Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms
Bingshan Li, Lam C Tsoi, William R Swindell, Johann E Gudjonsson, Trilokraj Tejasvi, Andrew Johnston, Jun Ding, Philip E Stuart, Xianying Xing, James J Kochkodan, John J Voorhees, Hyun M Kang, Rajan P Nair, Goncalo R Abecasis, James T Elder, Bingshan Li, Lam C Tsoi, William R Swindell, Johann E Gudjonsson, Trilokraj Tejasvi, Andrew Johnston, Jun Ding, Philip E Stuart, Xianying Xing, James J Kochkodan, John J Voorhees, Hyun M Kang, Rajan P Nair, Goncalo R Abecasis, James T Elder
Abstract
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.
Conflict of interest statement
Conflict of Interest
The authors declare no competing interests.
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References
- Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNAseq data. Genome Res. 2012;22:2008–2017.
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–29.
- Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004;5:101–113.
- Bazzi H, Getz A, Mahoney MG, Ishida-Yamamoto A, Langbein L, Wahl JK, 3rd, et al. Desmoglein 4 is expressed in highly differentiated keratinocytes and trichocytes in human epidermis and hair follicle. Differentiation. 2006;74:129–140.
- Birnbaum RY, Hayashi G, Cohen I, Poon A, Chen H, Lam ET, et al. Association analysis identifies ZNF750 regulatory variants in psoriasis. BMC medical genetics. 2011;12:167.
- Bowcock AM, Shannon W, Du F, Duncan J, Cao K, Aftergut K, et al. Insights into psoriasis and other inflammatory diseases from large-scale gene expression studies. Hum Mol Genet. 2001;10:1793–1805.
- Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics. 2010;11:282.
- Caruso R, Botti E, Sarra M, Esposito M, Stolfi C, Diluvio L, et al. Involvement of interleukin-21 in the epidermal hyperplasia of psoriasis. Nat Med. 2009;15:1013–1015.
- De Las Rivas J, Fontanillo C. Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol. 2010;6:e1000807.
- Di Meglio P, Perera GK, Nestle FO. The multitasking organ: recent insights into skin immune function. Immunity. 2011;35:857–869.
- Dong S, Kanno T, Yamaki A, Kojima T, Shiraiwa M, Kawada A, et al. NF-Y and Sp1/Sp3 are involved in the transcriptional regulation of the peptidylarginine deiminase type III gene (PADI3) in human keratinocytes. Biochem J. 2006;397:449–459.
- Elder J, Hammerberg C, Cooper K, Kojimas T, Nair R, Ellis C, et al. Cyclosporin A rapidly inhibits epidermal cytokine expression in psoriasis lesions, but not in cytokine-stimulated cultured keratinocytes. J Invest Dermatol. 1993;101:761–766.
- Elder JT, Zhao X. Evidence for local control of gene expression in the epidermal differentiation complex. Exp Dermatol. 2002;11:406–412.
- Fujiwara H, Ferreira M, Donati G, Marciano DK, Linton JM, Sato Y, et al. The basement membrane of hair follicle stem cells is a muscle cell niche. Cell. 2011;144:577–589.
- Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011;8:469–477.
- Garza LA, Liu Y, Yang Z, Alagesan B, Lawson JA, Norberg SM, et al. Prostaglandin D2 inhibits hair growth and is elevated in bald scalp of men with androgenetic alopecia. Sci Transl Med. 2012;4 126ra34.
- Gudjonsson JE, Ding J, Johnston A, Tejasvi T, Guzman AM, Nair RP, et al. Assessment of the psoriatic transcriptome in a large sample: additional regulated genes and comparisons with in vitro models. The Journal of investigative dermatology. 2010;130:1829–1840.
- Gudjonsson JE, Ding J, Li X, Nair RP, Tejasvi T, Qin ZS, et al. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. The Journal of investigative dermatology. 2009;129:2795–2804.
- Gudjonsson JE, Elder JT. Psoriasis. In: Goldsmith L, Katz SI, Gilchrest BA, Paller AS, Woolf K, Leffell DJ, editors. Dermatology in General Medicine. 8th ed. Vol. 1. New York: McGraw-Hill; 2012. pp. 197–231.
- Hardas BD, Zhao X, Zhang J, Longqing X, Stoll S, Elder JT. Assignment of psoriasin to human chromosomal band 1q21: Coordinate overexpression of clustered genes in psoriasis. J Invest Dermatol. 1996;106:753–758.
- Horvath S, Dong J. Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol. 2008;4:e1000117.
- Hsu YC, Pasolli HA, Fuchs E. Dynamics between stem cells, niche, and progeny in the hair follicle. Cell. 2011;144:92–105.
- Jabbari A, Suarez-Farinas M, Dewell S, Krueger JG. Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes. The Journal of investigative dermatology. 2012;132:246–249.
- Jiang YJ, Kim P, Lu YF, Feingold KR. PPARgamma activators stimulate aquaporin 3 expression in keratinocytes/epidermis. Exp Dermatol. 2011;20:595–599.
- Joyce CE, Zhou X, Xia J, Ryan C, Thrash B, Menter A, et al. Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome. Hum Mol Genet. 2011;20:4025–4040.
- Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109–D114.
- Kizawa K, Takahara H, Unno M, Heizmann CW. S100 and S100 fused-type protein families in epidermal maturation with special focus on S100A3 in mammalian hair cuticles. Biochimie. 2011;93:2038–2047.
- Kojima T, Cromie MA, Fisher GJ, Voorhees JJ, Elder JT. Gro-alpha mRNA is selectively overexpressed in psoriatic epidermis and is reduced by cyclosporin A in vivo, but not in cultured keratinocytes. J Invest Dermatol. 1994;101:501–507.
- Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2012;493:231–235.
- Kryczek I, Bruce AT, Gudjonsson JE, Johnston A, Aphale A, Vatan L, et al. Induction of IL-17+ T cell trafficking and development by IFN-gamma: mechanism and pathological relevance in psoriasis. J Immunol. 2008;181:4733–4741.
- Langfelder P, Horvath S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol. 2007;1:54.
- Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
- Lee E, Trepicchio WL, Oestreicher JL, Pittman D, Wang F, Chamian F, et al. Increased expression of interleukin 23 p19 and p40 in lesional skin of patients with psoriasis vulgaris. J Exp Med. 2004;199:125–130.
- Lever WF, Schaumburg-Lever G. Histopathology of the Skin. Seventh edition edn. Philadelphia: J. B. Lippincott; 1990. ; p. 909.
- Liu S, Lin L, Jiang P, Wang D, Xing Y. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res. 2011;39:578–588.
- Lowes MA, Russell CB, Martin DA, Towne JE, Krueger JG. The IL-23/T17 pathogenic axis in psoriasis is amplified by keratinocyte responses. Trends Immunol. 2012
- Mardaryev AN, Meier N, Poterlowicz K, Sharov AA, Sharova TY, Ahmed MI, et al. Lhx2 differentially regulates Sox9, Tcf4 and Lgr5 in hair follicle stem cells to promote epidermal regeneration after injury. Development. 2011;138:4843–4852.
- Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18:1509–1517.
- Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009;37:D619–D622.
- Mattiuzzo NR, Toulza E, Jonca N, Serre G, Guerrin M. A large-scale multi-technique approach identifies forty-nine new players of keratinocyte terminal differentiation in human epidermis. Exp Dermatol. 2011;20:113–118.
- Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31–46.
- Mitsui H, Suarez-Farinas M, Belkin DA, Levenkova N, Fuentes-Duculan J, Coats I, et al. Combined use of laser capture microdissection and cDNA microarray analysis identifies locally expressed disease-related genes in focal regions of psoriasis vulgaris skin lesions. The Journal of investigative dermatology. 2012;132:1615–1626.
- Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–628.
- Nestle FO, Kaplan DH, Barker J. Psoriasis. N Engl J Med. 2009;361:496–509.
- Nold MF, Nold-Petry CA, Zepp JA, Palmer BE, Bufler P, Dinarello CA. IL-37 is a fundamental inhibitor of innate immunity. Nat Immunol. 2012;11:1014–1022.
- Obarzanek-Fojt M, Favre B, Kypriotou M, Ryser S, Huber M, Hohl D. Homeodomain-only protein HOP is a novel modulator of late differentiation in keratinocytes. Eur J Cell Biol. 2010;90:279–290.
- Ouyang W, Kolls JK, Zheng Y. The biological functions of T helper 17 cell effector cytokines in inflammation. Immunity. 2008;28:454–467.
- Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011;12:87–98.
- Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera MF, Tusie-Luna T, et al. A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet. 2009;5:e1000642.
- Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61–D65.
- Quigley D, Balmain A. Systems genetics analysis of cancer susceptibility: from mouse models to humans. Nat Rev Genet. 2009;10:651–657.
- Quigley DA, To MD, Kim IJ, Lin KK, Albertson DG, Sjolund J, et al. Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility. Genome Biol. 2011;12:R5.
- Quigley DA, To MD, Perez-Losada J, Pelorosso FG, Mao JH, Nagase H, et al. Genetic architecture of mouse skin inflammation and tumour susceptibility. Nature. 2009;458:505–508.
- Reischl J, Schwenke S, Beekman JM, Mrowietz U, Sturzebecher S, Heubach JF. Increased expression of Wnt5a in psoriatic plaques. The Journal of investigative dermatology. 2007;127:163–169.
- Rogers MA, Langbein L, Praetzel-Wunder S, Winter H, Schweizer J. Human hair keratin-associated proteins (KAPs) Int Rev Cytol. 2006;251:209–263.
- Roy NC, Altermann E, Park ZA, McNabb WC. A comparison of analog and Next-Generation transcriptomic tools for mammalian studies. Brief Funct Genomics. 2011;10:135–150.
- Schuster M, Zouboulis CC, Ochsendorf F, Muller J, Thaci D, Bernd A, et al. Peroxisome proliferator-activated receptor activators protect sebocytes from apoptosis: a new treatment modality for acne? Br J Dermatol. 2011;164:182–186.
- Schweizer J, Langbein L, Rogers MA, Winter H. Hair follicle-specific keratins and their diseases. Exp Cell Res. 2007;313:2010–2020.
- Sen GL, Boxer LD, Webster DE, Bussat RT, Qu K, Zarnegar BJ, et al. ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation. Dev Cell. 2012;22:669–677.
- Shi X, Jin L, Dang E, Chang T, Feng Z, Liu Y, et al. IL-17A upregulates keratin 17 expression in keratinocytes through STAT1- and STAT3-dependent mechanisms. The Journal of investigative dermatology. 2012;131:2401–2408.
- Soccio RE, Tuteja G, Everett LJ, Li Z, Lazar MA, Kaestner KH. Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol. 2011;25:694–706.
- Steinert PM, Parry DA, Marekov LN. Trichohyalin mechanically strengthens the hair follicle: multiple cross-bridging roles in the inner root shealth. J Biol Chem. 2003;278:41409–41419.
- Suarez-Farinas M, Li K, Fuentes-Duculan J, Hayden K, Brodmerkel C, Krueger JG. Expanding the psoriasis disease profile: interrogation of the skin and serum of patients with moderate-to-severe psoriasis. The Journal of investigative dermatology. 2012;132:2552–2564.
- Suarez-Farinas M, Lowes MA, Zaba LC, Krueger JG. Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA) PLoS One. 2010;5:e10247.
- Swindell WR, Johnston A, Voorhees JJ, Elder JT, Gudjonsson JE. Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients. BMC Genomics. 2013;14:527.
- Swindell WR, Xing X, Stuart PE, Chen CS, Aphale A, Nair RP, et al. Heterogeneity of inflammatory and cytokine networks in chronic plaque psoriasis. PLoS One. 2012;7:e34594.
- Teunissen MB, Koomen CW, de Waal Malefyt R, Wierenga EA, Bos JD. Interleukin-17 and interferon-gamma synergize in the enhancement of proinflammatory cytokine production by human keratinocytes. The Journal of investigative dermatology. 1998;111:645–649.
- Tian S, Krueger JG, Li K, Jabbari A, Brodmerkel C, Lowes MA, et al. Metaanalysis derived (MAD) transcriptome of psoriasis defines the "core" pathogenesis of disease. PLoS One. 2012;7:e44274.
- Toulza E, Mattiuzzo NR, Galliano MF, Jonca N, Dossat C, Jacob D, et al. Large-scale identification of human genes implicated in epidermal barrier function. Genome Biol. 2007;8:R107.
- Trivedi NR, Cong Z, Nelson AM, Albert AJ, Rosamilia LL, Sivarajah S, et al. Peroxisome proliferator-activated receptors increase human sebum production. The Journal of investigative dermatology. 2006;126:2002–2009.
- Tsoi LC, Spain SL, Knight J, Ellinghaus E, Stuart PE, Capon F, et al. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet. 2012;44:1341–1348.
- Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
- Yang CF, Hwu WL, Yang LC, Chung WH, Chien YH, Hung CF, et al. A promoter sequence variant of ZNF750 is linked with familial psoriasis. The Journal of investigative dermatology. 2008;128:1662–1668.
- Yao Y, Richman L, Morehouse C, de los Reyes M, Higgs BW, Boutrin A, et al. Type I interferon: potential therapeutic target for psoriasis? PLoS One. 2008;3:e2737.
- Yessoufou A, Wahli W. Multifaceted roles of peroxisome proliferator-activated receptors (PPARs) at the cellular and whole organism levels. Swiss Med Wkly. 2010;140:w13071.
- Yip AM, Horvath S. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics. 2007;8:22.
- Zaba LC, Suarez-Farinas M, Fuentes-Duculan J, Nograles KE, Guttman-Yassky E, Cardinale I, et al. Effective treatment of psoriasis with etanercept is linked to suppression of IL-17 signaling, not immediate response TNF genes. J Allergy Clin Immunol. 2009;124 1022-10 e1-395.
- Zarnegar BJ, Webster DE, Lopez-Pajares V, Vander Stoep Hunt B, Qu K, Yan KJ, et al. Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63. Am J Hum Genet. 2012;91:435–443.
- Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4 Article17.
- Zhang W, Dang E, Shi X, Jin L, Feng Z, Hu L, et al. The pro-inflammatory cytokine IL-22 up-regulates keratin 17 expression in keratinocytes via STAT3 and ERK1/2. PLoS One. 2011;7:e40797.
- Zhou X, Krueger JG, Kao MC, Lee E, Du F, Menter A, et al. Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array. Physiol Genomics. 2003;13:69–78.
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