Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH
Tóm tắt
Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail. We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6. ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets.
Tài liệu tham khảo
Schutte BC, Carpten JD, Forus A, Gregory SG, Horii A, White PS: Report and abstracts of the sixth international workshop on human chromosome 1 mapping 2000. Cytogenet Cell Genet. 2001, 92 (1-2): 23-48. 10.1159/000056867
Szymanska J, Tarkkanen M, Wiklund T, Virolainen M, Blomqvist C, Asko-Seljavaara S, Tukiainen E, Elomaa I, Knuutila S: Gains and losses of DNA sequences in liposarcomas evaluated by comparative genomic hybridization. Genes Chromosomes Cancer. 1996, 15 (2): 89-94. 10.1002/(SICI)1098-2264(199602)15:2<89::AID-GCC2>3.0.CO;2-#
Forus A, Weghuis DO, Smeets D, Fodstad O, Myklebost O, van Kessel AG: Comparative genomic hybridization analysis of human sarcomas: I. Occurrence of genomic imbalances and identification of a novel major amplicon at 1q21-q22 in soft tissue sarcomas. Genes Chromosomes Cancer. 1995, 14 (1): 8-14.
Forus A, Weghuis DO, Smeets D, Fodstad O, Myklebost O, van Kessel AG: Comparative genomic hybridization analysis of human sarcomas: II. Identification of novel amplicons at 6p and 17p in osteosarcomas. Genes Chromosomes Cancer. 1995, 14 (1): 15-21.
Enzinger FM, Weiss SW: Soft tissue tumors. 1995, St. Louis, Mosby, 3rd.
Oliner JD, Kinzler KW, Meltzer PS, George DL, Vogelstein B: Amplification of a gene encoding a p53-associated protein in human sarcomas. Nature. 1992, 358 (6381): 80-83. 10.1038/358080a0
Khatib ZA, Matsushime H, Valentine M, Shapiro DN, Sherr CJ, Look AT: Coamplification of the CDK4 gene with MDM2 and GLI in human sarcomas. Cancer Res. 1993, 53 (22): 5535-5541.
Wong N, Lai P, Lee SW, Fan S, Pang E, Liew CT, Sheng Z, Lau JW, Johnson PJ: Assessment of genetic changes in hepatocellular carcinoma by comparative genomic hybridization analysis: relationship to disease stage, tumor size, and cirrhosis. Am J Pathol. 1999, 154 (1): 37-43.
Zimonjic DB, Keck CL, Thorgeirsson SS, Popescu NC: Novel recurrent genetic imbalances in human hepatocellular carcinoma cell lines identified by comparative genomic hybridization. Hepatology. 1999, 29 (4): 1208-1214. 10.1002/hep.510290410
Gronwald J, Storkel S, Holtgreve-Grez H, Hadaczek P, Brinkschmidt C, Jauch A, Lubinski J, Cremer T: Comparison of DNA gains and losses in primary renal clear cell carcinomas and metastatic sites: importance of 1q and 3p copy number changes in metastatic events. Cancer Res. 1997, 57 (3): 481-487.
Qin LX, Tang ZY, Sham JS, Ma ZC, Ye SL, Zhou XD, Wu ZQ, Trent JM, Guan XY: The association of chromosome 8p deletion and tumor metastasis in human hepatocellular carcinoma. Cancer Res. 1999, 59 (22): 5662-5665.
Tarkkanen M, Elomaa I, Blomqvist C, Kivioja AH, Kellokumpu-Lehtinen P, Bohling T, Valle J, Knuutila S: DNA sequence copy number increase at 8q: a potential new prognostic marker in high-grade osteosarcoma. Int J Cancer. 1999, 84 (2): 114-121. 10.1002/(SICI)1097-0215(19990420)84:2<114::AID-IJC4>3.0.CO;2-Q
Hirai M, Yoshida S, Kashiwagi H, Kawamura T, Ishikawa T, Kaneko M, Ohkawa H, Nakagawara A, Miwa M, Uchida K: 1q23 gain is associated with progressive neuroblastoma resistant to aggressive treatment. Genes Chromosomes Cancer. 1999, 25 (3): 261-269. 10.1002/(SICI)1098-2264(199907)25:3<261::AID-GCC8>3.0.CO;2-#
Pedeutour F, Forus A, Coindre JM, Berner JM, Nicolo G, Michiels JF, Terrier P, Ranchere-Vince D, Collin F, Myklebost O, Turc-Carel C: Structure of the supernumerary ring and giant rod chromosomes in adipose tissue tumors. Genes Chromosomes Cancer. 1999, 24 (1): 30-41. 10.1002/(SICI)1098-2264(199901)24:1<30::AID-GCC5>3.0.CO;2-P
Larramendy ML, Virolainen M, Tukiainen E, Elomaa I, Knuutila S: Chromosome band 1q21 is recurrently gained in desmoid tumors. Genes Chromosomes Cancer. 1998, 23 (2): 183-186. 10.1002/(SICI)1098-2264(199810)23:2<183::AID-GCC12>3.0.CO;2-P
Forus A, Berner JM, Meza-Zepeda LA, Saeter G, Mischke D, Fodstad O, Myklebost O: Molecular characterization of a novel amplicon at 1q21-q22 frequently observed in human sarcomas. Br J Cancer. 1998, 78 (4): 495-503.
Meza-Zepeda LA, Forus A, Lygren B, Dahlberg AB, Godager LH, South AP, Marenholz I, Lioumi M, Florenes VA, Maelandsmo GM, Serra M, Mischke D, Nizetic D, Ragoussis J, Tarkkanen M, Nesland JM, Knuutila S, Myklebost O: Positional cloning identifies a novel cyclophilin as a candidate amplified oncogene in 1q21. Oncogene. 2002, 21 (14): 2261-2269. 10.1038/sj.onc.1205339
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic Acids Res. 2002, 30 (1): 38-41. 10.1093/nar/30.1.38
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006. 10.1101/gr.229102. Article published online before print in May 2002
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA: ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003, 31 (1): 68-71. 10.1093/nar/gkg091
Fauman EB, Saper MA: Structure and function of the protein tyrosine phosphatases. Trends Biochem Sci. 1996, 21 (11): 413-417. 10.1016/S0968-0004(96)10059-1
Park HD, Beeser AE, Clancy MJ, Cooper TG: The S. cerevisiae nitrogen starvation-induced Yvh1p and Ptp2p phosphatases play a role in control of sporulation. Yeast. 1996, 12 (11): 1135-1151. 10.1002/(SICI)1097-0061(19960915)12:11<1135::AID-YEA11>3.0.CO;2-L
Guan K, Hakes DJ, Wang Y, Park HD, Cooper TG, Dixon JE: A yeast protein phosphatase related to the vaccinia virus VH1 phosphatase is induced by nitrogen starvation. Proc Natl Acad Sci U S A. 1992, 89 (24): 12175-12179.
Hanaoka N, Umeyama T, Ueno K, Ueda K, Beppu T, Fugo H, Uehara Y, Niimi M: A putative dual-specific protein phosphatase encoded by YVH1 controls growth, filamentation and virulence in Candida albicans. Microbiology. 2005, 151: 2223-2232. 10.1099/mic.0.27999-0
Muda M, Manning ER, Orth K, Dixon JE: Identification of the human YVH1 protein-tyrosine phosphatase orthologue reveals a novel zinc binding domain essential for in vivo function. J Biol Chem. 1999, 274 (34): 23991-23995. 10.1074/jbc.274.34.23991
Sakumoto N, Yamashita H, Mukai Y, Kaneko Y, Harashima S: Dual-specificity protein phosphatase Yvh1p, which is required for vegetative growth and sporulation, interacts with yeast pescadillo homolog in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2001, 289 (2): 608-615. 10.1006/bbrc.2001.6021
Kumar R, Musiyenko A, Cioffi E, Oldenburg A, Adams B, Bitko V, Krishna SS, Barik S: A zinc-binding dual-specificity YVH1 phosphatase in the malaria parasite, Plasmodium falciparum, and its interaction with the nuclear protein, pescadillo. Mol Biochem Parasitol. 2004, 133 (2): 297-310. 10.1016/j.molbiopara.2003.11.005
Kinoshita Y, Jarell AD, Flaman JM, Foltz G, Schuster J, Sopher BL, Irvin DK, Kanning K, Kornblum HI, Nelson PS, Hieter P, Morrison RS: Pescadillo, a novel cell cycle regulatory protein abnormally expressed in malignant cells. J Biol Chem. 2001, 276 (9): 6656-6665. 10.1074/jbc.M008536200
Lerch-Gaggl A, Haque J, Li J, Ning G, Traktman P, Duncan SA: Pescadillo is essential for nucleolar assembly, ribosome biogenesis, and mammalian cell proliferation. J Biol Chem. 2002, 277 (47): 45347-45355. 10.1074/jbc.M208338200
Hai T, Hartman MG: The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis. Gene. 2001, 273 (1): 1-11. 10.1016/S0378-1119(01)00551-0
Wang XZ, Lawson B, Brewer JW, Zinszner H, Sanjay A, Mi LJ, Boorstein R, Kreibich G, Hendershot LM, Ron D: Signals from the stressed endoplasmic reticulum induce C/EBP-homologous protein (CHOP/GADD153). Mol Cell Biol. 1996, 16 (8): 4273-4280.
Aman P, Ron D, Mandahl N, Fioretos T, Heim S, Arheden K, Willen H, Rydholm A, Mitelman F: Rearrangement of the transcription factor gene CHOP in myxoid liposarcomas with t(12;16)(q13;p11). Genes Chromosomes Cancer. 1992, 5 (4): 278-285.
Forus A, Florenes VA, Maelandsmo GM, Fodstad O, Myklebost O: The protooncogene CHOP/GADD153, involved in growth arrest and DNA damage response, is amplified in a subset of human sarcomas. Cancer Genet Cytogenet. 1994, 78 (2): 165-171. 10.1016/0165-4608(94)90085-X
Yoshida H, Haze K, Yanagi H, Yura T, Mori K: Identification of the cis-acting endoplasmic reticulum stress response element responsible for transcriptional induction of mammalian glucose-regulated proteins. Involvement of basic leucine zipper transcription factors. J Biol Chem. 1998, 273 (50): 33741-33749. 10.1074/jbc.273.50.33741
Haze K, Yoshida H, Yanagi H, Yura T, Mori K: Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress. Mol Biol Cell. 1999, 10 (11): 3787-3799.
Little E, Ramakrishnan M, Roy B, Gazit G, Lee AS: The glucose-regulated proteins (GRP78 and GRP94): functions, gene regulation, and applications. Crit Rev Eukaryot Gene Expr. 1994, 4 (1): 1-18.
Lee AS: The glucose-regulated proteins: stress induction and clinical applications. Trends Biochem Sci. 2001, 26 (8): 504-510. 10.1016/S0968-0004(01)01908-9
Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ: A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001, 11 (3): 483-496. 10.1101/gr.169601
Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP: DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer. 2003, 36 (4): 361-374. 10.1002/gcc.10155
Forus A, Florenes VA, Maelandsmo GM, Meltzer PS, Fodstad O, Myklebost O: Mapping of amplification units in the q13-14 region of chromosome 12 in human sarcomas: some amplica do not include MDM2. Cell Growth Differ. 1993, 4 (12): 1065-1070.
Wang J, Meza-Zepeda LA, Kresse SH, Myklebost O: M-CGH: Analysing microarray-based CGH experiments. BMC Bioinformatics. 2004, 5 (1): 74- 10.1186/1471-2105-5-74
Lennon G, Auffray C, Polymeropoulos M, Soares MB: The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics. 1996, 33 (1): 151-152. 10.1006/geno.1996.0177
Rogne S, Myklebost O, Hoyheim B, Olaisen B, Gedde-Dahl TJ: The genes for apolipoprotein all (APOA2) and the Duffy blood group (FY) are linked on chromosome 1 in man. Genomics. 1989, 4 (2): 169-173. 10.1016/0888-7543(89)90296-6
Huang LS, Bock SC, Feinstein SI, Breslow JL: Human apolipoprotein B cDNA clone isolation and demonstration that liver apolipoprotein B mRNA is 22 kilobases in length. Proc Natl Acad Sci U S A. 1985, 82 (20): 6825-6829.
Simons A, Schepens M, Jeuken J, Sprenger S, van de Zande G, Bjerkehagen B, Forus A, Weibolt V, Molenaar I, van den Berg E, Myklebost O, Bridge J, van Kessel AG, Suijkerbuijk R: Frequent loss of 9p21 (p16(INK4A)) and other genomic imbalances in human malignant fibrous histiocytoma. Cancer Genet Cytogenet. 2000, 118 (2): 89-98. 10.1016/S0165-4608(99)00178-8
Parente F, Grosgeorge J, Coindre JM, Terrier P, Vilain O, Turc-Carel C: Comparative genomic hybridization reveals novel chromosome deletions in 90 primary soft tissue tumors. Cancer Genet Cytogenet. 1999, 115 (2): 89-95. 10.1016/S0165-4608(99)00082-5