GSE131359

Differential pathogenic Th17 profile in mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients

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

6 case / 6 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.

Source
GEO
Assay
microarray
Organism
Homo sapiens
Whole-study samples
12 samples
Specimen
Unclear specimen/source
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Bsat M, Sarfati M
Contact name
Marika Sarfati
Submission date
2019-05-16
Last update
2019-06-24
Organization
CRCHUM
Department
Neurology
Public date
2019-05-17
Experiment types
Expression profiling by array
Platforms
GPL21847 nCounter Nanostring Human Immunology v2 (Catalog #115000061)
Series type
Series
SubSeries
Not available
BioProject
PRJNA543335

Summary

The drug targets IL23 and IL12 regulate pathogenicity and plasticity of intestinal Th17 cells in Crohn’s disease (CD) and ulcerative colitis (UC), the two most common inflammatory bowel diseases (IBD). However, studies examining Th17 dysregulation in mesenteric lymph nodes (mLNs) of these patients are rare. We showed that in mLNs, CD could be distinguished from UC by increased frequencies of CCR6+CXCR3-RORg+Tbet-CD4+ (Th17) memory T cells enriched in CD62Llow effector memory T cells (TEM), and their differentially expressed molecular profile. Th17 TEM cells (expressing IL17A, IL17F, RORC and STAT3) displayed a higher pathogenic/cytotoxic (IL23R, IL18RAP, and GZMB, CD160, PRF1) gene signature in CD relative to UC, while non-pathogenic/regulatory genes (IL9, FOXP3, CTLA4) were more elevated in UC. In both CD and UC, IL12 but not IL23, augmented IFNg expression in Th17 TEM and switched their molecular profile towards an ex-Th17 (Th1*)-biased transcriptomic signature (increased IFNG, and decreased TCF7, IL17A), suggesting that Th17 plasticity occurs in mLNs before their recruitment to inflamed colon. We propose that differences observed between Th17 cell frequencies and their molecular profile in CD and UC might have implications in understanding disease pathogenesis, and thus, therapeutic management of patients with IBD.

Overall design

For microarray study, we sorted CCR6+CXCR3-CD62LlowCD45RO+CD45RA-CD25-CD8-CD4+ Th17 TEM cells from mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients. Th17 TEM cells were stimulated with anti-CD3/CD28 beads and cultured with or without IL12 for 6 days. NanoString Human Immunology v2 panel was performed on samples.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
12 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. Differential Pathogenic Th17 Profile in Mesenteric Lymph Nodes of Crohn's Disease and Ulcerative Colitis Patients. Frontiers in immunology, 2019
Available

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review
97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

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

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

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.

Assay context may require expert handling before DESeq2-style 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

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Crohn's disease, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Crohn's disease 6 samples
  • Likely control group Control 6 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 31191543.
  • Publication context: Differential Pathogenic Th17 Profile in Mesenteric Lymph Nodes of Crohn's Disease and Ulcerative Colitis Patients.. Frontiers in immunology, 2019. PMID 31191543. DOI 10.3389/fimmu.2019.01177.

Cautions

  • Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Missing or unclear metadata. Comparison - Disease/model vs control. Specimen - Unclear 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

19 fields

Sample Group Preview

12 rows shown Show Hide
Study totals: Case 6 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM3771348 CD_IL12_rep1 MLN, CD, IL12 Disease: Crohn's disease; Culture condition: IL12 Case marker detected.
Crohn's disease Case GSM3771350 CD_IL12_rep2 MLN, CD, IL12 Disease: Crohn's disease; Culture condition: IL12 Case marker detected.
Crohn's disease Case GSM3771352 CD_IL12_rep3 MLN, CD, IL12 Disease: Crohn's disease; Culture condition: IL12 Case marker detected.
Ulcerative colitis Case GSM3771354 UC_IL12_rep1 MLN, UC, IL12 Disease: Ulcerative colitis; Culture condition: IL12 Case marker detected.
Ulcerative colitis Case GSM3771356 UC_IL12_rep2 MLN, UC, IL12 Disease: Ulcerative colitis; Culture condition: IL12 Case marker detected.
Ulcerative colitis Case GSM3771358 UC_IL12_rep3 MLN, UC, IL12 Disease: Ulcerative colitis; Culture condition: IL12 Case marker detected.
Control Control GSM3771347 CD_Control_rep1 MLN, CD, Control Disease: Crohn's disease; Culture condition: Medium Sample-local control marker detected.
Control Control GSM3771349 CD_Control_rep2 MLN, CD, Control Disease: Crohn's disease; Culture condition: Medium Sample-local control marker detected.
Control Control GSM3771351 CD_Control_rep3 MLN, CD, Control Disease: Crohn's disease; Culture condition: Medium Sample-local control marker detected.
Control Control GSM3771353 UC_Control_rep1 MLN, UC, Control Disease: Ulcerative colitis; Culture condition: Medium Sample-local control marker detected.
Control Control GSM3771355 UC_Control_rep2 MLN, UC, Control Disease: Ulcerative colitis; Culture condition: Medium Sample-local control marker detected.
Control Control GSM3771357 UC_Control_rep3 MLN, UC, Control Disease: Ulcerative colitis; Culture condition: Medium Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.