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| Status |
Public on Jun 30, 2009 |
| Title |
Expression Signatures in Polyarticular JIA Show Heterogeneity and Offer a Molecular Classification of Disease Subsets |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Objective. Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC). Methods. Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization. Results. Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA and controls. Hierarchical clustering of these probe sets distinguished three subgroups within polyarticular JIA. Prototypical subjects within each subgroup were identified and used to define subgroup-specific gene expression signatures. One of these signatures was associated with monocyte markers, another with transforming growth factor-beta-inducible genes, and a third with immediate-early genes. Correlation of these gene expression signatures with clinical and biological features of JIA subgroups suggests direct relevance to aspects of disease activity and supports the division of polyarticular JIA into distinct subsets. Conclusions. PBMC gene expression signatures in recent onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease.
Keywords: Patient vs. control, reassessment of phenotype
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| Overall design |
PBMC samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.
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| Contributor(s) |
Griffin TA, Barnes MG, Ilowite NT, Olson JC, Sherry DD, Gottlieb BS, Aronow BJ, Pavlidis P, Hinze C, Thornton S, Thompson SD, Grom AA, Colbert RA, Glass DN |
| Citation(s) |
19565504 |
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| Submission date |
Dec 05, 2008 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Michael Barnes |
| E-mail(s) |
[email protected]
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| Phone |
513-636-1319
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| Organization name |
Cincinnati Childrens Hospital Medical Center
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| Department |
Rheumatology
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| Lab |
Dr. David Glass
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (120)
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| Relations |
| BioProject |
PRJNA110529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13849_RAW.tar |
546.0 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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