The genomic landscape of breast cancer as a therapeutic roadmap

Cancer Discovery

Volumn 3, Issue 1, 2013, Pages 27-34

  Ellis, Matthew J ^a,b,c   Perou, Charles M ^b,c,d  

^a USA   (United States)

^b University Genomics   (United States)

^c Bioclassifier LLC   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

6 ACETYL 8 CYCLOPENTYL 5 METHYL 2 [5 (1 PIPERAZINYL) 2 PYRIDINYLAMINO] 8H PYRIDO [2, 3 D] PYRIMIDIN 7 ONE; 6 ACETYL 8 CYCLOPENTYL 5 METHYL 2 [5 (1 PIPERAZINYL) 2 PYRIDINYLAMINO] 8H PYRIDO[2,3 D]PYRIMIDIN 7 ONE; 8 [4 (1 AMINOCYCLOBUTYL) PHENYL] 9 PHENYL 1, 2, 4 TRIAZOLO [3, 4 F] [1, 6] NAPHTHYRIDIN 3 (2H) ONE; 8 [4 (1 AMINOCYCLOBUTYL)PHENYL] 9 PHENYL 1,2,4 TRIAZOLO[3,4 F][1,6]NAPHTHYRIDIN 3(2H) ONE; ANTINEOPLASTIC AGENT; BGJ 398; BUPARLISIB; BYL 719; CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE 6; E 3800; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; HISTONE DEACETYLASE; LAPATINIB; MITOGEN ACTIVATED PROTEIN KINASE; NERATINIB; OLAPARIB; PERTUZUMAB; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3, 4, 5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN MDM2; PROTEIN P53; RO 5503781; STRESS ACTIVATED PROTEIN KINASE; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTION FACTOR RUNX1; TRASTUZUMAB; UNCLASSIFIED DRUG; VELIPARIB; Z 1031;

ARTICLE; BIOINFORMATICS; BREAST CANCER; CELL CYCLE PROGRESSION; DNA DAMAGE; DNA REPAIR; DRUG RESPONSE; DRUG SENSITIVITY; DRUG TARGETING; GENE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE MUTATION; GENE OVEREXPRESSION; HUMAN; MIXED LINEAGE LEUKEMIA GENE; OVARY CANCER; PHASE 1 CLINICAL TRIAL (TOPIC); PHASE 2 CLINICAL TRIAL (TOPIC); RANDOMIZED CONTROLLED TRIAL (TOPIC); SIGNAL TRANSDUCTION;

BREAST NEOPLASMS; FEMALE; GENOMICS; HUMANS; MUTATION; OVARIAN NEOPLASMS; PROTEIN KINASES; RECEPTOR, ERBB-2; RECEPTORS, ESTROGEN;

EID: 84872847361     PISSN: 21598274     EISSN: 21598290     Source Type: Journal    
DOI: 10.1158/2159-8290.CD-12-0462     Document Type: Article

References (50)

1. Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012;486:395-399.
2. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 2012;486:400-404.
3. Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 2012;486:405-409.
4. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Wholegenome analysis informs breast cancer response to aromatase inhibition. Nature 2012;486:353-360.
5. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012;486:346-352.
6. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
7. Chia SK, Bramwell VH, Tu D, Shepherd LE, 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: 4465-4472.
8. 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;24:3726-3734.
9. Albain KS, Barlow WE, Shak S, Hortobagyi GN, Livingston RB, Yeh IT, et al. Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogenreceptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial. Lancet Oncol 2010;11:55-65.
10. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009;27:1160-1167.
11. Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, et al. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res 2010;16:5222-5232.
12. 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;351:2817-2826.
13. Ellis MJ, Tao Y, Young O, White S, Proia AD, Murray J, et al. Estrogen-independent proliferation is present in estrogen-receptor HER2-positive primary breast cancer after neoadjuvant letrozole. J Clin Oncol 2006;24:3019-3025.
14. Stemke-Hale K, Gonzalez-Angulo AM, Lluch A, Neve RM, Kuo WL, Davies M, et al. An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res 2008;68:6084-6091.
15. Crowder RJ, Phommaly C, Tao Y, Hoog J, Luo J, Perou CM, et al. PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in estrogen receptor-positive breast cancer. Cancer Res 2009;69:3955-3962.
16. Sanchez CG, Ma CX, Crowder RJ, Guintoli T, Phommaly C, Gao F, et al. Preclinical modeling of combined phosphatidylinositol3-kinase inhibition with endocrine therapy for estrogen receptorpositive breast cancer. Breast Cancer Res 2011;13:R21.
17. Baselga J, Campone M, Piccart M, Burris HA, Rugo HS, Sahmoud T, et al. Everolimus in postmenopausal hormone-receptor-positive advanced breast cancer. N Engl J Med 2012;366:520-529.
18. Juric D, Rodon J, Gonzalez-Angulo AM, Burris HA, Bendell J, Berlin JD, et al. BYL719, a next generation PI3K alpha specific inhibitor: Preliminary safety, PK, and efficacy results from the first-in-human study [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; 2012. Abstract nr CT-01.
19. Small GW, Shi YY, Higgins LS, Orlowski RZ. Mitogen-activated protein kinase phosphatase-1 is a mediator of breast cancer chemoresistance. Cancer Res 2007;67:4459-4466.
20. Deisenroth C, Thorner AR, Enomoto T, Perou CM, Zhang Y. Mitochondrial Hep27 is a c-Myb target gene that inhibits Mdm2 and stabilizes p53. Mol Cell Biol 2010;30:3981-3993.
21. Stender JD, Kim K, Charn TH, Komm B, Chang KC, Kraus WL, et al. Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol 2010;30:3943-3955.
22. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010; 26:i237-i245.
23. Won Jeong K, Chodankar R, Purcell DJ, Bittencourt D, Stallcup MR. Gene-specific patterns of coregulator requirements by estrogen receptor-alpha in breast cancer cells. Mol Endocrinol 2012;26:955-966.
24. Huang Y, Nayak S, Jankowitz R, Davidson NE, Oesterreich S. Epigenetics in breast cancer: what's new? Breast Cancer Res 2011;13:225.
25. Stumpel DJ, Schneider P, Seslija L, Osaki H, Williams O, Pieters R, et al. Connectivity mapping identifi es HDAC inhibitors for the treatment of t(4;11)-positive infant acute lymphoblastic leukemia. Leukemia 2012;26:682-692.
26. Yardley DA, Ismail-Khan R, Klein P. Results of ENCORE 301, a randomized, phase II, double-blind, placebo-controlled study of exemestane with or without entinostat in postmenopausal women with locally recurrent or metastatic estrogen receptor-positive (ER+) breast cancer progressing on a nonsteroidal aromatase inhibitor (AI). J Clin Oncol 29, 2011(suppl 27; abstr 268).
27. Vassilev LT. MDM2 inhibitors for cancer therapy. Trends Mol Med 2007;13:23-31.
28. Bond GL, Hu W, Levine AJ. MDM2 is a central node in the p53 pathway: 12 years and counting. Curr Cancer Drug Targets 2005;5:3-8.
29. Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, Filipovic Z, et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 2004;303:844-848.
30. Shangary S, Qin D, McEachern D, Liu M, Miller RS, Qiu S, et al. Temporal activation of p53 by a specifi c MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci U S A 2008;105:3933-3938.
31. Shangary S, Wang S. Targeting the MDM2-p53 interaction for cancer therapy. Clin Cancer Res 2008;14:5318-5324.
32. Harbour JW, Luo RX, Dei Santi A, Postigo AA, Dean DC. Cdk phosphorylation triggers sequential intramolecular interactions that progressively block Rb functions as cells move through G1. Cell 1999; 98:859-869.
33. Leung BS, Potter AH. Mode of estrogen action on cell proliferative kinetics in CAMA-1 cells. I. Effect of serum and estrogen. Cancer Invest 1987;5:187-194.
34. Sherr CJ. Cancer cell cycles. Science 1996;274:1672-1677.
35. Sherr CJ, Roberts JM. CDK inhibitors: positive and negative regulators of G1-phase progression. Genes Dev 1999;13:1501-1512.
36. van den Heuvel S, Harlow E. Distinct roles for cyclin-dependent kinases in cell cycle control. Science 1993;262:2050-2054.
37. Weinberg RA. The retinoblastoma protein and cell cycle control. Cell 1995;81:323-330.
38. Miller TW, Balko JM, Fox EM, Ghazoui Z, Dunbier A, Anderson H, et al. ERalpha-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer. Cancer Discov 2011;1:338-351.
39. Herschkowitz JI, He X, Fan C, Perou CM. The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas. Breast Cancer Res 2008;10:R75.
40. Finn RS, Crown JP, Boer K, Lang I, Parikh RJ, Breazna A, et al. Results of a randomized Phase 2 study of PD0332991, a cyclin-dependent kinase (CDK) 4/6 inhibitor, in combination with letrozole vs letrozole alone for first-line treatment of ER+/HER2advanced breast cancer. Ann Oncol 2012;23:243.
41. Leonard JP, LaCasce AS, Smith MR, Noy A, Chirieac LR, Rodig SJ, et al. Selective CDK4/6 inhibition with tumor responses by PD0332991 in patients with mantle cell lymphoma. Blood 2012;119:4597-4607.
42. Roberts PJ, Bisi JE, Strum JC, Combest AJ, Darr DB, Usary JE, et al. Multiple roles of cyclin-dependent kinase 4/6 inhibitors in cancer therapy. J Natl Cancer Inst 2012;104:476-487.
43. Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, et al. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clin Cancer Res 2012;18:2402-2412.
44. Bell D, Berchuck A, Birrer M, Chien J, Cramer D, Dao F, et al. Integrated genomic analyses of ovarian carcinoma. Nature 2011;474: 609-615.
45. Fong PC, Boss DS, Yap TA, Tutt A, Wu P, Mergui-Roelvink M, et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 2009;361:123-134.
46. Turner N, Pearson A, Sharpe R, Lambros M, Geyer F, Lopez-Garcia MA, et al. FGFR1 amplification drives endocrine therapy resistance and is a therapeutic target in breast cancer. Cancer Res 2010; 70: 2085-2094.
47. Dienstmann R. Significant antitumor activity of E-3810, a novel FGFR and VEGFR inhibitor, in patients with FGFR1 amplified breast cancer. Proceedings of the European Society for Medical Oncology; 2012 Sept 28-Oct. 2; Vienna, Austria. Ann Oncol 2012 (suppl 9; abstr 3190).
48. Wolf J, LoRusso P, Camidge R, Perez J, Tabernero J, Hidalgo M, et al. A phase I dose escalation study of NVP-BGJ398, a selective pan FGFR inhibitor in genetically preselected advanced solid tumors [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; 2012. Abstract nr LB-122.
49. Tutt A, Robson M, Garber JE, Domchek SM, Audeh MW, Weitzel JN, et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and advanced breast cancer: a proof-of-concept trial. Lancet 2010;376:235-244.
50. Bose R, Kavuri SM, Searleman AC, Shen W, Shen D, Koboldt DC, et al. Activating HER2 mutations in HER2 gene amplification megative breast cancer. Cancer Discov 2012 Dec 7. [Epub ahead of print].