-system or unclear and should be reviewed before analysis.

Mixed specimen/source groups must be separated before analysis.

Why This Is Ranked Here

Tumor vs normal
Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

  • Disease context Crohn's disease, inflammatory bowel disease Disease context came from Normalization rules.
  • Likely case group Crohn's disease 265 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 41821786.
  • Publication context: A blood-based transcriptomic signature stratifies severe Crohn's disease and defines potentially targetable therapeutic pathways.. Frontiers in gastroenterology (Lausanne, Switzerland), 2023. PMID 41821786. DOI 10.3389/fgstr.2023.1251133.

Cautions

  • Comparison: Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%.
  • Downgraded for tissue search because specimen/source classes are mixed.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Mixed specimen/source. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 568 fields

Sample Group Preview

showing 50 of 265 preview rows
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Study totals: Case 265 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 265 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM6715698 Patient226432_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715699 Patient226432_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715700 Patient226946_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715701 Patient226946_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715702 Patient224667_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715703 Patient224667_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715704 Patient226434_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715705 Patient226434_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715706 Patient239853_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715707 Patient239853_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715708 Patient227440_CD_PostSurgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: PostSurgery Case marker detected.
Crohn's disease Case GSM6715709 Patient226425_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715710 Patient226425_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715711 Patient225295_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715712 Patient225295_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715713 Patient226536_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715714 Patient226536_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715715 Patient227440_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715716 Patient226260_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715717 Patient226260_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715718 Patient226218_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715719 Patient226218_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715720 Patient226262_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715721 Patient226262_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715722 Patient226536_CD_PostSurgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: PostSurgery Case marker detected.
Crohn's disease Case GSM6715723 Patient225781_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715724 Patient225781_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715725 Patient226946_CD_PostSurgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: PostSurgery Case marker detected.
Crohn's disease Case GSM6715726 Patient226432_CD_PostSurgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: PostSurgery Case marker detected.
Crohn's disease Case GSM6715727 Patient226001_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715728 Patient226001_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715729 Patient226649_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715730 Patient226649_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715731 Patient225302_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715732 Patient225302_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715733 Patient225601_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715734 Patient225601_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715735 Patient224667_CD_PostSurgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: PostSurgery Case marker detected.
Crohn's disease Case GSM6715736 Patient227596_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715737 Patient227596_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715738 Patient225439_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715739 Patient225439_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715740 Patient226190_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715741 Patient226190_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715742 Patient226712_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715743 Patient226712_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715744 Patient239153_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715745 Patient239153_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715746 Patient261956_CD_Surgery_LPT Lamina propria mucosa-derived T cell Tissue: Lamina propria mucosa-derived T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
Crohn's disease Case GSM6715747 Patient261956_CD_Surgery_PBT Peripheral blood T cell Tissue: Peripheral blood T cell; Cell type: CD3+; Phenotype: Crohn's disease; Time: Surgery Case marker detected.
215 additional case samples are hidden from this preview.

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