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| Status |
Public on Jul 20, 2018 |
| Title |
RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
It has long been recognized that anatomic location is an important feature for defining distinct subtypes of plaque psoriasis. However, little is known about the molecular differences between scalp, palmoplantar, and conventional plaque psoriasis. To investigate the molecular heterogeneity of these psoriasis subtypes, we performed RNA-seq and flow cytometry on skin samples from individuals with scalp, palmoplantar, and conventional plaque psoriasis, along with samples from healthy control patients. We performed differential expression analysis and network analysis using weighted gene coexpression network analysis (WGCNA). Our analysis revealed a core set of 763 differentially expressed genes common to all sub-types of psoriasis. In contrast, we identified 605, 632, and 262 genes uniquely differentially expressed in conventional, scalp, and palmoplantar psoriasis, respectively. WGCNA and pathway analysis revealed biological processes for the core genes as well as subtype-specific genes. Flow cytometry analysis revealed a shared increase in the percentage of CD4+ T regulatory cells in all psoriasis subtypes relative to controls, whereas distinct psoriasis subtypes displayed differences in IL-17A, IFN-gamma, and IL-22 production. This work reveals the molecular heterogeneity of plaque psoriasis and identifies subtype-specific signaling pathways that will aid in the development of therapy that is appropriate for each subtype of plaque psoriasis.
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| Overall design |
Transcriptomic profiles were obtained from palmoplantar (n = 3), scalp (n = 8), and conventional psoriatic skin (n = 8) as well as healthy control skin (n = 9) biopsies on the Illumina HiSeq 2000/4000 platforms. Multi-parameter FACS was also performed on each biopsy sample to obtain T cell populations (CD4+ T effectors, CD8+ T cells, and CD4+Foxp3+ Tregs).
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| Contributor(s) |
Ahn R, Yan D, Chang H, Lee K, Bhattarai S, Huang Z, Nakamura M, Singh R, Afifi L, Taravati K, Munoz-Sandoval P, Pauli M, Rosenblum MD, Liao W |
| Citation(s) |
30054515 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| T32 AR007175 |
UCSF Dermatology Training Grant |
University of California San Francisco |
Pui-Yan KWOK |
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| Submission date |
Jul 19, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Richard Sungho Ahn |
| Organization name |
University of California Los Angeles
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| Department |
Microbiology, Immunology, and Molecular Genetics
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| Street address |
611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA481993 |
| SRA |
SRP154474 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117405_SCALP_HF_P_KT_FPKM_Table_05_18_2017.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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