Landscape of Long Noncoding RNAs in Psoriatic and Healthy Skin

• Published in: Journal of investigative dermatology Vol. 136; no. 3; pp. 603 - 609
• Main Authors: Gupta, Rashmi, Ahn, Richard, Lai, Kevin, Mullins, Elizabeth, Debbaneh, Maya, Dimon, Michelle, Arron, Sarah, Liao, Wilson
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2016
• Subjects: Adalimumab - administration & dosage; Adult; Biopsy, Needle; Case-Control Studies; Female; Gene Expression Profiling; Humans; Immunohistochemistry; Male; Middle Aged; Psoriasis - drug therapy; Psoriasis - genetics; Psoriasis - pathology; Real-Time Polymerase Chain Reaction - methods; Reference Values; RNA, Long Noncoding - genetics; RNA, Messenger - metabolism; Sequence Analysis, RNA - methods; Severity of Illness Index; Transcriptome; Young Adult; NN; PP; DE; lncRNA; PT; TNF-α; CNC; qPCR; FPKM
• ISSN: 0022-202X; 1523-1747
• DOI: 10.1016/j.jid.2015.12.009

We used RNA sequencing to study and characterize the long noncoding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). To this end, we sequenced total RNA from 18 psoriasis patients and 16 healthy controls. We merged three lncRNA reference datasets to create a single combined reference of 67,157 lncRNA transcripts with no overlaps. We identified differential expression of 971 lncRNAs between PP and NN, 157 between PP and PT, and 377 between PT and NN. Using differentially expressed lncRNAs between PP and NN, we identified a molecular lncRNA signature that distinguishes psoriatic skin from healthy skin. Furthermore, we performed an unsupervised hierarchical analysis that revealed distinct clustering of PP samples from NN. A coding noncoding network analysis revealed a large network of highly correlated lncRNA and protein coding transcripts that provided insight into the potential functions of unannotated lncRNAs. To the best of our knowledge, this description of both polyadenylated as well as nonpolyadenylated lncRNA transcripts in psoriasis has not been previously reported. Our findings highlight the potential importance of lncRNAs in the biology of psoriasis and response to treatment.