Gene-expression signatures in breast cancer

New England Journal of Medicine

Volumn 360, Issue 8, 2009, Pages 790-

  Sotiriou, Christos ^a   Pusztai, Lajos ^b  

^a JULES BORDET INSTITUTE   (Belgium)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRACYCLINE; BIOLOGICAL MARKER; CAPECITABINE; CYCLOPHOSPHAMIDE; DNA; DOCETAXEL; DOXORUBICIN; ESTROGEN RECEPTOR; FLUOROURACIL; LETROZOLE; MESSENGER RNA; METHOTREXATE; PACLITAXEL; TAMOXIFEN; TRASTUZUMAB;

ACCURACY; ADJUVANT THERAPY; BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER CLASSIFICATION; CANCER COMBINATION CHEMOTHERAPY; CANCER GROWTH; CANCER RISK; CANCER STAGING; CELL DIFFERENTIATION; CELL PROLIFERATION; CELL TYPE; CLINICAL ASSESSMENT; CLINICAL FEATURE; CLINICAL TRIAL; DISEASE ASSOCIATION; DNA MICROARRAY; DRUG METABOLISM; DRUG RESPONSE; GENE ACTIVITY; GENE EXPRESSION PROFILING; HORMONAL THERAPY; HUMAN; MORPHOLOGICAL TRAIT; OUTCOME ASSESSMENT; PATIENT CODING; PRIORITY JOURNAL; PROGNOSIS; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RISK ASSESSMENT;

EID: 60849097255     PISSN: 00284793     EISSN: 15334406     Source Type: Journal    
DOI: 10.1056/NEJMra0801289     Document Type: Review

References (90)

1. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747-52.
2. Sorlie 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;98:10869-74.
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 USA 2003;100:8418-23.
4. Sotiriou C, Neo SY, McShane LM, et al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci USA 2003;100:10393-8.
5. Hu Z, Fan C, Oh DS, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006;7:96.
6. Rakha EA, El-Sayed ME, Green AR, et al. Biologic and clinical characteristics of breast cancer with single hormone receptor positive phenotype. J Clin Oncol 2007;25:4772-8.
7. Rakha EA, Tan DS, Foulkes WD, et al. Are triple-negative tumours and basal-like breast cancer synonymous? Breast Cancer Res 2007;9:404.
8. Matros E, Wang ZC, Lodeiro G, Miron A, Iglehart JD, Richardson AL. BRCA1 promoter methylation in sporadic breast tumors: relationship to gene expression profiles. Breast Cancer Res Treat 2005;91:179-86.
9. Turner N, Tutt A, Ashworth A. Hallmarks of 'BRCAness' in sporadic cancers. Nat Rev 2004;4:814-9.
10. Turner NC, Reis-Filho JS, Russell AM, et al. BRCA1 dysfunction in sporadic basal-like breast cancer. Oncogene 2007;26:2126-32.
11. Hedenfalk I, Duggan D, Chen Y, et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001;344:539-48.
12. Liu S, Ginestier C, Charafe-Jauffret E, et al. BRCA1 regulates human mammary stem/progenitor cell fate. Proc Natl Acad Sci U S A 2008;105:1680-5.
13. Foulkes WD, Brunet JS, Stefansson IM, et al. The prognostic implication of the basal-like (cyclin E high/p27 low/p53+/glomeruloid-microvascular- proliferation+) phenotype of BRCA1-related breast cancer. Cancer Res 2004;64:830-5.
14. Foulkes WD, Stefansson IM, Chap-puis PO, et al. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 2003;95:1482-5.
15. Kreike B, van Kouwenhove M, Hor-lings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9:R65.
16. Loi S, Haibe-Kains B, Desmedt C, et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 2007;25:1239-46. [Erratum, J Clin Oncol 2007;25:3790.]
17. Chin K, DeVries S, Fridlyand J, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006;10:529-41.
18. Melchor L, Honrado E, Garcia MJ, et al. Distinct genomic aberration patterns are found in familial breast cancer associated with different immunohistochemical subtypes. Oncogene 2008;27:3165-75.
19. Chin SF, Teschendorff AE, Marioni JC, et al. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007;8:R215.
20. Melchor L, Honrado E, Huang J, et al. Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer. Clin Cancer Res 2007;13:7305-13.
21. Bergamaschi A, Kim YH, Wang P, et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006;45:1033-40.
22. Vincent-Salomon A, Gruel N, Lucchesi C, et al. Identification of typical medullary breast carcinoma as a genomic subgroup of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res 2007;9:R24.
23. Richardson AL, Wang ZC, De Nicolo A, et al. X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell 2006;9:121-32.
24. Wessels LF, van Welsem T, Hart AA, van't Veer LJ, Reinders MJ, Nederlof PM. Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res 2002;62:7110-7.
25. Glinsky GV. Stem cell origin of death-from-cancer phenotypes of human prostate and breast cancers. Stem Cell Rev 2007;3:79-93.
26. Idem. "Sternness" genomics law governs clinical behavior of human cancer: implications for decision making in disease management. J Clin Oncol 2008;26:2846-53.
27. Kakarala M, Wicha MS. Implications of the cancer stem-cell hypothesis for breast cancer prevention and therapy. J Clin Oncol 2008;26:2813-20.
28. Rouzier R, Perou CM, Symmans WF, et al. Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 2005;11:5678-85.
29. 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;347:1999-2009.
30. Farmer P, Bonnefoi H, Becette V, et al. Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 2005;24:4660-71.
31. Doane AS, Danso M, Lal P, et al. An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 2006;25:3994-4008.
32. Ashworth A. A synthetic lethal therapeutic approach: poly(ADP) ribose poly-merase inhibitors for the treatment of cancers deficient in DNA double-strand break repair. J Clin Oncol 2008;26:3785-90.
33. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530-6.
34. Wang Y, Klijn JG, Zhang Y, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005;365:671-9.
35. Foekens JA, Atkins D, Zhang Y, et al. Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol 2006;24:1665-71.
36. Naderi A, Teschendorff AE, Barbosa-Morais NL, et al. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 2007;26:1507-16.
37. Teschendorff AE, Naderi A, Barbosa-Morais NL, et al. A consensus prognostic gene expression classifier for ER positive breast cancer. Genome Biol 2006;7:R101.
38. Chang HY, Nuyten DS, Sneddon JB, et al. Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci USA 2005;102:3738-43.
39. Sotiriou C, Wirapati P, Loi S, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006;98:262-72.
40. Miller LD, Smeds J, George J, et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 2005;102:13550-5.
41. Glinsky GV, Berezovska O, Glinskii AB. Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. J Clin Invest 2005;115:1503-21.
42. Liu R, Wang X, Chen GY, et al. The prognostic role of a gene signature from tumorigenic breast-cancer cells. N Engl J Med 2007;356:217-26.
43. Paik S, Shak S, Tang G, et al. A multi-gene assay to predict recurrence of tamox-ifen-treated, node-negative breast cancer. N Engl J Med 2004;351:2817-26.
44. Ma XJ, Wang Z, Ryan PD, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004;5:607-16.
45. Buyse M, Loi S, van't Veer L, et al. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006;98:1183-92.
46. Bueno-de-Mesquita JM, van Harten WH, Retel VP, et al. Use of 70-gene signature to predict prognosis of patients with node-negative breast cancer: a prospective community-based feasibility study (RASTER). Lancet Oncol 2007;8:1079-87. [Erratum, Lancet Oncol 2008;9:10.]
47. Ma XJ, Salunga R, Tuggle JT, et al. Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003;100:5974-9.
48. Rhodes DR, Yu J, Shanker K, et al. Large-scale meta-analysis of cancer mi-croarray data identifies common transcrip-tional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 2004;101:9309-14.
49. Weinberg RA. Mechanisms of malignant progression. Carcinogenesis 2008;29:1092-5.
50. Dai H, van't Veer L, Lamb J, et al. A cell proliferation signature is a marker of extremely poor outcome in a subpopu-lation of breast cancer patients. Cancer Res 2005;65:4059-66.
51. Ivshina AV, George J, Senko O, et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006;66:10292-301.
52. Oh DS, Troester MA, Usary J, et al. Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers. J Clin Oncol 2006;24:1656-64.
53. Haibe-Kains B, Desmedt C, Piette F, et al. Comparison of prognostic gene expression signatures for breast cancer. BMC Genomics 2008;9:394.
54. Harris L, Fritsche H, Mennel R, et al. American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol 2007;25:5287-312.
55. Habel LA, Shak S, Jacobs MK, et al. A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients. Breast Cancer Res 2006;8:R25.
56. Paik S, Tang G, Shak S, et al. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 2006;24:3726-34.
57. Albain K, Barlow W, Shak S, et al. Prognostic and predictive value of the 21-gene recurrence score assay in postmeno-pausal, node-positive, ER-positive breast cancer (S8814,INT0100). Breast Cancer Res Treat 2007;106:Suppl:S10. abstract.
58. Liang H, Burfsky AM, Lembersky BB, et al. A retrospective analysis of the impact of OncotypeDX low recurrence score results on treatment decisio ns in a single ac ademic breast cancer center. Breast Cancer Res Treat 2007;106:Suppl:S105. abstract.
59. Mumby PB, Lo SS, Norton J, et al. Prospective multicenter study of the impact of the 21-gene recurrence score assay on patient satisfaction, anxiety and decision-al conflict for adjuvant breast cancer treatment selection. Breast Cancer Res Treat 2007;106:Suppl:S73. abstract.
60. Ma XJ, Hilsenbeck SG, Wang W, et al. The HOXB13:IL17BR expression index is a prognostic factor in early-stage breast cancer. J Clin Oncol 2006;24:4611-9.
61. Goetz MP, Suman VJ, Ingle JN, et al. A two-gene expression ratio of homeobox 13 and interleukin-17B receptor for prediction of recurrence and survival in women receiving adjuvant tamoxifen. Clin Cancer Res 2006;12:2080-7.
62. Jansen MP, Sieuwerts AM, Look MP, et al. HOXB13-to-IL17BR expression ratio is related with tumor aggressiveness and response to tamoxifen of recurrent breast cancer: a retrospective study. J Clin Oncol 2007;25:662-8.
63. Ma XJ, Salunga R, Dahiya S, et al. A five-gene molecular grade index and HOXB13:IL17BR are complementary prognostic factors in early stage breast cancer. Clin Cancer Res 2008;14:2601-8.
64. Fan C, Oh DS, Wessels L, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006;355:560-9.
65. Desmedt C, Haibe-Kains B, Wirapati P, et al. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 2008;14:5158-65.
66. Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Bioinformatics 2008;24:2200-8.
67. Wirapati P, Sotiriou C, Kunkel S, et al. Meta-analysis of gene-expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 2008;10:R65.
68. Finak G, Bertos N, Pepin F, et al. Stromal gene expression predicts clinical outcome in breast cancer. Nat Med 2008;14:518-27.
69. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 2006;38:1043-8.
70. Ben-Porath I, Thomson MW, Carey VJ, et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet 2008;40:499-507.
71. Kang Y, Siegel PM, Shu W, et al. A mul-tigenic program mediating breast cancer metastasis to bone. Cancer Cell 2003;3:537-49.
72. Minn AJ, Gupta GP, Siegel PM, et al. Genes that mediate breast cancer metastasis to lung. Nature 2005;436:518-24.
73. Minn AJ, Kang Y, Serganova I, et al. Distinct organ-specific metastatic potential of individual breast cancer cells and primary tumors. J Clin Invest 2005;115:44-55.
74. Schroth W, Antoniadou L, Fritz P, et al. Breast cancer treatment outcome with adjuvant tamoxifen relative to patient CYP2D6 and CYP2C19 genotypes. J Clin Oncol 2007;25:5187-93.
75. Gralow JR, Burstein HJ, Wood W, et al. Preoperative therapy in invasive breast cancer: pathologic assessment and systemic therapy issues in operable disease. J Clin Oncol 2008;26:814-9.
76. Ayers M, Symmans WF, Stec J, et al. Gene expression profiles predict complete pathologic response to neoadjuvant pacli-taxel and fluorouracil, doxorubicin, and cyclophosphamide chemotherapy in breast cancer. J Clin Oncol 2004;22:2284-93.
77. Hess KR, Anderson K, Symmans WF, et al. Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol 2006;24:4236-44.
78. Staunton JE, Slonim DK, Coller HA, et al. Chemosensitivity prediction by tran-scriptional profiling. Proc Natl Acad Sci USA 2001;98:10787-92.
79. Potti A, Dressman HK, Bild A, et al. Genomic signatures to guide the use of chemotherapeutics. Nat Med 2006;12:1294-300. [Errata, Nat Med 2007;13:1388, 2008;14:889.]
80. Lee JK, Havaleshko DM, Cho H, et al. A strategy for predicting the chemosensi-tivity of human cancers and its application to drug discovery. Proc Natl Acad Sci USA 2007;104:13086-91.
81. Bonnefoi H, Potti A, Delorenzi M, et al. Validation of gene signatures that predict the response of breast cancer to neo-adjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. Lancet Oncol 2007;8:1071-8.
82. Ross JS, Hatzis C, Symmans WF, Pusztai L, Hortobagyi GN. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist 2008;13:477-93.
83. Marchionni L, Wilson RF, Wolff AC, et al. Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med 2008;148:358-69.
84. Cardoso F, Van't Veer L, Rutgers E, Loi S, Mook S, Piccart-Gebhart MJ. Clinical application of the 70-gene profile: the MINDACT trial. J Clin Oncol 2008;26:729-35.
85. Sparano JA, Paik S. Development of the 21-gene assay and its application in clinical practice and clinical trials. J Clin Oncol 2008;26:721-8.
86. Hayes DF, Bast RC, Desch CE, et al. Tumor marker utility grading system: a framework to evaluate clinical utility of tumor markers. J Natl Cancer Inst 1996;88:1456-66.
87. Pusztai L, Ayers M, Stec J, et al. Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. Clin Cancer Res 2003;9:2406-15.
88. Symmans WF, Ayers M, Clark EA, et al. Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma. Cancer 2003;97:2960-71.
89. Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007;99:147-57.
90. Pusztai L, Hatzis C, Cardoso F. Combined use of genomic prognostic and treatment response predictors in lymph node-negative breast cancer. J Clin Oncol 2008;26:Suppl:15S. abstract. 801 sbnim@hanmail.net