|
| Status |
Public on Dec 05, 2018 |
| Title |
DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [sarcmeth] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays.
We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. We identified 2,726 differentially methylated CpGs mapping to 1,944 unique genes when comparing CBD patients to beryllium-sensitized (BeS) individuals without disease. 69% of these genes were also differentially expressed in CBD. Sarcoidosis patients exhibited directional consistency at many loci, but genome-wide significance was not achieved, likely due to heterogeneity in the patient population.
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|
| Overall design |
This cohort of 15 remitting and 9 progressive sarcoidosis patients, as defined in part by Scadding scale, were analyzed to detect epigenetic and transcriptomic differences within subsets of the heterogeneous sarcoidosis population. DNA and RNA were extracted from BAL fluid and analyzed on microarrays to define differential methylation and transcription genome-wide.
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| Contributor(s) |
Yang IV, Konigsberg IR, MacPhail K, Li L, Davidson EJ, Mroz PM, Hamzeh N, Gillespie M, Silveira LJ, Fingerlin TE, Maier LA |
| Citation(s) |
30141971 |
| |
| Submission date |
Feb 18, 2018 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Ivana Yang |
| E-mail(s) |
ivana.yang@cuanschutz.edu
|
| Organization name |
University of Colorado - Anschutz Medical Campus
|
| Street address |
12700 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
|
| Samples (24)
|
| GSM3016464 |
Remitting sarcoidosis sample 1 [sarcmeth] |
| GSM3016465 |
Remitting sarcoidosis sample 2 [sarcmeth] |
| GSM3016466 |
Remitting sarcoidosis sample 3 [sarcmeth] |
| GSM3016467 |
Remitting sarcoidosis sample 4 [sarcmeth] |
| GSM3016468 |
Remitting sarcoidosis sample 5 [sarcmeth] |
| GSM3016469 |
Progressive sarcoidosis sample 1 [sarcmeth] |
| GSM3016470 |
Remitting sarcoidosis sample 6 [sarcmeth] |
| GSM3016471 |
Remitting sarcoidosis sample 7 [sarcmeth] |
| GSM3016472 |
Progressive sarcoidosis sample 2 [sarcmeth] |
| GSM3016473 |
Remitting sarcoidosis sample 8 [sarcmeth] |
| GSM3016474 |
Remitting sarcoidosis sample 9 [sarcmeth] |
| GSM3016475 |
Remitting sarcoidosis sample 10 [sarcmeth] |
| GSM3016476 |
Remitting sarcoidosis sample 11 [sarcmeth] |
| GSM3016477 |
Remitting sarcoidosis sample 12 [sarcmeth] |
| GSM3016478 |
Progressive sarcoidosis sample 3 [sarcmeth] |
| GSM3016479 |
Remitting sarcoidosis sample 13 [sarcmeth] |
| GSM3016480 |
Progressive sarcoidosis sample 4 [sarcmeth] |
| GSM3016481 |
Progressive sarcoidosis sample 5 [sarcmeth] |
| GSM3016482 |
Progressive sarcoidosis sample 6 [sarcmeth] |
| GSM3016483 |
Progressive sarcoidosis sample 7 [sarcmeth] |
| GSM3016484 |
Progressive sarcoidosis sample 8 [sarcmeth] |
| GSM3016485 |
Progressive sarcoidosis sample 9 [sarcmeth] |
| GSM3016486 |
Remitting sarcoidosis sample 14 [sarcmeth] |
| GSM3016487 |
Remitting sarcoidosis sample 15 [sarcmeth] |
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| This SubSeries is part of SuperSeries: |
| GSE110780 |
DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease |
|
| Relations |
| BioProject |
PRJNA434525 |
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