Gene Expression Patterns and Gene Copy Number Changes in Dermatofibrosarcoma Protuberans

American Journal of Pathology

Volumn 163, Issue 6, 2003, Pages 2383-2395

  Linn, Sabine C ^a   West, Rob B ^a   Pollack, Jonathan R ^a   Zhu, Shirley ^a   Hernandez Boussard, Tina ^b   Nielsen, Torsten O ^d   Rubin, Brian P ^e   Patel, Rajiv ^f   Goldblum, John R ^f   Siegmund, David ^c   Botstein, David ^b   Brown, Patrick O ^b   Gilks, C Blake ^d   Van De Rijn, Matt ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^c STANFORD UNIVERSITY   (United States)

^d VANCOUVER GENERAL HOSPITAL   (Canada)

^e UNIVERSITY OF WASHINGTON MEDICAL CENTER   (United States)

^f LERNER RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLATELET DERIVED GROWTH FACTOR BETA RECEPTOR;

ADULT; AGED; ARTICLE; CHROMOSOME 17Q; CHROMOSOME 22Q; CLINICAL ARTICLE; CONTROLLED STUDY; DERMATOFIBROSARCOMA PROTUBERANS; DNA MICROARRAY; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MALE; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PRIORITY JOURNAL;

EID: 10744220575     PISSN: 00029440     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0002-9440(10)63593-6     Document Type: Article

References (58)

1. Bowne WB, Antonescu CR, Leung DH, Katz SC, Hawkins WG, Woodruff JM, Brennan MF, Lewis JJ: Dermatofibrosarcoma protuberans: a clinicopathologic analysis of patients treated and followed at a single institution Cancer 2000, 88:2711-2720
2. Suit HD, Spiro IJ, Spear M: Benign and low-grade tumors of the soft tissues: role for radiation therapy. Cancer Treat Res 1997, 91:95-105
3. Rubin BP, Schuetze SM, Eary JF, Norwood TH, Mirza S, Conrad EU, Bruckner JD: Molecular targeting of platelet-derived growth factor B by imatinib mesylate in a patient with metastatic dermatofibrosarcoma protuberans. J Clin Oncol 2002, 20:3586-3591
4. Maki RG, Awan RA, Dixon RH, Jhanwar S, Antonescu CR: Differential sensitivity to imatinib of 2 patients with metastatic sarcoma arising from dermatofibrosarcoma protuberans. Int J Cancer 2002, 100: 623-626
5. Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP: Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet 1997, 15:95-98
6. O'Brien KP, Seroussi E, Dal Cin P, Sciot R, Mandahl N, Fletcher JA, Turc-Carel C, Dumanski JP: Various regions within the alpha-helical domain of the COL1A1 gene are fused to the second exon of the PDGFB gene in dermatofibrosarcomas and giant-cell fibroblastomas Genes Chromosomes Cancer 1998, 23:187-193
7. Shimizu A, O'Brien KP, Sjoblom T, Pietras K, Buchdunger E, Collins VP, Heldin CH, Dumanski JP, Ostman A: The dermatofibrosarcoma protuberans-associated collagen type Iα1/platelet-derived growth factor (PDGF) B-chain fusion gene generates a transforming protein that is processed to functional PDGF- BB. Cancer Res 1999, 59: 3719-3723
8. Greco A, Fusetti L, Villa R, Sozzi G, Minoletti F, Mauri P, Pierotti MA: Transforming activity of the chimeric sequence formed by the fusion of collagen gene COL1A1 and the platelet derived growth factor b-chain gene in dermatofibrosarcoma protuberans. Oncogene 1998, 17:1313-1319
9. Nishio J, Iwasaki H, Ohjimi Y, Ishiguro M, Isayama T, Naito M, Kaneko Y, Kikuchi M: Supernumerary ring chromosomes in dermatofibrosarcoma protuberans may contain sequences from 8q11.2-qter and 17q21-qter: a combined cytogenetic and comparative genomic hybridization study. Cancer Genet Cytogenet 2001, 129:102-106
10. Nishio J, Iwasaki H, Ohjimi Y, Ishiguro M, Isayama T, Naito M, Iwashita A, Kikuchi M: Overrepresentation of 17q22-qter and 22q13 in dermatofibrosarcoma protuberans but not in dermatofibroma: a comparative genomic hybridization study. Cancer Genet Cytogenet 2002, 132:102-108
11. Kiuru-Kuhlefelt S, El Rifai W, Fanburg-Smith J, Kere J, Miettinen M, Knuutila S: Concomitant DNA copy number amplification at 17q and 22q in dermatofibrosarcoma protuberans. Cytogenet Cell Genet 2001, 92:192-195
12. Naeem R, Lux ML, Huang SF, Naber SP, Corson JM, Fletcher JA: Ring chromosomes in dermatofibrosarcoma protuberans are composed of interspersed sequences from chromosomes 17 and 22. Am J Pathol 1995, 147:1553-1558
13. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511
14. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I: diversity of gene expression in adenocarcinoma of the lung Proc Natl Acad Sci USA 2001, 98:13784-13789
15. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D: Molecular portraits of human breast tumours. Nature 2000, 406:747-752
16. Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M: Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 2002, 359:1301-1307
17. Allander SV, Illei PB, Chen Y, Antonescu CR, Bittner M, Ladanyi M, Meltzer PS: Expression profiling of synovial sarcoma by cDNA microarrays: association of ERBB2, IGFBP2, and ELF3 with epithelial differentiation. Am J Pathol 2002, 161:1587-1595
18. Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001, 7:673-679
19. Khan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013
20. Allander SV, Nupponen NN, Ringner M, Hostetter G, Maher GW, Goldberger N, Chen Y, Carpten J, Elkahloun AG, Meltzer PS: Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. Cancer Res 2001, 61: 8624-8628
21. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO: Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002, 99:12963-12968
22. Fletcher CD, Dal Cin P, De W, I, Mandahl N, Mertens F, Mitelman F, Rosai J, Rydholm A, Sciot R, Tallini G, van den Berghe H, Vanni R, Willen H: Correlation between clinicopathological features and karyotype in spindle cell sarcomas: a report of 130 cases from the CHAMP study group. Am J Pathol 1999, 154:1841-1847
23. Mitelman F, Johansson B, Mertens F: Mitelman Database of Chromosome Aberrations in Cancer (2003). CGAP Website. 11-26-2002, http://cgap.nci.nih.gov/Chromosomes/
24. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G: The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003, 31:94-96
25. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868
26. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121
27. Aiba S, Tabata N, Ishii H, Ootani H, Tagami H: Dermatofibrosarcoma protuberans is a unique fibrohistiocytic tumour expressing CD34. Br J Dermatol 1992, 127:79-84
28. Natkunam Y, Rouse RV, Zhu S, Fisher C, van de Rijn M: Immunoblot analysis of CD34 expression in histologically diverse neoplasms. Am J Pathol 2000, 156:21-27
29. Gloghini A, Rizzo A, Zanette I, Canal B, Rupolo G, Bassi P, Carbone A: KP1/CD68 expression in malignant neoplasms including lymphomas, sarcomas, and carcinomas. Am J Clin Pathol 1995, 103:425-431
30. Chleq-Deschamps CM, LeBrun DP, Huie P, Besnier DP, Warnke RA, Sibley RK, Cleary ML: Topographical dissociation of BCL-2 messenger RNA and protein expression in human lymphoid tissues. Blood 1993, 81:293-298
31. Siegmund D: Confidence sets in change-point problems. Int Statist Rev 1988, 56:31-48
32. Kempson RL, Fletcher CDM, Evans HE, Hendrickson MR, Sibley RK: Tumors of the soft tissues. Atlas of Tumor Pathology. Edited by J Rosai and LH Sobin. Washington DC, Armed Forces Institute of Pathology, 2001, pp 130-148
33. Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, Sallan SE, Lander ES, Golub TR, Korsmeyer SJ: MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia Nat Genet 2002, 30:41-47
34. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, 415:436-442
35. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein LP, Borresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874
36. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8:816-824
37. Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR: Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002, 1:203-209
38. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM: Delineation of prognostic biomarkers in prostate cancer. Nature 2001, 412:822-826
39. van de Rijn M, Rouse RV: CD34: a review. Appl Immunohistochem 1994, 2:71-80
40. Candia AF, Hu J, Crosby J, Lalley PA, Noden D, Nadeau JH, Wright CV: Mox-1 and Mox-2 define a novel homeobox gene subfamily and are differentially expressed during early mesodermal patterning in mouse embryos. Development 1992, 116:1123-1136
41. Candia AF, Wright CV: Differential localization of Mox-1 and Mox-2 proteins indicates distinct roles during development. Int J Dev Biol 1996, 40:1179-1184
42. Mankoo BS, Collins NS, Ashby P, Grigorieva E, Pevny LH, Candia A, Wright CV, Rigby PW, Pachnis V: Mox2 is a component of the genetic hierarchy controlling limb muscle development. Nature 1999, 400: 69-73
43. Leimeister C, Externbrink A, Klamt B, Gessler M: Hey genes: a novel subfamily of hairy- and enhancer of split related genes specifically expressed during mouse embryogenesis. Mech Dev 1999, 85:173-177
44. Steidl C, Leimeister C, Klamt B, Maier M, Nanda I, Dixon M, Clarke R, Schmid M, Gessler M: Characterization of the human and mouse HEY1, HEY2, and HEYL genes: cloning, mapping, and mutation screening of a new bHLH gene family. Genomics 2000, 66:195-203
45. Bridge JA, Neff JR, Sandberg AA: Cytogenetic analysis of dermatofibrosarcoma protuberans. Cancer Genet Cytogenet 1990, 49:199-202
46. Mandahl N, Heim S, Willen H, Rydholm A, Mitelman F: Supernumerary ring chromosome as the sole cytogenetic abnormality in a dermatofibrosarcoma protuberans. Cancer Genet Cytogenet 1990, 49:273-275
47. Pedeutour F, Coindre JM, Sozzi G, Nicolo G, Leroux A, Toma S, Miozzo M, Bouchot C, Hecht F, Ayraud N: Supernumerary ring chromosomes containing chromosome 17 sequences: a specific feature of dermatofibrosarcoma protuberans? Cancer Genet Cytogenet 1994, 76:1-9
48. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg P-J, Pinkel D, Schroder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, van Dekken H: High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol 2003, 162:763-770
49. Kallioniemi OP, Kallioniemi A, Piper J, Isola J, Waldman FM, Gray JW, Pinkel D: Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer 1994, 10:231-243
50. Jacobs JJ, Keblusek P, Robanus-Maandag E, Kristel P, Lingbeek M, Nederlof PM, van Welsem T, van de Vijver MJ, Koh EY, Daley GQ, van Lohuizen M: Senescence bypass screen identifies TBX2, which represses Cdkn2a (p19(ARF)) and is amplified in a subset of human breast cancers. Nat Genet 2000, 26:291-299
51. Leszczynski D, Joenvaara S, Foegh ML: Protein kinase C-α regulates proliferation but not apoptosis in rat coronary vascular smooth muscle cells. Life Sci 1996, 58:599-606
52. Wang XY, Repasky E, Liu HT: Antisense inhibition of protein kinase Ca reverses the transformed phenotype in human lung carcinoma cells. Exp Cell Res 1999, 250:253-263
53. Ihn H, Tamaki K: Mitogenic activity of dermatofibrosarcoma protuberans is mediated via an extracellular signal related kinase dependent pathway. J Invest Dermatol 2002, 119:954-960
54. Yuen AR, Sikic BI: Clinical studies of antisense therapy in cancer. Front Biosci 2000, 5:D588-D593
55. Nemunaitis J, Holmlund JT, Kraynak M, Richards D, Bruce J, Ognoskie N, Kwoh TJ, Geary R, Dorr A, Von Hoff D, Eckhardt SG: Phase I evaluation of ISIS 3521, an antisense oligodeoxynucleotide to protein kinase C-α, in patients with advanced cancer. J Clin Oncol 1999, 17:3586-3595
56. Cheng AM, Saxton TM, Sakai R, Kulkarni S, Mbamalu G, Vogel W, Tortorice CG, Cardiff RD, Cross JC, Muller WJ, Pawson T: Mammalian Grb2 regulates multiple steps in embryonic development and malignant transformation. Cell 1998, 95:793-803
57. Heldin CH, Ostman A, Ronnstrand L: Signal transduction via platelet-derived growth factor receptors. Biochim Biophys Acta 1998, 1378: F79-F113
58. Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen C-J, Joseph N, Singer S, Griffith DJ, Haley A, Town A, Demetri GD, Fletcher CDM, Fletcher JA: PDGFRA activating mutations in gastrointestinal stromal tumors. Science 2003, 299:708-710