Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics

Proteomics - Clinical Applications

Volumn 2, Issue 3, 2008, Pages 290-300

  Park, Yong Doo ^a,b   Park, Daeui ^c   Bhak, Jong ^c   Yang, Jun Mo ^b  

^a TSINGHUA UNIVERSITY   (China)

^b Sungkyunkwan University School of Medicine   (South Korea)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

Atopic dermatitis; Fibroblasts; Interactomics; Keratinocytes

Indexed keywords

ALDEHYDE DEHYDROGENASE; APOLIPOPROTEIN A; CD14 ANTIGEN; CELL PROTEIN; CERAMIDE; CHLORIDE INTRACELLULAR CHANNEL 1 PROTEIN; CHLORIDE INTRACELLULAR CHANNEL 4 PROTEIN; COMPLEMENT COMPONENT C1R; HEAT SHOCK PROTEIN; IMMUNOGLOBULIN E ANTIBODY; IMMUNOGLOBULIN FC FRAGMENT; LIPOCORTIN 1; MEMBRANE PROTEIN; POLYPEPTIDE ANTIBIOTIC AGENT; PROTEIN KINASE C INHIBITOR; SEMAPHORIN; SEMAPHORIN 4F; SPERMATOGENESIS ASSOCIATED FACTOR; SPHINGOMYELIN; TENASCIN; TOLL LIKE RECEPTOR 4; TUMOR REJECTION ANTIGEN; UNCLASSIFIED DRUG; VIMENTIN;

ATOPIC DERMATITIS; CELL CULTURE; DIAGNOSTIC VALUE; DNA MICROARRAY; DOWN REGULATION; ENZYME ACTIVITY; ENZYME LINKED IMMUNOSORBENT ASSAY; FIBROBLAST; GENETIC PREDISPOSITION; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; IMMUNOHISTOCHEMISTRY; KERATINOCYTE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOPHYSIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; PROTEOMICS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; TWO DIMENSIONAL GEL ELECTROPHORESIS; UNINDEXED SEQUENCE; WESTERN BLOTTING;

EID: 41149162157     PISSN: 18628346     EISSN: None     Source Type: Journal    
DOI: 10.1002/prca.200780063     Document Type: Review

References (55)

1. Kay, A. B., Allergy and allergic diseases. Second of two parts. N. Engl. J. Med. 2001, 344, 109-113.
2. Wright, R. J., Cohen, R. T., Cohen, S., The impact of stress on the development and expression of atopy. Curr. Opin. Allergy Clin. Immunol. 2005, 5, 23-29.
3. Blumenthal, M. N., The role of genetics in the development of asthma and atopy. Curr. Opin. Allergy Clin. Immunol. 2005, 5, 141-145.
4. Upham, J. W., Holt, P. G., Environment and development of atopy. Curr. Opin. Allergy Clin. Immunol. 2005, 5, 167-172.
5. Cookson, W., The immunogenetics of asthma and eczema: a new focus on the epithelium. Nat. Rev. Immunol. 2004, 4, 978-988.
6. Kim, E., Lee, J. E., Namkung, J. H., Park, J. H. et al., Association of the single-nucleotide polymorphism and haplotype of the interleukin 18 gene with atopic dermatitis in Koreans. Clin. Exp. Allergy 2007, 37, 865-871.
7. Kim, H. T., Lee, J. Y., Han, B. G., Kim, K. et al., Association analysis of sphingomyelinase 2 polymorphisms for the extrinsic type of atopic dermatitis in Koreans. J. Dermatol. Sci. 2007, 46, 143-146.
8. Ahmad-Nejad, P., Mrabet-Dahbi, S., Breuer, K., Klotz, M. et al., The toll-like receptor 2 R753Q polymorphism defines a subgroup of patients with atopic dermatitis having severe phenotype. J. Allergy Clin. Immunol. 2004, 113, 565-567.
9. Kusunoki, T., Okafuji, I., Yoshioka, T., Saito, M. et al., SPINK5 polymorphism is associated with disease severity and food allergy in children with atopic dermatitis. J. Allergy Clin. Immunol. 2005, 115, 636-638.
10. Bowcock, A. M., Cookson, W. O., The genetics of psoriasis, psoriatic arthritis and atopic dermatitis. Hum. Mol. Genet. 2004, 13, R43-R55.
11. Morar, N., Willis-Owen, S., Moffatt, M., Cookson, W., The genetics of atopic dermatitis. J. Allergy Clin. Immunol. 2006, 118, 24-34.
12. Abramovits, W., Atopic dermatitis. J. Am. Acad. Dermatol. 2005, 53, S86-S93.
13. Simpson, E. L., Hanifin, J. M., Atopic dermatitis. J. Am. Acad. Dermatol. 2005, 53, 115-128.
14. Leung, D. Y., Boguniewicz, M., Howell, M. D., Nomura, I. et al., New insights into atopic dermatitis. J. Clin. Invest. 2004, 113, 651-657.
15. Breuer, K., Werfel, T., Kapp, A., Allergic manifestations of skin diseases-atopic dermatitis. Chem. Immunol. Allergy 2006, 91, 76-86.
16. Lebwohl, M., Psoriasis. Lancet 2003, 361, 1197-1204.
17. Hamid, Q., Boguniewicz, M., Leung, D. Y., Differential in situ cytokine gene expression in acute versus chronic atopic dermatitis. J. Clin. Invest. 1994, 94, 870-876.
18. Heidecker, B., Hare, J. M., The use of transcriptomic biomarkers for personalized medicine. Heart Fail. Rev. 2007, 12, 1-11.
19. Drake, R. R., Schwegler, E. E., Malik, G., Diaz, J. et al., Lectin capture strategies combined with mass spectrometry for the discovery of serum glycoprotein biomarkers. Mol. Cell. Proteomics 2006, 5, 1957-1967.
20. Fischer, H. P., Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnol. Annu. Rev. 2005, 11, 1-68.
21. Bradshaw, R. A., Burlingame, A. L., From proteins to proteomics. IUBMB Life 2005, 57, 267-272.
22. Plager, D. A., Leontovich, A. A., Henke, S. A., Davis, M. D. et al., Early cutaneous gene transcription changes in adult atopic dermatitis and potential clinical implications. Exp. Dermatol. 2007, 16, 28-36.
23. Nomura, I., Gao, B., Boguniewicz, M., Darst, M. A. et al., 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.
24. Sonkoly, E., Muller, A., Lauerma, A. I., Pivarcsi, A. et al., IL-31: a new link between T cells and pruritus in atopic skin inflammation. J. Allergy Clin. Immunol. 2006, 117, 411-417.
25. de Jongh, G. J., Zeeuwen, P. L., Kucharekova, M., Pfundt, R. et al., High expression levels of keratinocyte antimicrobial proteins in psoriasis compared with atopic dermatitis. J. Invest. Dermatol. 2005, 125, 1163-1173.
26. Olsson, M., Broberg, A., Jernas, M., Carlsson, L. et al., Increased expression of aquaporin 3 in atopic eczema. Allergy 2006, 61, 1132-1137.
27. Park, Y. D., Lyou, Y. J., Lee, K. J., Lee, D. Y. et al., Towards profiling the gene expression of fibroblasts from atopic dermatitis patients: human 8K complementary DNA microarray. Clin. Exp. Allergy 2006, 36, 649-657.
28. Sugiura, H., Ebise, H., Tazawa, T., Tanaka, K. et al., Large-scale DNA microarray analysis of atopic skin lesions shows overexpression of an epidermal differentiation gene cluster in the alternative pathway and lack of protective gene expression in the cornified envelope. Br. J. Dermatol. 2005, 152, 146-149.
29. Nagata, N., Oshida, T., Yoshida, N. L., Yuyama, N. et al., Analysis of highly expressed genes in monocytes from atopic dermatitis patients. Int. Arch. Allergy Immunol. 2003, 132, 156-167.
30. von Bubnoff, D., Matz, H., Frahnert, C., Rao, M. L. et al., FcepsilonRI induces the tryptophan degradation pathway involved in regulating T cell responses. J. Immunol. 2002, 169, 1810-1816.
31. Seo, E. Y., Park, G. T., Lee, K. M., Kim, J. A. et al., Identification of the target genes of atopic dermatitis by real-time PCR. J. Invest. Dermatol. 2006, 126, 1187-1189.
32. Onishi, Y., Kuroda, M., Yasueda, H., Saito, A., et. al., Two-dimensional electrophoresis of Malassezia allergens for atopic dermatitis and isolation of Mal f 4 homologs with mitochondrial malate dehydrogenase. Eur. J. Biochem. 1999, 261, 148-154.
33. Park, Y. D., Lyou, Y. J., Yang, J. M., Two-dimensional electrophoresis analyses of atopic dermatitis and the chances to detect new candidate proteins by the variations in immobilized pH gradient strips. J. Dermatol. Sci. 2007, 47, 9-17.
34. Park, Y. D., Lyou, Y.J., Yang, J. M., Detection of down-regulated acetaldehyde dehydrogenase 1 in atopic dermatitis patients by two-dimensional electrophoresis. Exp. Dermatol. 2007, 16, 130-134.
35. Park, Y. D., Jang, H. S., Kim, S. Y., Ko, S. K. et al., Two-dimensional electrophoretic profiling of atopic dermatitis in primary cultured keratinocytes from patients. Proteomics 2006, 6, 1362-1370.
36. Park, Y. D., Kim, S. Y., Jang, H. S., Seo, E. Y. et al., Towards a proteomic analysis of atopic dermatitis: a two-dimensional-polyacrylamide gel electrophoresis/mass spectrometric analysis of cultured patient-derived fibroblasts. Proteomics 2004, 4, 3446-3455.
37. Yoon, S. W., Kim, T. Y., Sung, M. H., Kim, C. J. et al., Comparative proteomic analysis of peripheral blood easinophils from healthy donors and atopic dermatitis patients with eosinaphilia. Proteomics 2005, 5, 1987-1995.
38. Grone, A., Keratinocytes and cytokines. Vet. Immunol. Immunopathol. 2002, 88, 1-12.
39. Steinhoff, M., Brzoska, T., Luger, T. A., Keratinocytes in epidermal immune responses. Curr. Opin. Allergy Clin. Immunol. 2001, 1, 469-476.
40. Bhave, G., Gereau, R. W., Posttranslational mechanisms of peripheral sensitization. J. Neurobiol. 2004, 61, 88-106.
41. Smith-Beckerman, D. M., Fung, K. W., Williams, K. E., Auersperg, N., et al., Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer. Mol. Cell. Proteomics 2005, 4, 146-168.
42. Tonini, R., Ferroni, A., Valenzuela, S. M., Warton, K., et al., Functional characterization of the NCC27 nuclear protein in stable transfected CHO-K1 cells. FASEB J. 2000, 14, 1171-1178.
43. Valenzuela, S. M., Martin, D. K., Por, S. B., Robbins, J. M., Warton, K. et al., Molecular cloning and expression of a chloride ion channel of cell nuclei. J. Biol. Chem. 1997, 272, 12575-12582.
44. Berryman, M. A., Goldenring, J. R., CLIC4 is enriched at cell-cell junctions and colocalizes with AKAP350 at the centrosome and midbody of cultured mammalian cells. Cell Motil. Cytoskeleton 2003, 56, 159-172.
45. Suh, K. S., Mutoh, M., Nagashima, K., Fernandez-Salas, E. et al., The organellular chloride channel protein CLIC4/mtCLIC translocates to the nucleus in response to cellular stress and accelerates apoptosis. J. Biol. Chem. 2004, 279, 4632-4641.
46. Ronnov-Jessen, L., Villadsen, R., Edwards, J. C., Petersen, O. W., Differential expression of a chloride intracellular channel gene, CLIC4, in transforming growth factor-beta1-mediated conversion of fibroblasts to myofibroblasts. Am. J. Pathol. 2002, 161, 471-480.
47. Radice, P., Pensotti, V., Jones, C., Perry, H., Pierotti, M. A. et al., The human archain gene, ARCN1, has highly conserved homologs in rice and Drosophila. Genomics 1995, 26, 101-106.
48. Tunnacliffe, A., van de Vrugt, H., Pensotti, V., Radice, P., The coatomer protein delta-COP, encoded by the archain gene, is conserved across diverse eukaryotes. Mamm. Genome 1996, 7, 784-786.
49. Onishi, Y., Kuroda, M., Yasueda, H., Saito, A., et al., Two-dimensional electrophoresis of Malassezia allergens for atopic dermatitis and isolation of Mal f 4 homologs with mitochondrial malate dehydrogenase. Eur. J. Biochem. 1999, 261, 148-154.
50. Galter, D., Buervenich, S., Carmine, A. et al., ALDH1 mRNA: presence in human dopamine neurons and decreases in substantia nigra in Parkinson's disease and in the ventral tegmental area in schizophrenia. Neurobiol. Dis. 2003, 14, 637-647.
51. Fan, X., Molotkov, A., Manabe, S. I. et al., Targeted disruption of Aldh1a1 (Raldh1) provides evidence for a complex mechanism of retinoic acid synthesis in the developing retina. Mol. Cell Biol. 2003, 23, 4637-4648.
52. Park, J., Lappe, M., Teichmann, S. A., Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 2001, 307, 929-938.
53. Park, D., Lee, S., Bolser, D., Schroeder, M. et al., Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics 2005, 21, 3234-3240.
54. Gong, S., Yoon, G., Jang, I., Bolser, D. et al., PSIbase: a database of protein structural interactome map (PSIMAP). Bioinformatics 2005, 21, 2541-2543.
55. Murzin, A. G., Brenner, S. E., Hubbard, T., Chothia, C., SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.