Abstract
Breast cancer is a complex and heterogeneous disease where tumors of the same apparent prognostic type can vary widely in their responsiveness to therapy and survival rates. Traditionally the classification of breast cancer is performed based on clinical-histopathological parameters, such as age, tumor size, histological grade, lymph node status and by the analysis of estrogen (ER), progesterone (PR), and human epidermal growth factor 2 (HER2) receptors expression. The evaluation of these combined factors has been widely used in clinical practice and formed the basis to classify patients into various risk categories such as the St. Gallen criteria [1] and the Nottingham Prognostic Index [2]. However, the markedly extensive breast cancer heterogeneity combined with the lack of reliable predictive factors among these categories limits their ability to distinguish subtle phenotypic differences that may present relevant therapeutic implications.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Goldhirsch A, Ingle JN, Gelber RD et al (2009) Thresholds for therapies: highlights of the St. Gallen International Expert Consensus on the primary therapy of early breast cancer. Ann Oncol 8:1319–1329
Galea MH, Blamey RW, Elston CE et al (1992) The Nottingham Prognostic Index in primary breast cancer. Breast Cancer Res Treat 3:207–219
Perou CM, Sorlie T, Eisen MB et al (2000) Molecular portraits of human breast tumors. Nature 6797:747–752
Sorlie T, Perou CM, Tibshirani R et al (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 19:10869–10874
Prat A, Pineda E, Adamo B et al (2015) Clinical implications of the intrinsic molecular subtypes of breast cancer. Breast 24(Suppl 2):S26–S35
Lehmann BD, Pietenpol JA (2015) Clinical implications of molecular heterogeneity in triple negative breast cancer. Breast 24(Suppl 2):S36–S40
Cancer Genome Atlas (2012) Comprehensive molecular portraits of human breast tumours. Nature 490:61–70
Curtis C, Shah SP, Chin SF et al (2012) The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups. Nature 486:346–352
Gingras I, Desmedt C, Ignatiadis M et al (2015) CCR 20th Anniversary Commentary: gene-expression signature in breast cancer—where did it start and where are we now? Clin Cancer Res 21:4743–4746
Pinkel D, Segraves R, Sudar D et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207–211
Duggan DJ, Bittner M, Chen Y et al (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14
Pollack JR, Sørlie T, Perou CM et al (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 99:12963–12968
Shipitsin M, Campbell LL, Argani P et al (2007) Molecular definition of breast tumor heterogeneity. Cancer Cell 11:259–273
Stingl J, Caldas C (2007) Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. Nat Rev Cancer 7:791–799
Weigelt B, Reis-Filho JS (2009) Histological and molecular types of breast cancer: is there a unifying taxonomy? Nat Rev Clin Oncol 6:718–730
Laakso M, Loman N, Borg A et al (2005) Cytokeratin 5/14- positive breast cancer: true basal phenotype confined to BRCA1 tumors. Mod Pathol 18:1321–1328
Lakhani SR, Reis-Filho JS, Fulford L et al (2005) Prediction of BRCA1 status in patients with breast cancer using estrogen receptor and basal phenotype. Clin Cancer Res 11:5175–5180
Turner NC, Reis-Filho JS (2006) Basal-like breast cancer and the BRCA1 phenotype. Oncogene 25:5846–5853
Eerola H, Heinonen M, Heikkila P et al (2008) Basal cytokeratins in breast tumours among BRCA1, BRCA2 and mutation-negative breast cancer families. Breast Cancer Res 10:R17
Sorlie T, Tibshirani R, Parker J et al (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 100:8418–8423
Sorlie T, Wang Y, Xiao C et al (2006) Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms. BMC Genomics 7:127
Farmer P, Bonnefoi H, Becette V et al (2005) Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 24:4660–4671
Doane AS, Danso M, Lal P et al (2006) An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 25:3994–4008
Hu Z, Fan C, Oh DS et al (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 7:96
Teschendorff AE, Caldas C (2008) A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer. Breast Cancer Res 10:R73
Hennessy BT, Gonzalez-Angulo AM, Stemke-Hale K et al (2009) Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res 69:4116–4124
Banneau G, Guedj M, MacGrogan G et al (2010) Molecular apocrine differentiation is a common feature of breast cancer in patients with germline PTEN mutations. Breast Cancer Res 12:R63
Prat A, Parker JS, Karginova O et al (2010) Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 12:R68
Lehmann BD, Bauer JA, Chen X et al (2011) Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Investig 121:2750–2767
Prat A, Adamo B, Cheang MC et al (2013) Molecular characterization of basal-like and non-basal-like triple-negative breast cancer. Oncologist 18:123–133
Burstein MD, Tsimelzon A, Poage GM et al (2015) Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer. Clin Cancer Res 21:1688–1698
Purrington KS, Visscher DW, Wang C et al (2016) Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes. Breast Cancer Res Treat 157:117–131
Sotiriou C, Pusztai L (2009) Gene-expression signatures in breast cancer. N Engl J Med 360:790–800
Weigelt B, Baehner FL, Reis-Filho JS (2010) The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade. J Pathol 220:263–280
Rouzier R, Perou CM, Symmans WF et al (2005) Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 11:5678–5685
Martin M, Romero A, Cheang MC et al (2011) Genomic predictors of response to doxorubicin versus docetaxel in primary breast cancer. Breast Cancer Res Treat 128:127–136
Prat A, Lluch A, Albanell J et al (2014) Predicting response and survival in chemotherapy-treated triple-negative breast cancer. Br J Cancer 111:1532–1541
Cheang MCU, Chia SK, Voduc D et al (2009) Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst 101:736–750
Parker JS, Mullins M, Cheang MC et al (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27:1160–1167
Nielsen TO, Parker JS, Leung S 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 16:5222–5232
Iwamoto T, Bianchini G, Booser D et al (2011) Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst 103:264–272
Arteaga CL, Sliwkowski MX, Osborne CK et al (2011) Treatment of HER2-positive breast cancer: current status and future perspectives. Nat Rev Clin Oncol 9:16–32
Mukohara T (2011) Role of HER2-targeted agents in adjuvant treatment for breast cancer. Chemother Res Pract 2011:730360
Banerjee S, Reis-Filho JS, Ashley S et al (2006) Basal-like breast carcinomas: clinical outcome and response to chemotherapy. J Clin Pathol 59:729–735
Rakha EA, Reis-Filho JS, Ellis IO (2008) Basal-like breast cancer: a critical review. J Clin Oncol 26:2568–2581
Fong PC, Boss DS, Yap TA et al (2009) Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 361:123–134
Carey LA, Dees EC, Sawyer L et al (2007) The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res 13:2329–2334
Millikan RC, Newman B, Tse CK et al (2008) Epidemiology of basal-like breast cancer. Breast Cancer Res Treat 109:123–139
Lehmann BD, Jovanović B, Chen X et al (2016) Refinement of triple-negative breast cancer molecular subtypes: implications for neoadjuvant chemotherapy selection. PLoS One 11:e0157368
Wallden B, Storhoff J, Nielsen T et al (2015) Development and verification of the PAM50-based Prosigna breast cancer gene signature assay. BMC Med Genomics 8:54
Goldhirsch A, Wood WC, Coates AS 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 22:1736–1747
Goldhirsch A, Winer EP, Coates AS et al (2013) Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer. Ann Oncol 24:2206–2223
Coates AS, Winer EP, Goldrich A et al (2015) Tailoring therapies—improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015. Ann Oncol 26:1533–1546
Takahashi RU, Miyazaki H, Ochiya T (2015) The roles of microRNAs in breast cancer. Cancers (Basel) 7:598–616
Di Leva G, Garofalo M, Croce CM (2014) MicroRNAs in cancer. Annu Rev Pathol 9:287–314
Andorfer CA, Necela BM, Thompson EA et al (2011) MicroRNA signatures: clinical biomarkers for the diagnosis and treatment of breast cancer. Trends Mol Med 17:313–319
Friedman RC, Farh KK, Burge CB et al (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105
Calin GA, Sevignani C, Dumitru CD et al (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 101:2999–2104
Voorhoeve PM (2010) MicroRNAs: oncogenes, tumor suppressors or master regulators of cancer heterogeneity? Biochem Biophys Acta 1805:72–86
Blenkiron C, Goldstein LD, Thorne NP et al (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 8:R214
Sugita B, Gill M, Mahajan A et al (2016) Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women. Oncotarget 7:79274–79279
Lowery AJ, Miller N, Devaney A et al (2009) MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Breast Cancer Res 11:R27
Volinia S, Calin GA, Liu CG et al (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103:2257–2261
Foekens JA, Sieuwerts AM, Smid M et al (2008) Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer. Proc Natl Acad Sci U S A 105:13021–13026
Riaz M, van Jaarsveld MT, Hollestelle A et al (2015) miRNA expression profiling of 51 human breast cancer cell lines reveals subtype and driver mutation-specific miRNAs. Breast Cancer Res 15:R33
Bediaga NG, Acha Sagredo A, Guerra I et al (2010) DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res 12:R77
Holm K, Hegardt C, Staaf J et al (2010) Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 12:R36
Rønneberg JA, Fleischer T, Solvang HK et al (2011) Methylation profiling with a panel of cancer related genes: association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol Oncol 5:61–76
Flanagan JM, Cocciardi S, Waddell N et al (2010) DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 86:420–433
Conway K, Edmiston SN, May R et al (2014) DNA methylation profiling in the carolina breast cancer study defines cancer subclasses differing in clinicopathologic characteristics and survival. Breast Cancer Res 16:450
Stefansson OA, Moran S, Gomez A et al (2015) A DNA methylation-based definition of biologically distinct breast cancer subtypes. Mol Oncol 9:555–568
Sharma P, Stecklein SR, Kimler BF et al (2014) The prognostic value of promoter methylation in early stage triple negative breast cancer. J Cancer Ther Res 3:1–11
Watanabe Y, Maeda I, Oikawa R et al (2013) Aberrant DNA methylation status of DNA repair genes in breast cancer treated with neoadjuvant chemotherapy. Genes Cells 18:1120–1130
Xu Y, Diao L, Chen Y et al (2013) Promoter methylation of BRCA1 in triple-negative breast cancer predicts sensitivity to adjuvant chemotherapy. Ann Oncol 24:1498–1505
Ignatov T, Poehlmann A, Ignatov A et al (2013) BRCA1 promoter methylation is a marker of better response to anthracycline-based therapy in sporadic TNBC. Breast Cancer Res Treat 141:205–212
Ciriello G, Sinha R, Hoadley KA et al (2013) The molecular diversity of Luminal A breast tumors. Breast Cancer Res Treat 141:409–420
Cornen S, Guille A, Adélaïde J et al (2014) Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. PLoS One 9:e81843
He J, Yang J, Chen W et al (2015) Molecular features of triple negative breast cancer: microarray evidence and further integrated analysis. PLoS One 10:e0129842
Tishchenko I, Milioli HH, Riveros C et al (2016) Extensive transcriptomic and genomic analysis provides new insights about luminal breast cancers. PLoS One 11:e0158259
Netanely D, Avraham A, Ben-Baruch A et al (2016) Expression and methylation patterns partition luminal—a breast tumors into distinct prognostic subgroups. Breast Cancer Res 18:74
Liu YR, Jiang YZ, Xu XE et al (2016) Comprehensive transcriptome analysis identifies novel molecular subtypes and subtype-specific RNAs of triple-negative breast cancer. Breast Cancer Res 18:33
Weisman PS, Ng CK, Brogi E et al (2016) Genetic alterations of triple negative breast cancer by targeted next-generation sequencing and correlation with tumor morphology. Mod Pathol 29:476–488
Eifel P, Axelson JA, Costa J et al (2001) National Institutes of Health Consensus Development Conference Statement: adjuvant therapy for breast cancer. November 1-3, 2000. J Natl Cancer Inst 93:979–989
Harris LN, Ismaila N, McShane LM et al (2016) Use of biomarkers to guide decisions on adjuvant systemic therapy for women with early-stage invasive breast cancer: American Society of Clinical Oncology Clinical Practice Guideline Summary. J Oncol Pract 12:384–389
Duffy MJ, O’Donovan N, McDermott E et al (2016) Validated biomarkers: the key to precision treatment in patients with breast cancer. Breast 29:192–201
van’t Veer LJ, Dai H, van de Vijver MJ et al (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 6871:530–536
van de Vijver MJ, He YD, van’t Veer LJ et al (2002) A gene expression signature as a predictor of survival in breast cancer. N Engl J Med 347:1999–2009
Buyse M, Loi S, van’t Veer L et al (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98:1183–1192
Bueno-de-Mesquita JM, van Harten WH, Retel VP et al (2007) Use of 70-gene signature to predict prognosis of patients with node-negative breast cancer: a prospective community-based feasibility study (RASTER). Lancet Oncol 8:1079–1087
Mook S, Schmidt MK, Viale G et al (2009) 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 116:295–302
Cardoso F, van’t Veer LJ, Bogaerts J et al (2016) 70-Gene signature as an aid to treatment decisions in early-stage breast cancer. N Engl J Med 375:717–729
Emiel R et al (2011) The EORTC 10041/BIG 03-04 MINDACT trial is feasible: results of the pilot phase. Eur J Cancer 47:2742–2749
Piccart M, Rutgers E, van’t Veer L, et al. Primary analysis of the EORTC 10041/BIG 3-04 MINDACT study: a prospective, randomized study evaluating the clinical utility of the 70-gene signature (MammaPrint) combined with common clinical-pathological criteria for selection of patients for adjuvant chemotherapy in breast cancer with 0 to 3 positive nodes. 2016 American Association of Cancer Res Annual Meeting. Abstract CT039. Presented April 18, 2016
Cobleigh MA, Bitterman P, Baker J et al (2003) Tumor gene expression predicts distant disease-free survival (DDFS) in breast cancer patients with 10 or more positive nodes: high throughout RT-PCR assay of paraffin-embedded tumor tissues. Prog Proc Am Soc Clin Oncol 22:850–850
Esteban J, Baker J, Cronin M et al (2003) Tumor gene expression and prognosis in breast cancer: multi-gene RT-PCR assay of paraffin-embedded tissue. Prog Proc Am Soc Clin Oncol 22:850
Paik S, Shak S, Tang G et al (2003) Multi-gene RT-PCR assay for predicting recurrence in node negative breast cancer patients—NSABP studies B-20 and B-14. Breast Cancer Res Treat 82:A16
Fisher B, Dignam J, Wolmark N et al (1997) Tamoxifen and chemotherapy for lymph node-negative, estrogen receptor-positive breast cancer. J Natl Cancer Inst 89:1673–1682
Paik S, Shak S, Tang G et al (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351:2817–2826
Fisher B, Costantino J, Redmond C et al (1989) A randomized clinical trial evaluating tamoxifen in the treatment of patients with node-negative breast cancer who have estrogen-receptor-positive tumors. N Engl J Med 320:479–484
Habel LA, Shak S, Jacobs MK et al (2006) A population based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients. Breast Cancer Res 8:R25
Dowsett M, Cuzick J, Wale C et al (2010) Prediction of risk of distant recurrence using the 21-gene recurrence score in nodenegative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study. J Clin Oncol 11:1829–1834
Sparano JA (2006) TAILORx: trial assigning individualized options for treatment (Rx). Clin Breast Cancer 7:347–350
Sparano JA, Gray RJ, Makower DF et al (2015) Prospective validation of a 21-gene expression assay in breast cancer. N Engl J Med 373:2005–2014
Ma XJ, Salunga R, Dahiya S et al (2008) A five-gene molecular grade index and HOXB13:IL17BR are complementary prognostic factors in early stage breast cancer. Clin Cancer Res 14:2601–2608
Jerevall PL, Ma XJ, Li H et al (2011) Prognostic utility of HOXB13:IL17BR and molecular grade index in early-stage breast cancer patients from the Stockholm trial. Br J Cancer 104:1762–1769
Chang HY, Sneddon JB, Alizadeh AA et al (2004) Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2:E7
Laas E, Mallon P, Duhoux FP et al (2016) Low concordance between gene expression signatures in ER positive HER2 negative breast carcinoma could impair their clinical application. PLoS One 11:e0148957
Ma CX, Bose R, Ellis MJ (2016) Prognostic and predictive biomarkers of endocrine responsiveness for estrogen receptor positive breast cancer. Adv Exp Med Biol 882:125–154
Ernst B, Anderson KS (2015) Immunotherapy for the treatment of breast cancer. Curr Oncol Rep 17:5
Bedognetti D, Hnesdrickx W, Marincola FM et al (2015) Prognostic and predictive immune gene signatures in breast cancer. Curr Oncol Rep 27:433–444
Perez EA, Thompson EA, Ballman KV et al (2015) Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group N9831 Adjuvant Trastuzumab Trial. J Clin Oncol 33:701–708
Li X, Wetherilt CS, Krishnamurti U et al (2016) Stromal PD-L1 expression is associated with better disease-free survival in triple-negative breast cancer. Am J Clin Pathol 146:496–502
Mori H, Kubo M, Yamaguchi R et al (2017) The combination of PD-L1 expression and decreased tumor-infiltrating lymphocytes is associated with a poor prognosis in triple-negative breast cancer. Oncotarget 8(9):15584–15592. https://doi.org/10.18632/oncotarget.14698
Botti G, Collina F, Scognamiglio G et al (2017) Programmed death ligand 1 (PD-L1) tumor expression is associated with a better prognosis and diabetic disease in triple negative breast cancer patients. Int J Mol Sci 18(2):pii: E459
Li X, Li M, Lian Z et al (2016) Prognostic role of programmed death ligand-1 expression in breast cancer: a systematic review and meta-analysis. Target Oncol 11:753–761
GarcÃa-Teijido P, Cabal ML, Fernández IP et al (2016) Tumor-infiltrating lymphocytes in triple negative breast cancer: the future of immune targeting. Clin Med Insights Oncol 10(Suppl 1):31–39
Wang C, Zhu H, Zhou Y et al (2017) Prognostic value of PD-L1 in breast cancer: a meta-analysis. Breast J 23(4):436–443. https://doi.org/10.1111/tbj.12753
Fan C, Prat A, Parker JS et al (2011) Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics 9(4):3
Gyorffy B, Hatzis C, Sanft C et al (2015) Multigene prognostic tests in breast cancer: past, present, future. Breast Cancer Res 17:11
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Cavalli, L.R., Cavalli, I.J. (2019). Molecular Classification and Prognostic Signatures of Breast Tumors. In: Urban, C., Rietjens, M., El-Tamer, M., Sacchini, V.S. (eds) Oncoplastic and Reconstructive Breast Surgery. Springer, Cham. https://doi.org/10.1007/978-3-319-62927-8_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-62927-8_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-62925-4
Online ISBN: 978-3-319-62927-8
eBook Packages: MedicineMedicine (R0)