Global transcriptional analysis of psoriatic skin and blood confirms known disease-associated pathways and highlights novel genomic "hot spots" for differentially expressed genes

Genomics

Volumn 100, Issue 1, 2012, Pages 18-26

  Coda, Alvin B ^a   Icen, Murat ^a   Smith, Jason R ^a   Sinha, Animesh A ^b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

Global gene expression; Microarrays; Pathogenesis; Psoriasis; PSORS loci

Indexed keywords

MESSENGER RNA;

ADULT; AGED; ALOX12B GENE; APOPTOSIS; ARTICLE; BLOOD ANALYSIS; BLOOD SAMPLING; CLINICAL ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FABP5 GENE; FATTY ACID METABOLISM; FEMALE; GARS GENE; GENE; GENE EXPRESSION; GENE LOCATION; GENE LOCUS; GENE REPLICATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; IL1RN GENE; IMMUNOREACTIVITY; IVL GENE; LYN GENE; MALE; MICROARRAY ANALYSIS; MOLECULAR PATHOLOGY; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; OXIDATIVE STRESS; POLE3 GENE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PSORIASIS; SIGNAL TRANSDUCTION; TGM1 GENE; TRANSCRIPTION REGULATION; UPREGULATION;

ADULT; AGED; CASE-CONTROL STUDIES; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC LOCI; HUMANS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PSORIASIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SKIN;

EID: 84862756451     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.05.004     Document Type: Article

References (50)

1. Lowes M.A., Bowcock A.M., Krueger J.G. Pathogenesis and therapy of psoriasis. Nature 2007, 445:866-873.
2. Nestle F.O., Kaplan D.H., Barker J. Psoriasis. N. Engl. J. Med. 2009, 361:496-509.
3. Elder J.T., Bruce A.T., Gudjonsson J.E., Johnston A., Stuart P.E., Tejasvi T., Voorhees J.J., Abecasis G.R., Nair R.P. Molecular dissection of psoriasis: integrating genetics and biology. J. Invest. Dermatol. 2010, 130(5):1213-1226. Epub 2009 Oct 8.
4. Zhou X., Krueger J.G., Kao M.C., Lee E., Du F., Menter A., Wong W.H., Bowcock A.M. 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.
5. Bowcock A.M., Shannon W., Du F., Duncan J., Cao K., Aftergut K., Catier J., Fernandez-Vina M.A., Menter A. Insights into psoriasis and other inflammatory diseases from large-scale gene expression studies. Hum. Mol. Genet. 2001, 10:1793-1805.
6. Oestreicher J.L., Walters I.B., Kikuchi T., Gilleaudeau P., Surette J., Schwertschlag U., Dorner A.J., Krueger J.G., Trepicchio W.L. Molecular classification of psoriasis disease-associated genes through pharmacogenomic expression profiling. Pharmacogenomics J. 2001, 1:272-287.
7. Kulski J.K., Kenworthy W., Bellgard M., Taplin R., Okamoto K., Oka A., Mabuchi T., Ozawa A., Tamiya G., Inoko H. Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals. J. Mol. Med. 2005, 83:964-975.
8. Quekenborn-Trinquet V., Fogel P., Aldana-Jammayrac O., Ancian P., Demarchez M., Rossio P., Richards H.L., Kirby B., Nguyen C., Voegel J.J., Griffiths C.E. Gene expression profiles in psoriasis: analysis of impact of body site location and clinical severity. Br. J. Dermatol. 2005, 152:489-504.
9. Gudjonsson J.E., Ding J., Johnston A., Tejasvi T., Guzman A.M., Nair R.P., Voorhees J.J., Abecasis G.R., Elder J.T. Assessment of the psoriatic transcriptome in a large sample: additional regulated genes and comparisons with in vitro models. J. Invest. Dermatol. 2010, 130(7):1829-1840.
10. Yao Y., Richman L., Morehouse C., de los Reyes M., Higgs B.W., Boutrin A., White B., Coyle A., Krueger J., Kiener P.A., Jallal B. Type I interferon: potential therapeutic target for psoriasis?. PLoS One 2008, 3:e2737.
11. Reischl J., Schwenke S., Beekman J.M., Mrowietz U., Sturzebecher S., Heubach J.F. Increased expression of Wnt5a in psoriatic plaques. J. Invest. Dermatol. 2007, 127:163-169.
12. Mee J.B., Johnson C.M., Morar N., Burslem F., Groves R.W. The psoriatic transcriptome closely resembles that induced by interleukin-1 in cultured keratinocytes: dominance of innate immune responses in psoriasis. Am. J. Pathol. 2007, 171:32-42.
13. Suarez-Farinas M., Lowes M.A., Zaba L.C., Krueger J.G. Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA). PLoS One 2010, 5:e10247.
14. Chen R., Morgan A.A., Dudley J., Deshpande T., Li L., Kodama K., Chiang A.P., Butte A.J. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol. 2008, 9:R170.
15. Lee S.K., Jeon E.K., Kim Y.J., Seo S.H., Kim C.D., Lim J.S., Lee J.H. A global gene expression analysis of the peripheral blood mononuclear cells reveals the gene expression signature in psoriasis. Ann. Dermatol. 2009, 21:237-242.
16. Sinnaeve P.R., Donahue M.P., Grass P., Seo D., Vonderscher J., Chibout S.D., Kraus W.E., Sketch M., Nelson C., Ginsburg G.S., Goldschmidt-Clermont P.J., Granger C.B. Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease. PLoS One 2009, 4:e7037.
17. Wingrove J., Daniels S., Sehnert A., Tingley W., Elashoff M., Rosenberg S., Buellesfeld L., Grube E., Newby L., Ginsburg G., Kraus W. Correlation of peripheral-blood gene expression with the extent of coronary artery stenosis. Circ. Cardiovasc. Genet. 2008, 1:31-38.
18. Veal C.D., Clough R.L., Barber R.C., Mason S., Tillman D., Ferry B., Jones A.B., Ameen M., Balendran N., Powis S.H., Burden A.D., Barker J.N., Trembath R.C. Identification of a novel psoriasis susceptibility locus at 1p and evidence of epistasis between PSORS1 and candidate loci. J. Med. Genet. 2001, 38:7-13.
19. Samuelsson L., Enlund F., Torinsson A., Yhr M., Inerot A., Enerback C., Wahlstrom J., Swanbeck G., Martinsson T. A genome-wide search for genes predisposing to familial psoriasis by using a stratification approach. Hum. Genet. 1999, 105:523-529.
20. Foerster J., Nolte I., Schweiger S., Ehlert C., Bruinenberg M., Spaar K., van der Steege G., Mulder M., Kalscheuer V., Moser B., Kijas Z., Seeman P., Stander M., Sterry W., te Meerman G. Evaluation of the IRF-2 gene as a candidate for PSORS3. J. Invest. Dermatol. 2004, 122:61-64.
21. Zhang X.J., He P.P., Wang Z.X., Zhang J., Li Y.B., Wang H.Y., Wei S.C., Chen S.Y., Xu S.J., Jin L., Yang S., Huang W. Evidence for a major psoriasis susceptibility locus at 6p21(PSORS1) and a novel candidate region at 4q31 by genome-wide scan in Chinese Hans. J. Invest. Dermatol. 2002, 119:1361-1366.
22. Nair R.P., Duffin K.C., Helms C., Ding J., Stuart P.E., Goldgar D., Gudjonsson J.E., Li Y., Tejasvi T., Feng B.J., Ruether A., Schreiber S., Weichenthal M., Gladman D., Rahman P., Schrodi S.J., Prahalad S., Guthery S.L., Fischer J., Liao W., Kwok P.Y., Menter A., Lathrop G.M., Wise C.A., Begovich A.B., Voorhees J.J., Elder J.T., Krueger G.G., Bowcock A.M., Abecasis G.R. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat. Genet. 2009, 41:199-204.
23. Trembath R.C., Clough R.L., Rosbotham J.L., Jones A.B., Camp R.D., Frodsham A., Browne J., Barber R., Terwilliger J., Lathrop G.M., Barker J.N. Identification of a major susceptibility locus on chromosome 6p and evidence for further disease loci revealed by a two stage genome-wide search in psoriasis. Hum. Mol. Genet. 1997, 6:813-820.
24. Nair R.P., Henseler T., Jenisch S., Stuart P., Bichakjian C.K., Lenk W., Westphal E., Guo S.W., Christophers E., Voorhees J.J., Elder J.T. Evidence for two psoriasis susceptibility loci (HLA and 17q) and two novel candidate regions (16q and 20p) by genome-wide scan. Hum. Mol. Genet. 1997, 6:1349-1356.
25. Tomfohrde J., Silverman A., Barnes R., Fernandez-Vina M.A., Young M., Lory D., Morris L., Wuepper K.D., Stastny P., Menter A., et al. Gene for familial psoriasis susceptibility mapped to the distal end of human chromosome 17q. Science 1994, 264:1141-1145.
26. Lee Y.A., Ruschendorf F., Windemuth C., Schmitt-Egenolf M., Stadelmann A., Nurnberg G., Stander M., Wienker T.F., Reis A., Traupe H. Genomewide scan in German families reveals evidence for a novel psoriasis-susceptibility locus on chromosome 19p13. Am. J. Hum. Genet. 2000, 67:1020-1024.
27. Capon F., Bijlmakers M.J., Wolf N., Quaranta M., Huffmeier U., Allen M., Timms K., Abkevich V., Gutin A., Smith R., Warren R.B., Young H.S., Worthington J., Burden A.D., Griffiths C.E., Hayday A., Nestle F.O., Reis A., Lanchbury J., Barker J.N., Trembath R.C. Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene. Hum. Mol. Genet. 2008, 17:1938-1945.
28. Sun L.D., Yang S., Liu J.J., Ren Y.Q., Fan X., Xu S.X., Zhou L., Yang C.J., Xiao F.L., Gao M., Cui Y., Du W.H., Huang W., Zhang X.J. Follow-up analysis of 180 Chinese Han families: identification of a novel locus for psoriasis at 2p22.3-11.2. Br. J. Dermatol. 2008, 158:512-517.
29. Bhalerao J., Bowcock A.M. The genetics of psoriasis: a complex disorder of the skin and immune system. Hum. Mol. Genet. 1998, 7:1537-1545.
30. Romanowska M., al Yacoub N., Seidel H., Donandt S., Gerken H., Phillip S., Haritonova N., Artuc M., Schweiger S., Sterry W., Foerster J. PPARdelta enhances keratinocyte proliferation in psoriasis and induces heparin-binding EGF-like growth factor. J. Invest. Dermatol. 2008, 128:110-124.
31. Nomura I., Gao B., Boguniewicz M., Darst M.A., Travers J.B., Leung D.Y. Distinct patterns of gene expression in the skin lesions of atopic dermatitis and psoriasis: a gene microarray analysis. J. Allergy Clin. Immunol. 2003, 112:1195-1202.
32. Van Haren R., Feldman D., Sinha A.A. Systematic comparison of nonmelanoma skin cancer microarray datasets reveals lack of consensus genes. Br. J. Dermatol. 2009, 161:1278-1287.
33. Cahan P., Rovegno F., Mooney D., Newman J.C., St Laurent G., McCaffrey T.A. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401:12-18.
34. Jabbari A., Suarez-Farinas M., Dewell S., Krueger J.G. Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes. J. Invest. Dermatol. 2012, 132:246-249.
35. Piskin G., Sylva-Steenland R.M., Bos J.D., Teunissen M.B. In vitro and in situ expression of IL-23 by keratinocytes in healthy skin and psoriasis lesions: enhanced expression in psoriatic skin. J. Immunol. 2006, 176:1908-1915.
36. Chan J.R., Blumenschein W., Murphy E., Diveu C., Wiekowski M., Abbondanzo S., Lucian L., Geissler R., Brodie S., Kimball A.B., Gorman D.M., Smith K., de Waal Malefyt R., Kastelein R.A., McClanahan T.K., Bowman E.P. IL-23 stimulates epidermal hyperplasia via TNF and IL-20R2-dependent mechanisms with implications for psoriasis pathogenesis. J. Exp. Med. 2006, 203:2577-2587.
37. Kunz M. DNA microarray technology in dermatology. Semin. Cutan. Med. Surg. 2008, 27:16-24.
38. Gudjonsson J.E., Ding J., Li X., Nair R.P., Tejasvi T., Qin Z.S., Ghosh D., Aphale A., Gumucio D.L., Voorhees J.J., Abecasis G.R., Elder J.T. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J. Invest. Dermatol. 2009, 129:2795-2804.
39. van de Kerkhof P.C. The evolution of the psoriatic lesion. Br. J. Dermatol. 2007, 157:4-15.
40. Zhou Q., Mrowietz U., Rostami-Yazdi M. Oxidative stress in the pathogenesis of psoriasis. Free Radic. Biol. Med. 2009, 47:891-905.
41. McDonald C.J., Calabresi P. Psoriasis and occlusive vascular disease. Br. J. Dermatol. 1978, 99:469-475.
42. Lindegard B. Diseases associated with psoriasis in a general population of 159,200 middle-aged, urban, native Swedes. Dermatologica 1986, 172:298-304.
43. Poikolainen K., Karvonen J., Pukkala E. Excess mortality related to alcohol and smoking among hospital-treated patients with psoriasis. Arch. Dermatol. 1999, 135:1490-1493.
44. Gelfand J.M., Neimann A.L., Shin D.B., Wang X., Margolis D.J., Troxel A.B. Risk of myocardial infarction in patients with psoriasis. JAMA 2006, 296:1735-1741.
45. Brauchli Y.B., Jick S.S., Miret M., Meier C.R. Psoriasis and risk of incident myocardial infarction, stroke or transient ischaemic attack: an inception cohort study with a nested case-control analysis. Br. J. Dermatol. 2009, 160:1048-1056.
46. Mehta N.N., Azfar R.S., Shin D.B., Neimann A.L., Troxel A.B., Gelfand J.M. Patients with severe psoriasis are at increased risk of cardiovascular mortality: cohort study using the General Practice Research Database. Eur. Heart J. 2010, 31(8):1000-1006.
47. Nair R.P., Stuart P.E., Nistor I., Hiremagalore R., Chia N.V., Jenisch S., Weichenthal M., Abecasis G.R., Lim H.W., Christophers E., Voorhees J.J., Elder J.T. Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene. Am. J. Hum. Genet. 2006, 78:827-851.
48. Hoffjan S., Stemmler S. On the role of the epidermal differentiation complex in ichthyosis vulgaris, atopic dermatitis and psoriasis. Br. J. Dermatol. 2007, 157:441-449.
49. Enerback C., Holmqvist D., Inerot A., Enlund F., Samuelsson L., Torinsson A., Wahlstrom J., Swanbeck G., Martinsson T. Cytogenetic analysis of 477 psoriatics revealed an increased frequency of aberrations involving chromosome region 11q. Eur. J. Hum. Genet. 1999, 7:339-344.
50. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.