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| Status |
Public on Apr 03, 2018 |
| Title |
NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Employing microarray assays, a total of 267 genes were identified that were significantly up- or downregulated in PBMCs of WT-NOD2 patients, compared to healthy donors after challenge with vitamin D (+/-D) and/or a combination (+/-LP) of LPS (lipopolysaccharide) and PGN (peptidoglycan) (p < 0.05; threshold: ≥ 2-fold change). For further analysis by real-time PCR, 12 genes with known impact on inflammation and immunity were selected that fulfilled predefined expression criteria. In a larger cohort of patients and controls, a disease-associated expression pattern, with higher transcript levels in vitamin D-treated PBMCs from 5 patients, was observed for three of these genes, CLEC5A (p < 0.030), lysozyme (LYZ; p < 0.047) and TREM1 (p < 0.023). Six genes were found to be expressed in a NOD2- dependent manner (CD101, p < 0.002; CLEC5A, p < 0.020; CXCL5, p < 0.009; IL-24, p < 0.044; ITGB2, p < 0.041; LYZ, p < 0.042). Interestingly, the highest transcript levels were observed in patients with heterozygous NOD2 mutations.
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| Overall design |
PBMC`s of 3 patient and 3 controls were treated with vitamin D and/or a combination of LPS and PGN resulting in 8 triplicates (24 hybridization samples)
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| Contributor(s) |
Schäffler H, Rohde M, Rohde S, Huth A, Gittel N, Hollborn H, Koczan D, Glass Ä, Lamprecht G, Jaster R |
| Citation(s) |
29568200 |
| Submission date |
Feb 06, 2018 |
| Last update date |
Feb 01, 2019 |
| Contact name |
Dirk Koczan |
| E-mail(s) |
dirk.koczan@med.uni-rostock.de
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| Phone |
+493814945885
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| Organization name |
University of Rostock
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| Department |
Institute for Immunology
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| Street address |
Schillingallee 70
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| City |
Rostock |
| ZIP/Postal code |
18057 |
| Country |
Germany |
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| Platforms (1) |
| GPL23159 |
[Clariom_S_Human] Affymetrix Clariom S Assay, Human (Includes Pico Assay) |
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| Samples (24)
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| GSM2981862 |
Control_1_+D+LP, biological replicate 1 |
| GSM2981863 |
Control_2_+D+LP, biological replicate 2 |
| GSM2981864 |
Control_3_+D+LP, biological replicate 3 |
| GSM2981865 |
Control_1_+D-LP, biological replicate 1 |
| GSM2981866 |
Control_2_+D-LP, biological replicate 2 |
| GSM2981867 |
Control_3_+D-LP, biological replicate 3 |
| GSM2981868 |
Control_1_-D+LP, biological replicate 1 |
| GSM2981869 |
Control_2_-D+LP, biological replicate 2 |
| GSM2981870 |
Control_3_-D+LP, biological replicate 3 |
| GSM2981871 |
Control_1_-D-LP, biological replicate 1 |
| GSM2981872 |
Control_2_-D-LP, biological replicate 2 |
| GSM2981873 |
Control_3_-D-LP, biological replicate 3 |
| GSM2981874 |
Patient_1_+D+LP, biological replicate 1 |
| GSM2981875 |
Patient_2_+D+LP, biological replicate 2 |
| GSM2981876 |
Patient_3_+D+LP, biological replicate 3 |
| GSM2981877 |
Patient_1_+D-LP, biological replicate 1 |
| GSM2981878 |
Patient_2_+D-LP, biological replicate 2 |
| GSM2981879 |
Patient_3_+D-LP, biological replicate 3 |
| GSM2981880 |
Patient_1_-D+LP, biological replicate 1 |
| GSM2981881 |
Patient_2_-D+LP, biological replicate 2 |
| GSM2981882 |
Patient_3_-D+LP, biological replicate 3 |
| GSM2981883 |
Patient_1_-D-LP, biological replicate 1 |
| GSM2981884 |
Patient_2_-D-LP, biological replicate 2 |
| GSM2981885 |
Patient_3_-D-LP, biological replicate 3 |
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| Relations |
| BioProject |
PRJNA433092 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110186_RAW.tar |
30.8 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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