Breast cancer biomarker discovery in the functional genomic age: A systematic review of 42 gene expression signatures

Biomarker Insights

Volumn 2010, Issue 5, 2010, Pages 103-118

  Abba, M C ^a   Lacunza, E ^a   Butti, M ^a   Aldaz, C M ^b  

^a UNIVERSIDAD NACIONAL DE LA PLATA   (Argentina)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Biomarkers; Breast cancer; Gene expression signatures

Indexed keywords

APC PROTEIN; AURORA A KINASE; BACULOVIRAL IAP REPEAT CONTAING 5 PROTEIN; BUB1 RELATED PROTEIN; CELL CYCLE PROTEIN; CELL CYCLE PROTEIN 20; CELL CYCLE PROTEIN 8; CENTROMERE PROTEIN A; CYCLIN A2; CYTIDINE TRIPHOSPHATE SYNTHASE; DNA TOPOISOMERASE (ATP HYDROLYSING); EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR ALPHA; FORKHEAD TRANSCRIPTION FACTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; KINESIN 2; MANGANESE SUPEROXIDE DISMUTASE; MUCIN 1; PROTEIN BCL 2; PROTEIN MAD2; SECURIN; SEPARASE; TRANSCRIPTION FACTOR EZH2; TRANSCRIPTION FACTOR GATA 3; TTK PROTEIN KINASE; TUMOR MARKER; UBIQUITIN CONJUGATING ENZYME E2; UBIQUITIN CONJUGATING ENZYME E2C; UNCLASSIFIED DRUG; X BOX BINDING PROTEIN 1;

BREAST CANCER; CANCER GRADING; CANCER STAGING; CANCER SURVIVAL; CELL CYCLE; CLUSTER ANALYSIS; DATA MINING; DISEASE FREE SURVIVAL; EXTRACELLULAR MATRIX; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; HUMAN; MICROARRAY ANALYSIS; MITOSIS SPINDLE; OVERALL SURVIVAL; PROGNOSIS; REVIEW; SIGNAL TRANSDUCTION; SYSTEMATIC REVIEW; TUMOR VOLUME; UPREGULATION;

EID: 78650555583     PISSN: None     EISSN: 11772719     Source Type: Journal    
DOI: 10.4137/BMI.S5740     Document Type: Review

References (77)

1. Perou CM, Sørlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature. 2000;406(6797):747-752.
2. Sørlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001;98(19):10869-10874.
3. Sorlie T, Tibshirani R, Parker J, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A. 2003;100(14):8418-8423.
4. Weisz A, Basile W, Scafoglio C, et al. Molecular identifcation of ERalpha-positive breast cancer cells by the expression profle of an intrinsic set of estrogen regulated genes. J Cell Physiol. 2004;200(3):440-450.
5. Abba MC, Hu Y, Sun H, et al. Gene expression signature of estrogen receptor alpha status in breast cancer. BMC Genomics. 2005;6(1):37.
6. Sørlie T, Perou CM, Fan C, et al. Gene expression profles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol Cancer Ther. 2006;5(11):2914-2918.
7. Yu J, Yu J, Cordero KE, et al. A transcriptional fngerprint of estrogen in human breast cancer predicts patient survival. Neoplasia. 2008;10(1):79-88.
8. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profl-ing predicts clinical outcome of breast cancer. Nature. 2002;415(6871): 530-536.
9. Glinsky GV, Higashiyama T, Glinskii AB. Classifcation of human breast cancer using gene expression profling as a component of the survival predictor algorithm. Clin Cancer Res. 2004;10(7):2272-2283.
10. Sotiriou C, Pusztai L. Gene-expression signatures in breast cancer. N Engl J Med. 2009;360(8):790-800.
11. Fan C, Oh DS, Wessels L, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med. 2006;355(6):560-569.
12. Ein-Dor L, Kela I, Getz G, Givol D, Domany E. Outcome signature genes in breast cancer: is there a unique set? Bioinformatics. 2005;21(2):171-178.
13. Culhane AC, Schwarzl T, Sultana R, et al. GeneSigDB-a curated database of gene expression signatures. Nucleic Acids Res. 2010;38(Database issue):D716-D725.
14. Saeed AI, Sharov V, White J, et al. TM4: a free, open-source system for microar-ray data management and analysis. Bio Techniques. 2003;34(2):374-378.
15. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57.
16. Jensen LJ, Kuhn M, Stark M. STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009;37(Database issue):D412-D416.
17. van de Vijver MJ, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002;347(25):1999-2009.
18. Shek LL, Godolphin W. Survival with breast cancer: the importance of estrogen receptor quantity. Eur J Cancer Clin Oncol. 1989;25(2):243-250.
19. Sotiriou C, Neo S, McShane LM, et al. Breast cancer classifcation and prognosis based on gene expression profles from a population-based study. Proc Natl Acad Sci. U S A. 2003;100(18):10393-10398.
20. Liu ET, Sotiriou C. Defning the galaxy of gene expression in breast cancer. Breast Cancer Res. 2002;4(4):141-144.
21. Ding L, Yan J, Zhu J, et al. Ligand-independent activation of estrogen receptor alpha by XBP-1. Nucleic Acids Res. 2003;31(18):5266-5274.
22. Wang MM, Traystman RJ, Hurn PD, Liu T. Non-classical regulation of estrogen receptor-alpha by ICI182,780. J Steroid Biochem Mol Biol. 2004;92(1-2):51-62.
23. Carroll JS, Liu XS, Brodsky AS, et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005;122(1):33-43.
24. Eeckhoute J, Keeton EK, Lupien M, et al. Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer. Cancer Res. 2007;67(13):6477-6483.
25. Usary J, Llaca V, Karaca G, et al. Mutation of GATA3 in human breast tumors. Oncogene. 2004;23(46):7669-7678.
26. Parikh P, Palazzo JP, Rose LJ, Daskalakis C, Weigel RJ. GATA-3 expression as a predictor of hormone response in breast cancer. J Am Coll Surg. 2005;200(5):705-710.
27. Abba MC, Nunez MI, Colussi AG, et al. GATA3 protein as a MUC1 transcrip-tional regulator in breast cancer cells. Breast Cancer Res. 2006;8(6):R64.
28. Gendler SJ. MUC1, the renaissance molecule. J Mammary Gland Biol Neoplasia. 2001;6(3):339-353.
29. Raina D, Ahmad R, Joshi MD, et al. Direct targeting of the mucin 1 onco-protein blocks survival and tumorigenicity of human breast carcinoma cells. Cancer Res. 2009;69(12):5133-41.
30. Li Y, Liu D, Chen D, Kharbanda S, Kufe D. Human DF3/MUC1 carcinoma-associated protein functions as an oncogene. Oncogene. 2003;22(38): 6107-6110.
31. Huang L, Chen D, Liu D, et al. MUC1 oncoprotein blocks glycogen syn-thase kinase 3beta-mediated phosphorylation and degradation of beta-catenin. Cancer Res. 2005;65(22):10413-10422.
32. Ahmad R, Raina D, Trivedi V, et al. MUC1 oncoprotein activates the Ikap-paB kinase beta complex and constitutive NF-kappaB signalling. Nat Cell Biol. 2007;9(12):1419-1427.
33. Wei X, Xu H, Kufe D. MUC1 oncoprotein stabilizes and activates estrogen receptor alpha. Mol Cell. 2006;21(2):295-305.
34. Zaretsky JZ, Barnea I, Aylon Y, et al. MUC1 gene overexpressed in breast cancer: structure and transcriptional activity of the MUC1 promoter and role of estrogen receptor alpha (ERalpha) in regulation of the MUC1 gene expression. Mol Cancer. 2006;5:57.
35. Kakar SS. Assignment of the human tumor transforming gene TUTR1 to chromosome band 5q35.1 by fuorescence in situ hybridization. Cytogenet. Cell Genet. 1998;83(1-2):93-95.
36. Ishikawa H, Heaney AP, Yu R, Horwitz GA, Melmed S. Human pituitary tumor-transforming gene induces angiogenesis. J Clin Endocrinol Metab. 2001;86(2):867-874.
37. Solbach C, Roller M, Fellbaum C, Nicoletti M, Kaufmann M. PTTG mRNA expression in primary breast cancer: a prognostic marker for lymph node invasion and tumor recurrence. Breast. 2004;13(1):80-81.
38. Jacobson KK, Morrison LE, Henderson BT, et al. Gene copy mapping of the ERBB2/TOP2 A region in breast cancer. Genes Chromosomes Cancer. 2004;40(1):19-31.
39. Tsunoda N, Kokuryo T, Oda K, et al. Nek2 as a novel molecular target for the treatment of breast carcinoma. Cancer Sci. 2009;100(1):111-116.
40. Fu J, Bian M, Jiang Q, Zhang C. Roles of Aurora kinases in mitosis and tumorigenesis. Mol Cancer Res. 2007;5(1):1-10.
41. Gautschi O, Heighway J, Mack PC, et al. Aurora kinases as anticancer drug targets. Clin Cancer Res. 2008;14(6):1639-1648.
42. Kufer TA, Silljé HHW, Körner R, et al. Human TPX2 is required for targeting Aurora-A kinase to the spindle. J Cell Biol. 2002;158(4):617-623.
43. Wittmann T, Wilm M, Karsenti E, Vernos I. TPX2, A novel xenopus MAP involved in spindle pole organization. J Cell Biol. 2000;149(7):1405-1418.
44. Gruss OJ, Carazo-Salas RE, Schatz CA, et al. Ran induces spindle assembly by reversing the inhibitory effect of importin alpha on TPX2 activity. Cell. 2001;104(1):83-93.
45. Andrews PD. Aurora kinases: shining lights on the therapeutic horizon?. Oncogene. 2005;24(32):5005-5015.
46. Du J, Hannon GJ. Suppression of p160ROCK bypasses cell cycle arrest after Aurora-A/STK15 depletion. Proc Natl Acad Sci USA. 2004;101(24): 8975-8980.
47. Cazales M, Schmitt E, Montembault E, et al. CDC25B phosphorylation by Aurora-A occurs at the G2/M transition and is inhibited by DNA damage. Cell Cycle. 2005;4(9):1233-8.
48. Takaki T, Trenz K, Costanzo V, Petronczki M. Polo-like kinase 1 reaches beyond mitosis-cytokinesis, DNA damage response, and development. Curr. Opin. Cell Biol. 2008;20(6):650-660.
49. Macůrek L, Lindqvist A, Lim D, et al. Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery. Nature. 2008;455(7209):119-123.
50. Rizki A, Mott JD, Bissell MJ. Polo-like kinase 1 is involved in invasion through extracellular matrix. Cancer Res. 2007;67(23):11106-11110.
51. Chopra P, Sethi G, Dastidar SG, Ray A. Polo-like kinase inhibitors: an emerging opportunity for cancer therapeutics. Expert Opin Investig Drugs. 2010;19(1):27-43.
52. Weichert W, Kristiansen G, Winzer K, et al. Polo-like kinase isoforms in breast cancer: expression patterns and prognostic implications. Virchows Arch. 2005;446(4):442-450.
53. Laoukili J, Kooistra MRH, Brás A, et al. FoxM1 is required for execution of the mitotic programme and chromosome stability. Nat Cell Biol. 2005;7(2):126-136.
54. Wang I, Chen Y, Hughes D, et al. Forkhead box M1 regulates the tran-scriptional network of genes essential for mitotic progression and genes encoding the SCF (Skp2-Cks1) ubiquitin ligase. Mol Cell Biol. 2005;25(24):10875-10894.
55. Fu Z, Malureanu L, Huang J, et al. Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression. Nat Cell Biol. 2008;10(9):1076-1082.
56. Teh M, Wong S, Neill GW, et al. FOXM1 is a downstream target of Gli1 in basal cell carcinomas. Cancer Res. 2002;62(16):4773-4780.
57. Wonsey DR, Follettie MT. Loss of the forkhead transcription factor FoxM1 causes centrosome amplifcation and mitotic catastrophe. Cancer Res. 2005;65(12):5181-5189.
58. Strausfeld UP, Howell M, Descombes P, et al. Both cyclin A and cyclin E have S-phase promoting (SPF) activity in Xenopus egg extracts. J Cell Sci. 1996;109(Pt 6):1555-1563.
59. Carroll CW, Silva MCC, Godek KM, Jansen LET, Straight AF. Centromere assembly requires the direct recognition of CENP-A nucleosomes by CENP-N. Nat Cell Biol. 2009;11(7):896-902.
60. O'Brien N, O'Donovan N, Foley D, et al. Use of a panel of novel genes for differentiating breast cancer from non-breast tissues. Tumour Biol. 2007;28(6):312-317.
61. Taylor SS, Ha E, McKeon F. The human homologue of Bub3 is required for kinetochore localization of Bub1 and a Mad3/Bub1-related protein kinase. J Cell Biol. 1998;142(1):1-11.
62. Taylor SS, Hussein D, Wang Y, Elderkin S, Morrow CJ. Kinetochore localisation and phosphorylation of the mitotic checkpoint components Bub1 and BubR1 are differentially regulated by spindle events in human cells. J Cell Sci. 2001;114(Pt 24):4385-4395.
63. Jablonski SA, Chan GK, Cooke CA, Earnshaw WC, Yen TJ. The hBUB1 and hBUBR1 kinases sequentially assemble onto kinetochores during pro-phase with hBUBR1 concentrating at the kinetochore plates in mitosis. Chromosoma. 1998;107(6-7):386-396.
64. Johnson VL, Scott MIF, Holt SV, Hussein D, Taylor SS. Bub1 is required for kinetochore localization of BubR1, Cenp-E, Cenp-F and Mad2, and chromosome congression. J Cell Sci. 2004;117(Pt 8):1577-1589.
65. Yang Z, Guo J, Chen Q, et al. Silencing mitosin induces misaligned chromosomes, premature chromosome decondensation before anaphase onset, and mitotic cell death. Mol Cell Biol. 2005;25(10):4062-4074.
66. Wang H, Hu X, Ding X, et al. Human Zwint-1 specifes localization of Zeste White 10 to kinetochores and is essential for mitotic checkpoint signaling. J Biol Chem. 2004;279(52):54590-54598.
67. Weaver BAA, Bonday ZQ, Putkey FR, et al. Centromere-associated protein-E is essential for the mammalian mitotic checkpoint to prevent ane-uploidy due to single chromosome loss. J Cell Biol. 2003;162(4):551-563.
68. Yuan B, Xu Y, Woo J, et al. Increased expression of mitotic checkpoint genes in breast cancer cells with chromosomal instability. Clin. Cancer Res. 2006;12(2):405-410.
69. Scintu M, Vitale R, Prencipe M, et al. Genomic instability and increased expression of BUB1B and MAD2L1 genes in ductal breast carcinoma. Cancer Lett. 2007;254(2):298-307.
70. Neef R, Preisinger C, Sutcliffe J, et al. Phosphorylation of mitotic kinesin-like protein 2 by polo-like kinase 1 is required for cytokinesis. J Cell Biol. 2003;162(5):863-875.
71. Zhao W, Seki A, Fang G. Cep55, a microtubule-bundling protein, associates with centralspindlin to control the midbody integrity and cell abscission during cytokinesis. Mol Biol Cell. 2006;17(9):3881-3896.
72. Shimo A, Nishidate T, Ohta T, et al. Elevated expression of protein regulator of cytokinesis 1, involved in the growth of breast cancer cells. Cancer Sci. 2007;98(2):174-181.
73. Vendrell JA, Magnino F, Danis E, et al. Estrogen regulation in human breast cancer cells of new downstream gene targets involved in estrogen metabolism, cell proliferation and cell transformation. J Mol Endocrinol. 2004;32(2):397-414.
74. Suzuki T, Urano T, Miki Y, et al. Nuclear cyclin B1 in human breast carcinoma as a potent prognostic factor. Cancer Sci. 2007;98(5):644-651.
75. Payton M, Scully S, Chung G, Coats S. Deregulation of cyclin E2 expression and associated kinase activity in primary breast tumors. Oncogene. 2002;21(55):8529-8534.
76. Ha S, Shin SM, Namkoong H, et al. Cancer-associated expression of minichromosome maintenance 3 gene in several human cancers and its involvement in tumorigenesis. Clin Cancer Res. 2004;10(24):8386-8395.
77. Reena RMZ, Mastura M, Siti-Aishah MA, et al. Minichromosome maintenance protein 2 is a reliable proliferative marker in breast carcinoma. Ann Diagn Pathol. 2008;12(5):340-343.