Sub theme 3.10
Translational cancer genomics and proteomics

Goals of research: general outline
Scientific achievements
Future plans: special goals and approach
Running projects
Associated staff

Workgroup leaders   Department
dr.  J.A.  Foekens   Medical Oncology

Goals of research: general outline

The Erasmus MC-Daniel den Hoed is specialized in the detection and treatment of cancer and has long-standing tradition in preclinical as well as clinical cancer research. The section of Translational Cancer Genomics and Proteomics (prof. dr. J.A. Foekens/dr. S. Sleijfer) is part of the department of Medical Oncology and consists of both a clinical section and laboratories of Genomics and Proteomics of Breast Cancer (PI: dr. J.W.M. Martens, dr. A. Umar, dr. A.M. Sieuwerts), and Integrated Genomics of Treatment Resistance (PI: dr. E.M.J.J. Berns, dr. M.P.H.M. Jansen). The overall aim of the section Translational Cancer Genomics and Proteomics is to investigate the cell biological and genetic factors involved in the development of sporadic and hereditary breast and ovarian cancer, the processes of tumor progression and treatment failure, and to move toward tailored treatments (for subgroups of patients) that are based on identified risk factors and phenotypes of individual tumors as well as circulating tumor cells. Our research programs involve clinical, translational and functional genomic and proteomic studies performed on sporadic and hereditary cancer types. Our laboratories have available breast and ovarian tissue (>15,000 samples stored in liquid nitrogen) and serum banks (>50,000 samples), >80 well-characterized breast and ovarian cancer cell lines, and various metastasizing and non-metastasizing rat and mouse tumor models. Since 1990, ~1,500 families have been registered at our family cancer clinic, the great majority of whom display site-specific hereditary breast cancer or hereditary breast/ovarian cancer syndrome. In our clinic, phase I, II and III trails with various (targeted) drugs are performed. The major research line of the section of Translational Cancer Genomics and Proteomics makes use of various high-throughput genomics (mRNA, miRNA, DNA-methylation and SNP profiling) and proteomics techniques (mass spectrometry, phopspho-protein profiling, reverse phase protein arrays) for the molecular characterization of clinical breast cancer, including circulating tumor cells, with respect to prognosis and response to systemic therapy, and extensive molecular characterization of a collection of over 40 human breast cancer cell lines (mRNA and exon arrays), including mutational analyses of a large panel of known cancer genes.

Scientific achievements

Using our high-throughput technology and bioinformatics, a large number of papers in the field of discovery and validation of cell biological factors that are associated with prognosis or therapy resistance in breast and ovarian cancer have been published in high impact journals. Many of the (validation) studies have been carried out in collaboration with research groups within the EU and the United States, and with commercial partners. In 2005 we published our established prognostic and predictive mRNA expression signatures for primary and metastatic breast cancer, respectively. The 76-gene prognostic gene signature established in untreated lymph node-negative patients has now been validated in one uni-center and three multi-center studies, also including patients who had received adjuvant tamoxifen therapy. Our 44-gene signature that predicts tamoxifen resistance in ER-positive metastatic breast cancer has successfully been validated in an independent cohort of the Dutch Cancer Institute, Amsterdam. In addition to these two algorithms we have developed and published a 31-gene mRNA signature that predicts bone metastasis in breast cancer, and a 9-gene signature to identify ovarian cancer patients who will not respond to platinum-based chemotherapy. More recently we have also established, validated, and published an 81-gene copy number signature to predict prognosis in lymph node-negative breast cancer, and a panel of 4 miRNAs that are associated with prognosis in ER-positive breast cancer. In the context of the EpiBreast consortium and and EU-FP6 project, which we coordinated, we have identified and validated several DNA-methylation markers that are associated with prognosis in tamoxifen-treated lymph-node negative and anthracycline-treated lymph node-positive primary breast cancer, and with the efficacy of response to tamoxifen therapy in advanced disease. In addition to the high-throughput genomic analyses, many quantitative RT-PCR assays have been developed for RNA and miRNA isolated from frozen as well as from formalin-fixed paraffin-embedded tissues to validate the prognostic and/or predictive value of many candidate genes we, and others, have identified. With respect to our proteomic studies using state-of-the art mass spectrometry approaches after laser capture microdissection of tissue sections, we have identified a panel of putatively differentially abundant proteins between tamoxifen-sensitive and tamoxifen-resistant tumors. Subsequent validation was performed using our tissue microarrays. Since the number of circulating tumor cells (CTC) may resemble the metastatic burden of the patient and the likelihood of the success of systemic therapy, we have recently put efforts on their enumeration and in addition their molecular characterization. It was shown that cells of one of the major genomic breast cancer subtypes (the normal-like) are overlooked by the CellSearch machine, approved by the Food and Drug Administration in the United States for the enumeration of CTC in metastatic breast cancer. In addition, to identify potential targets for treatment on an individual basis, we have developed a method to measure quantitatively the mRNA expression level of 96 selected genes in RNA of as little as two breast cancer cells in an environment of an excess leukocytes. Further information, also on our studies on hereditary cancer syndromes, and in vitro studies, including the extensive molecular characterization of >40 breast cancer cell lines, can be found at our website.

Future plans: special goals and approach

We will continue our various research lines as described by the workgroupleaders (see annexes) with the aim to identify drugable targets (pathways) and to develop individualized treatment schedules for (subgroups) of breast and ovarian cancer patients. In our genomic and proteomic studies new generation sequencing technologies and state-of-the-art mass spectrometry will be implemented. These technologies have advanced significantly over the years and to establish new prognostic and predictive algorithms, in addition to our frozen tumor bank samples, we will also use our large collection of formalin-fixed paraffin-embedded tissues, where appropriate. Our collaborations with partners of the Cancer Genomics Centre (CGC)/Netherlands Organization for Scientific Research (NWO), Top Institute Pharma (TI-Pharma), the Center for Translational Molecular Medicine (CTMM), the EU-FP7 Consortium Breast Cancer Somatic Genetic Study, as part of the International Cancer Genomics Consortium (ICGC) Breast Cancer Working Group, the EORTC – PathoBiology Group (PBG), the EORTC-Gynaecological Cancer Group (GCG), the EU-FP6 Consortium OVCAD, ovarian cancer diagnosis of a silent killer, and commercial partners, will continue to be very important for technological advancement in the discovery phase and for our large-scale clinical validation studies. The magnitude of genomic and proteomic information that we already have collected and which will significantly increase during the coming years, makes the implementation of systems biology imperative. We will therefore expand our efforts in this direction. Once potential drugable targets (pathways) have been identified we will perform mechanistic in vitro and in vivo studies. We will use our large panel of extensively characterized breast and ovarian cancer cell lines and specifically silence the target gene using RNAi in cell lines that express it. The subsequent effect of the silencing on cell proliferation, invasion/migration, apoptosis and cellular senescence will be monitored to unravel the mechanistic function of the target genes. These studies will pave the way for in debt in vivo follow-up studies yielding the true leads for the urgently needed targeted therapy development.

Most recent publications

1.                 Wang Y, Klijn JGM, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EMJJ, Atkins D, Foekens JA. Gene expression profiles to predict distant metastasis of early breast cancer. Lancet 365: 671-679 (2005). IF 28.4

2.                 Jansen MPHM, Foekens JA, van Staveren IL, Dirkszwager-Kiel MM, Ritsier K, Look MP, Meijer-van Gelder ME, Portengen H, Dorssers LCJ, Klijn JGM, Berns EMJJ. Molecular classification of tamoxifen resistant breast carcinomas by gene expression profiling. J Clin Oncol 23: 732-640 (2005). IF 17.2

3.                 Foekens JA, Atkins D, Zhang Y, Sweep CGJ, Harbeck N, Paradiso A, Cufer T, Sieuwerts AM, Talantov D, Timmermans M, Span PN, Tjan-Heijnen VCG, Mangia A, Zito AF, Specht K, Hoefler H, Meijer-van Gelder ME, Golouh R, Schittulli F, Schmitt M, Beex LVAM, Klijn JGM, Wang Y. Multicenter validation of a gene expression based prognostic signature in lymph-node-negative primary breast cancer. J Clin Oncol 24: 1665-1671 (2006). IF 17.2

4.                 Smid M, Wang Y, Klijn JGM, Sieuwerts AM, Zhang Y, Atkins D, Martens JWM, Foekens JA. Genes associated with breast cancer metastatic to bone. J Clin Oncol 24: 2261-2267 (2006). IF 17.2

5.                 Jansen MPHM, Sieuwerts AM, Look MP, Ritstier K, Meijer-van Gelder ME,  van Staveren IL, Klijn JGM, Foekens JA, Berns EMJJ. The HOXB13-to-IL17BR expression ratio is related with tumor aggressiveness and response to tamoxifen of recurrent breast cancer: a retrospective study. J Clin Oncol 25: 662-668 (2007). IF 17.2

6.                 Sleijfer S, Ray-Coquard I, Papai Z, Le Cesne A, Scurr M, Schöffski P, Collin F, Pandite L, Marreaud S, De Brauwer A, van Glabbeke M, Verweij J, Blay JY. Pazopanib, a multikinase angiogenesis inhibitor, in patients with relapsed or refractory advanced tissue sarcoma: a phase II study from the European organisation for reaserach and treatment of cancer-soft tissue and bone sarcoma group (EORTC study 62043). J Clin Oncol 27: 3126-3132 (2009). IF 17.2

7.                 Sieuwerts AM, Kraan J, Bolt-de Vries J, van der Spoel P, Elstrodt F, Schutte M, Martens JWM, Gratama JW, Sleijfer S, Foekens JA. Anti-epithelial cell adhesion molecule antibodies and the detection of circulating normal-like breast tumor cells. J Natl Cancer Inst 100: 62-66 (2009). IF 14.9

8.                 Van Agthoven T, Sieuwerts AM, Meijer-van Gelder ME, Look MP, Smid M, Veldscholte J, Sleijfer S, Foekens JA, Dorssers LCJ. Relevance of breast cancer anti-estrogen resistance (BCAR) genes in human breast cancer progression and tamoxifen resistance. J Clin Oncol 27: 542-549 (2009). IF 17.2

9.                 Zhang XHF, Wang Q, Gerald W, Hudis CA, Norton L, Smid M, Foekens JA, Massagué J. Latent bone metastasis in breast cancer tied to Src-dependent survival signals. Cancer Cell 16: 67-78 (2009). IF 25.0

10.             Bos PD, Zhang XHF, nadal C, Shu W, Gomis RR, Nguyen D, Minn AJ, van de Vijver MJ, Gerald W, Foekens JA, Massagué J. Genes that mediate breast cancer metastasis through the blood-brain barrier. Nature 459: 105-109 (2009). IF 31.4