Interrogating differences in expression of targeted gene sets to predict breast cancer outcome

BMC Cancer

Volumn 13, Issue , 2013, Pages

  Andres, Sarah A ^a   Brock, Guy N ^a   Wittliff, James L ^a  

^a UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

Breast cancer; Invasive ductal carcinoma; Prognostic test; Risk of recurrence

Indexed keywords

ACCURACY; ADULT; ARTICLE; BREAST CARCINOMA; CANCER MORTALITY; CANCER RECURRENCE; CANCER TISSUE; ESR1 GENE; EVL GENE; FOLLOW UP; FUT8 GENE; GABRP GENE; GENE EXPRESSION; HUMAN; HUMAN TISSUE; LRBA GENE; MAJOR CLINICAL STUDY; NAT1 GENE; OUTCOME ASSESSMENT; PGR GENE; PREDICTION; PROGNOSIS; PTP4A2 GENE; RABEP1 GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; SCUBE2 GENE; SLC39A6 GENE; TBC1D9 GENE; TUMOR GENE; BREAST TUMOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; KAPLAN MEIER METHOD; MIDDLE AGED; MORTALITY; PAGET NIPPLE DISEASE; PROCEDURES; PROPORTIONAL HAZARDS MODEL;

TRANSCRIPTOME; TUMOR MARKER;

BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KAPLAN-MEIER ESTIMATE; MIDDLE AGED; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL;

EID: 84879828588     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-13-326     Document Type: Article

References (62)

1. Bonner RF, Emmert-Buck M, Cole K, Pohida T, Chuaqui R, Goldstein S, Liotta LA. Laser capture microdissection: molecular analysis of tissue. Science 1997, 278:1481-1483. 10.1126/science.278.5342.1481, 9411767.
2. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. Science 1996, 274:998-1001. 10.1126/science.274.5289.998, 8875945.
3. Wittliff JL, Kunitake ST, Chu SS, Travis JC. Applications of laser capture microdissection in genomics and proteomics. J Clin Ligand Assay 2000, 23:66.
4. Wittliff JL, Erlander MG. Laser capture microdissection and its applications in genomics and proteomics. Methods Enzymol 2002, 356:12-25.
5. Kang Y, Siegel PM, Shu W, Drobnjak M, Kakonen SM, Cordon-Cardo C, Guise TA, Massague J. A multigenic program mediating breast cancer metastasis to bone. Cancer Cell 2003, 3:537-549. 10.1016/S1535-6108(03)00132-6, 12842083.
6. Jansen MP, Foekens JA, van Staveren IL, Dirkzwager-Kiel MM, Ritstier K, Look MP, Meijer-van Gelder ME, Sieuwerts AM, Portengen H, Dorssers LC, Klijn JG, Berns EM. Molecular classification of tamoxifen-resistant breast carcinomas by gene expression profiling. J Clin Oncol 2005, 23:732-740. 10.1200/JCO.2005.05.145, 15681518.
7. Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat Genet 2003, 33:49-54.
8. 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. 10.1073/pnas.191367098, 58566, 11553815.
9. Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET. Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci USA 2003, 100:10393-10398. 10.1073/pnas.1732912100, 193572, 12917485.
10. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536. 10.1038/415530a, 11823860.
11. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679.
12. Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, Zhou YX, Varnholt H, Smith B, Gadd M, Chatfield E, Kessler J, Baer TM, Erlander MG, Sgroi DC. Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003, 100:5974-5979. 10.1073/pnas.0931261100, 156311, 12714683.
13. Ma XJ, Wang W, Salunga R, Tuggle JT, Stecker K, Baer TM, et al. Gene expression associated with clinical outcome in breast cancer via laser capture microdissection. Breast Cancer Res Treat 2003, 82:S15.
14. Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, Tran Y, Tran D, Tassin A, Amon P, Wang W, Wang W, Enright E, Stecker K, Estepa-Sabal E, Smith B, Younger J, Balis U, Michaelson J, Bhan A, Habin K, Baer TM, Brugge J, Haber DA, Erlander MG, Sgroi DC. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004, 5:607-616. 10.1016/j.ccr.2004.05.015, 15193263.
15. Wittliff JL, Ma XJ, Wang W, Salunga R, Tuggle JT, Stecker K, et al. Expression of estrogen receptor-associated genes in breast cancer cells procured by laser capture microdissection. Jensen Symp Abs 2003, 64:81.
16. Cox DR. Regression models and life tables. J R Stat Soc 1972, 34:187-220.
17. Kaplan ELMP. Nonparametric estimation from incomplete observations. J American Statistical Assoc 2012, 53:481.
18. Katz MH, Hauck WW. Proportional hazards (Cox) regression. J Gen Intern Med 1993, 8:702-711. 10.1007/BF02598295, 8120690.
19. Tibshirani R. The lasso method for variable selection in the Cox model. Stat Med 1997, 16:385-395. 10.1002/(SICI)1097-0258(19970228)16:4<385::AID-SIM380>3.0.CO;2-3, 9044528.
20. Wittliff JL, Pasic R, Bland KI. The breast: comprehensive management of benign and malignant diseases 1998, Philadelphia, PA: W.B. Saunders Co.
21. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM. Reporting recommendations for tumor marker prognostic studies. J Clin Oncol 2005, 23:9067-9072. 10.1200/JCO.2004.01.0454, 16172462.
22. Andres SA, Wittliff JL. Co-expression of genes with estrogen receptor-a and progesterone receptor in human breast carcinoma tissue. Horm Mol Biol Clin Investig 2012, 12:377-390.
23. Kerr DA, Wittliff JL. A five-gene model predicts clinical outcome in ER+/PR+, early-stage breast cancers treated with adjuvant tamoxifen. Horm Cancer 2011, 2:261-271. 10.1007/s12672-011-0080-8, 21826535.
24. Wittliff JL, Raffelsberger W. Mechanisms of signal transduction: sex hormones, their receptors and clinical utility. J Clin Ligand Assay 1995, 18:211-235.
25. Hammond ME, Hayes DF, Dowsett M, Allred DC, Hagerty KL, Badve S, Fitzgibbons PL, Francis G, Goldstein NS, Hayes M, Hicks DG, Lester S, Love R, Mangu PB, McShane L, Miller K, Osborne CK, Paik S, Perlmutter J, Rhodes A, Sasano H, Schwartz JN, Sweep FC, Taube S, Torlakovic EE, Valenstein P, Viale G, Visscher D, Wheeler T, Williams RB, et al. American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. J Clin Oncol 2010, 28:2784-2795. 10.1200/JCO.2009.25.6529, 2881855, 20404251.
26. Collett D. Modeling survival data in medical research 2003, Boca Raton, FL: Chapman & Hall/CRC, 2.
27. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple hypothesis testing under dependency. Ann Stat 2001, 29:1165-1188.
28. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 1995, 57:289-300.
29. Dupont WD. Statisical modeling for biomedical researchers: a simple introduction to the analysis of complex data 2002, Cambridge, UK: Cambridge University Press.
30. Austin PC, Tu JV. Automated variable selection methods for logistic regression produced unstable models for predicting acute myocardial infarction mortality. J Clin Epidemiol 2004, 57:1138-1146. 10.1016/j.jclinepi.2004.04.003, 15567629.
31. Harrell FE, Lee KL, Mark DB. Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat Med 1996, 15:361-387. 10.1002/(SICI)1097-0258(19960229)15:4<361::AID-SIM168>3.0.CO;2-4, 8668867.
32. R Development Core Team R: a language and environment for statistical computing 2011, Vienna, Austria: R Foundation for Statisical Computing, R Development Core Team.
33. Thereau T. Survival: survival analysis, including penalised likelihood. 2011, R package version 2.36-10.
34. Goeman JJ. L1 penalized estimation in the Cox proportional hazards model. Biom J 2010, 52:70-84.
35. Harrell FE. Hmisc: Harrell Miscellaneous. 2011, R package version 3.9-0.
36. Pollard KS, Gilbert HN, Ge Y, Taylor S, Dudoit S. Multtest: resampling-based multiple hypothesis testing. 2011, R package version 2.10.0.
37. Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris A, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, Piccart MJ. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006, 98:1183-1192. 10.1093/jnci/djj329, 16954471.
38. Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris AL, Klijn JG, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res 2007, 13:3207-3214. 10.1158/1078-0432.CCR-06-2765, 17545524.
39. Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G, Quackenbush J. breastCancerTRANSBIG. 2011, R package version 1.0.4.
40. McGuire WL, Carbone PP, Vollmer EP. Estrogen receptors in human breast cancer 1975, New York: Raven.
41. DeSombre ER, Carbone PP, Jensen EV, McGuire WL, Wells SA, Wittliff JL, Lipsett MB. Special report. Steriod receptors in breast cancer. N Engl J Med 1979, 301:1011-1012. 10.1056/NEJM197911013011826, 492228.
42. Payne SJ, Bowen RL, Jones JL, Wells CA. Predictive markers in breast cancer-the present. Histopathology 2008, 52:82-90.
43. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826. 10.1056/NEJMoa041588, 15591335.
44. Taylor KM, Morgan HE, Johnson A, Hadley LJ, Nicholson RI. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters. Biochem J 2003, 375:51-59. 10.1042/BJ20030478, 1223660, 12839489.
45. Taylor KM, Morgan HE, Smart K, Zahari NM, Pumford S, Ellis IO, Robertson JF, Nicholson RI. The emerging role of the LIV-1 subfamily of zinc transporters in breast cancer. Mol Med 2007, 13:396-406. 1936980, 17673939.
46. Lue HW, Yang X, Wang R, Qian W, Xu RZ, Lyles R, Osunkoya AO, Zhou BP, Vessella RL, Zayzafoon M, Liu ZR, Zhau HE, Chung LW. LIV-1 promotes prostate cancer epithelial-to-mesenchymal transition and metastasis through HB-EGF shedding and EGFR-mediated ERK signaling. PLoS One 2011, 6:e27720. 10.1371/journal.pone.0027720, 3218022, 22110740.
47. Unno J, Satoh K, Hirota M, Kanno A, Hamada S, Ito H, Masamune A, Tsukamoto N, Motoi F, Egawa S, Unno M, Horii A, Shimosegawa T. LIV-1 enhances the aggressive phenotype through the induction of epithelial to mesenchymal transition in human pancreatic carcinoma cells. Int J Oncol 2009, 35:813-821.
48. Kasper G, Weiser AA, Rump A, Sparbier K, Dahl E, Hartmann A, Wild P, Schwidetzky U, Castanos-Velez E, Lehmann K. Expression levels of the putative zinc transporter LIV-1 are associated with a better outcome of breast cancer patients. Int J Cancer 2005, 117:961-973. 10.1002/ijc.21235, 15986450.
49. Symmans WF, Fiterman DJ, Anderson SK, Ayers M, Rouzier R, Dunmire V, Stec J, Valero V, Sneige N, Albarracin C, Wu Y, Ross JS, Wagner P, Theriault RL, Arun B, Kuerer H, Hess KR, Zhang W, Hortobagyi GN, Pusztai L. A single-gene biomarker identifies breast cancers associated with immature cell type and short duration of prior breastfeeding. Endocr Relat Cancer 2005, 12:1059-1069. 10.1677/erc.1.01051, 16322343.
50. Zafrakas M, Chorovicer M, Klaman I, Kristiansen G, Wild PJ, Heindrichs U, Knuchel R, Dahl E. Systematic characterisation of GABRP expression in sporadic breast cancer and normal breast tissue. Int J Cancer 2006, 118:1453-1459. 10.1002/ijc.21517, 16187283.
51. Wang JW, Gamsby JJ, Highfill SL, Mora LB, Bloom GC, Yeatman TJ, Pan TC, Ramne AL, Chodosh LA, Cress WD, Chen J, Kerr WG. Deregulated expression of LRBA facilitates cancer cell growth. Oncogene 2004, 23:4089-4097. 10.1038/sj.onc.1207567, 15064745.
52. Tozlu S, Girault I, Vacher S, Vendrell J, Andrieu C, Spyratos F, Cohen P, Lidereau R, Bieche I. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach. Endocr Relat Cancer 2006, 13:1109-1120. 10.1677/erc.1.01120, 17158757.
53. Hodzic D, Kong C, Wainszelbaum MJ, Charron AJ, Su X, Stahl PD. TBC1D3, a hominoid oncoprotein, is encoded by a cluster of paralogues located on chromosome 17q12. Genomics 2006, 88:731-736. 10.1016/j.ygeno.2006.05.009, 16863688.
54. Cheng KW, Lahad JP, Gray JW, Mills GB. Emerging role of RAB GTPases in cancer and human disease. Cancer Res 2005, 65:2516-2519. 10.1158/0008-5472.CAN-05-0573, 15805241.
55. Hein DW. Molecular genetics and function of NAT1 and NAT2: role in aromatic amine metabolism and carcinogenesis. Mutat Res 2002, 506-507:65-77.
56. Ragunathan N, Dairou J, Pluvinage B, Martins M, Petit E, Janel N, Dupret JM, Rodrigues-Lima F. Identification of the xenobiotic-metabolizing enzyme arylamine N-acetyltransferase 1 as a new target of cisplatin in breast cancer cells: molecular and cellular mechanisms of inhibition. Mol Pharmacol 2008, 73:1761-1768. 10.1124/mol.108.045328, 18310302.
57. Kim SJ, Kang HS, Chang HL, Jung YC, Sim HB, Lee KS, Ro J, Lee ES. Promoter hypomethylation of the N-acetyltransferase 1 gene in breast cancer. Oncol Rep 2008, 19:663-668.
58. Tiang JM, Butcher NJ, Minchin RF. Small molecule inhibition of arylamine N-acetyltransferase Type I inhibits proliferation and invasiveness of MDA-MB-231 breast cancer cells. Biochem Biophys Res Commun 2010, 393:95-100. 10.1016/j.bbrc.2010.01.087, 20100460.
59. Gui J, Moore JH, Kelsey KT, Marsit CJ, Karagas MR, Andrew AS. A novel survival multifactor dimensionality reduction method for detecting gene-gene interactions with application to bladder cancer prognosis. Hum Genet 2011, 129:101-110. 10.1007/s00439-010-0905-5, 3255326, 20981448.
60. Ishwaran H, Kogalur UB, Blackstone EH, Lauer MS. Random survival forests. Ann Appl Stat 2008, 2:841-860.
61. Wittliff JL, Ma XJ, Stecker KK, Salunga RC, Tuggle JT, Tran YK, et al. Gene expression profiles and tumor marker signatures of human breast carcinoma cells procured by laser capture microdissection. Endocrine Soc Abs 2002, P3-198:538.
62. Wittliff JL, Kruer TL, Andres SA, Smolenkova I. Molecular signatures of estrogen receptor-associated genes in breast cancer predict clinical outcome. Adv Exp Med Biol 2008, 617:349-357. 10.1007/978-0-387-69080-3_33, 18497058.