Homogeneous datasets of triple negative breast cancers enable the identification of novel prognostic and predictive signatures

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Karn, Thomas ^a   Pusztai, Lajos ^b   Holtrich, Uwe ^a   Iwamoto, Takayuki ^b   Shiang, Christine Y ^b   Schmidt, Marcus ^c   Müller, Volkmar ^d   Solbach, Christine ^a   Gaetje, Regine ^a   Hanker, Lars ^a   Ahr, Andre ^a   Liedtke, Cornelia ^e   Ruckhäberle, Eugen ^a   Kaufmann, Manfred ^a   Rody, Achim ^f  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c JOHANNES GUTENBERG UNIVERSITY   (Germany)

^d UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^e UNIVERSITY OF MÜNSTER   (Germany)

^f SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; HEMOGLOBIN; HISTONE; INTERLEUKIN 8; PROGESTERONE RECEPTOR; VASCULOTROPIN; TUMOR MARKER;

ADJUVANT THERAPY; AREA UNDER THE CURVE; ARTICLE; B LYMPHOCYTE; CANCER GRADING; CANCER RECURRENCE; CANCER REGRESSION; COHORT ANALYSIS; CONFIDENCE INTERVAL; CORRELATION ANALYSIS; DISEASE FREE SURVIVAL; EVENT FREE SURVIVAL; GENE; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC DATABASE; HAZARD RATIO; HEMOGLOBIN GENE; HIGH RISK PATIENT; HISTONE GENE; HUMAN; IL8 GENE; IMMUNE RESPONSE; LYMPHOCYTIC INFILTRATION; MICROARRAY ANALYSIS; MULTIVARIATE ANALYSIS; PHENOTYPE; PREDICTION; PROGNOSIS; RECEIVER OPERATING CHARACTERISTIC; RECURRENCE FREE SURVIVAL; STROMA GENE; T LYMPHOCYTE; TREATMENT OUTCOME; TRIPLE NEGATIVE BREAST CANCER; VEGF GENE; BREAST TUMOR; FEMALE; GENE EXPRESSION REGULATION; GENETICS; KAPLAN MEIER METHOD; METABOLISM; PREDICTIVE VALUE; REPRODUCIBILITY; TUMOR GENE;

BREAST NEOPLASMS; COHORT STUDIES; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; KAPLAN-MEIER ESTIMATE; NEOADJUVANT THERAPY; PREDICTIVE VALUE OF TESTS; PROGNOSIS; RECEPTOR, ERBB-2; RECEPTORS, ESTROGEN; RECEPTORS, PROGESTERONE; REPRODUCIBILITY OF RESULTS; TUMOR MARKERS, BIOLOGICAL;

EID: 84855273818     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028403     Document Type: Article

References (61)

1. Goldhirsch A, Wood WC, Coates AS, Gelber RD, Thürlimann B, et al. (2011) Strategies for subtypes-dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011. Ann Oncol 2011 Jun 27. [Epub ahead of print].
2. Kaufmann M, Pusztai L, Biedenkopf Expert Panel Members (2011) Use of standard markers and incorporation of molecular markers into breast cancer therapy: Consensus recommendations from an International Expert Panel. Cancer 117 (8): 1575-82 doi:10.1002/cncr.25660.
3. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. (2000) Molecular portraits of human breast tumours. Nature 406 (6797): 747-52.
4. Sotiriou C, Pusztai L, (2009) Gene-expression signatures in breast cancer. N Engl J Med 60 (8): 790-800.
5. Weigelt B, Mackay A, A'hern R, Natrajan R, Tan DS, et al. (2010) Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol 11 (4): 339-49.
6. Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, et al. (2010) A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res 16 (21): 5222-32.
7. Tabchy A, Valero V, Vidaurre T, Lluch A, Gomez HL, et al. (2010) Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clin Cancer Res 2010 Sep 9. [Epub ahead of print].
8. Foulkes WD, Smith IE, Reis-Filho JS, (2010) Triple-negative breast cancer. N Engl J Med 363 (20): 1938-48.
9. Rody A, Karn T, Liedtke C, Pusztai L, Ruckhaeberle E, et al. (2011) A Clinically Relevant Gene Signature in Triple Negative and Basal Like Breast Cancer. Breast Cancer Res 13 (5): R97.
10. Karn T, Pusztai L, Ruckhäberle E, Liedtke C, Müller V, et al. (2011) Melanoma antigen family A identified by the bimodality index defines a subset of triple negative breast cancers as candidates for immune response augmentation. Eur J Cancer 2011 Jul 7. [Epub ahead of print].
11. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, et al. (2005) Reporting recommendations for tumor marker prognostic studies. J Clin Oncol 23 (36): 9067-72.
12. (2011) The R Project for Statistical Computing. Available: http://www.r-project.org/. Accessed: 2011 Nov 30.
13. Gong Y, Yan K, Lin F, Anderson K, Sotiriou C, et al. (2007) Determination of oestrogen-receptor status and ERBB2 status of breast carcinoma: a gene-expression profiling study. Lancet Oncol 8 (3): 203-11.
14. Karn T, Metzler D, Ruckhäberle E, Hanker L, Gätje R, et al. (2010) Data driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer. Breast Cancer Res Treat 120 (3): 567-79.
15. Affymetrix (2001) Statistical algorithms reference guide, Technical report, Affymetrix.
16. Gautier L, Cope L, Bolstad BM, Irizarry RA, (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20 (3): 307-15.
17. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5 (10): R80.
18. Sabatier R, Finetti P, Cervera N, Lambaudie E, Esterni B, et al. (2011) A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res Treat 126 (2): 407-20.
19. Tusher VG, Tibshirani R, Chu G, (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98 (9): 5116-21.
20. Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, et al. (2005) Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 24 (29): 4660-71.
21. Doane AS, Danso M, Lal P, Donaton M, Zhang L, et al. (2006) An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 25 (28): 3994-4008.
22. Rody A, Holtrich U, Pusztai L, Liedtke C, Gaetje R, et al. (2009) T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Res 11 (2): R15.
23. Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, et al. (2008) Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 14 (16): 5158-65.
24. Schmidt M, Böhm D, von Törne C, Steiner E, Puhl A, et al. (2008) The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res 68 (13): 5405-13.
25. Bianchini G, Qi Y, Alvarez RH, Iwamoto T, Coutant C, et al. (2010) Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and-negative cancers. J Clin Oncol 28 (28): 4316-23.
26. Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, et al. (2009) A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer. Nat Med 15 (1): 68-74.
27. Hennessy BT, Gonzalez-Angulo AM, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, et al. (2009) Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res 69 (10): 4116-24.
28. Creighton CJ, Li X, Landis M, Dixon JM, Neumeister VM, et al. (2009) Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features. Proc Natl Acad Sci U S A 106 (33): 13820-5.
29. Prat A, Parker JS, Karginova O, Fan C, Livasy C, et al. (2010) Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 12 (5): R68.
30. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, et al. (2003) Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A 100 (4): 1896-901.
31. Hu Z, Fan C, Livasy C, He X, Oh DS, et al. (2009) A compact VEGF signature associated with distant metastases and poor outcomes. BMC Med 7: 9.
32. Waugh DJ, Wilson C, (2008) The interleukin-8 pathway in cancer. Clin Cancer Res 14 (21): 6735-41.
33. Angelo LS, Kurzrock R, (2007) Vascular endothelial growth factor and its relationship to inflammatory mediators. Clin Cancer Res 13 (10): 2825-30.
34. Bièche I, Chavey C, Andrieu C, Busson M, Vacher S, et al. (2007) CXC chemokines located in the 4q21 region are up-regulated in breast cancer. Endocr Relat Cancer 14 (4): 1039-52.
35. Paik S, Shak S, Tang G, Kim C, Baker J, et al. (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351 (27): 2817-26.
36. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, et al. (2006) Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98 (4): 262-72.
37. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415 (6871): 530-6.
38. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, et al. (2004) Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2 (2): E7.
39. Teschendorff AE, Miremadi A, Pinder SE, Ellis IO, Caldas C, (2007) An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol 8 (8): R157.
40. Finak G, Bertos N, Pepin F, Sadekova S, Souleimanova M, et al. (2008) Stromal gene expression predicts clinical outcome in breast cancer. Nat Med 14 (5): 518-27.
41. (2011) genefu R package: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. Available: http://www.bioconductor.org/packages/release/bioc/html/genefu.html. Accessed: 2011 Nov 30.
42. Haibe-Kains B, Desmedt C, Rothé F, Piccart M, Sotiriou C, et al. (2010) A fuzzy gene expression-based computational approach improves breast cancer prognostication. Genome Biol 11 (2): R18.
43. Desmedt C, Di Leo A, de Azambuja E, Larsimont D, Haibe-Kains B, et al. (2011) Multifactorial approach to predicting resistance to anthracyclines. J Clin Oncol 29 (12): 1578-86.
44. Ahr A, Karn T, Solbach C, Seiter T, et al. (2002) Identification of high risk breast-cancer patients by gene expression profiling. Lancet 359 (9301): 131-2.
45. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347 (25): 1999-2009.
46. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, et al. (2003) Gene expression predictors of breast cancer outcomes. Lancet 361 (9369): 1590-6.
47. Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck SG, Gutierrez MC, et al. (2003) Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet 362 (9381): 362-9.
48. Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, et al. (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 7 (6): R953-64.
49. Hess KR, Anderson K, Symmans WF, Valero V, Ibrahim N, et al. (2006) Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol 24 (26): 4236-44.
50. Rody A, Karn T, Solbach C, Gaetje R, Munnes M, et al. (2007) The erbB2+ cluster of the intrinsic gene set predicts tumor response of breast cancer patients receiving neoadjuvant chemotherapy with docetaxel, doxorubicin and cyclophosphamide within the GEPARTRIO trial. Breast 16 (3): 235-40.
51. Liu S, Wicha MS, (2010) Targeting breast cancer stem cells. J Clin Oncol 28 (25): 4006-12.
52. Ginestier C, Liu S, Diebel ME, Korkaya H, Luo M, et al. (2010) CXCR1 blockade selectively targets human breast cancer stem cells in vitro and in xenografts. J Clin Invest 120 (2): 485-97.
53. Korkaya H, Liu S, Wicha MS, (2011) Regulation of Cancer Stem Cells by Cytokine Networks: Attacking Cancers Inflammatory Roots. Clin Cancer Res 2011 Jun 17. [Epub ahead of print].
54. Rakha EA, El-Sayed ME, Green AR, Lee AH, Robertson JF, et al. (2007) Prognostic markers in triple-negative breast cancer. Cancer 109 (1): 25-32.
55. Rakha EA, Elsheikh SE, Aleskandarany MA, Habashi HO, Green AR, et al. (2009) Triple-negative breast cancer: distinguishing between basal and nonbasal subtypes. Clin Cancer Res 15 (7): 2302-10.
56. Foulkes WD, Reis-Filho JS, Narod SA, (2010) Tumor size and survival in breast cancer-a reappraisal. Nat Rev Clin Oncol 7 (6): 348-53.
57. Eklund AC, Szallasi Z, (2008) Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol 9 (2): R26.
58. Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, et al. (2011) Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinformatics 12 (1): 310.
59. Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, et al. (2011) Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest 121 (7): 2750-67.
60. Hu Z, Fan C, Oh DS, Marron JS, He X, et al. (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 7: 96.
61. Weigelt B, Mackay A, A'hern R, Natrajan R, Tan DS, et al. (2010) Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol 11 (4): 339-49.