Signaling networks in cutaneous melanoma metastasis identified by complementary DNA microarrays

Archives of Dermatology

Volumn 141, Issue 2, 2005, Pages 165-173

  Nambiar, Sandeep ^a,c   Mirmohammadsadegh, Alireza ^a   Doroudi, Roya ^a   Gustrau, Annett ^a   Marini, Alessandra ^a   Roeder, Gernot ^b   Ruzicka, Thomas ^a   Hengge, Ulrich R ^a  

^a Heinrich HeineUniversity ^*  (Germany)

^b Oncol Clin Immunol Heinrich H   (Germany)

^c HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; COMPLEMENTARY DNA; GROWTH FACTOR RECEPTOR; GROWTH FACTOR RECEPTOR BOUND PROTEIN 10; MITOGEN ACTIVATED PROTEIN KINASE KINASE; PROTEIN; SCATTER FACTOR RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; CANCER CLASSIFICATION; CELL LINE; CONTROLLED STUDY; DNA MICROARRAY; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; HORMONE PROTEIN COMPLEX; HUMAN; HUMAN CELL; MELANOCYTE; MELANOMA; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTO ONCOGENE; REAL TIME POLYMERASE CHAIN REACTION; RECEPTOR BINDING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; SKIN METASTASIS; UPREGULATION;

CASE-CONTROL STUDIES; CELL LINE, TUMOR; DNA, NEOPLASM; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; JNK MITOGEN-ACTIVATED PROTEIN KINASES; MALE; MELANOMA; NEOPLASM INVASIVENESS; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; SKIN NEOPLASMS; TUMOR MARKERS, BIOLOGICAL; UP-REGULATION;

EID: 13444309138     PISSN: 0003987X     EISSN: None     Source Type: Journal    
DOI: 10.1001/archderm.141.2.165     Document Type: Article

References (71)

1. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed spatially addressable chemical synthesis. Science. 1991;251:767-773.
2. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL. Multiplexed biochemical assays with biological chips. Nature. 1993;364:555-556.
3. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science. 1995;270:467-470.
4. Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996;14:1675-1680.
5. Eickhoff H, Konthur Z, Lueking A, et al. Protein array technology: the tool to bridge genomics and proteomics. Adv Biochem Eng Biotechnol. 2002;77:103-112.
6. Schraml P, Kononen J, Bubendorf L, et al. Tissue microarrays for gene amplification surveys in many different tumor types. Clin Cancer Res. 1999;5:1966-1975.
7. Rao J, Seligson D, Hemstreet GP. Protein expression analysis using quantitative fluorescence image analysis on tissue microarray slides. Biotechniques. 2002;32:924-932.
8. Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation sing comparative genomic hybridization to microarrays. Nat Genet. 1998;20:207-211.
9. Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.
10. Marks R, Whiteman D. Sunburn and melanoma: how strong is the evidence? BMJ. 1994;308:75-76.
11. Whiteman DC, Whiteman CA, Green AC. Childhood sun exposure as a risk factor for melanoma: a systematic review of epidemiologic studies. Cancer Causes Control. 2001;12:69-82.
12. Clark WH Jr, From L, Bernardino EA, Mihm MC. The histogenesis and biologic behavior of primary human malignant melanomas of the skin. Cancer Res. 1969;29:705-727.
13. Breslow A. Thickness, cross-sectional areas and depth of invasion in the prognosis of cutaneous melanoma. Ann Surg. 1970;172:902-908.
14. Breslow A. Tumor thickness, level of invasion and node dissection in stage I cutaneous melanoma. Ann Surg. 1975;182:572-575.
15. Balch CM, Murad TM, Soong SJ, Ingalls AL, Halpern NB, Maddox WA. A multifactorial analysis of melanoma: prognostic histopathological features comparing Clark's and Breslow's staging methods. Ann Surg. 1978;188:732-742.
16. Armstrong SA, Staunton JE, Silverman LB, et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet. 2002;30:41-47.
17. Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531-537.
18. Bittner M, Meltzer P, Chen Y, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000;406:536-540.
19. Bhattacharjee A, Richards WG, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A. 2001;98:13790-13795.
20. Pomeroy SL, Tamayo P, Gaasenbeek M, et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002;415:436-442.
21. Kamb A, Gruis N, Weaver-Feldhaus J, et al. A cell cycle regulator potentially involved in genesis of many tumor types. Science. 1994;264:436-444.
22. Cairns P, Polascik T, Eby Y, et al. Frequency of homozygous deletion at p16/CDKN2 in primary human tumours. Nat Genet. 1995;11:210-212.
23. Sherr CJ. Tumor surveillance via the ARF-p53 pathway. Genes Dev. 1998;12:2984-2991.
24. ARF. J Biol Chem. 2001;276:41424-41434.
25. Walker GJ, Hayward NK. Pathways to melanoma development: lessons from the mouse. J Invest Dermatol. 2002;119:783-792.
26. Bardeesy N, Bastian BC, Hezel A, Pinkel D, DePinho RA, Chin L. Dual inactivation of RB and p53 pathways in RAS-induced melanomas. Mol Cell Biol. 2001;21:2144-2153.
27. Gorden A, Osman I, Gai W, et al. Analysis of BRAF and N-RAS mutations in metastatic melanoma tissues. Cancer Res. 2003;63:3955-3957.
28. Cruz F, Rubin BP, Wilson D, et al. Absence of BRAF and NRAS mutations in uveal melanoma. Cancer Res. 2003;63:5761-5766.
29. Weber A, Hengge UR, Urbanik D, et al. Absence of mutations of the BRAF gene and constitutive activation of extracellular-regulated kinase in malignant melanomas of the uvea. Lab Invest. 2003;83:1771-1776.
30. Clark EA, Golub TR, Lander ES, Hynes RO. Genomic analysis of metastasis reveals an essential role for RhoC. Nature. 2000;406:532-535.
31. Weeraratna AT, Jiang Y, Hostetter G, et al. Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma. Cancer Cell. 2002;1:279-288.
32. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response [published correction appears in Proc Natl Acad Sci U S A. 2001;98:10515] Proc Natl Acad Sci U S A. 2001;98:5116-5121.
33. Dysvik B, Jonassen I. J-Express: exploring gene expression data using Java. Bioinformatics. 2001;17:369-370.
34. SOURCE. Stanford University Web site. Available at: http://source. stanford.edu/cgi-bin/source/sourceSearch. Accessed April 24, 2004.
35. KEGG. Kyoto Encyclopedia of Genes and Genomes. Available at: http://www.genome.jp/kegg/kegg.html. Accessed April 24, 2004.
36. Signaling pathway database. Available at: http://www.grt.kyushu-u.ac.jp/ spad/index.html. Accessed April 24, 2004.
37. Cell signaling networks database. Available at: http://geo.nihs.go.jp/ csndb.html. Accessed April 24, 2004.
38. Human protein reference database. Available at: http://www.hprd.org. Accessed April 24, 2004.
39. Biocarta. Available at: http://www.biocarta.com/genes/allpathways.asp. Accessed April 24, 2004.
40. Furge KA, Zhang YW, Vande Woude GF. Met receptor tyrosine kinase: enhanced signaling through adapter proteins. Oncogene. 2000;19:5582-5589.
41. Jeffers M, Rong S, Woude GF. Hepatocyte growth factor/scatter factor-Met signaling in tumorigenicity and invasion/metastasis. J Mol Med. 1996;74:505-513.
42. Halaban R, Rubin JS, Funasaka Y, et al. Met and hepatocyte growth factor/scatter factor signal transduction in normal melanocytes and melanoma cells. Oncogene. 1992;7:2195-2206.
43. Otsuka T, Takayama H, Sharp R, et al. c-Met autocrine activation induces development of malignant melanoma and acquisition of the metastatic phenotype. Cancer Res. 1998;58:5157-5167.
44. Natali PG, Nicotra MR, Di Renzo MF, et al. Expression of the c-Met/HGF receptor in human melanocytic neoplasms: demonstration of the relationship to malignant melanoma tumour progression. Br J Cancer. 1993;68:746-750.
45. Mirmohammadsadegh A, Baer A, Nambiar S, Bardenheuer W, Hengge UR. Rapid identification of dysregulated genes in cutaneous malignant melanoma metastases using cDNA technology. Cells Tissues Organs. 2004;177:119-123.
46. Ooi J, Yajnik V, Immanuel D, et al. The cloning of Grb10 reveals a new family of SH2 domain proteins. Oncogene. 1995;10:1621-1630.
47. Nantel A, Mohammad-Ali K, Sherk J, Posner BI, Thomas DY. Interaction of the Grb10 adapter protein with the Raf1 and MEK1 kinases. J Biol Chem. 1998; 273:10475-10484.
48. Jahn T, Seipel P, Urschel S, Peschel C, Duyster J. Role for the adaptor protein Grb10 in the activation of Akt. Mol Cell Biol. 2002;22:979-991.
49. Morrione A, Plant P, Valentinis B, et al. mGrb10 interacts with Nedd4. J Biol Chem. 1999;274:24094-24099.
50. O'Neill TJ, Rose DW, Pillay TS, Hotta K, Olefsky JM, Gustafson TA. Interaction of a GRBIR splice variant (a human GRB10 homolog) with the insulin and insulin-like growth factor I receptors: evidence for a role in mitogenic signaling. J Biol Chem. 1996;271:22506-22513.
51. Wang J, Dai H, Yousaf N, et al. Grb10, a positive, stimulatory signaling adapter in platelet-derived growth factor BB-, insulin-like growth factor I-, and insulin-mediated mitogenesis. Mol Cell Biol. 1999;19:6217-6228.
52. Liu F, Roth RA. GrbIR: a SH2-domain-containing protein that binds to the insulin receptor and inhibits its function. Proc Natl Acad Sci U S A. 1995;92:10287-10291.
53. Liu F, Roth RA. Binding of SH2 containing proteins to the insulin receptor: a new way for modulating insulin signalling. Mol Cell Biochem. 1998;182:73-78.
54. Stein EG, Gustafson TA, Hubbard SR. The BPS domain of Grb10 inhibits the catalytic activity of the insulin and IGF1 receptors. FEBS Lett. 2001:493:106-111.
55. Morrione A, Valentinis B, Resnicoff M, Xu S, Baserga R. The role of mGrb10alpha in insulin-like growth factor I-mediated growth. J Biol Chem. 1997;272:26382-26387.
56. Langlais P, Dong LQ, Ramos FJ, et al. Negative regulation of insulin-stimulated mitogen-activated protein kinase signaling by Grb10. Mol Endocrinol. 2003; 18:350-358.
57. Tschentscher F, Husing J, Holter T, et al. Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res. 2003;63:2578-2584.
58. Alonso SR, Ortiz P, Pollan M, et al. Progression in cutaneous malignant melanoma is associated with distinct expression profiles: a tissue microarray-based study. Am J Pathol. 2004;164:193-203.
59. St Croix B, Rago C, Velculescu V, et al. Genes expressed in human tumor endothelium. Science. 2000;289:1197-1202.
60. Macaulay VM, Salisbury AJ, Bohula EA, Playford MP, Smorodinsky NI, Shiloh Y. Downregulation of the type 1 insulin-like growth factor receptor in mouse melanoma cells is associated with enhanced radiosensitivity and impaired activation of Atm kinase. Oncogene. 2001;20:4029-4040.
61. Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000;97:9834-9839.
62. Yang YH, Buckley MJ, Speed TP. Analysis of cDNA microarray images. Brief Bioinform. 2001;2:341-349.
63. DeRisi J, Penland L, Brown PO, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996;14:457-460.
64. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95:14863-14868.
65. Alon U, Barkai N, Notterman DA, et al. Patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A. 1999;96:6745-6750.
66. Chen Y, Dougherty ER, Bittner ML. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J Biomed Opt. 1997;2:367-374.
67. Newton MA, Kenziorski CM, Richmond CS, Blattner FR, Tsui KW. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol. 2001;8:37-52.
68. Antoniadis A, Lambert-Lacroix S, Leblanc F. Effective dimension reduction methods for tumor classification using gene expression data. Bioinformatics. 2003;19:563-570.
69. Kerr MK, Churchill GA. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc Natl Acad Sci U S A. 2001; 98:8961-8965.
70. Chuaqui RF, Bonner RF, Best CJ, et al. Post-analysis follow-up and validation of microarray experiments. Nat Genet. 2002;32:509-514.
71. Rajeevan MS, Ranamukhaarachchi DG, Vernon SD, Unger ER. Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Methods. 2001;25:443-451.