Integrative molecular and functional profiling of erbb2-amplified breast cancers identifies new genetic dependencies

Integrative molecular and functional profiling of erbb2-amplified breast cancers identifies new genetic dependencies

Play all audios:

Loading...

ABSTRACT Overexpression of the receptor tyrosine kinase ERBB2 (also known as HER2) occurs in around 15% of breast cancers and is driven by amplification of the _ERBB2_ gene. _ERBB2_


amplification is a marker of poor prognosis, and although anti-ERBB2-targeted therapies have shown significant clinical benefit, _de novo_ and acquired resistance remains an important


problem. Genomic profiling has demonstrated that ERBB2+ve breast cancers are distinguished from ER+ve and ‘triple-negative’ breast cancers by harbouring not only the _ERBB2_ amplification on


17q12, but also a number of co-amplified genes on 17q12 and amplification events on other chromosomes. Some of these genes may have important roles in influencing clinical outcome, and


could represent genetic dependencies in ERBB2+ve cancers and therefore potential therapeutic targets. Here, we describe an integrated genomic, gene expression and functional analysis to


determine whether the genes present within amplicons are critical for the survival of ERBB2+ve breast tumour cells. We show that only a fraction of the _ERBB2_-amplified breast tumour lines


are truly addicted to the _ERBB2_ oncogene at the mRNA level and display a heterogeneous set of additional genetic dependencies. These include an addiction to the transcription factor gene


_TFAP2C_ when it is amplified and overexpressed, suggesting that _TFAP2C_ represents a genetic dependency in some ERBB2+ve breast cancer cells. Access through your institution Buy or


subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Subscribe to this journal Receive 50 print issues and online


access $259.00 per year only $5.18 per issue Learn more Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which


are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS


COMPLEX REARRANGEMENTS FUEL ER+ AND HER2+ BREAST TUMOURS Article Open access 08 January 2025 IDENTIFICATION OF PUTATIVE ACTIONABLE ALTERATIONS IN CLINICALLY RELEVANT GENES IN BREAST CANCER


Article 28 August 2021 THE ROLE OF HER2 AND HER3 IN HER2-AMPLIFIED CANCERS BEYOND BREAST CANCERS Article Open access 27 April 2021 ACCESSION CODES ACCESSIONS GENBANK/EMBL/DDBJ * E-TABM-543


REFERENCES * Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A _et al_. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that


overexpresses HER2. _N Engl J Med_ 2001; 344: 783–792. Article  CAS  Google Scholar  * Geyer CE, Forster J, Lindquist D, Chan S, Romieu CG, Pienkowski T _et al_. Lapatinib plus capecitabine


for HER2-positive advanced breast cancer. _N Engl J Med_ 2006; 355: 2733–2743. Article  CAS  Google Scholar  * Vogel C, Cobleigh MA, Tripathy D, Gutheil JC, Harris LN, Fehrenbacher L _et


al_. First-line, single-agent Herceptin(R) (trastuzumab) in metastatic breast cancer. A preliminary report. _Eur J Cancer_ 2001; 37 (Suppl 1): 25–29. Article  Google Scholar  * Romond EH,


Perez EA, Bryant J, Suman VJ, Geyer CE, Davidson NE _et al_. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. _N Engl J Med_ 2005; 353: 1673–1684. Article 


CAS  Google Scholar  * Smith I, Procter M, Gelber RD, Guillaume S, Feyereislova A, Dowsett M _et al_. 2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast


cancer: a randomised controlled trial. _Lancet_ 2007; 369: 29–36. Article  CAS  Google Scholar  * Gianni L, Dafni U, Gelber RD, Azambuja E, Muehlbauer S, Goldhirsch A _et al_. Treatment with


trastuzumab for 1 year after adjuvant chemotherapy in patients with HER2-positive early breast cancer: a 4-year follow-up of a randomised controlled trial. _Lancet Oncol_ 2011; 12: 236–244.


Article  CAS  Google Scholar  * Perez EA, Romond EH, Suman VJ, Jeong JH, Davidson NE, Geyer CE _et al_. Four-year follow-up of trastuzumab plus adjuvant chemotherapy for operable human


epidermal growth factor receptor 2-positive breast cancer: joint analysis of data from NCCTG N9831 and NSABP B-31. _J Clin Oncol_ 2011; 29: 3366–3373. Article  CAS  Google Scholar  * Chin K,


DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL _et al_. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. _Cancer Cell_ 2006; 10: 529–541. CAS 


Google Scholar  * Arriola E, Marchio C, Tan DS, Drury SC, Lambros MB, Natrajan R _et al_. Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. _Lab


Invest_ 2008; 88: 491–503. Article  CAS  Google Scholar  * Staaf J, Jonsson G, Ringner M, Vallon-Christersson J, Grabau D, Arason A _et al_. High-resolution genomic and expression analyses


of copy number alterations in HER2-amplified breast cancer. _Breast Cancer Res_ 2010; 12: R25. Article  Google Scholar  * Shiu KK, Natrajan R, Geyer FC, Ashworth A, Reis-Filho JS . DNA


amplifications in breast cancer: genotypic-phenotypic correlations. _Future Oncol_ 2010; 6: 967–984. Article  CAS  Google Scholar  * Santarius T, Shipley J, Brewer D, Stratton MR, Cooper CS


. A census of amplified and overexpressed human cancer genes. _Nat Rev Cancer_ 2010; 10: 59–64. Article  CAS  Google Scholar  * Natrajan R, Lambros MB, Rodriguez-Pinilla SM, Moreno-Bueno G,


Tan DS, Marchio C _et al_. Tiling path genomic profiling of grade 3 invasive ductal breast cancers. _Clin Cancer Res_ 2009; 15: 2711–2722. Article  CAS  Google Scholar  * Mackay A, Tamber N,


Fenwick K, Iravani M, Grigoriadis A, Dexter T _et al_. A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines. _Breast Cancer Res Treat_ 2009;


118: 481–498. Article  CAS  Google Scholar  * Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Goransson H, Liljedahl U _et al_. Screening for copy-number alterations and loss of heterozygosity


in chronic lymphocytic leukemia—a comparative study of four differently designed, high resolution microarray platforms. _Genes Chromosomes Cancer_ 2008; 47: 697–711. Article  CAS  Google


Scholar  * Cleator SJ, Powles TJ, Dexter T, Fulford L, Mackay A, Smith IE _et al_. The effect of the stromal component of breast tumours on prediction of clinical outcome using gene


expression microarray analysis. _Breast Cancer Res_ 2006; 8: R32. Article  Google Scholar  * Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E _et al_. Novel patterns of genome


rearrangement and their association with survival in breast cancer. _Genome Res_ 2006; 16: 1465–1479. Article  CAS  Google Scholar  * Sims D, Bursteinas B, Gao Q, Jain E, MacKay A,


Mitsopoulos C _et al_. ROCK: a breast cancer functional genomics resource. _Breast Cancer Res Treat_ 2010; 124: 567–572. Article  CAS  Google Scholar  * Sircoulomb F, Bekhouche I, Finetti P,


Adelaide J, Ben Hamida A, Bonansea J _et al_. Genome profiling of ERBB2-amplified breast cancers. _BMC Cancer_ 2010; 10: 539. Article  Google Scholar  * Natrajan R, Weigelt B, Mackay A,


Geyer FC, Grigoriadis A, Tan DS _et al_. An integrative genomic and transcriptomic analysis reveals molecular pathways and networks regulated by copy number aberrations in basal-like, HER2


and luminal cancers. _Breast Cancer Res Treat_ 2010; 121: 575–589. Article  CAS  Google Scholar  * Tan DS, Reis-Filho JS . Comparative genomic hybridisation arrays: high-throughput tools to


determine targeted therapy in breast cancer. _Pathobiology_ 2008; 75: 63–74. Article  CAS  Google Scholar  * Kreike B, van Kouwenhove M, Horlings H, Weigelt B, Peterse H, Bartelink H _et


al_. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. _Breast Cancer Res_ 2007; 9: R65. Article  Google Scholar  * Turner N,


Lambros MB, Horlings HM, Pearson A, Sharpe R, Natrajan R _et al_. Integrative molecular profiling of triple negative breast cancers identifies amplicon drivers and potential therapeutic


targets. _Oncogene_ 2010; 29: 2013–2023. Article  CAS  Google Scholar  * Santarius T, Shipley J, Brewer D, Stratton MR, Cooper CS . A census of amplified and overexpressed human cancer


genes. _Nat Rev_ 2009; 10: 59–64. Article  Google Scholar  * Kao J, Pollack JR . RNA interference-based functional dissection of the 17q12 amplicon in breast cancer reveals contribution of


coamplified genes. _Genes Chromosomes Cancer_ 2006; 45: 761–769. Article  CAS  Google Scholar  * Boutros M, Bras LP, Huber W . Analysis of cell-based RNAi screens. _Genome Biol_ 2006; 7:


R66. Article  Google Scholar  * Zhang JH, Chung TD, Oldenburg KR . A simple statistical parameter for use in evaluation and validation of high throughput screening assays. _J Biomol Screen_


1999; 4: 67–73. Article  CAS  Google Scholar  * Lee-Hoeflich ST, Crocker L, Yao E, Pham T, Munroe X, Hoeflich KP _et al_. A central role for HER3 in HER2-amplified breast cancer:


implications for targeted therapy. _Cancer Res_ 2008; 68: 5878–5887. Article  CAS  Google Scholar  * Schoeberl B, Pace EA, Fitzgerald JB, Harms BD, Xu L, Nie L _et al_. Therapeutically


targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. _Sci Signal_ 2009; 2: ra31. Article  Google Scholar  * Bosher JM, Williams T, Hurst HC . The


developmentally regulated transcription factor AP-2 is involved in c-erbB-2 overexpression in human mammary carcinoma. _Proc Natl Acad Sci USA_ 1995; 92: 744–747. Article  CAS  Google


Scholar  * Vernimmen D, Begon D, Salvador C, Gofflot S, Grooteclaes M, Winkler R . Identification of HTF (HER2 transcription factor) as an AP-2 (activator protein-2) transcription factor and


contribution of the HTF binding site to ERBB2 gene overexpression. _Biochem J_ 2003; 370 (Pt 1): 323–329. Article  CAS  Google Scholar  * Ailan H, Xiangwen X, Daolong R, Lu G, Xiaofeng D,


Xi Q _et al_. Identification of target genes of transcription factor activator protein 2 gamma in breast cancer cells. _BMC Cancer_ 2009; 9: 279. Article  Google Scholar  * Chin SF, Wang Y,


Thorne NP, Teschendorff AE, Pinder SE, Vias M _et al_. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. _Oncogene_ 2007; 26: 1959–1970.


Article  CAS  Google Scholar  * Turner BC, Zhang J, Gumbs AA, Maher MG, Kaplan L, Carter D _et al_. Expression of AP-2 transcription factors in human breast cancer correlates with the


regulation of multiple growth factor signalling pathways. _Cancer Res_ 1998; 58: 5466–5472. CAS  PubMed  Google Scholar  * Zhao C, Yasui K, Lee CJ, Kurioka H, Hosokawa Y, Oka T _et al_.


Elevated expression levels of NCOA3, TOP1, and TFAP2C in breast tumors as predictors of poor prognosis. _Cancer_ 2003; 98: 18–23. Article  CAS  Google Scholar  * Gee JM, Eloranta JJ, Ibbitt


JC, Robertson JF, Ellis IO, Williams T _et al_. Overexpression of TFAP2C in invasive breast cancer correlates with a poorer response to anti-hormone therapy and reduced patient survival. _J


Pathol_ 2009; 217: 32–41. Article  CAS  Google Scholar  * Guler G, Iliopoulos D, Guler N, Himmetoglu C, Hayran M, Huebner K . Wwox and Ap2gamma expression levels predict tamoxifen response.


_Clin Cancer Res_ 2007; 13: 6115–6121. Article  CAS  Google Scholar  * Woodfield GW, Chen Y, Bair TB, Domann FE, Weigel RJ . Identification of primary gene targets of TFAP2C in hormone


responsive breast carcinoma cells. _Genes Chromosomes Cancer_ 2010; 49: 948–962. Article  CAS  Google Scholar  * Williams CM, Scibetta AG, Friedrich JK, Canosa M, Berlato C, Moss CH _et al_.


AP-2gamma promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene. _EMBO J_ 2009; 28: 3591–3601. Article  CAS  Google Scholar  * Delacroix L, Begon D, Chatel


G, Jackers P, Winkler R . Distal ERBB2 promoter fragment displays specific transcriptional and nuclear binding activities in ERBB2 overexpressing breast cancer cells. _DNA Cell Biol_ 2005;


24: 582–594. Article  CAS  Google Scholar  * Weinstein IB . Cancer. Addiction to oncogenes—the Achilles heal of cancer. _Science_ 2002; 297: 63–64. Article  CAS  Google Scholar  * Scaltriti


M, Eichhorn PJ, Cortes J, Prudkin L, Aura C, Jimenez J _et al_. Cyclin E amplification/overexpression is a mechanism of trastuzumab resistance in HER2+ breast cancer patients. _Proc Natl


Acad Sci USA_ 2011; 108: 3761–3766. Article  CAS  Google Scholar  * O’Brien NA, Browne BC, Chow L, Wang Y, Ginther C, Arboleda J _et al_. Activated phosphoinositide 3-kinase/AKT signaling


confers resistance to trastuzumab but not lapatinib. _Mol Cancer Ther_ 2010; 9: 1489–1502. Article  Google Scholar  * Scaltriti M, Rojo F, Ocana A, Anido J, Guzman M, Cortes J _et al_.


Expression of p95HER2, a truncated form of the HER2 receptor, and response to anti-HER2 therapies in breast cancer. _J Natl Cancer Inst_ 2007; 99: 628–638. Article  CAS  Google Scholar  *


Eichhorn PJ, Gili M, Scaltriti M, Serra V, Guzman M, Nijkamp W _et al_. Phosphatidylinositol 3-kinase hyperactivation results in lapatinib resistance that is reversed by the


mTOR/phosphatidylinositol 3-kinase inhibitor NVP-BEZ235. _Cancer Res_ 2008; 68: 9221–9230. Article  CAS  Google Scholar  * Harris LN, You F, Schnitt SJ, Witkiewicz A, Lu X, Sgroi D _et al_.


Predictors of resistance to preoperative trastuzumab and vinorelbine for HER2-positive early breast cancer. _Clin Cancer Res_ 2007; 13: 1198–1207. Article  CAS  Google Scholar  * Dave B,


Migliaccio I, Gutierrez MC, Wu MF, Chamness GC, Wong H _et al_. Loss of phosphatase and tensin homolog or phosphoinositol-3 kinase activation and response to trastuzumab or lapatinib in


human epidermal growth factor receptor 2-overexpressing locally advanced breast cancers. _J Clin Oncol_ 2011; 29: 166–173. Article  CAS  Google Scholar  * Baselga J, Gelmon KA, Verma S,


Wardley A, Conte P, Miles D _et al_. Phase II trial of pertuzumab and trastuzumab in patients with human epidermal growth factor receptor 2-positive metastatic breast cancer that progressed


during prior trastuzumab therapy. _J Clin Oncol_ 2010; 28: 1138–1144. Article  CAS  Google Scholar  * Marchio C, Natrajan R, Shiu KK, Lambros MB, Rodriguez-Pinilla SM, Tan DS _et al_. The


genomic profile of HER2-amplified breast cancers: the influence of ER status. _J Pathol_ 2008; 216: 399–407. Article  CAS  Google Scholar  * Pietersen AM, Horlings HM, Hauptmann M, Langerod


A, Ajouaou A, Cornelissen-Steijger P _et al_. EZH2 and BMI1 inversely correlate with prognosis and TP53 mutation in breast cancer. _Breast Cancer Res_ 2008; 10: R109. Article  Google Scholar


  * Hollestelle A, Nagel JH, Smid M, Lam S, Elstrodt F, Wasielewski M _et al_. Distinct gene mutation profiles among luminal-type and basal-type breast cancer cell lines. _Breast Cancer Res


Treat_ 2010; 121: 53–64. Article  Google Scholar  * Brough R, Frankum JR, Sims D, Mackay A, Mendes-Pereira AM, Bajrami I _et al_. Functional viability profiles of breast cancer. _Cancer


Discov_ 2011; 1: 260–273. Article  CAS  Google Scholar  * Farmer H, McCabe N, Lord CJ, Tutt AN, Johnson DA, Richardson TB _et al_. Targeting the DNA repair defect in BRCA mutant cells as a


therapeutic strategy. _Nature_ 2005; 434: 917–921. Article  CAS  Google Scholar  * Lambros MB, Simpson PT, Jones C, Natrajan R, Westbury C, Steele D _et al_. Unlocking pathology archives for


molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent _in situ_ hybridization. _Lab Invest_ 2006; 86: 398–408. Article  CAS  Google Scholar 


Download references ACKNOWLEDGEMENTS This work was supported by grants from Cancer Research UK, AACR as part of the Stand Up To Cancer Breast Cancer Dream Team Initiative, and Breakthrough


Breast Cancer. Dr Kai-Keen Shiu is an Avon Clinical Fellow. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research,


London, UK K-K Shiu, D Wetterskog, A Mackay, R Natrajan, M Lambros, D Sims, I Bajrami, R Brough, J Frankum, R Sharpe, N Turner, J S Reis-Filho, C J Lord & A Ashworth * Department of


Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy C Marchio * Department of Pathology, Academic Medical Centre, Amsterdam, The Netherlands H Horlings, F Reyal & M


van der Vijver Authors * K-K Shiu View author publications You can also search for this author inPubMed Google Scholar * D Wetterskog View author publications You can also search for this


author inPubMed Google Scholar * A Mackay View author publications You can also search for this author inPubMed Google Scholar * R Natrajan View author publications You can also search for


this author inPubMed Google Scholar * M Lambros View author publications You can also search for this author inPubMed Google Scholar * D Sims View author publications You can also search for


this author inPubMed Google Scholar * I Bajrami View author publications You can also search for this author inPubMed Google Scholar * R Brough View author publications You can also search


for this author inPubMed Google Scholar * J Frankum View author publications You can also search for this author inPubMed Google Scholar * R Sharpe View author publications You can also


search for this author inPubMed Google Scholar * C Marchio View author publications You can also search for this author inPubMed Google Scholar * H Horlings View author publications You can


also search for this author inPubMed Google Scholar * F Reyal View author publications You can also search for this author inPubMed Google Scholar * M van der Vijver View author publications


You can also search for this author inPubMed Google Scholar * N Turner View author publications You can also search for this author inPubMed Google Scholar * J S Reis-Filho View author


publications You can also search for this author inPubMed Google Scholar * C J Lord View author publications You can also search for this author inPubMed Google Scholar * A Ashworth View


author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHORS Correspondence to J S Reis-Filho, C J Lord or A Ashworth. ETHICS DECLARATIONS COMPETING


INTERESTS The authors declare no conflict of interest. ADDITIONAL INFORMATION Supplementary Information accompanies the paper on the Oncogene website SUPPLEMENTARY INFORMATION SUPPLEMENTARY


FIGURES (PDF 759 KB) SUPPLEMENTARY TABLES (XLS 116 KB) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Shiu, KK., Wetterskog, D., Mackay, A. _et al._


Integrative molecular and functional profiling of _ERBB2-_amplified breast cancers identifies new genetic dependencies. _Oncogene_ 33, 619–631 (2014). https://doi.org/10.1038/onc.2012.625


Download citation * Received: 29 May 2012 * Revised: 04 November 2012 * Accepted: 14 November 2012 * Published: 21 January 2013 * Issue Date: 30 January 2014 * DOI:


https://doi.org/10.1038/onc.2012.625 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not


currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative KEYWORDS * HER2-positive breast cancer * microarrays * gene


expression * comparative genomic hybridization * siRNA screens * TFAP2C