Gene expression profiling in breast cancer: A clinical perspective

Breast

Volumn 22, Issue 2, 2013, Pages 109-120

  Arpino, Grazia ^a   Generali, Daniele ^h   Sapino, Anna ^b   Lucia, Del Matro ^c   Frassoldati, Antonio ^d   de Laurentis, Michelino ^a   Paolo, Pronzato ^c   Mustacchi, Giorgio ^e   Cazzaniga, Marina ^f   De Placido, Sabino ^a   Conte, Pierfranco ^d   Cappelletti, Mariarosa ^g,h   Zanoni, Vanessa ^g,h   Antonelli, Andrea ^g,h   Martinotti, Mario ^h   Puglisi, Fabio ^g   Berruti, Alfredo ^b   Bottini, Alberto ^h   Dogliotti, Luigi ^b  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF TURIN   (Italy)

^c UNIVERSITY OF GENOA   (Italy)

^d UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^e UNIVERSITY OF TRIESTE   (Italy)

^f SAN GERARDO HOSPITAL   (Italy)

^g UNIVERSITY HOSPITAL OF UDINE   (Italy)

^h CREMONA HOSPITAL   (Italy)

Author keywords

Breast cancer; Gene arrays; Gene profiles; Prognostic factors

Indexed keywords

ANASTROZOLE; ANTHRACYCLINE DERIVATIVE; AURORA A KINASE; BAG 1 PROTEIN; CD68 ANTIGEN; CYCLOPHOSPHAMIDE; DOXORUBICIN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; EXEMESTANE; FLUOROURACIL; GLUTATHIONE TRANSFERASE M1; GROWTH FACTOR RECEPTOR BOUND PROTEIN 7; KI 67 ANTIGEN; MESSENGER RNA; METHOTREXATE; PACLITAXEL; PLACEBO; PROGESTERONE RECEPTOR; PROTEIN BCL 2; PROTEIN P53; STROMELYSIN 3; SURVIVIN; TAMOXIFEN; TAXANE DERIVATIVE;

BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER CHEMOTHERAPY; CANCER GRADING; CANCER HORMONE THERAPY; CANCER PROGNOSIS; CANCER RECURRENCE; CELERA METASTASIS SCORE; CLASSIFIER; DIAGNOSTIC TEST; DISEASE FREE SURVIVAL; DISTANT METASTASIS; DISTANT METASTASIS FREE SURVIVAL; ESTROGEN RECEPTOR POSITIVE BREAST CANCER; GENE; GENE EXPRESSION PROFILING; GENOMICS; HIGH RISK PATIENT; HOXB13 GENE; HUMAN; IMMUNOHISTOCHEMISTRY; INTERLEUKIN 17B RECEPTOR GENE; PERSONALIZED MEDICINE; POSTMENOPAUSE; PREDICTIVE VALUE; PREMENOPAUSE; PRIORITY JOURNAL; PROGRESSION FREE SURVIVAL; RECURRENCE FREE SURVIVAL; RECURRENCE RISK; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RISK ASSESSMENT; SCORING SYSTEM;

EID: 84875534675     PISSN: 09609776     EISSN: 15323080     Source Type: Journal    
DOI: 10.1016/j.breast.2013.01.016     Document Type: Review

References (74)

1. Olivotto I.A., Bajdik C.D., Ravdin P.M., Speers C.H., Coldman A.J., Norris B.D., et al. Population-based validation of the prognostic model ADJUVANT! for early breast cancer. J Clin Oncol 2005, 23(12):2716-2725.
2. Ravdin P.M., Siminoff L.A., Davis G.J., Mercer M.B., Hewlett J., Gerson N., et al. Computer program to assist in making decisions about adjuvant therapy for women with early breast cancer. J Clin Oncol 2001, 19(4):980-991.
3. Eifel P., Axelson J.A., Costa J., Crowley J., Curran W.J., Deshler A., et al. National Institutes of Health Consensus Development Conference Statement: adjuvant therapy for breast cancer, November 1-3, 2000. J Natl Cancer Inst 2001, 93(13):979-989.
4. Harris L., Fritsche H., Mennel R., Norton L., Ravdin P., Taube S., 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(33):5287-5312. American Society of Clinical Oncology.
5. Goldhirsch A., Ingle J.N., Gelber R.D., Coates A.S., Thurlimann B., Senn H.J. Thresholds for therapies: highlights of the St Gallen International Expert Consensus on the primary therapy of early breast cancer 2009. Ann Oncol 2009, 20(8):1319-1329. Panel members.
6. Perou C.M., Sorlie T., Eisen M.B., van de Rijn M., Jeffrey S.S., Rees C.A., et al. Molecular portraits of human breast tumours. Nature 2000, 406(6797):747-752.
7. van 't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415(6871):530-536.
8. Paik S., Shak S., Tang G., Kim C., Baker J., Cronin M., et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351(27):2817-2826.
9. Sotiriou C., Wirapati P., Loi S., Harris A., Fox S., Smeds J., et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006, 98(4):262-272.
10. Rouzier R., Perou C.M., Symmans W.F., Ibrahim N., Cristofanilli M., Anderson K., et al. Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 2005, 11(16):5678-5685.
11. Wirapati P., Sotiriou C., Kunkel S., Farmer P., Pradervand S., Haibe-Kains B., 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(4):R65.
12. Sotiriou C., Pusztai L. Gene-expression signatures in breast cancer. N Engl J Med 2009, 360(8):790-800.
13. Sorlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., Johnsen H., 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.
14. Recommendations from the EGAPP Working Group: can tumor gene expression profiling improve outcomes in patients with breast cancer?. Genet Med 2009, 11(1):66-73.
15. van de Vijver M.J., He Y.D., van't Veer L.J., Dai H., Hart A.A., Voskuil D.W., et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347(25):1999-2009.
16. Buyse M., Loi S., van't Veer L., Viale G., Delorenzi M., Glas A.M., 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(17):1183-1192.
17. Bueno-de-Mesquita J.M., Linn S.C., Keijzer R., Wesseling J., Nuyten D.S., van Krimpen C., et al. Validation of 70-gene prognosis signature in node-negative breast cancer. Breast Cancer Res Treat 2009, 117(3):483-495.
18. Wittner B.S., Sgroi D.C., Ryan P.D., Bruinsma T.J., Glas A.M., Male A., et al. Analysis of the MammaPrint breast cancer assay in a predominantly postmenopausal cohort. Clin Cancer Res 2008, 14(10):2988-2993.
19. Mook S., Schmidt M.K., Viale G., Pruneri G., Eekhout I., Floore A., et al. The 70-gene prognosis-signature predicts disease outcome in breast cancer patients with 1-3 positive lymph nodes in an independent validation study. Breast Cancer Res Treat 2009, 116(2):295-302.
20. Mook S., Schmidt M.K., Weigelt B., Kreike B., Eekhout I., van de Vijver M.J., et al. The 70-gene prognosis signature predicts early metastasis in breast cancer patients between 55 and 70 years of age. Ann Oncol 2010, 21(4):717-722.
21. Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 2005, 365(9472):1687-1717.
22. Ravdin P. Overview of randomized trials of systemic adjuvant therapy. Cancer Treat Res 2008, 141:55-62.
23. Bender R.A.K.M., Rutgers E.J., Glas A.M., de Snoo F.A., Linn S.C., et al. The 70-gene profile and chemotherapy benefit in 1,600 breast cancer patients. J Clin Oncol 2009, 27:15S. [abstr 512].
24. Knauer M.S.M., Rutgers E.J.T., Bender R.A., Cardoso F., Mook S., et al. The 70-gene MammaPrint signature is predictive for chemotherapy benefit in early breast cancer. The Breast 2009, 18:S36e7.
25. Glas A.M., Floore A., Delahaye L.J., Witteveen A.T., Pover R.C., Bakx N., et al. Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 2006, 7:278.
26. Ach R.A., Floore A., Curry B., Lazar V., Glas A.M., Pover R., et al. Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools. BMC Genomics 2007, 8:148.
27. Cronin M., Pho M., Dutta D., Stephans J.C., Shak S., Kiefer M.C., et al. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol 2004, 164(1):35-42.
28. Cobleigh M.A., Tabesh B., Bitterman P., Baker J., Cronin M., Liu M.L., et al. Tumor gene expression and prognosis in breast cancer patients with 10 or more positive lymph nodes. Clin Cancer Res 2005, 11(24 Pt 1):8623-8631.
29. Cronin M., Sangli C., Liu M.L., Pho M., Dutta D., Nguyen A., et al. Analytical validation of the Oncotype DX genomic diagnostic test for recurrence prognosis and therapeutic response prediction in node-negative, estrogen receptor-positive breast cancer. Clin Chem 2007, 53(6):1084-1091.
30. Esteva F.J., Sahin A.A., Cristofanilli M., Coombes K., Lee S.J., Baker J., et al. Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy. Clin Cancer Res 2005, 11(9):3315-3319.
31. Habel L.A., Shak S., Jacobs M.K., Capra A., Alexander C., Pho M., 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(3):R25.
32. Dowsett M.C.J., Wales C., Forbes J., Mallon L., Salter J., et al. Risk of distant recurrence using Oncotype DX in postmenopausal primary breast cancer patients treated with anastrozole or tamoxifen: a TransATAC study. Cancer Res 2009, 69:75s. [abstr 53].
33. Tang G., Cuzick J., Costantino J.P., Dowsett M., Forbes J.F., Crager M., et al. Risk of recurrence and chemotherapy benefit for patients with node-negative, estrogen receptor-positive breast cancer: recurrence score alone and integrated with pathologic and clinical factors. J Clin Oncol 2011, 29(33):4365-4372.
34. NSABP halts B-14 trial: no benefit seen beyond 5 years of tamoxifen use. J Natl Cancer Inst 1995, 87(24):1829.
35. Paik S., Tang G., Shak S., Kim C., Baker J., Kim W., et al. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 2006, 24(23):3726-3734.
36. Chang J.C., Makris A., Gutierrez M.C., Hilsenbeck S.G., Hackett J.R., Jeong J., et al. Gene expression patterns in formalin-fixed, paraffin-embedded core biopsies predict docetaxel chemosensitivity in breast cancer patients. Breast Cancer Res Treat 2008, 108(2):233-240.
37. Cardoso F., Van't Veer L., Rutgers E., Loi S., Mook S., Piccart-Gebhart M.J. Clinical application of the 70-gene profile: the MINDACT trial. J Clin Oncol 2008, 26(5):729-735.
38. Ma X.J., Wang Z., Ryan P.D., Isakoff S.J., Barmettler A., Fuller A., et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004, 5(6):607-616.
39. Ma X.J., Hilsenbeck S.G., Wang W., Ding L., Sgroi D.C., Bender R.A., et al. The HOXB13:IL17BR expression index is a prognostic factor in early-stage breast cancer. J Clin Oncol 2006, 24(28):4611-4619.
40. Jerevall P.L., Brommesson S., Strand C., Gruvberger-Saal S., Malmstrom P., Nordenskjold B., et al. Exploring the two-gene ratio in breast cancer - independent roles for HOXB13 and IL17BR in prediction of clinical outcome. Breast Cancer Res Treat 2008, 107(2):225-234.
41. Jansen M.P., Sieuwerts A.M., Look M.P., Ritstier K., Meijer-van Gelder M.E., van Staveren I.L., 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(6):662-668.
42. Reid J.F., Lusa L., De Cecco L., Coradini D., Veneroni S., Daidone M.G., et al. Limits of predictive models using microarray data for breast cancer clinical treatment outcome. J Natl Cancer Inst 2005, 97(12):927-930.
43. Ma X.J., Salunga R., Dahiya S., Wang W., Carney E., Durbecq V., 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(9):2601-2608.
44. Loi S., Haibe-Kains B., Desmedt C., Lallemand F., Tutt A.M., Gillet C., et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 2007, 25(10):1239-1246.
45. Liedtke C., Broglio K., Moulder S., Hsu L., Kau S.W., Symmans W.F., et al. Prognostic impact of discordance between triple-receptor measurements in primary and recurrent breast cancer. Ann Oncol 2009, 20(12):1953-1958.
46. Sorlie T. Introducing molecular subtyping of breast cancer into the clinic?. J Clin Oncol 2009, 27(8):1153-1154.
47. Desmedt C., Haibe-Kains B., Wirapati P., Buyse M., Larsimont D., Bontempi G., et al. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 2008, 14(16):5158-5165.
48. Parker P.A., Pettaway C.A., Babaian R.J., Pisters L.L., Miles B., Fortier A., et al. The effects of a presurgical stress management intervention for men with prostate cancer undergoing radical prostatectomy. J Clin Oncol 2009, 27(19):3169-3176.
49. Chia S.K., Bramwell V.H., Tu D., Shepherd L.E., Jiang S., Vickery T., et al. A 50-Gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Clin Cancer Res 2012, 18(16):4465-4472.
50. Harvell D.M., Spoelstra N.S., Singh M., McManaman J.L., Finlayson C., Phang T., et al. Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance. Breast Cancer Res Treat 2008, 112(3):475-488.
51. Kelly C.M., Bernard P.S., Krishnamurthy S., Wang B., Ebbert M.T., Bastien R.R., et al. Agreement in risk prediction between the 21-gene recurrence score assay (oncotype DX(R)) and the PAM50 breast cancer intrinsic classifier in early-stage estrogen receptor-positive breast cancer. Oncologist 2012, 17(4):492-498.
52. Ring B.Z., Seitz R.S., Beck R., Shasteen W.J., Tarr S.M., Cheang M.C., et al. Novel prognostic immunohistochemical biomarker panel for estrogen receptor-positive breast cancer. J Clin Oncol 2006, 24(19):3039-3047.
53. Ross D.T., Kim C.Y., Tang G., Bohn O.L., Beck R.A., Ring B.Z., et al. Chemosensitivity and stratification by a five monoclonal antibody immunohistochemistry test in the NSABP B14 and B20 trials. Clin Cancer Res 2008, 14(20):6602-6609.
54. Cuzick J., Dowsett M., Pineda S., Wale C., Salter J., Quinn E., et al. Prognostic value of a combined estrogen receptor, progesterone receptor, Ki-67, and human epidermal growth factor receptor 2 immunohistochemical score and comparison with the genomic health recurrence score in early breast cancer. J Clin Oncol 2011, 29(32):4273-4278.
55. Dowsett M., Cuzick J., Wale C., Forbes J., Mallon E.A., Salter J., et al. Prediction of risk of distant recurrence using the 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study. J Clin Oncol 2010, 28(11):1829-1834.
56. Foekens J.A., Atkins D., Zhang Y., Sweep F.C., Harbeck N., Paradiso A., et al. Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol 2006, 24(11):1665-1671.
57. Desmedt C., Piette F., Loi S., Wang Y., Lallemand F., Haibe-Kains B., et al. 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(11):3207-3214.
58. Liu R., Wang X., Chen G.Y., Dalerba P., Gurney A., Hoey T., et al. The prognostic role of a gene signature from tumorigenic breast-cancer cells. N Engl J Med 2007, 356(3):217-226.
59. Zhang Y., Sieuwerts A.M., McGreevy M., Casey G., Cufer T., Paradiso A., et al. The 76-gene signature defines high-risk patients that benefit from adjuvant tamoxifen therapy. Breast Cancer Res Treat 2009, 116(2):303-309.
60. Staaf J., Ringner M., Vallon-Christersson J., Jonsson G., Bendahl P.O., Holm K., et al. Identification of subtypes in human epidermal growth factor receptor 2 - positive breast cancer reveals a gene signature prognostic of outcome. J Clin Oncol 2010, 28(11):1813-1820.
61. Liu J.C., Voisin V., Bader G.D., Deng T., Pusztai L., Symmans W.F., et al. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+: ERalpha- breast cancer. Proc Natl Acad Sci U S A 2012, 109(15):5832-5837.
62. Tutt A., Wang A., Rowland C., Gillett C., Lau K., Chew K., et al. Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature. BMC Cancer 2008, 8:339.
63. Goldhirsch A., Wood W.C., Coates A.S., Gelber R.D., Thurlimann B., Senn H.J. 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, 22(8):1736-1747. Panel members.
64. Cusumano G., Generali D., Lifrange E., Jerusalem G., Andreis D., Hilderink-Koertshuis R., et al. Inter-institutional comparison of impact of MammaPrint on the routine treatment decision-making process in early breast cancer patient populations from three European hospitals. The Breast 2011, P503.
65. Hornberger J., Alvarado M.D., Rebecca C., Gutierrez H.R., Yu T.M., Gradishar W.J. Clinical validity/utility, change in practice patterns, and economic implications of risk stratifiers to predict outcomes for early-stage breast cancer: a systematic review. J Natl Cancer Inst 2012, 104(14):1068-1079.
66. Simon R.M., Paik S., Hayes D.F. Use of archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst 2009, 101(21):1446-1452.
67. Hayes D.F., Bast R.C., Desch C.E., Fritsche H., Kemeny N.E., Jessup J.M., et al. Tumor marker utility grading system: a framework to evaluate clinical utility of tumor markers. J Natl Cancer Inst 1996, 88(20):1456-1466.
68. Tang G., Shak S., Paik S., Anderson S.J., Costantino J.P., Geyer C.E., et al. Comparison of the prognostic and predictive utilities of the 21-gene recurrence score assay and adjuvant! for women with node-negative, ER-positive breast cancer: results from NSABP B-14 and NSABP B-20. Breast Cancer Res Treat 2011, 127(1):133-142.
69. Geyer F.C., Marchio C., Reis-Filho J.S. The role of molecular analysis in breast cancer. Pathology 2009, 41(1):77-88.
70. Albain K.S., Barlow W.E., Ravdin P.M., Farrar W.B., Burton G.V., Ketchel S.J., et al. Adjuvant chemotherapy and timing of tamoxifen in postmenopausal patients with endocrine-responsive, node-positive breast cancer: a phase 3, open-label, randomised controlled trial. Lancet 2009, 374(9707):2055-2063.
71. Ayers M., Symmans W.F., Stec J., Damokosh A.I., Clark E., Hess K., et al. Gene expression profiles predict complete pathologic response to neoadjuvant paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide chemotherapy in breast cancer. J Clin Oncol 2004, 22(12):2284-2293.
72. Sparano J.A. TAILORx: trial assigning individualized options for treatment (Rx). Clin Breast Cancer 2006, 7(4):347-350.
73. Bogaerts J., Cardoso F., Buyse M., Braga S., Loi S., Harrison J.A., et al. Gene signature evaluation as a prognostic tool: challenges in the design of the MINDACT trial. Nat Clin Pract Oncol 2006, 3(10):540-551.
74. Rutgers E., Piccart-Gebhart M.J., Bogaerts J., Delaloge S., Veer L.V., Rubio I.T., et al. The EORTC 10041/BIG 03-04 MINDACT trial is feasible: results of the pilot phase. Eur J Cancer 2011, 47(18):2742-2749.