Scientific Annual Report Scientific Annual Report 2012

Transcription

1 Contents 2 Introduction Director of Research 8 Board members Scientific Annual Report 2012 Scientific Annual Report Group leaders 12 Neil Aaronson 14 Reuven Agami 16 Roderick Beijersbergen 18 Andre Bergman 20 Rene Bernards 22 Anton Berns 24 Christian Blank 26 Eveline Bleiker 28 Jannie Borst 30 Piet Borst 32 Thijn Brummelkamp 34 Jan-Hermen Dannenberg 36 Karin de Visser 38 John Haanen 40 Michael Hauptmann 42 John Hilkens 44 Metello Innocenti 46 Heinz Jacobs 48 Jacqueline Jacobs 50 Kees Jalink 52 Jos Jonkers 54 Sabine Linn 56 Rene Medema 58 Wouter Moolenaar 60 Sach Mukherjee 62 Jacques Neefjes 64 Huib Ovaa 66 Daniel Peeper 68 Anastassis Perrakis 70 Peter Peters 72 Sven Rottenberg 74 Sanne Schagen 76 Jan Schellens 80 Alfred Schinkel 82 Marjanka Schmidt 84 Ton Schumacher 86 Titia Sixma 88 Arnoud Sonnenberg 90 Fiona Stewart 92 Hein Te Riele 94 Wim Van Harten 96 Flora Van Leeuwen & Matti Rookus 100 Fred Van Leeuwen 102 Maarten Van Lohuizen 104 Bas Van Steensel 106 Marcel Verheij 108 Jelle Wesseling 110 Lodewyk Wessels 112 Rob Wolthuis 114 Wilbert Zwart Division of Diagnostic Oncology Division of Surgical Oncology Biometrics Department Education in oncology Invited speakers Personnel index Division of Medical Oncology Division of Radiotherapy Research facilities Clinical trials Research projects

2 Netherlands Cancer Institute Plesmanlaan CX Amsterdam The Netherlands redactie Suzanne Corsetto Copyright Netherlands Cancer Institute, Amsterdam Ontwerp Room for ID s, Nieuwegein fotografie Martin Hogeboom, Epe Drukker True Colours, Utrecht

3 Scientific Annual Report 2012

4 Director of Research René Medema Introduction I am pleased to present our Scientific Annual Report. It showcases the scientific achievements of the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital (NKI-AVL) in More background information on our research programs and principle investigators can be found on our website ( or in our Scientific Brochure that is available for download on our website. The Antoni van Leeuwenhoek is a Comprehensive Cancer Center, combining a dedicated cancer hospital and cancer research institute in a single organization. The hospital has 180 beds, an outpatient clinic, a large radiotherapy department and an extensive infrastructure for clinical research that includes clinical data management, a large array of diagnostic facilities, and a pharmacy with a production unit for experimental drugs and clinical grade biologicals. Over the years the hospital has built a large repository of patient data and a large collection of tumor and normal tissues. Clinical research spans across medical, surgical and diagnostic oncology, radiotherapy, pharmacology, epidemiology and psychosocial oncology and research into cost effectiveness of health care and efficiency of planning and organization. Our hospital has seen steady growth in patient numbers over the last years, with an average annual growth of 7%. This growth is part of a planned expansion that projects a growth of our clinical production by 70% in 2020 (compared to 2010). To facilitate this growth, construction is underway to increase the capacity of our outpatient clinic, operating rooms and intensive care. Construction is planned to be completed in 2015 and will give room to 4 additional operating rooms and the necessary expansion of our intensive care unit. In 2012, building activities for the radiotherapy satellite in Hoofddorp (Spaarne Ziekenhuis) reached completion, and this site will open its doors early in We have also continued our discussions with the University Medical Center Utrecht (UMC Utrecht) to establish a joint cancer hospital next to the UMC Utrecht, and aim to start reorganizing oncological activities in Utrecht in The joint activity aims to improve the quality of cancer care, and will bring together a large critical mass in areas such as radiology, radiotherapy and personalized cancer treatment. This will facilitate further innovations in minimally invasive and non-invasive interventions as well as in tailored therapies, areas that hold great promise for further improvements in cancer care. Finally, we aim to establish a proton therapy center next to the Antoni van Leeuwenhoek, in a joint venture with the Academic Medical Center and the Free University Medical Centre and supported in a collaborative effort with the UMC Utrecht and the Princess Máxima Center for Pediatric Oncology (PMC). The proton therapy center is expected to be operational in 2016 and will treat the patients of the PMC requiring moderate to high irradiation, as well as a range of inoperable tumors in adult patients surrounded by radiation-sensitive healthy tissue. We concluded 2012 again with a modest profit for the hospital, but the growth in numbers of patients has resulted in a significant increase in the workload per employee and per square meter. An important challenge for our institute is to accommodate this growth in order to provide the required clinical care for the growing numbers of cancer patients. Yet, this growth must not compromise the high level of quality care that we strive to provide. Unfortunately, the sizeable increase of our clinical activities cannot be matched by a comparable growth in our research program. Due to the dire national economic situation, our research budget from the Ministry of Health, Welfare and Sport will face an annual reduction up to a total of 6% by the end of In addition, funding options at the Netherlands Organization for Scientific Research have seen a steady reduction under previous governments. As a result, it is becoming increasingly difficult for bottom-up research initiatives to secure funding, despite the fact that project proposals from the Netherlands Cancer Institute continue to rank well above the national average in funding percentile. On top of this shrinkage in external funding sources, emphasis in our national funding schemes has undergone a dramatic shift towards short-term valorization of scientific research. While our institute performs very well in such projects, and serves as a role model for clinical translation, we do foresee a serious bottleneck to arise in the near future. The cuts we are facing now in fundamental cancer research will inevitably become rate-limiting for further innovation and progress in a few years from now. In recent years, several of our principle investigators have been able to compensate the reductions in national funding of fundamental research by obtaining funding from the European Research Council. It is unclear how the EU research budget will develop in the next years, but the current economic situation makes it likely that this funding source will either also face reductions or not be able to compensate reductions elsewhere. table 1 Core research funding the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital by the Dutch Cancer Society and the Ministry of Health, Welfare and Sport in the period in million euros Dutch Cancer Society Ministry of Health, Welfare & Sport (excluded are the reimbursement for interest and depreciation of buildings) Total Fortunately, the Dutch Cancer Society has increased their financial support for our research by allowing a gradual increase of the core grant given by the Dutch Cancer Society to the Netherlands Cancer Institute. This funding becomes ever more important for our success, because the continuity of our research activities critically depends on a healthy ratio between core funding and external funding. That ratio has steadily shifted towards external grants, donations and short-term research agreements with third parties. Currently 65% of our total research budget comes from such sources, making it difficult to maintain sufficient manpower in the underlying infrastructure that is increasingly important to deal with the complexity of present-day cancer research. The dependence of our research activities on high-throughput screening facilities, next generation sequencing, proteomics, a state of the art animal facility, bio-informatics, analysis and maintenance of large datasets requires steady investments that cannot be easily accommodated by external grants. In an attempt to deal with this problem, we have, together with the Dutch Cancer Society, established a foundation (NKI-AVL fund) that will raise additional funds for the Netherlands Cancer Institute. In its first full year, this fund managed to raise a little over 1 million euros. Nonetheless, the large majority of those funds were earmarked for specific projects, leaving us with the continued problem of limited core funding

5 Highlights It is impossible to provide a complete overview of the total impact generated by our Institute in 2012 in this introduction. Many of the highlights can be found in the reports of the individual group leaders further on in this annual report or on our website. I have chosen to mention just a few highlights here. Let me begin with an unprecedented success of clinical translation. In March of 2012, the Bernards group published a manuscript explaining how colon carcinomas carrying a B-Raf mutation fail to respond to B-Raf inhibitory drugs that are successfully used in the treatment of melanomas carrying the same mutations. They subsequently showed how the resistance to B-Raf inhibitors could be overcome in colon cancer in tissue culture and in mice. In November 2012, the first colon carcinoma patient entered a clinical trial in our hospital to validate this conceptual advance, an unprecedented timeline between discovery and clinical trial. This example very nicely demonstrates how crosstalk between research and clinic can lead to rapid translation at The Netherlands Cancer Institute. The Bernards group recently identified another mechanism of resistance that might soon lead to new clinical trials. They identified MED12, a component of the transcriptional MEDIATOR complex, as a determinant of response to ALK and EGFR inhibitor drugs in lung cancer. Inhibition of TGFβR signaling can restore drug responsiveness, suggesting a strategy to treat tumors that have acquired drug resistance as a result of activated TGFβ signaling. Liesbeth Vredeveld and Patricia Possik in the group of Daniel Peeper showed that targeted inhibition of PI(3) Kinase restores senescence features in melanoma cells, providing another concept that can be tested for clinical applicability. Janneke Jaspers in the groups of Jos Jonkers and Sven Rottenberg, found that Brca1-mutated mouse mammary tumors acquire resistance to PARP inhibitors through inactivation of 53BP1, suggesting that 53BP1 may play an important role in therapy response and resistance of BRCA1-mutated and BRCA1-like cancers. Piet Borst and Henri van Luenen elucidated the long sought-after function of a modified base in the DNA (called base J). With the help of our deep sequencing facility and the group of Peter Myler in Seattle, they showed that Base J is clustered at chromosomeinternal RNA polymerase II termination sites. These findings have broad implications for our understanding of the formation of repressive chromatin and how chromatin marks can define transcriptional boundaries. Mathias Jenal, Ran Elkon and Fabricio Loayza-Puch in the group of Reuven Agami identified the PABPN1 gene as a regulator of alternative cleavage and poly-adenylation of messenger RNAs (mrnas), a process linked to proliferation and cancer. Intriguingly, PABPN1 is causal of oculopharyngeal muscular dystrophy (OPMD), and cellular and mouse model systems showed induction of alternative polyadenylation by mutant PABP1, linking this for the first time with a genetic disease. In the group of Arnoud Sonnenberg, Coert Margadant identified a novel missense mutation in the gene encoding the integrin a3 subunit that causes interstitial lung disease and nephrotic syndrome. Francesca Mattiroli in the group of Titia Sixma studied the role of ubiquitination in the DNA damage response, showing that RNF168, not RNF8 ubiquitinates H2A after ionizing radiation. Her studies revealed that this mark is positioned at a novel site on the histone protein, and that this modification, rather than the RNF168-dependent chain formation, is essential for recruitment of downstream effectors such as Brca1 and 53BP1. Karim Nacerddine and colleagues in the group of Maarten van Lohuizen showed that the key Polycomb E3 ubiquitin ligase Bmi/Ring1B is regulated by phosphorylation, coupling Pi3K/AKT signaling to epigenetic gene regulation. Phosphorylation of Bmi1 correlates with PTEN-loss and PI3K activation in prostate cancer with high grade and poor prognosis, whereas mutation of the phosphorylation sites diminishes the oncogenic effects of Bmi1 in prostate cancer cells. Jonathan Coquet and coworkers in the group of Jannie Borst identified novel signaling pathways that suppress the function of pathogenic T-helper 17 cells, a class of T cells that promotes inflammation and auto-immunity. Nienke van Rooij and Marit van Buuren in the Schumacher lab provided the first evidence that information on the mutations present within individual tumors can be used to successfully predict mutant T cell epitopes that are recognized by cytotoxic T cells. This approach may in future studies be utilized for the development of personalized immunotherapies. Metamia Ciampricotti from the group of Karin de Visser demonstrated that -against the prevailing dogmaadaptive immune cells do not affect the outcome of chemotherapy treatment of established spontaneous mammary tumors. The division of Radiotherapy reported the long-term results of the EORTC breast cancer trial. This multi-centric trial was the first to investigate the efficacy of breastconserving therapy in early breast cancer up to 5 cm. Importantly, the study concluded that survival outcomes are similar in patients treated with breast-conserving therapy or modified radical mastectomy, confirming that breast-conserving therapy can be safely applied in patients with early breast cancer up to 5 cm. The group also showed that local recurrence in prostate cancer is significantly lower when patients are irradiated with a higher local dose. The Epidemiology Group showed that diagnostic radiation exposure of BRCA1/2 mutation carriers is associated with an increased breast cancer risk. Any exposure to diagnostic radiation before the age of 30 was associated with a 1.9-fold increased risk of breast cancer, with a dose-response pattern. The results of this study support the use of nonionizing radiation imaging techniques (such as magnetic resonance imaging) as the main tool for surveillance in young women with BRCA1/2 mutations. The psychosocial research group of Neil Aaronson demonstrated the efficacy of cognitive behavioral therapy and physical exercise in helping to alleviate endocrine symptom burden in young women with breast cancer who experience chemotherapyinduced menopause. Such behavioral approaches to treating menopausal symptoms are important, as available medicines are either contraindicated for women with breast cancer or have significant side effects. Quality of Research The quality of our research can be monitored in several ways. First of all, objective bibliometric parameters (citations and impact of scientific articles published by NKI staff) demonstrate that our scientific productivity continues to be outstanding (see table 2). The year 2012 is no exception to this trend and it is gratifying to note, that despite the difficulties to obtain sufficient funds for our research, we manage to maintain our position at the international forefront of cancer research. Secondly, our prominent international standing in cancer research is reflected by the frequency with which our staff members are invited to present at international meetings and in the awards and grants that they obtain. We score high on all of these accounts. Several NKI-postdocs have received competitive grants from national and international organizations. In addition, a number of our principle investigators received prestigious (inter)national research grants. Jacqueline Jacobs and Thijn Brummelkamp were awarded an ERC Starting Grant, Reuven Agami received an ERC Advanced Grant. Fred van Leeuwen received a prestigious VICI grant and Rene Bernards received the Queen Wilhelmina Research Award. Anton Berns coordinated the Mouse Clinic for Cancer and Ageing, together with the European Institute for the Biology of Ageing (ERIBA). They received 18 million euros from the National Roadmap to build a national research facility for the generation of mouse models for cancer and ageing. The ERC Synergy proposal of Anton Berns, Daniel Peeper, Lodewyk Wessels and groups of the Sanger Institute was selected out of over 700 proposals and was awarded with 15 million euros for the next 5 years. This project, entitled COMBATCANCER, will seek to optimize personalized medicine for lung and melanoma cancer. Finally, Rene Bernards coordinated a Zwaartekracht proposal that was awarded 30 million euros for the next 10 years. In this project several other groups from the NKI, as well as groups from several academic institutions, will 4 5

6 work together to study (targeted) drug responses and optimize targeted therapies. The quality of research within each division is assessed every 5 years by external site visit teams. In 2012 we have organized several site visits. On March 5th and 6th, a site visit team composed of Hidde Ploegh (MIT, Boston), Reinhard Faessler (Max- Planck Institute, Martinsried), Vivek Malhotra (CRG, Barcelona), Rienk Offringa (DKFZ, Heidelberg) and Benjamin Geiger (Weizmann Institute, Rehovot) evaluated the divisions of Cell Biology I, Cell Biology II and Immunology. On May 14th, a site visit committee formed by Johann De Bono (ICR, London), Antoni Ribas (Jonsson Comprehensive Cancer Center, UCLA), Rolf Stahel (UZH, Zurich) and Ian Tannock (The Princess Margeret, Toronto) evaluated the research program of the division of Medical Oncology. Finally, on December 18th and 19th, a site visit team formed by Roel Nusse (Stanford, CA), Kristian Helin (BRIC, Copenhagen), David Livingston (DFCI, Boston), Simon Boulton (Clare Hall Laboratories, London) and Michael Gottesman (NCI, Center for Cancer Research, Bethesda) evaluated the research of the divisions of Molecular Pathology, Molecular Oncology, Molecular Genetics and Biological Stress Response. The overall impression of each of these committees was very positive and the ranking of the majority of the evaluated principle investigators was outstanding. All committee members were impressed with the international standing of our research programs, considering the relatively small size of our institute. Several valuable suggestions were made; how to further strengthen the ties between fundamental and clinical research, how to provide more support for our junior investigators. We will implement these suggestions where possible in the next years. Honors and Appointments The NKI-AVL cannot award university degrees, but many of our staff members hold special part-time chairs at Dutch Universities. This allows them to award PhD degrees to graduate students who receive their training at the Netherlands Cancer Institute. Currently, 33 staff members have professorships at one of the Dutch Universities. In 2012, Huib Ovaa was appointed Professor of Chemical Biology at Leiden University, Lodewyk Wessels as Professor of Bioinformatics at the Technical University in Delft and Sabine Linn as Professor of Translational Oncology at the University Medical Center in Utrecht. table 2 Short term citations and impact of scientific articles published by the Netherlands Cancer Institute research staff /2012 Publication publications citations citations/ impact year Publications , , , , , , , , , , , There were several changes in our staff. Karin de Visser was appointed as junior group leader, Sven Rottenberg was appointed as staff member and head of the intervention unit of our mouse cancer clinic, and Jacqueline Jacobs was appointed as tenured staff member. With my appointment as Scientific Director, my research group also took up base at the The Netherlands Cancer Institute, in the division of Cell Biology I. Staff of the NKI-AVL fulfilled numerous functions in national and international organizations, on boards of scientific journals, as members of study sections, site visit committees and as organizers or co-organizers of scientific meetings, workshops and conferences. Jannie Borst and Jos Jonkers were elected as members of the European Molecular Biology Organization (EMBO). Outlook and Acknowledgements For the last decennia our Institute has been at the international forefront in cancer research and innovative cancer treatments. It has demonstrated to be able to maintain that position, despite the difficult economic situation of the last few years. We have been very successful in obtaining external grants for our research and I am convinced that we will continue to do so. Provided that we can match this with a healthy ratio of core funding, I foresee that the Netherlands Cancer Institute can continue to deliver important breakthroughs that will prove beneficial in the treatment of cancer. Particularly in a time when our ever growing molecular understanding of cancer meets up with a new generation of anti-cancer drugs that target well-defined nodal points in the cancer cell. This calls for a more individualized treatment of cancer, in which molecular pathology in the form of a genetic and/or immunological fingerprint of the tumor is extensively used in making clinical decisions how to treat the individual patient. Success in this area will critically depend on a close collaboration between basic and clinical research; where basic research can provide the concepts for new drug combinations that can be taken to the clinic, and vice-versa, where response failure of a genetically and immunologically defined tumor in the clinic can be taken to the lab to identify alternative strategies. The integration of research and clinic in a single Comprehensive Cancer Center provides us with the ideal setting to facilitate this collaboration, and our first concrete steps in this area hold great promise for the future. However, these promising developments bring new demands for our research infrastructure that cannot be financed from external project grants. It is therefore imperative that we raise additional funds through alternative routes to enable us to maximize our research efforts in this area. This will receive high priority in the coming years. Our newly established NKI-AVL fund and our upcoming anniversary provide us with great opportunities to obtain such funds. In 2013, The Netherlands Cancer Institute will celebrate its 100th year anniversary. We will use this year to bring our new ambitions to the attention of a large audience, ranging from individuals to large organizations. By showcasing our past performance and by providing a clear explanation of the opportunities that lie within our grasp, combined with the drive and enthusiasm of our employees, we should be able to convince a wide audience to support our cause. I want to end by thanking all of our employees and everyone that supported us; the Dutch Cancer Society that has been a very significant sponsor of our research for many years; the Ministry of Health Welfare and Sport that provides a substantial core grant to our Institute and has provided the funds to renovate our research facilities; and all of those individuals that provided us with financial, moral and practical support. Their support is making it possible for us to continue to strive for better treatments to improve the outlook of cancer patients. And last but not least, I would like to extend my sincere gratitude to all of our patients willing to participate in our clinical studies; they are vital to the progress that we can make. René Medema Director of Research 6 7

7 Board members Chairman of Board of Governors T de Swaan Board of Directors Scientific Advisory Council International scientific advisory board National scientific advisory board RH Medema Chairman and Director of Research S Rodenhuis Director Clinical Research and Development WH Van Harten Director Organization and Management RH Medema Chairman TNM Schumacher Secretary S Rodenhuis B Van Steensel (until October 1, 2012) T Ruers T De Lange Leon Hess Professor, The Rockefeller University, New York, USA RA Flavell Professor of Immunobiology, Yale University School of Medicine, New Haven, USA WGJ Ho Professor of Biochemistry and Biological Structure, University of Washington, Seattle, USA DD Breimer Professor of Pharmacology, Leiden University JL Bos Professor of Physiological Chemistry, University of Utrecht EGE De Vries Professor of Medical Oncology, University of Groningen J Jonkers ML Van Lohuizen J Mendelsohn President MD Anderson Cancer Center, University of Texas, Houston, USA JHF Falkenburg Professor of Experimental Hematology, Leiden University Board of Governors P Nurse Professor of Microbiology, President of The Rockefeller University, New York, USA CG Figdor Professor of Experimental Immunology, Radboud University Nijmegen T De Swaan President EH Swaab Vice-president R Nusse Professor of Developmental Biology, Stanford University, Stanford, USA HL Ploegh Professor of Biology, Whitehead Institute for Biomedical Research, Cambridge, USA JHJ Hoeijmakers Professor of Molecular Genetics, Erasmus University Rotterdam P Lambin Professor of Radiation Oncology, Maastricht University JP Balkenende GH Blijham S Powell Chairman, Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, USA CJH Van de Velde Professor of Surgical Oncology, Leiden University FH Schröder MC Smeets F Sijbesma (from October 1, 2012) PC Van der Vliet MJ Van Mourik IF Tannock Daniel E. Bergsagel Professor of Medical Oncology, Princess Margaret Hospital and University of Toronto, Toronto, Ontario, Canada (from June 1, 2012). K Vousden Director, Beatson Institute for Cancer Research, Glasgow, UK RA Weinberg Professor of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, USA 8 9

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9 A A Group leader Neil Aaronson Neil Aaronson PhD Group leader Marieke Van Leeuwen PhD Post-doc Chantal Lammens PhD Post-doc Willem Eijzenga MSc PhD student Lisanne Hummel MSc PhD student Hanna Van Waart MSc PhD studentt Marijke Wevers MD MSc PhD student Jacobien Kieffer MSc Senior statistical analyst Marianne Berkhof Research assistant Miranda Gerritsma Research assistant Marianne Kuenen Research assistant Jacoline Melis MSc Research assistant Grace Sidharta Research assistant Publications Duijts SFA, van Beurden M, Oldenburg HSA, Hunter MS, Kieffer JM, Stuiver MM, Gerritsma MA, Menke-Pluymers MBE, Plaisier PW, Rijna H, Lopes Cardozo AMF, Timmers GJ, van der Meij S, van der Veen H, Bijker N, de Widt-Levert LM, Geenen MM, Heuff G, van Dulken EJ, Boven E, Aaronson NK. Efficacy of cognitive behavioral therapy and physical exercise in alleviating treatment-induced menopausal symptoms in patients with breast cancer: Results of a randomized controlled multicenter trial. J Clin Oncol 2012;30: Gundy CM, Fayers PM, Groenvold M, Petersen MA, Scott NW, Sprangers MAG, Velikova G, Aaronson NK. Comparing higher order models for the EORTC QLQ-C30. Qual Life Res 2012;21: Hilarius DL, Kloeg PH, van der Wall E, van den Heuvel JJG, Gundy CM, Aaronson NK. Chemotherapy-induced nausea and vomiting in daily clinical practice: A community hospitalbased study. J Support Care Cancer 2012;20: Holzner B, Efficace F, Basso U, Incrocci L, Johnson C, Aaronson N, Arraras J, King M, Chow E, Oberguggenberger A, Bottomley A, Steiner H, Giesinger J. Cross-cultural development of an EORTC questionnaire to assess health-related quality of life in patients with testicular cancer: The EORTC TC26. Qual Life Res, 2012 Khoshnevisan A, Yekaninejad MS, Ardakani SK, Pakpour AH, Mardani A, Aaronson NK Translation and validation of the EORTC brain cancer module (EORTC QLQ-BN20) for use in Iran. Health Qual Life Outcomes 2012;10:54 Lagerwaard FJ, Aaronson NK, Gundy CM, Cornelis JA, Slotman BJ, Senan S. Patient-reported quality of life after stereotactic ablative radiotherapy for early stage lung cancer. J Thorac Oncol 2012;7: Nieuwenhuis MH, Douma KFL, Bleiker EMA, Aaronson NK, Clevers H, Vasen HFA. Clinical evidence for an association between familial adenomatous polyposis (FAP) and type II diabetes. Int J Cancer 2012;131: Scott NW, Etta JA, Aaronson NK, Bottomley A, Fayers PM, Groenvold M, Koller M, Kuli D, Marais D, Petersen MA, Sprangers MA. An evaluation of the response category translations of the EORTC QLQ-C30 questionnaire. Qual Life Res 2012 Snyder C, Aaronson N, Choucair A, Elliott T, Greenhalgh J, Halyard M, Hess R, Miller D, Reeve B, Santana M. Implementing patient-reported outcomes assessment in clinical practice: A review of the options and considerations Qual Life Res 2012;21: Snyder CF, Blackford AL, Wolff AC, Carducci MA, Herman JM, Wu AW, Aaronson N, Gotay C, Halyard M, Hynes D, Jones JB, Yount S, Velikova G. Feasibility and value of PatientViewpoint: A web system for patient-reported outcomes assessment in clinical practice. Qual Life Res, 2012 Wevers MR, Hahn DE, Verhoef S, Bolhaar MD, Ausems MG, Aaronson NK, Bleiker EM. Breast cancer genetic counseling after diagnosis but before treatment: Treatment consequences and psychological impact. Pat Educ Counsel 2012;89:89-95 Health-related quality of life assessment and behavioral interventions in clinical oncology This research line has two primary foci: (1) development of methods and applications of health-related quality of life (HRQL) assessment in clinical research and clinical practice; and (2) development and testing of behavioral and psychosocial interventions to reduce symptom burden and improve the HRQL of patients with cancer. Methods and measures for assessing the HRQL of long-term survivors of testicular and prostate cancer This study, a collaboration between the EORTC Quality of Life and Genitourinary Cancer Groups, has two primary objectives: (1) to test the logistics required to conduct long-term survivorship studies within the context of the EORTC; (2) to pilot test questionnaires for assessing the HRQL of long-term cancer survivors (> 10 years disease free). We recruited 280 long-term prostate and testicular cancer survivors who had participated in EORTC phase III clinical trials. Patients were drawn from 3 broad geographic/cultural regions: (1) Northern Europe; (2) Southern Europe; and (3) the United Kingdom. HRQL was assessed at 3 levels: (1) generic (the SF-36 Health Survey); (2) cancer-specific (the EORTC QLQ-C30 plus condition-specific modules; and (3) cancer survivor-specific (the Impact of Cancer). Time required to obtain medical ethical approval for the patient survey ranged from 1.5 to 25 months. We encountered most problems with obtaining ethical approval in the UK, Italy and Belgium. The average time to recruit patients and field the survey questionnaire was 3 months. Completed questionnaires were received from 242 patients. Although many survivors scored at the upper extremes of the questionnaires, in general, the SF36, the QLQ-C30 and the IOCv2 exhibited adequate reliability (< 0.70), and known groups validity (e.g., discriminated between subgroups formed on the basis of comorbidity and age). The QLQ-C30 condition-specific modules could benefit from modification for cancer survivor populations (e.g., by deleting acute, treatment-related side effects). Identifying symptom clusters in the endocrine scale of the Functional Assessment of Cancer Therapy Measurement System (The FACT-ES) The FACT-ES is an 18-item questionnaire assessing treatmentinduced endocrine symptoms. Currently, the scoring algorithm for the FACT-ES yields a single, overall score. We carried out a psychometric study to identify a potential subscale structure for the FACT-ES, reflecting symptom clusters. We used questionnaire data from 422 breast cancer patients who had experienced chemotherapy-induced menopause. Using exploratory factor analysis, we identified 6 symptom clusters: vasomotor symptoms, gynaecological symptoms, sexual symptoms, mood, weight, and other endocrine symptoms. Confirmatory factor analysis confirmed this subscale structure in a second sample of 141 women who had undergone prophylactic oophorectomy due to a heightened risk of familial breast/ovarian cancer, and who had experienced treatment-induced menopause. These findings support the tenability of generating both subscale and overall scores for the FACT-ES. This will allow a more detailed assessment and reporting of endocrine symptoms. Physical exercise during chemotherapy to improve physical fitness and reduce fatigue (PACES) In this multicenter RCT we are evaluating the effectiveness of two physical exercise interventions in maintaining or enhancing physical fitness and minimizing fatigue in patients undergoing adjuvant chemotherapy for breast or colon cancer: (1) a low intensity, home-based, self-management program; and (2) a moderate intensity, structured, supervised program. All participants undergo physical performance tests and complete selfreport questionnaires at baseline, at the completion of chemotherapy, and at 6 month follow-up. We completed patient recruitment in December In total, we have entered 253 patients (230 and 23 with breast and colon cancer, respectively), of whom 190 have completed the first follow-up (T1) and 140 the 6-month follow-up (T2). Data collection will continue until December Behavioral and psychosocial effects of rapid genetic counseling and testing (RGCT) in newly diagnosed breast cancer patients In this multicenter, randomized trial, carried out in collaboration with the University Medical Center Utrecht (Dr. Margreet Ausems), we are investigating the uptake of RGCT when offered routinely to newly diagnosed breast cancer patients who, prior to receiving primary treatment, are identified as having at least a 10% risk of carrying a mutation in the BRCA1/2 gene, and the impact of RGCT on choice of surgery and psychosocial well-being. Women were recruited from 12 hospitals in the Amsterdam and Utrecht regions of the Netherlands and were randomized to either the RGCT group or a usual care group (2:1 ratio). The study endpoints include: (1) uptake of RGCT; (2) choice of clinical management strategy, including direct bilateral mastectomy or delayed preventive contralateral mastectomy; (3) cancer risk perception and cancer-related distress; (4) knowledge of genetic aspects of breast cancer; (5) decisional satisfaction; (6) HRQL; and (6) satisfaction with RGCT. Between 2008 and 2010, 265 women were randomized into the study. Questionnaires were administered at study entry, and at 6 month (response 92.5%) and 12 month follow-up (response 90.6%). A subset of women has been interviewed to obtain supplementary, qualitative data. Follow-up was completed in 2012 and data analysis is currently ongoing. Online cognitive behavioral therapy (CBT) for climacteric symptoms in breast cancer patients experiencing treatment-induced menopause Menopausal symptoms are common, and may be particularly severe in younger women with breast cancer who undergo treatment-induced menopause. Effective and safe treatment options for these symptoms in breast cancer patients are needed. In a recently completed RCT, we demonstrated the efficacy of a group-based, CBT program that included psychoeducation, cognitive restructuring, behavioral strategies and relaxation training. However, compliance with the program was problematic. In attempt to increase the accessibility to and compliance with this CBT program, we are developing a web-based version in collaboration with MindDistrict and King s College, London. The program is currently under development and will be tested iteratively for feasibility and effectiveness. Wolf SL, Barton DL, Qin R, Wos EJ, Sloan JA, Liu H, Aaronson NK, Satele DV, Mattar BI, Green Nb, Loprinzi CL. The relationship between numbness, tingling and shooting/burning pain in patients with chemotherapy induced peripheral neuropathy (CIPN) as measured by the EORTC QLQ-CIPN20 instrument. Support Care Cancer 2012;20: Petersen MA, Aaronson NK, Arraras JI, Chie W-C, Conroy T, Costantini A, Giesinger JM, Holzner B, King MT, Singer S, Velikova G, Verdonck-de Leeuw IM, Young T, Groenvold M. The EORTC computer-adaptive tests (CATs) measuring physical functioning and fatigue exhibited high levels of measurement precision and efficiency J Clin Epidemiol (in press) Victorson DE, Brucker PS, Bode RK, Eton DT, Talcott JA, Clark JA, Knight SJ, Litwin MS, Moinpour CM, Reeve BB, Aaronson NK, Bennett CL, Herr HW, McGuire M, Shevrin D, McVary K, Cella D. Ensuring Comprehensive Assessment of Urinary Problems in Prostate Cancer through Patient- Physician Concordance. Urol Oncol (in press) Chinapaw MJM, Buffart LM, van Mechelen W, Schep G, Aaronson NK, van Harten WH, Stuiver MM, Kersten MJ, Nollet F, Kaspers GJK, van Dulmen-den Broeder E, Huisman J, Takken T, van Tulder M, Brug J. Alpe d HuZes Cancer Rehabilitation (A-CaRe) research: Four randomized controlled exercise trials and economic evaluations in cancer patients and survivors. Int J Behav Med 2012;19: Reeve BB, Wyrwich KW, Wu AW, Velikova G, Terwee CB, Snyder CF, Schwartz C, Revicki DA, Moinpour CM, McLeod LD, Lyons JC, Lenderking WR, Hinds Ps, Hays RD, Greenhalgh J, Gershon R, Feeny D, Fayers PM, Cella D, Brundage M, Ahmed S, Aaronson NK, Butt Z on behalf of the International Society for Quality of Life Research (ISOQOL). ISOQOL recommends minimum standards for patientreported Outcome Measures Used in Patient-Centered Outcomes Research. Qual Life Res 2013 Kuijpers W, Groen WG, Aaronson NK, van Harten WH. A systematic review of web-based interventions for patient empowerment and physical activity in chronic diseases: Relevance for cancer survivors. J Med Internet Res (in press) Smith EML, Barton DL, Qin R, Steen PD, Aaronson NK, Loprinzi CL. Assessing patient-reported peripheral neuropathy: The reliability and validity of the European Organization for Research and Treatment of Cancer QLQ-CIPN20 Questionnaire. Qual Life Res (in press) 12 13

10 A A Division head, group leader Reuven Agami Reuven Agami Group leader Rani Elkon PhD Post-doc Nicolas Léveillé PhD Post-doc Mathias Jenal PhD Post-doc Fabricio Loayza Puch PhD Post-doc Pieter Van Breugel PhD Post-doc Boris Slobodin PhD Post-doc Jarno Drost MSc PhD student Marieke Van Kouwenhove MSc PhD student Arnold Bos MSc PhD student Carlos Melo MSc PhD student Koos Rooijers MSc PhD student Rui Lopes MSc PhD student Mariëtte Schrier PhD Technical staff Joachim Oude Vrielink Technical staff Publications Melo CA, Drost J, Wijchers, PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Leveille N, Kalluri R, de Laat W and Agami R. ernas Are Required for p53-dependent Enhancer Activity and Gene Transcription. Mol Cell Elkon R, Drost J, van Haaften G, Jenal M, Schrier M, Oude Vrielink JA, and Agami R. E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol 2012;13:R59 Morris AR, Bos A, Diosdado B, Rooijers K, Elkon R, Bolijn AS, Carvalho B, Meijer GA and Agami R. Alternative Cleavage and Polyadenylation during Colorectal Cancer Development. Clin Cancer Res. 2012;18: Korkmaz G, le Sage C, Tekirdag KA, Agami R and Gozuacik D. mir- 376b controls starvation and mtor inhibition-related autophagy by targeting ATG4C and BECN1. Autophagy 2012;8: Jenal M, Elkon R, Loayza-Puch F, van Haaften G, Kuhn U, Menzies FM, Oude Vrielink JA, Bos AJ, Drost J, Rooijers, K, Rubinsztein DC, Agami R. The poly(a)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 2012;149: Wilting SM, Snijders PJ, Verlaat W, Jaspers A, van de Wiel MA, van Wieringen WN, Meijer GA, Kenter GG, Yi Y, le Sage C, Agami R, Meijer CJ, Steenbergen RD. Altered microrna expression associated with chromosomal changes contributes to cervical carcinogenesis. Oncogene 2012;3;32: Wilting SM, Verlaat W, Jaspers A, Makazaji NA, Agami R, Meijer CJ, Snijders PJ, Steenbergen RD. Methylation-mediated transcriptional repression of micrornas during cervical carcinogenesis. Epigenetics. 2013;8 Tekirdag KA, Korkmaz G, Ozturk DG, Agami R, Gozuacik D. MIR181A regulates starvation- and rapamycininduced autophagy through targeting of ATG5. Autophagy. 2013;9: Identifying and characterizing novel cancerous processes Our main research objective is to understand the cancerous process in humans with the focus on RNA-directed gene regulation. We either use RNA as a tool to interfere with cellular gene expression or study various cellular RNA types to uncover novel cancer causing or inhibiting genetic programs. The knowledge we gather is used to design novel therapeutic approaches. Research line 1: Functional screens using RNA interference (RNAi) All human tumors harbor multiple genetic alterations that activate oncogenes, inhibit tumor suppressors and induce genomic instability. As each tumor contains many genetic alterations, the study of the contribution of each alteration to the cancerous phenotype was obscured. We developed and successfully used an RNA interference (RNAi) approach to inactivate genes in mammalian cells to identify and characterize cancerous genes. As an example, we lately identified and characterized the role of the gene BRD7 (bromodomaincontaining 7) as a protein whose inhibition allows full neoplastic transformation in the presence of the tumor suppressor p53. Our results proposed a tumor suppressive role in breast cancer. Now, we generate a mouse model system for BRD7 to study in detail its in vivo role as a tumor suppressor, and to assess novel therapeutic strategies. Research line 2: Functional screens to identify cancerous mirnas In the past years we initiated studies to identify cancerous micrornas (mirnas), a newly emerging gene family encoding for endogenous small RNAs. We developed novel and unique genetic approaches to screen for cancer-causing and cancerpreventing mirnas. With these tools we discovered and characterized the role of the micrornas in autophagy, tumor growth, cancer and metastasis. Research line 3: Interplay between mirnas and RNA binding proteins in cancer We recently noticed that the regions surrounding some functional mirna targets are highly conserved throughout evolution. We hypothesized that these regions recruit RNA binding proteins (RBPs) to control mirna function during induction of various stress responses. We performed genetic screens and identified and characterized RBPs that can inhibit or potentiate the accessibility of mirnas to their target mrnas. We suggest that the genetic interaction between mirnas and RBPs influence developmental processes, cellular proliferation, and cancer. Research line 4: Regulation of alternative cleavage and polyadenylation of mrnas The 3 -end of most message RNAs (mrnas) is cleaved and polyadenylated, a process that is required for mrna function. Recent discoveries revealed that a large proportion of human genes contain more than one polyadenylation site. Therefore, alternative cleavage and polyadenylation (APA) is a widespread phenomenon that generates mrnas with alternative 3 ends. Potentially, APA generates isoforms differing in their coding and non-coding regions, thereby affecting gene function and its regulation by mirnas and RBPs. Thus, APA provides an important regulatory layer of gene expression. Interestingly, very strong genome-wide switches in APA are observed when cells are stimulated to proliferate, differentiate, and during cancer progression. However, how APA is regulated and what is its function, are largely unknown. To identify regulators of APA we developed a reporter-based RNAi screen and devised a genome-wide approach to detect 3 ends of mrnas (named 3 Seq). With these tools we identified the gene PABPN1 as a regulator of APA. Loss-of PABPN1 resulted in extensive 3 UTR shortening and a compromised mirna-mediated repression. Interestingly mutations in PABPN1 causes the autosomal dominant oculopharyngeal muscular dystrophy (OPMD). Intriguingly, the expression of mutant PABPN1 in both a mouse model of OPMD and human cells elicited 3 UTR shortening, linking for the first time APA with a genetic disease. We conclude that PABPN1 is a suppressor of APA (figure 1). Additionally, we explored, on a transcriptome-wide scale, APA events that are associated with cancer. First, we comprehensively mapped APA events associated with cellular proliferation and transformation, and cancer. Second, we demonstrated that E2F-mediated transcriptional regulation of 3 -end processing genes is one of the key mechanisms that links APA to proliferation. Increase in E2F activity enhances 3 -end processing expression that results in more potent usage of alternative polyadenylation sites (figure 2). Research line 5: Role of enhancer RNAs in controlling gene expression and in cancer It is well known that the p53 tumor suppressor gene regulates transcription and cell cycle progression by binding within or nearby target genes controlling cell proliferation and survival. We found that p53 binds genomic regions located distantly from any known p53 target gene. Interestingly, many of these regions possess conserved p53-binding sites and all known hallmarks of enhancer regions. We demonstrate that these p53-bound regions are indeed enhancers. Moreover, these p53-binding sites produce enhancer RNAs (ernas) that are required for enhancer activity. The production of ernas is interesting, as they can be used to control enhancer activity and phenotype (figure 3). Figure 1: A model for PABPN1 s Mode of Action in Regultion of APA. Schematic model for PABPN1 s role in suppressing APA (upper and middele panels). Normally, PABPN1 binds APA sites and competes with the 3 -end cleavage and polyadenylation machinery (CPSF). Expression of an OPMD mutant PABPN1 (trepabpn1) sequesters wild type PABPN1 in aggregates causing 3 UTR shortening. Figure 2: E2F controls alternative cleavage and polyadenylation of mrnas. Many 3 -end enzymes are under the control of the E2F transcription factor. When cell enter proliferation, E2F level and activity increase, resulting in more 3 -end cleavage activity and induction of broad mrna shortening. Figure 3: p53-induced ernas are required for p53 function. The p53 tumor suppressor gene binds enhancers to generate ernas and activate distal genes. Knocking down ernas results in reduced enhancer activity

11 B B Group leader Roderick Beijersbergen Roderick Beijersbergen PhD Group leader Pasi Halonen PhD Post-doc Kathy Jastrzebski PhD Post-doc Jos Poell PhD Post-doc Jordi Vidal-Rodriguez PhD Post-doc Johan Kuiken MSc PhD student Klaas De Lint MSc PhD student Cor Lieftink MSc Bioinformatician Ben Morris Technical staff Wouter Nijkamp Technical staff Publications Kuiken HJ, Egan DA, Laman H, Bernards R, Beijersbergen RL, Dirac AM. Identification of F-box only protein 7 as a negative regulator of NF-kappaB signalling. J Cell Mol Med. 2012;16: Prahallad A, Sun C, Huang S, Di Nico lan tonio F, Salazar R, Zecchin D, Beijers bergen RL, Bardelli A, Bernards R. Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature. 2012;483:100-3 Huang S, Holzel M, Knijnenburg T, Schlicker A, Roepman P, McDermott U, Garnett M, Grernrum W, Sun C, Prahallad A, Groenendijk FH, Mittempergher L, Nijkamp W, Neefjes J, Salazar R, Ten Dijke P, Uramoto H, Tanaka F, Beijersbergen RL, Wessels LF, Bernards R. MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-beta Receptor Signalling. Cell. 2012;151: Unraveling signalling networks in cancer The complexity and heterogeneity of cancer poses an enormous challenge for the identification and selection of effective cancer therapies. Genomic alterations occurring in human tumours frequently affect components of signalling networks, thereby contributing to cancerous phenotypes. As a result, components of these signalling networks represent potential targets for cancer therapy. However, the complex structure of these networks, the extensive crosstalk between pathways and unanticipated feedback control pose a major challenge in the selection of the right targets for individual patients. Our research evolves around the development and application of RNAi technologies in largescale cell based screening to identify critical components of signalling networks deregulated in cancer that can be explored as drug targets in cancer therapy. Furthermore, we use these RNAi technologies to search for potential mechanisms of resistance and thereby potential combination treatments. We use dynamic phosphoproteomic profiling of signalling pathways in the context of specific tumour associated mutations with the goal to generate predictive models for therapy response to pathway targeted therapeutics in cancer. Generation of computational models for predicting response to therapy in breast cancer The understanding of the complex dynamic circuitry of signalling pathways in the context of targeted inhibition is highly valuable for identifying biomarkers to stratify patients, and to enable the identification of more effective combination therapies. In this project our focus is on the PI3-Kinase and MAP-kinase signalling pathways, both of which are strongly implicated in breast cancer. Although genetic alterations in these pathways are frequently observed, drugs targeting specific components display limited success in the clinic. The understanding and modelling of these pathways and the complex regulatory feedback regulation will allow for the generation of predictive models for therapy response in individual cancers. We have characterized a set of more than 30 human breast cancer lines for their sensitivity to more than 15 different pathway targeted drugs. We have analysed genomic alterations present in these tumour cell lines together with gene expression analysis. We have used reverse phosphoprotein arrays to analyse the activation state of a large number of individual components in the PI3K and MAPK signalling networks. In a parallel approach we are generating a panel of cell lines, derived from normal mammary epithelial cells, carrying specific genetic alterations in the PI3K and MAPK signalling pathways e.g. PIK3CA mutation or PTEN loss. We use RNAi for perturbation experiments and Luminex technology for the quantification of the activation status of individual pathway components in a dynamic fashion. The data obtained from these different experimental model systems is used to create a dynamic and quantitative computational model of pathway status and the response to perturbation using clinically relevant pathway-targeted drugs. Enhancers for response to targeted therapeutics Examples of successes with pathway-targeted drugs have fuelled the expectation that this type of drugs holds great promise in cancer treatment. At present, many of these drugs are in clinical development, but their successes are limited. Complicated interactions with other signalling pathways and unexpected feedback loops underlie the limited effectiveness and, in some instances, even accelerate the tumourigenic process. In this project we apply large-scale RNAi screens to identify genes that upon knockdown increase the response to specific inhibitors in the PI3K and MAPK pathways. To this end, we use the pooled shrna screening technology in combination with next generation sequencing in different model systems including breast, lung and colon cancer. We have screened the colon cancer cell line HCT116, carrying activating mutations in both the PI3K and MAPK pathway, for genes that upon knockdown enhance the response to either PI3-kinase or MEK kinase inhibition or both simultaneously. As expected, we identify mtorc1 as a crucial intersection of these 2 pathways controlling cell survival. However, apart from this crucial node, we also find a number of receptor tyrosine kinase receptors that are selectively required for the survival of cells only in the presence of either or both inhibitors. We are currently exploring these interactions in several cancer cell lines carrying similar alterations in these pathways. Synthetic lethal interactions with oncogenic RAS For the effective treatment of cancer, there is a great need for drugs that specifically target tumour cells without affecting normal cells. With the use of RNA interference, we explore synthetic lethal phenotypes in mammalian cells. By using our isogenic cell line pair of primary human BJ fibroblasts harbouring an oncogenic RAS V12 allele we identified, among others, kinesin family member 18A (KIF18A) as synthetic lethal interaction with oncogenic RAS. We have shown that silencing of KIF18A has a detrimental effect on human fibroblasts expressing a HRAS, KRAS or NRAS oncogene. Time-lapse imaging of mitotic events showed that silencing of KIF18A resulted in a more pronounced mitotic arrest associated with an increase in apoptosis in cells expressing oncogenic RAS V12 (see figure). Furthermore, we observe a strong correlation between the effects of KIF18A silencing and the RAS mutation status in a panel of Non-Small-Cell Lung Cancer cell lines. Together these results suggest that KIF18A synthetic lethality is context independent and could be explored as a therapeutic target in tumours carrying an activated RAS oncogene. Time-lapse microscopy of cells and analysis of duration of mitosis and subsequent cellular faith. Comparison between RAS wild-type cells and cells expression oncogenic RAS in the absence or presence of KIF18A knockdown