Research interest
The focus of this group is on the application of innovative functional genomics tools to identify novel genes that have a role in the biology of cancer. We use both high-throughput gain-of-function genetic screens with retroviral cDNA expression libraries and loss-of-function RNA interference genetic screens to identify novel components of cancer-relevant pathways.
Gain-of-function genetic screens
We use retroviral cDNA expression libraries to identify novel genes that act in pathways, which are frequently deregulated in human cancer. In short, these genetic screens involve the infection of a cell population with a high-complexity retroviral cDNA expression library, selection of cells with altered phenotype, followed by identification of the cDNA responsible for the phenotype. In the past years, we have successfully used this approach to identify novel genes that act in several cancer-relevant pathways and to identify biomarkers of drug resistance.
Loss-of-function genetic screens
Mammalian genetic approaches to study gene function have been hampered by the lack of tools to efficiently generate stable loss-of-function phenotypes. To overcome this limitation, we designed a mammalian expression vector (pSUPER) that directs the synthesis of short hairpin transcripts that get processed intracellularly into siRNA-like molecules. Using this technology, we have generated a number of “gene family” knockdown libraries, in which all members of a gene family are individually targeted for suppression by shRNA vectors. One particular focus has been the family of de-ubiquitinating enzymes (DUBs), which act as antagonists of ubiquitin ligases to remove ubiquitin moieties from proteins. Using this DUB knockdown library, we have identified the cylindromatosis tumor suppressor gene (CYLD) as a regulator of the anti apoptotic transcription factor NF-kB and USP1 as a regulator of the Fanconi anemia D2 protein (FANCD2). More recently, we have completed the construction of a collection of some 55,000 shRNA vectors, targeting 23,000 mouse and human genes.
One of our recent innovation in the screening of such complex shRNA libraries is the development of so called “bar code screening” technology, in which tens of thousands of shRNA vectors can be screened in parallel for their role in a specific process. We have used large-scale loss of function genetic screens to identify novel components of the p53 pathway and to identify biomarkers of resistance to specific cancer therapeutics.
Key publications
Agami, R., and Bernards, R. (2000). Distinct initiation and maintenance mechanisms cooperate to induce G1 cell cycle arrest in response to DNA damage. Cell 102, 55-66.
Shvarts, A., Brummelkamp, T., Koh, E., Daley, G.Q., and Bernards, R (2002). A senescence rescue screen identifies BCL6 as an inhibitor of antiproliferative p19ARF-p53 signalling. Genes, Dev. 16, 681-686.
Van de Vijver, M.J., He, Y.D., van ’t Veer, L.J., Dai, H., A M Hart, A.A.M., Voskuil, D., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J., Parrish, M., Atsma, D., Witteveen, A., Glas, A., Delahaye, L., van der Velde, T., Bartelink, H., Rodenhuis, S., Rutgers,E. Th., Friend, S.H. and Bernards, R.. (2002). A gene expression signature as a predictor of survival in breast cancer. New England J. Med. 347, 1999-2009.
Brummelkamp, T.R., Nijman, S.M.B., Dirac, A.M.G., and Bernards, R. (2003). Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kB. Nature, 424, 797-801.
Berns, K., Hijmans, E.M., Mullenders, J., Brummelkamp, T.R., Velds, A., Heimerikx, Kerkhoven, R. M., Madiredjo, M., Nijkamp, W., Weigelt, B., Agami, R., Ge, W., Cavet, G., Linsley, P.S., Beijersbergen, R.L. and Bernards, R. (2004). A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature, 428, 431-437.
Nijman, S.M.B., Huang, T.T., Dirac, A.M.G., Brummelkamp, T.R., Kerkhoven, R.M., D’Andrea, A.D and Bernards, R. (2005). The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway. Mol. Cell, 17, 331-339.
Epping, M.T., Wang, L, Edel, M.J., Hernandez, M, and Bernards, R. (2005). The human tumor antigen PRAME is a dominant repressor of retinoic acid receptor signaling. Cell, 122, 835-847.
Brummelkamp, T.R., Fabius, A., Mullenders, J., Madiredjo, M., Velds, A., Kerkhoven, R.M., Bernards, R., and Beijersbergen, R.L. (2006). An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors. Nature Chem. Biol. 2, 202-206.
Kortlever, R.M., Higgins, P.J., Bernards, R. (2006). Plasminogen activator inhibitor-1 is a critical downstream target of p53 in the induction of replicative senescence. Nature Cell Biol. 8, 878-884.
Berns, K., Horlings, H., Hennessy, B.T., Madiredjo, M., Hijmans, E.M., Beelen, K., Linn, S.C., Gonzalez-Angulo, A.M., Stemke-Hale, K., Hauptmann, M., Beijersbergen, R.L., Mills, G.B., van de Vijver, M.J., and Bernards, R. (2007). A functional genetic approach identifies the PI3K pathway as a major determinant of Trastuzumab resistance in breast cancer. Cancer Cell 12, 395-402.
Reviews
Bernards, R. and Weinberg, R.A. (2002). Metastasis genes: A progression puzzle. Nature, 418, 823.
Brummelkamp, T.R. and Bernards, R (2003). New tools for functional mammalian cancer genetics. Nature Rev. Cancer, 3, 781-789.
Nijman, S.M.B., Luna-Vargas, M.P.A., Velds, A., Brummelkamp, T.R., Dirac, A.M.G., Sixma, T.K., and Bernards, R. (2005). A Genomic and Functional Inventory of Deubiquitinating Enzymes. Cell, 123, 773-786.
Rowland, B.D., and Bernards, R. (2006). Re-evaluating cell cycle regulation by E2Fs. Cell 127, 871-874.
Bernards, R., Brummelkamp, T.R., and Beijersbergen, R.L. (2006). shRNA libraries and their use in cancer genetics. Nature Methods 3, 701-706.
Van ‘t Veer, L.J., and Bernards, R (2008). Enabling personalized cancer medicine through analysis of gene expression patterns. Nature, 452, 564-570.
More publications by René Bernards on PubMed
List of relevant websites
Centre for Biomedical Genetics:
http://www.biomedicalgenetics.nl/participant.php?participant_id=1
Biographic sketch
René Bernards received his Ph.D. in 1984 from the University of Leiden where he studied cell transformation by adenovirus in the laboratory of Alex van der Eb. He joined the group of Robert Weinberg at the Whitehead Institute in Cambridge, USA for his postdoctoral training. Here, he was involved in the identification of the retinoblastoma tumor suppressor gene and studied the role of myc oncogenes in tumor progression. He joined the Massachusetts General Hospital Cancer Center as an assistant professor in 1988 to study function of oncogenes and tumor suppressor genes. In 1992 he was appointed senior staff scientist at the Netherlands Cancer Institute where he studies mammalian cell cycle regulation. In addition, he has been a part time professor of molecular carcinogenesis at Utrecht University since 1994.
More recently, his group has focused on the development of new tools to carry out genome-wide genetic screens for the identification of genes that act in cancer-relevant pathways. His laboratory employs both retroviral cDNA expression libraries in gain-of-function genetic screens as well as RNA interference to carry out large-scale loss-of-function genetic screens.
He has also set up a large DNA microarray facility to study gene expression patterns in cancer. This work has demonstrated that breast cancer patients with poor clinical outcome have a distinctive 70 gene "poor prognosis" gene expression signature. This work also led to the formulation of the hypothesis that a metastatic phenotype is acquired relatively early in tumor development, rather than late. In 2003 he co-founded a company named Agendia to introduce microarray technology in the clinical management of cancer.
He received several awards for his research, including the Pezcoller Foundation-FECS Recognition for Contribution to Oncology, the Ernst W. Bertner Award for Cancer Research from the M.D. Anderson Cancer Center, the ESMO Lifetime Achievement Award in Translational Research in Breast Cancer and the Spinoza award from the Netherlands Organization for Scientific Research. He is a member of the Royal Netherlands Academy of Arts and Sciences.
Co-workers
Katrien Berns PhD (Post-doc)
Annette Dirac PhD (Post-doc)
Michael Holzel MD, PhD (Post-doc)
Sidong Huang PhD (Post-doc)
Rianne Oosterkamp MD (Clinical fellow)
Ernst-Jan Geutjes MSc (Graduate student)
Guus Heynen MSc (Graduate Student)
Jasper Mullenders Msc Graduate Student)
Marielle Hijmans MSc (Technical staff)
Vacancies