Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms.

Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT
J Invest Dermatol. 2014 134 (7): 1828-1838

PMID: 24441097 · PMCID: PMC4057954 · DOI:10.1038/jid.2014.28

To increase our understanding of psoriasis, we used high-throughput complementary DNA sequencing (RNA-seq) to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived complementary DNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ∼38 million single-end 80-bp reads per sample. Comparison of 42 samples examined by both RNA-seq and microarray revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes. Weighted gene coexpression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long noncoding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally expressed genes were significantly downregulated in psoriatic biopsies, most likely because of expansion of the epidermal compartment. These results show the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and coexpression analysis.

MeSH Terms (16)

Case-Control Studies Cytoskeletal Proteins Down-Regulation Epidermis Gene Expression Profiling High-Throughput Nucleotide Sequencing Humans Interleukin-17 Keratinocytes Kruppel-Like Transcription Factors Oligonucleotide Array Sequence Analysis Psoriasis RNA, Long Noncoding RNA-Binding Proteins Transcription Factors Transcriptome

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