Review
. 2011 Jul;13(3).
doi: 10.1186/bcr2890.

Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction

Pierre-Emmanuel Colombo 1 Fernanda Milanezi  Britta Weigelt  Jorge S Reis-Filho  
Affiliations
  • PMID: 21787441
  •     111 References
  •     49 citations

Abstract

Breast cancer comprises a collection of diseases with distinctive clinical, histopathological, and molecular features. Importantly, tumors with similar histological features may display disparate clinical behaviors. Gene expression profiling using microarray technologies has improved our understanding of breast cancer biology and has led to the development of a breast cancer molecular taxonomy and of multigene 'signatures' to predict outcome and response to systemic therapies. The use of these prognostic and predictive signatures in routine clinical decision-making remains controversial. Here, we review the clinical relevance of microarray-based profiling of breast cancer and discuss its impact on patient management.

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H R Ali, S-J Dawson, +3 authors, C Caldas.
Br J Cancer, 2012 Apr 28; 106(11). PMID: 22538974    Free PMC article.
Strategies for the discovery and development of therapies for metastatic breast cancer.
Bedrich L Eckhardt, Prudence A Francis, Belinda S Parker, Robin L Anderson.
Nat Rev Drug Discov, 2012 Jun 02; 11(6). PMID: 22653217
Highly Cited. Review.
Prognostic signatures in breast cancer: correlation does not imply causation.
Charlotte Ng, Britta Weigelt, Anita Grigoriadis, Jorge S Reis-Filho.
Breast Cancer Res, 2012 Jun 21; 14(3). PMID: 22713235    Free PMC article.
Stromal genes add prognostic information to proliferation and histoclinical markers: a basis for the next generation of breast cancer gene signatures.
Dwain Mefford, Joel Mefford.
PLoS One, 2012 Jun 22; 7(6). PMID: 22719844    Free PMC article.
Proteomic studies in breast cancer (Review).
Xian-Ju Qin, Bruce X Ling.
Oncol Lett, 2012 Jun 29; 3(4). PMID: 22740985    Free PMC article.
Integrin β5 contributes to the tumorigenic potential of breast cancer cells through the Src-FAK and MEK-ERK signaling pathways.
A Bianchi-Smiraglia, S Paesante, A V Bakin.
Oncogene, 2012 Jul 25; 32(25). PMID: 22824793    Free PMC article.
Genomic instability at the 13q31 locus and somatic mtDNA mutation in the D-loop site correlate with tumor aggressiveness in sporadic Brazilian breast cancer cases.
Gilson Costa dos Santos, Andréa Carla de Souza Góes, +4 authors, Claudia Vitoria de Moura Gallo.
Clinics (Sao Paulo), 2012 Oct 17; 67(10). PMID: 23070345    Free PMC article.
Transcriptional shift identifies a set of genes driving breast cancer chemoresistance.
Laura Vera-Ramirez, Pedro Sanchez-Rovira, +3 authors, Jose A Lorente.
PLoS One, 2013 Jan 18; 8(1). PMID: 23326553    Free PMC article.
Chemoprevention activity of dipyridamole in the MMTV-PyMT transgenic mouse model of breast cancer.
Chunmei Wang, Luciana P Schwab, +2 authors, John K Buolamwini.
Cancer Prev Res (Phila), 2013 Mar 01; 6(5). PMID: 23447563    Free PMC article.
A prognosis classifier for breast cancer based on conserved gene regulation between mammary gland development and tumorigenesis: a multiscale statistical model.
Yingpu Tian, Baozhen Chen, +2 authors, Zhongxian Lu.
PLoS One, 2013 Apr 09; 8(4). PMID: 23565194    Free PMC article.
Interleukin-8 in breast cancer progression.
Nataša Todorović-Raković, Jelena Milovanović.
J Interferon Cytokine Res, 2013 May 24; 33(10). PMID: 23697558    Free PMC article.
Review.
Transcriptome Analysis Reveals Novel Entry Mechanisms and a Central Role of SRC in Host Defense during High Multiplicity Mycobacterial Infection.
Jay Zhang.
PLoS One, 2013 Jul 05; 8(6). PMID: 23824656    Free PMC article.
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers.
Xianxiao Zhou, Tongwei Shi, +6 authors, Zheng Guo.
PLoS One, 2013 Jul 23; 8(7). PMID: 23875016    Free PMC article.
Dual-color fluorescence in situ hybridization reveals an association of chromosome 8q22 but not 8p21 imbalance with high grade invasive breast carcinoma.
Logan C Walker, Margaret McDonald, +3 authors, Christine M Morris.
PLoS One, 2013 Aug 13; 8(7). PMID: 23936250    Free PMC article.
Thermodynamically inspired classifier for molecular phenotypes of health and disease.
Marc T Facciotti.
Proc Natl Acad Sci U S A, 2013 Nov 10; 110(48). PMID: 24204030    Free PMC article.
Are breast cancer molecular classes predictive of survival in patients with long follow-up?
Danae Pracella, Serena Bonin, +4 authors, Giorgio Stanta.
Dis Markers, 2013 Nov 30; 35(6). PMID: 24288429    Free PMC article.
Intrinsic subtypes from PAM50 gene expression assay in a population-based breast cancer cohort: differences by age, race, and tumor characteristics.
Carol Sweeney, Philip S Bernard, +11 authors, Bette J Caan.
Cancer Epidemiol Biomarkers Prev, 2014 Feb 14; 23(5). PMID: 24521995    Free PMC article.
A novel approach for discovering condition-specific correlations of gene expressions within biological pathways by using cloud computing technology.
Tzu-Hao Chang, Shih-Lin Wu, +2 authors, Cheng-Wei Chang.
Biomed Res Int, 2014 Mar 01; 2014. PMID: 24579087    Free PMC article.
Gene expression analysis in RA: towards personalized medicine.
A N Burska, K Roget, +8 authors, F Ponchel.
Pharmacogenomics J, 2014 Mar 05; 14(2). PMID: 24589910    Free PMC article.
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Biomarker identification in breast cancer: Beta-adrenergic receptor signaling and pathways to therapeutic response.
Liana E Kafetzopoulou, David J Boocock, +2 authors, Graham R Ball.
Comput Struct Biotechnol J, 2013 Jan 01; 6. PMID: 24688711    Free PMC article.
The association of the expression of miR-122-5p and its target ADAM10 with human breast cancer.
Sercan Ergün, Mustafa Ulasli, +9 authors, Serdar Oztuzcu.
Mol Biol Rep, 2014 Oct 17; 42(2). PMID: 25318895
MiR-363 sensitizes cisplatin-induced apoptosis targeting in Mcl-1 in breast cancer.
Ruiguang Zhang, Yan Li, +2 authors, Xiu Nie.
Med Oncol, 2014 Nov 25; 31(12). PMID: 25416050
Identification of a microRNA signature associated with risk of distant metastasis in nasopharyngeal carcinoma.
Jeff P Bruce, Angela B Y Hui, +12 authors, Fei-Fei Liu.
Oncotarget, 2015 Mar 05; 6(6). PMID: 25738365    Free PMC article.
Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer--the INNODIAG study.
Tatiana Kempowsky-Hamon, Carine Valle, +12 authors, Véronique Anton-Leberre.
BMC Med Genomics, 2015 Apr 19; 8. PMID: 25888889    Free PMC article.
The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set.
Heloisa Helena Milioli, Renato Vimieiro, +3 authors, Pablo Moscato.
PLoS One, 2015 Jul 02; 10(7). PMID: 26132585    Free PMC article.
GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature.
Ning Ye, Hengfu Yin, +2 authors, Tongming Yin.
Biomed Res Int, 2015 Jul 23; 2015. PMID: 26199946    Free PMC article.
4-IHC classification of breast cancer subtypes in a large cohort of a clinical cancer registry: use in clinical routine for therapeutic decisions and its effect on survival.
Elisabeth Christine Inwald, M Koller, +5 authors, O Ortmann.
Breast Cancer Res Treat, 2015 Sep 16; 153(3). PMID: 26369534    Free PMC article.
Molecular classification and prediction in gastric cancer.
Xiandong Lin, Yongzhong Zhao, Won-Min Song, Bin Zhang.
Comput Struct Biotechnol J, 2015 Sep 19; 13. PMID: 26380657    Free PMC article.
Review.
Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production.
Vytautas Leoncikas, Huihai Wu, +2 authors, Nick J Plant.
Sci Rep, 2016 Jan 28; 6. PMID: 26813959    Free PMC article.
Synergistic Effects Induced by Combined Treatments of Aqueous Extract of Propolis and Venom.
Flaviu Drigla, Ovidiu Balacescu, +3 authors, Liviu Alexandru Marghitas.
Clujul Med, 2016 Mar 24; 89(1). PMID: 27004032    Free PMC article.
Identification of novel biomarkers associated with poor patient outcomes in invasive breast carcinoma.
Renata A Canevari, Fabio A Marchi, +5 authors, Eduardo M Reis.
Tumour Biol, 2016 Aug 04; 37(10). PMID: 27485113
Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis.
Zsuzsanna Mihály, Balázs Győrffy.
Microarrays (Basel), 2013 Jan 01; 2(3). PMID: 27605190    Free PMC article.
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Breast cancer classification and prognostication through diverse systems along with recent emerging findings in this respect; the dawn of new perspectives in the clinical applications.
Vida Pourteimoor, Samira Mohammadi-Yeganeh, Mahdi Paryan.
Tumour Biol, 2016 Sep 22; 37(11). PMID: 27651157
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First report on molecular breast cancer subtypes and their clinico-pathological characteristics in Eastern Morocco: series of 2260 cases.
Manal Elidrissi Errahhali, Mounia Elidrissi Errahhali, +3 authors, Mohammed Bellaoui.
BMC Womens Health, 2017 Jan 11; 17(1). PMID: 28068979    Free PMC article.
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm.
Wei-Sheng Wu, Meng-Jhun Jhou.
BMC Bioinformatics, 2017 Jan 15; 18(1). PMID: 28086746    Free PMC article.
Screening-relevant age threshold of 70 years and older is a stronger determinant for the choice of adjuvant treatment in breast cancer patients than tumor biology.
E C Inwald, O Ortmann, +5 authors, M Klinkhammer-Schalke.
Breast Cancer Res Treat, 2017 Feb 17; 163(1). PMID: 28205042    Free PMC article.
Gene Expression Signatures for Head and Neck Cancer Patient Stratification: Are Results Ready for Clinical Application?
Luca Tonella, Marco Giannoccaro, +2 authors, Loris De Cecco.
Curr Treat Options Oncol, 2017 May 06; 18(5). PMID: 28474265
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Targeting Intracellular Calcium Signaling ([Ca2+]i) to Overcome Acquired Multidrug Resistance of Cancer Cells: A Mini-Overview.
Dietrich Büsselberg, Ana-Maria Florea.
Cancers (Basel), 2017 May 10; 9(5). PMID: 28486397    Free PMC article.
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Dipalmitoylphosphatidic acid inhibits tumor growth in triple-negative breast cancer.
Qian-Qian Zhang, Jian Chen, +7 authors, Lijing Wang.
Int J Biol Sci, 2017 May 23; 13(4). PMID: 28529455    Free PMC article.
Profiling of gene expression regulated by 17β-estradiol and tamoxifen in estrogen receptor-positive and estrogen receptor-negative human breast cancer cell lines.
Nelson Rangel, Victoria E Villegas, Milena Rondón-Lagos.
Breast Cancer (Dove Med Press), 2017 Oct 17; 9. PMID: 29033607    Free PMC article.
Relationships between Reproductive Risk Factors for Breast Cancer and Tumor Molecular Subtypes
Nahid Nafissi, Maryam Faraji, +4 authors, Seyed Hamzeh Mousavie.
Asian Pac J Cancer Prev, 2018 Jul 28; 19(7). PMID: 30049185    Free PMC article.
SET Overexpression is Associated with Worse Recurrence-Free Survival in Patients with Primary Breast Cancer Receiving Adjuvant Tamoxifen Treatment.
Yu-Hsiang Huang, Pei-Yi Chu, +8 authors, Chun-Yu Liu.
J Clin Med, 2018 Aug 30; 7(9). PMID: 30154367    Free PMC article.
GSIAR: gene-subcategory interaction-based improved deep representation learning for breast cancer subcategorical analysis using gene expression, applicable for precision medicine.
Chiranjib Sur.
Med Biol Eng Comput, 2019 Oct 09; 57(11). PMID: 31591679
Towards the early detection of ductal carcinoma (a common type of breast cancer) using biomarkers linked to the PPAR(γ) signaling pathway.
Ghazala Sultan, Swaleha Zubair, +2 authors, Inamul Hasan Madar.
Bioinformation, 2020 Jan 07; 15(11). PMID: 31902979    Free PMC article.
Six novel immunoglobulin genes as biomarkers for better prognosis in triple-negative breast cancer by gene co-expression network analysis.
Huan-Ming Hsu, Chi-Ming Chu, +7 authors, Yu-Tien Chang.
Sci Rep, 2019 Mar 16; 9(1). PMID: 30872752    Free PMC article.
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.
Jessica Gliozzo, Paolo Perlasca, +9 authors, Giorgio Valentini.
Sci Rep, 2020 Feb 29; 10(1). PMID: 32107391    Free PMC article.
SHON expression predicts response and relapse risk of breast cancer patients after anthracycline-based combination chemotherapy or tamoxifen treatment.
Tarek M A Abdel-Fatah, Reuben J Broom, +20 authors, Dong-Xu Liu.
Br J Cancer, 2019 Mar 01; 120(7). PMID: 30816325    Free PMC article.
Epidemiological characteristics, clinical outcomes and management patterns of metastatic breast cancer patients in routine clinical care settings of Greece: Results from the EMERGE multicenter retrospective chart review study.
Athanasios Kotsakis, Alexandros Ardavanis, +3 authors, Christos Papadimitriou.
BMC Cancer, 2019 Jan 20; 19(1). PMID: 30658600    Free PMC article.