GSE60083

Genome-wide analysis of monocyte derived macrophages from Crohn's Disease patients and controls

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

0 case / 100 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

Crohn's disease (CD) is a complex and highly heterogeneous chronic inflammatory disorder, primarily affecting the gastrointestinal tract. Genetic and functional studies have highlighted a key role for innate immunity in its pathogenesis. Profound systemic defects in innate immunity and acute inflammation are understood to result in markedly delayed clearance of bacteria from the tissues, leading to local chronic granulomatous inflammation and compensatory adaptive immunological changes. Macrophages, key orchestrators of acute inflammation, are likely to play an important role in the initial impaired innate immune response. Monocyte-derived macrophages from CD patients stimulated with E. coli were shown to release attenuated levels of TNF and IFNγ with normal secretion of IL8, IL10 and IL6. In controls, the secretion of these cytokines was strongly positively correlated, which was not seen with CD macrophages. The transcriptomes of CD and control macrophages were examined in an attempt to understand the molecular basis of this defect. There were no differentially expressed genes identified between the two groups, consistent with genetic heterogeneity; however, a number of molecules were found to be under-expressed in subgroups of CD patients. The most common of these was optineurin (OPTN) which was under-expressed in approximately 10% of the CD patients. Reduced OPTN expression coincided with lower intracellular protein levels and diminished cytokine secretion after bacterial stimulation both in the patients and with siRNA knockdown in THP-1 cells. Identifying and studying subgroups of patients with shared defective gene expression could aid our understanding of the mechanisms underlying highly heterogeneous diseases such as CD.

Overall design

Total RNA obtained from monocyte derived macrophages from Crohn's disease patients (n=58) or healthy volenteers (n=42) were cultured for six days before being stimulated with heat killed E. coli for four hours or left unstimulated.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
100 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. Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients. Immunology, 2015
Available

Metadata Quality Components

Analysis Readiness

Not ready
59% 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

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • No complete case/control contrast is available.

Next Steps

  • Review blockers and update sample grouping or dataset selection before 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.

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

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Crohn's disease Disease context came from Normalization rules.
  • Likely case group No case group detected 0 samples
  • Likely control group Untreated 100 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Interpreted disease metadata: Crohn's disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 24943399.
  • Publication context: Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients.. Immunology, 2015. PMID 24943399. DOI 10.1111/imm.12338.

Cautions

  • Comparison: Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%.
  • Downgraded for tissue search because it is a model-system experiment.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Organoid or cell-line experiment downgraded for patient tissue search intent.
  • 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.
  • Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Cultured cells. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Publication context: Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients.. Immunology, 2015. PMID 24943399. DOI 10.1111/imm.12338.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

387 fields

Sample Group Preview

showing 50 of 100 preview rows
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Study totals: Case 0 | Control 100 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 100 preview rows
Group Role Accession Title Source / characteristics Reason
Untreated Control GSM1464665 HC139 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464666 HC158 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464667 CD232 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464668 HC160 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464669 CD383 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464670 CD316 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464671 CD278 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464672 CD384 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464673 HC125 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464674 CD381 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464675 CD200 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464676 CD389 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464677 HC175 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464678 CD141 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464679 CD382 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464680 CD22 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464681 HC120 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464682 CD328 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464683 CD48 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464684 HC169 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464685 HC136 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464686 HC154 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464687 CD359 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464688 CD385 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464689 CD386 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464690 CD17 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464691 CD369 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464692 HC165 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464693 CD377 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464694 CD50 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch1 Treatment control marker detected.
Untreated Control GSM1464695 HC119 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464696 CD374 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464697 CD273 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464698 CD367 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464699 CD319 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464700 CD121 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464701 HC167 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464702 CD387 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464703 CD56 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464704 CD388 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464705 CD128 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464706 HC186 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464707 CD330 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464708 HC15 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464709 CD352 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464710 CD368 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464711 CD394 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Crohn's Disease; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464712 HC86 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464713 HC196 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: M; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
Untreated Control GSM1464714 HC203 Monocyte derived macrophage_Unstimulated Monocyte derived macrophage_Unstimulated Gender: F; Disease: Healthy Control; Stimulation: Unstimulated; Batch: Batch2 Treatment control marker detected.
50 additional control 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.