GSE101817

Association between colonic level of microRNA 31 and subtypes of adult and pediatric Crohn's disease [pediatric]

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

234 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.

Source
GEO
Assay
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
234 samples
Specimen
Biopsy
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Keith BP, Furey TS, Sethupathy P, Sheikh SZ, Furey T
Contact name
Terry Furey
Submission date
2017-07-24
Last update
2024-04-04
Organization
The University of North Carolina at Chapel Hill
Department
Department of Genetics
Public date
2018-10-01
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA395580

Summary

The course of Crohn's disease (CD) is heterogeneous, confounding effective personalized therapy. A previous analysis of differences in gene expression between patients with versus without CD groups revealed 2 subsets of patients with CD -- a group characterized by genes more highly expressed in the colon (colon-like CD) and a group with increased expression of ileum marker genes (ileum-like CD). We compared differences in microRNAs between these groups. We performed genome-wide microRNA profile analyses of colon tissues from 18 adults with CD and 12 adults without CD (controls). We performed principal component analyses to associate levels of microRNAs with CD subtypes. Colonic epithelial cells and lamina propria immune cells were isolated from intestinal tissues and levels of microRNA 31 (miR-31) were measured by real-time quantitative PCR. We validated the differential expression of miR-31 between the subtypes by measuring miR-31 levels in an independent cohort of 32 adult patients with CD and 23 controls. We generated epithelial colonoid cultures from controls and patients with CD, and measured levels of miR-31 in crypts. We performed genome-wide microRNA profile analyses of formalin-fixed paraffin-embedded colon and ileum biopsies from 76 treatment-naive pediatric patients with CD and 51 controls (234 samples) and collected data on disease features and outcomes. In comparing miRNA expression profiles between 9 patients with colon-like CD and 9 patients with ileum-like CD, we identified 19 miRNAs with significant differences in levels. We observed a 13.5-fold difference in level of miR-31-5p between tissues from patients with colon-like vs. ileum-like CD (Padj = 1.43 x 10-18). Principal component analysis found miR-31 to be the top contributor to the variance observed. Levels of miR-31 were increased 60-fold in tissues from patients with ileum-like CD compared with controls (Padj = 2.59 × 10-51). We validated the differential expression of miR-31 between the subtypes in the independent set of tissues. Colonoids derived from patients with CD had significantly higher levels of miR-31 than colonoids derived from control tissues (day 2 P=.041 and day 6 P=.0095). Levels of miR-31 were significantly increased in colon tissues from pediatric patients with CD compared with controls (~7.8-fold, P=4.64 ×10-7) and in ileum tissues from patients with CD patients vs. controls (~1.5-fold, P=9.97 × 10-7). A high level of miR-31 in index biopsies from pediatric patients with only inflammation and no other complications at time of diagnosis associated with development of fibrostenotic ileal CD. We identified differences in miR-31 levels in colon tissues from adult and pediatric patients with CD compared with controls, and in patients with ileum-like CD compared with colon-like CD. Further studies are needed to determine the mechanisms by which miR-31 might contribute to pathogenesis of this subtype of CD, or affect response to therapy.

Overall design

234 small RNA-seq samples from Crohn's disease and non-IBD control FFPE tissue, 124 of which are from ascending colon biopsies at the time of surgery, and 110 from the terminal ileum at the time of surgery. Raw data not available due to patient privacy concerns.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
234 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.

3 linked publications 3 DOIs

Primary publication

  1. Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease. Cellular and molecular gastroenterology and hepatology, 2020
  2. Colonic epithelial miR-31 associates with the development of Crohn's phenotypes. JCI insight, 2018
  3. Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease. JCI insight, 2024
Available

Metadata Quality Components

Persisted metadata quality

93 pts
Clarity
93%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. 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

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.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

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.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed 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 234 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biopsy. 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 3 publications; 3 DOIs available: PMID 30282822, PMID 32561494, PMID 38385744.
  • Publication context: Colonic epithelial miR-31 associates with the development of Crohn's phenotypes.. JCI insight, 2018. PMID 30282822. DOI 10.1172/jci.insight.122788.
  • Publication context: Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease.. Cellular and molecular gastroenterology and hepatology, 2020. PMID 32561494. DOI 10.1016/j.jcmgh.2020.06.005.
  • Publication context: Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease.. JCI insight, 2024. PMID 38385744. DOI 10.1172/jci.insight.168800.

Cautions

  • Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • 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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biopsy. 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 1300 fields

Sample Group Preview

showing 50 of 234 preview rows Show Hide
Study totals: Case 234 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 234 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM3034800 Peds CD Colon 101 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034801 Peds CD Colon 102 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034802 Peds CD Colon 103 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034803 Peds CD Colon 104 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034804 Peds CD Colon 105 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034805 Peds CD Colon 106 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034806 Peds CD Colon 107 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034807 Peds CD Colon 108 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034808 Peds CD Colon 109 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034809 Peds CD Colon 110 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034810 Peds CD Colon 111 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034811 Peds CD Colon 112 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034812 Peds CD Colon 113 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034813 Peds CD Colon 114 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034814 Peds CD Colon 115 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034815 Peds CD Colon 116 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034816 Peds CD Colon 120 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034817 Peds CD Colon 121 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034818 Peds CD Colon 122 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034819 Peds CD Colon 123 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034820 Peds CD Colon 124 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034821 Peds CD Colon 125 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034822 Peds CD Colon 126 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034823 Peds CD Colon 128 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034824 Peds CD Colon 129 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034825 Peds CD Colon 130 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034826 Peds CD Colon 131 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034827 Peds CD Colon 132 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034828 Peds CD Colon 133 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034829 Peds CD Colon 134 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034830 Peds CD Colon 135 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034831 Peds CD Colon 136 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034832 Peds CD Colon 137 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034833 Peds CD Colon 139 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034834 Peds CD Colon 140 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034835 Peds CD Colon 141 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034836 Peds CD Colon 142 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034837 Peds CD Colon 143 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034838 Peds CD Colon 144 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034839 Peds CD Colon 145 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034840 Peds CD Colon 146 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034841 Peds CD Colon 147 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034842 Peds CD Colon 148 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034843 Peds CD Colon 149 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: High Case marker detected.
Crohn's disease Case GSM3034844 Peds CD Colon 150 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034845 Peds CD Colon 201 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034846 Peds CD Colon 202 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034847 Peds CD Colon 204 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034848 Peds CD Colon 205 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
Crohn's disease Case GSM3034849 Peds CD Colon 206 Ascending colon mucosal biopsy Age: Pediatric; Tissue: Ascending colon mucosa; Phenotypic status: Crohn's disease; Treatment: Naive; Mir-31: Low Case marker detected.
184 additional case samples are hidden from this preview.

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.