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| Status |
Public on Nov 11, 2011 |
| Title |
Global methylation analysis of psoriatic (involved and uninvolved) and control skin |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Psoriasis is a chronic inflammatory immune-mediated disorder affecting the skin and other organs including joints. Over 1,300 transcripts are altered in psoriatic involved skin compared to normal skin. Global epigenetic profiles of psoriatic skin have not been described. Here we describe the first genome-wide study of altered CpG methylation in psoriatic skin. We determined the methylation levels at 27,578 CpG sites in skin samples from individuals with psoriasis (12 involved, 8 uninvolved) and 10 unaffected individuals. CpG methylation of involved skin differed from normal skin at 1,108 sites. Twelve mapped to the epidermal differentiation complex, upstream or within genes that are highly up-regulated in psoriasis. Hierarchical clustering of 50 of the top differentially methylated (DM) sites separated psoriatic from normal skin samples. CpG sites where methylation was correlated with gene expression are reported. Sites with inverse correlations between methylation and nearby gene expression include those of KYNU, OAS2, S100A12, and SERPINB3, whose strong transcriptional up-regulation are important discriminators of psoriasis. We observed intrinsic epigenetic differences in uninvolved skin. Pyrosequencing of bisulfite-treated DNA from skin biopsies at three DM loci confirmed earlier findings and revealed a reversion of methylation levels towards the non-psoriatic state after one month of anti-TNF-a therapy.
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| Overall design |
Control n=8 (NN), psoriasis involved n = 19 (PP), psoriasis uninvolved n=8 (PN). Hybridized to Illumina Human 27k methylation array.
Paired samples are as follows:
PN1 and PP1
PN2 and PP2
PN3 and PP3
PN4 and PP4
PN5 and PP5
PN6 and PP6
PN7 and PP7
PN8 and PP8
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| Contributor(s) |
Roberson ED, Liu Y, Ryan C, Joyce CE, Duan S, Cao L, Martin A, Liao W, Menter A, Bowcock AM |
| Citation(s) |
22071477 |
| Submission date |
Sep 01, 2011 |
| Last update date |
Jan 02, 2015 |
| Contact name |
Elisha D.O. Roberson |
| E-mail(s) |
eroberso@dom.wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Internal Medicine & Genetics
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| Lab |
Roberson Lab
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| Street address |
660 South Euclid Ave., CB 8045
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
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| Samples (37)
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| GSM789521 |
Biopsy, control skin (NN4) |
| GSM789522 |
Biopsy, control skin (NN5) |
| GSM789523 |
Biopsy, control skin (NN6) |
| GSM789524 |
Biopsy, control skin (NN7) |
| GSM789525 |
Biopsy, control skin (NN8) |
| GSM789526 |
Biopsy, control skin (NN9) |
| GSM789527 |
Biopsy, control skin (NN10) |
| GSM789528 |
Biopsy, uninvolved psoriatic skin (PN1) |
| GSM789529 |
Biopsy, uninvolved psoriatic skin (PN2) |
| GSM789530 |
Biopsy, uninvolved psoriatic skin (PN3) |
| GSM789531 |
Biopsy, uninvolved psoriatic skin (PN4) |
| GSM789532 |
Biopsy, uninvolved psoriatic skin (PN5) |
| GSM789533 |
Biopsy, uninvolved psoriatic skin (PN6) |
| GSM789534 |
Biopsy, uninvolved psoriatic skin (PN7) |
| GSM789535 |
Biopsy, uninvolved psoriatic skin (PN8) |
| GSM789536 |
Biopsy, involved psoriatic skin (PP1) |
| GSM789537 |
Biopsy, involved psoriatic skin (PP2) |
| GSM789538 |
Biopsy, involved psoriatic skin (PP3) |
| GSM789539 |
Biopsy, involved psoriatic skin (PP4) |
| GSM789540 |
Biopsy, involved psoriatic skin (PP5) |
| GSM789541 |
Biopsy, involved psoriatic skin (PP6) |
| GSM789542 |
Biopsy, involved psoriatic skin (PP7) |
| GSM789543 |
Biopsy, involved psoriatic skin (PP8) |
| GSM789544 |
Biopsy, involved psoriatic skin (PP9) |
| GSM789545 |
Biopsy, involved psoriatic skin (PP10) |
| GSM789546 |
Biopsy, involved psoriatic skin (PP11) |
| GSM789547 |
Biopsy, involved psoriatic skin (PP12) |
| GSM789548 |
Biopsy, involved psoriatic skin (PP13) |
| GSM789549 |
Biopsy, involved psoriatic skin (PP14) |
| GSM789550 |
Biopsy, involved psoriatic skin (PP15) |
| GSM789551 |
Biopsy, involved psoriatic skin (PP16) |
| GSM789552 |
Biopsy, involved psoriatic skin (PP17) |
| GSM789553 |
Biopsy, involved psoriatic skin (PP18) |
| GSM789554 |
Biopsy, involved psoriatic skin (PP19) |
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| Relations |
| BioProject |
PRJNA145123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31835_RAW.tar |
5.8 Mb |
(http)(custom) |
TAR |
| GSE31835_signals.txt.gz |
6.7 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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