Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes

Breast Cancer Research

Volumn 11, Issue 6, 2009, Pages

  Melchor, Lorenzo ^a,e   Saucedo Cuevas, Laura Paula ^a   Muñoz Repeto, Iván ^a   Rodríguez Pinilla, Socorro María ^a   Honrado, Emiliano ^a   Campoverde, Alfredo ^b   Palacios, Jose ^a   Nathanson, Katherine L ^c   García, María José ^a,d   Benítez, Javier ^a,d  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

^b Institute of Cancer SOLCA   (Ecuador)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^e INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; BRCA1 PROTEIN; CELL MARKER; CYTOKERATIN 5; CYTOKERATIN 6; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; ESTROGEN RECEPTOR; MEMBRANE PROTEIN; MESSENGER RNA; P CADHERIN; PROGESTERONE RECEPTOR; PROTEIN CUL4A; PROTEIN P16; PROTEIN P21; PROTEIN P27; RETINOBLASTOMA PROTEIN; TRANSCRIPTION FACTOR DP1; UNCLASSIFIED DRUG; UVOMORULIN; CUL4A PROTEIN, HUMAN; CULLIN; TFDP1 PROTEIN, HUMAN;

ADULT; ARTICLE; BASAL CELL; BREAST CANCER; BREAST CARCINOGENESIS; CANCER GENETICS; CANCER GRADING; CELL CYCLE PROGRESSION; CHROMOSOME 13; COMPARATIVE GENOMIC HYBRIDIZATION; DNA ISOLATION; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE DOSAGE; GENE LOCATION; GENETIC ANALYSIS; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; TISSUE MICROARRAY; TUMOR GROWTH; BIOSYNTHESIS; BREAST TUMOR; CHROMOSOME ABERRATION; GENETICS; METABOLISM; PATHOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

BREAST NEOPLASMS; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 13; COMPARATIVE GENOMIC HYBRIDIZATION; CULLIN PROTEINS; DNA, NEOPLASM; FEMALE; GENE AMPLIFICATION; HUMANS; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION, FLUORESCENCE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TRANSCRIPTION FACTOR DP1;

EID: 77954614896     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2456     Document Type: Article

References (47)

1. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W, et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 1994, 266:66-71. 10.1126/science.7545954, 7545954.
2. Wooster R, Neuhausen SL, Mangion J, Quirk Y, Ford D, Collins N, Nguyen K, Seal S, Tran T, Averill D, et al. Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science 1994, 265:2088-2090. 10.1126/science.8091231, 8091231.
3. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006, 7:96. 10.1186/1471-2164-7-96, 1468408, 16643655.
4. Perou CM, Sorlie T, Eisen MB, 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. 10.1038/35021093, 10963602.
5. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006, 45:1033-1040. 10.1002/gcc.20366, 16897746.
6. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J, Raffeld M, Yakhini Z, Ben-Dor A, Dougherty E, Kononen J, Bubendorf L, Fehrle W, Pittaluga S, Gruvberger S, Loman N, Johannsson O, Olsson H, Sauter G. Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001, 344:539-548. 10.1056/NEJM200102223440801, 11207349.
7. Jonsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR, Greshock JD, Luts L, Olsson H, Rahman N, Stratton M, Ringner M, Borg A, Weber BL. Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 2005, 65:7612-7621.
8. Lakhani SR, Vijver MJ, Jacquemier J, Anderson TJ, Osin PP, McGuffog L, Easton DF. The pathology of familial breast cancer: predictive value of immunohistochemical markers estrogen receptor, progesterone receptor, HER-2, and p53 in patients with mutations in BRCA1 and BRCA2. J Clin Oncol 2002, 20:2310-2318. 10.1200/JCO.2002.09.023, 11981002.
9. Palacios J, Honrado E, Osorio A, Cazorla A, Sarrio D, Barroso A, Rodriguez S, Cigudosa JC, Diez O, Alonso C, Lerma E, Sanchez L, Rivas C, Benitez J. Immunohistochemical characteristics defined by tissue microarray of hereditary breast cancer not attributable to BRCA1 or BRCA2 mutations: differences from breast carcinomas arising in BRCA1 and BRCA2 mutation carriers. Clin Cancer Res 2003, 9:3606-3614.
10. Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, Nederlof PM. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat 2008,
11. Melchor L, Honrado E, Garcia MJ, Alvarez S, Palacios J, Osorio A, Nathanson KL, Benitez J. Distinct genomic aberration patterns are found in familial breast cancer associated with different immunohistochemical subtypes. Oncogene 2008, 27:3165-3175. 10.1038/sj.onc.1210975, 18071313.
12. Al-Kuraya K, Schraml P, Torhorst J, Tapia C, Zaharieva B, Novotny H, Spichtin H, Maurer R, Mirlacher M, Kochli O, Zuber M, Dieterich H, Mross F, Wilber K, Simon R, Sauter G. Prognostic relevance of gene amplifications and coamplifications in breast cancer. Cancer Res 2004, 64:8534-8540. 10.1158/0008-5472.CAN-04-1945, 15574759.
13. Albertson DG, Snijders AM, Fridlyand J, Jordan R, Pinkel D, Schmidt BL. Genomic analysis of tumors by array comparative genomic hybridization: more is better. Cancer Res 2006, 66:3955-3956. author reply 3956., 10.1158/0008-5472.CAN-05-3611, 16585227.
14. Adelaide J, Finetti P, Bekhouche I, Repellini L, Geneix J, Sircoulomb F, Charafe-Jauffret E, Cervera N, Desplans J, Parzy D, Schoenmakers E, Viens P, Jacquemier J, Birnbaum D, Bertucci F, Chaffanet M. Integrated profiling of basal and luminal breast cancers. Cancer Res 2007, 67:11565-11575. 10.1158/0008-5472.CAN-07-2536, 18089785.
15. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10:529-541. 10.1016/j.ccr.2006.10.009, 17157792.
16. Natrajan R, Lambros MB, Rodriguez-Pinilla SM, Moreno-Bueno G, Tan DS, Marchio C, Vatcheva R, Rayter S, Mahler-Araujo B, Fulford LG, Hungermann D, Mackay A, Grigoriadis A, Fenwick K, Tamber N, Hardisson D, Tutt A, Palacios J, Lord CJ, Buerger H, Ashworth A, Reis-Filho JS. Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin Cancer Res 2009, 15:2711-2722. 10.1158/1078-0432.CCR-08-1878, 19318498.
17. Shinomiya T, Mori T, Ariyama Y, Sakabe T, Fukuda Y, Murakami Y, Nakamura Y, Inazawa J. Comparative genomic hybridization of squamous cell carcinoma of the esophagus: the possible involvement of the DPI gene in the 13q34 amplicon. Genes Chromosomes Cancer 1999, 24:337-344. 10.1002/(SICI)1098-2264(199904)24:4<337::AID-GCC7>3.0.CO;2-O, 10092132.
18. Dohna M, Reincke M, Mincheva A, Allolio B, Solinas-Toldo S, Lichter P. Adrenocortical carcinoma is characterized by a high frequency of chromosomal gains and high-level amplifications. Genes Chromosomes Cancer 2000, 28:145-152. 10.1002/(SICI)1098-2264(200006)28:2<145::AID-GCC3>3.0.CO;2-7, 10824999.
19. Michiels EM, Weiss MM, Hoovers JM, Baak JP, Voute PA, Baas F, Hermsen MA. Genetic alterations in childhood medulloblastoma analyzed by comparative genomic hybridization. J Pediatr Hematol Oncol 2002, 24:205-210. 10.1097/00043426-200203000-00009, 11990307.
20. Yasui K, Arii S, Zhao C, Imoto I, Ueda M, Nagai H, Emi M, Inazawa J. TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in hepatocellular carcinomas. Hepatology 2002, 35:1476-1484. 10.1053/jhep.2002.33683, 12029633.
21. Melchor L, Alvarez S, Honrado E, Palacios J, Barroso A, Diez O, Osorio A, Benitez J. The accumulation of specific amplifications characterizes two different genomic pathways of evolution of familial breast tumors. Clin Cancer Res 2005, 11:8577-8584. 10.1158/1078-0432.CCR-05-1278, 16361540.
22. Abba MC, Fabris VT, Hu Y, Kittrell FS, Cai WW, Donehower LA, Sahin A, Medina D, Aldaz CM. Identification of novel amplification gene targets in mouse and human breast cancer at a syntenic cluster mapping to mouse ch8A1 and human ch13q34. Cancer Res 2007, 67:4104-4112. 10.1158/0008-5472.CAN-06-4672, 17483321.
23. Chen LC, Manjeshwar S, Lu Y, Moore D, Ljung BM, Kuo WL, Dairkee SH, Wernick M, Collins C, Smith HS. The human homologue for the Caenorhabditis elegans cul-4 gene is amplified and overexpressed in primary breast cancers. Cancer Res 1998, 58:3677-3683.
24. Mc Cormack O, Chung WY, Fitzpatrick P, Cooke F, Flynn B, Harrison M, Fox E, Gallagher E, Goldrick AM, Dervan PA, Mc Cann A, Kerin MJ. Growth arrest-specific gene 6 expression in human breast cancer. Br J Cancer 2008, 98:1141-1146. 10.1038/sj.bjc.6604260, 2275480, 18283315.
25. Schindl M, Gnant M, Schoppmann SF, Horvat R, Birner P. Overexpression of the human homologue for Caenorhabditis elegans cul-4 gene is associated with poor outcome in node-negative breast cancer. Anticancer Res 2007, 27:949-952.
26. Yasui K, Okamoto H, Arii S, Inazawa J. Association of over-expressed TFDP1 with progression of hepatocellular carcinomas. J Hum Genet 2003, 48:609-613. 10.1007/s10038-003-0086-3, 14618416.
27. Diez O, Osorio A, Duran M, Martinez-Ferrandis JI, de la Hoya M, Salazar R, Vega A, Campos B, Rodriguez-Lopez R, Velasco E, Chaves J, Diaz-Rubio E, Jesus Cruz J, Torres M, Esteban E, Cervantes A, Alonso C, San Roman JM, Gonzalez-Sarmiento R, Miner C, Carracedo A, Eugenia Armengod M, Caldes T, Benitez J, Baiget M. Analysis of BRCA1 and BRCA2 genes in Spanish breast/ovarian cancer patients: a high proportion of mutations unique to Spain and evidence of founder effects. Hum Mutat 2003, 22:301-312. 10.1002/humu.10260, 12955716.
28. Melchor L, Honrado E, Huang J, Alvarez S, Naylor TL, Garcia MJ, Osorio A, Blesa D, Stratton MR, Weber BL, Cigudosa JC, Rahman N, Nathanson KL, Benitez J. Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer. Clin Cancer Res 2007, 13:7305-7313. 10.1158/1078-0432.CCR-07-0711, 18094411.
29. Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004, 14:179-187. 10.1101/gr.1847304, 314295, 14672980.
30. Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 2005, 33:W616-620. 10.1093/nar/gki500, 1160260, 15980548.
31. Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21:3763-3770. 10.1093/bioinformatics/bti611, 16081473.
32. Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007, 23:657-663. 10.1093/bioinformatics/btl646, 17234643.
33. Honrado E, Osorio A, Palacios J, Milne RL, Sanchez L, Diez O, Cazorla A, Syrjakoski K, Huntsman D, Heikkila P, Lerma E, Kallioniemi A, Rivas C, Foulkes WD, Nevanlinna H, Benitez J. Immunohistochemical expression of DNA repair proteins in familial breast cancer differentiate BRCA2-associated tumors. J Clin Oncol 2005, 23:7503-7511. 10.1200/JCO.2005.01.3698, 16234517.
34. Palacios J, Honrado E, Osorio A, Cazorla A, Sarrio D, Barroso A, Rodriguez S, Cigudosa JC, Diez O, Alonso C, Lerma E, Dopazo J, Rivas C, Benitez J. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res Treat 2005, 90:5-14. 10.1007/s10549-004-1536-0, 15770521.
35. Taron M, Rosell R, Felip E, Mendez P, Souglakos J, Ronco MS, Queralt C, Majo J, Sanchez JM, Sanchez JJ, Maestre J. BRCA1 mRNA expression levels as an indicator of chemoresistance in lung cancer. Hum Mol Genet 2004, 13:2443-2449. 10.1093/hmg/ddh260, 15317748.
36. Roche Applied Science. , http://www.roche-applied-science.com
37. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 2007, 8:R19. 10.1186/gb-2007-8-2-r19, 1852402, 17291332.
38. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006, 6:96. 10.1186/1471-2407-6-96, 1459181, 16620391.
39. Vincent-Salomon A, Gruel N, Lucchesi C, MacGrogan G, Dendale R, Sigal-Zafrani B, Longy M, Raynal V, Pierron G, de Mascarel I, Taris C, Stoppa-Lyonnet D, Pierga JY, Salmon R, Sastre-Garau X, Fourquet A, Delattre O, de Cremoux P, Aurias A. Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res 2007, 9:R24. 10.1186/bcr1666, 1868916, 17417968.
40. Kipreos ET, Lander LE, Wing JP, He WW, Hedgecock EM. cul-1 is required for cell cycle exit in C. elegans and identifies a novel gene family. Cell 1996, 85:829-839. 10.1016/S0092-8674(00)81267-2, 8681378.
41. Gupta A, Yang LX, Chen L. Study of the G2/M cell cycle checkpoint in irradiated mammary epithelial cells overexpressing Cul-4A gene. Int J Radiat Oncol Biol Phys 2002, 52:822-830. 10.1016/S0360-3016(01)02739-0, 11849807.
42. Kotake Y, Zeng Y, Xiong Y. DDB1-CUL4 and MLL1 mediate oncogene-induced p16INK4a activation. Cancer Res 2009, 69:1809-1814. 10.1158/0008-5472.CAN-08-2739, 19208841.
43. Leung-Pineda V, Huh J, Piwnica-Worms H. DDB1 targets Chk1 to the Cul4 E3 ligase complex in normal cycling cells and in cells experiencing replication stress. Cancer Res 2009, 69:2630-2637. 10.1158/0008-5472.CAN-08-3382, 19276361.
44. Miranda-Carboni GA, Krum SA, Yee K, Nava M, Deng QE, Pervin S, Collado-Hidalgo A, Galic Z, Zack JA, Nakayama K, Nakayama KI, Lane TF. A functional link between Wnt signaling and SKP2-independent p27 turnover in mammary tumors. Genes Dev 2008, 22:3121-3134. 10.1101/gad.1692808, 2593606, 19056892.
45. Shan B, Farmer AA, Lee WH. The molecular basis of E2F-1/DP-1-induced S-phase entry and apoptosis. Cell Growth Differ 1996, 7:689-697.
46. Chan JA, Olvera M, Lai R, Naing W, Rezk SA, Brynes RK. Immunohistochemical expression of the transcription factor DP-1 and its heterodimeric partner E2F-1 in non-Hodgkin lymphoma. Appl Immunohistochem Mol Morphol 2002, 10:322-326. 10.1097/00022744-200212000-00006, 12607600.
47. Johnson DG, Cress WD, Jakoi L, Nevins JR. Oncogenic capacity of the E2F1 gene. Proc Natl Acad Sci USA 1994, 91:12823-12827. 10.1073/pnas.91.26.12823, 45532, 7809128.