Amsterdam UMC

Louis Vermeulen Group

Cancer molecular subtypes, stem cell dynamics, colorectal cancer, microenvironment

Kép

Our Focus

Our group seeks to elucidate the origin and evolution colorectal cancer (CRC). We have set up and developed a collection of state-of-the-art tools and techniques to study cancer stem cell dynamics. Stem cells are essential for the homeostasis of most adult human tissues. Previously we identified stem-like cells that fuel the growth and progression of CRC. We defined the impact of oncogenic mutations on stem cell dynamics in the intestine. We use this knowledge and state-of-the-art research tools to develop novel, and more effective therapies for CRC.  

 

We elucidate mode of growth of colon cancer tissue and study how the microenvironment determines clonogenicity. Furthermore, we investgate microenvironmental factors that regulate stem cell function in cancers.  

About Louis Vermeulen

My Research

Louis Vermeulen MD PhD studied medicine at the University of Amsterdam. In 2010 he obtained his PhD (cum laude) on the topic of cancer stem cells in colorectal cancer. He spent several years at the Cancer Research UK institute in Cambridge as a postdoctoral Fellow. Louis trained as a medical oncologist and established his independent research group at the Cancer Center Amsterdam of the Amsterdam UMC. Currently he is Vice President and head of Discovery Oncology at Genentech inc., and professor of molecular oncology at the Amsterdam UMC – University of Amsterdam.

Awards
  • NYSCF Robertson Stem Cell Investigator Award

  • ERC Starting Grant (2015);ERC Consolidator Grant (2021)

  • Vidi (2015) ;Vici (2021)

  • Ammodo-KNAW Life Science Award

Key Publications
  1. Molecular characterization of colorectal cancer related peritoneal metastatic disease.
    Lenos KJ, Bach S, Ferreira Moreno L, Ten Hoorn S, Sluiter NR, Bootsma S, Vieira Braga FA, Nijman LE, van den Bosch T, Miedema DM, van Dijk E, Ylstra B, Kulicke R, Davis FP, Stransky N, Smolen GA, Coebergh van den Braak RRJ, IJzermans JNM, Martens JWM, Hallam S, Beggs AD, Kops GJPL, Lansu N, Bastiaenen VP, Klaver CEL, Lecca MC, El Makrini K, Elbers CC, Dings MPG, van Noesel CJM, Medema JP, Koster J, Koens L, Punt CJA, Tanis PJ, de Hingh IH, Bijlsma MF, Tuynman JB, Vermeulen L.Nat Commun. 2022 Aug 4;13(1):4443. doi: 10.1038/s41467-022-32198-z.

  2. Apc-mutant cells act as supercompetitors in intestinal tumour initiation.
    van Neerven SM, de Groot NE, Nijman LE, Scicluna BP, van Driel MS, Lecca MC, Warmerdam DO, Kakkar V, Moreno LF, Vieira Braga FA, Sanches DR, Ramesh P, Ten Hoorn S, Aelvoet AS, van Boxel MF, Koens L, Krawczyk PM, Koster J, Dekker E, Medema JP, Winton DJ, Bijlsma MF, Morrissey E, Léveillé N, Vermeulen L.Nature. 2021 Jun;594(7863):436-441. doi: 10.1038/s41586-021-03558-4. Epub 2021 Jun 2.

  3. Continuous clonal labeling reveals uniform progenitor potential in the adult exocrine pancreas.
    Lodestijn SC, van den Bosch T, Nijman LE, Moreno LF, Schlingemann S, Sheraton VM, van Neerven SM, Koning JJ, Vieira Braga FA, Paauw NJ, Lecca MC, Lenos KJ, Morrissey E, Miedema DM, Winton DJ, Bijlsma MF, Vermeulen L.Cell Stem Cell. 2021 Nov 4;28(11):2009-2019.e4. doi: 10.1016/j.stem.2021.07.004. Epub 2021 Aug 5.

  4. Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts.
    van der Heijden M, Miedema DM, Waclaw B, Veenstra VL, Lecca MC, Nijman LE, van Dijk E, van Neerven SM, Lodestijn SC, Lenos KJ, de Groot NE, Prasetyanti PR, Arricibita Varea A, Winton DJ, Medema JP, Morrissey E, Ylstra B, Nowak MA, Bijlsma MF, Vermeulen L.Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6140-6145. doi: 10.1073/pnas.1813417116. Epub 2019 Mar 8.

  5. Stem cell functionality is microenvironmentally defined during tumour expansion and therapy response in colon cancer.
    Lenos KJ, Miedema DM, Lodestijn SC, Nijman LE, van den Bosch T, Romero Ros X, Lourenço FC, Lecca MC, van der Heijden M, van Neerven SM, van Oort A, Leveille N, Adam RS, de Sousa E Melo F, Otten J, Veerman P, Hypolite G, Koens L, Lyons SK, Stassi G, Winton DJ, Medema JP, Morrissey E, Bijlsma MF, Vermeulen L.Nat Cell Biol. 2018 Oct;20(10):1193-1202. doi: 10.1038/s41556-018-0179-z. Epub 2018 Sep 3.

Members

Louis Vermeulen
Group leader
Adrian Logiantara    
Research Technician
Chiara Jongerius    
Post Doc
Clara Elbers    
Research Manager
Isabel Mora Martinez    
Research analyst
Jasmijn Linssen    
Phd Candidate
Job Kesselaar    
PhD student
Joyaditya Saha    
Phd Candidate
Kristiaan Lenos    
Post Doc
Laura Swart    
PhD Student
Lauri Borghuis    
PhD student
Lisanne Nijman    
Research technician
Milou van Driel    
PhD student
Nicolas Leveille    
Post Doc
Nina de Groot    
Research technician
Oscar Bril    
PhD Student
Pascale Schafrat    
Phd Candidate
Rodrigo Leite de Oliveira    
Postdoc fellow
Sander van Hooff     
Bioinformatician
Sanne van Neerven    
PhD student
Sinejan Ozcan    
Phd Candidate
Steven Eleonora    
Phd Candidate
Tim van der Plas    
PhD student
Tineke Buffart    
Senior Scientist
Jan Paul Medema Group

Experimental Oncology and Radiobiology

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Our Focus

The laboratory of Experimental Oncology and Radiobiology houses multiple research teams under my supervision and the supervision of L. Vermeulen. These teams study cancers of the gastrointestinal tract, specifically oesophageal, pancreas and colorectal cancer. The aim is to understand the heterogeneity present within cancers and between distinct cancer patients. For pancreas and colorectal cancer, we have been instrumental in the design of molecular subtypes that identify patient groups with clearly distinctive tumours from a biological point of view. Understanding the way these molecular subtypes arise and how they are wired in molecular terms is key to our research program. In addition, we aim to reveal subtype -specific vulnerabilities in order to design better therapies. Interaction with the microenvironment, the ECM, nutrients, microvasculature and immune components is part of our studies to unravel the subtypes and to find novel targets for therapy.   

For our studies we depend on primary tumour material from patients and hence we have optimal connection to several clinical departments. Moreover, organoids and xenografts derived from human tumour as well as a wide range of mouse models is part of our research infrastructure.   

About Jan Paul Medema

Name

Jan Paul Medema

Position
Oncode Investigator at AMC
Awards
  • 2009: Dutch Society of Gastroenterology Tytgat award
  • 2007: VICI laureate of the Dutch Science Organization
  • 2002: C.J.Kok prize
  • 2000: VIDI laureate of the Dutch Science Organization
  • 1996: Dutch Cancer Society Fellowship
  • Honorary Professorship Brunel University London, UK
Key publications
  1. Ramesh, P., Di Franco, S., Atencia Taboada, L., Zhang, L.,…..& Medema, J.P. (2022). BCL-XL inhibition induces an FGFR4-mediated rescue response in colorectal cancer. Cell Reports, 38(7):110374.
  2. Ramesh, P., Lannagan, T.R.M., Jackstadt, R,, Atencia Taboada, L., Lansu, N.,….& Medema, J.P. (2021) BCL-XL is crucial for progression through the adenoma-to-carcinoma sequence of colorectal cancer. Cell Death Differentiation, 28(12):3282-3296.
  3. Linnekamp, J.F., Hooff, S.R.V., Prasetyanti, P.R., Kandimalla, R., Buikhuisen, J.Y.,…..& Medema JP. (2018)Consensus molecular subtypes of colorectal cancer are recapitulated in in vitro and in vivo models. Cell Death Differentiation, 25(3):616-633.
  4. Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., …., Medema, J.P.* &….. Tejpar S.* (2015). The consensus molecular subtypes of colorectal cancer. Nature Medicine, 21(11):1350-6.
  5. Felipe De Sousa, E. M., Wang, X., Jansen, M., Fessler, E., Trinh, A., De Rooij, L. P., ... Medema J.P.* & Vermeulen, L.* (2013). Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nature Medicine19(5), 614.
  6. Vermeulen, L., Felipe De Sousa, E. M., Van Der Heijden, M., Cameron, K., De Jong, J. H., Borovski, T., ... & Medema J.P. (2010). Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nature Cell Biology12(5), 468.
  7. *shared senior authorships
Awards
  • 2009: Dutch Society of Gastroenterology Tytgat award

  • 2007: VICI laureate of the Dutch Science Organization

  • 2002: C.J.Kok prize

  • 2000: VIDI laureate of the Dutch Science Organization

  • 1996: Dutch Cancer Society Fellowship

  • Honorary Professorship Brunel University London, UK

Key Publications
  1. Ramesh, P., Di Franco, S., Atencia Taboada, L., Zhang, L.,…..& Medema, J.P. (2022). BCL-XL inhibition induces an FGFR4-mediated rescue response in colorectal cancer. Cell Reports, 38(7):110374.

  2. Ramesh, P., Lannagan, T.R.M., Jackstadt, R,, Atencia Taboada, L., Lansu, N.,….& Medema, J.P. (2021) BCL-XL is crucial for progression through the adenoma-to-carcinoma sequence of colorectal cancer. Cell Death Differentiation, 28(12):3282-3296.

  3. Linnekamp, J.F., Hooff, S.R.V., Prasetyanti, P.R., Kandimalla, R., Buikhuisen, J.Y.,…..& Medema JP. (2018)Consensus molecular subtypes of colorectal cancer are recapitulated in in vitro and in vivo models. Cell Death Differentiation, 25(3):616-633.

  4. Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., …., Medema, J.P.* &….. Tejpar S.* (2015). The consensus molecular subtypes of colorectal cancer. Nature Medicine, 21(11):1350-6.

  5. Felipe De Sousa, E. M., Wang, X., Jansen, M., Fessler, E., Trinh, A., De Rooij, L. P., ... Medema J.P.* & Vermeulen, L.* (2013). Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nature Medicine19(5), 614.

  6. Vermeulen, L., Felipe De Sousa, E. M., Van Der Heijden, M., Cameron, K., De Jong, J. H., Borovski, T., ... & Medema J.P. (2010). Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nature Cell Biology12(5), 468.

*shared senior authorships

Members

Jan Paul Medema
Oncode Investigator
Arezo Torang    
PhD student
Benthe H. Doeve    
PhD student
Ciro Longobardi    
PhD student
Joan de Jong     
Technician
Katherine Cameron     
Technician
Lidia Atencia Taboada    
PhD student
Martin Huisman    
Technician
Polina Deenichina    
Phd student
Rebecca Roessler    
Phd student
Roxan Helderman    
Postdoc
Saskia van den Bergh    
Technician
Selami Baglamis    
Technician
Tobias Ackermann    
PostDoc
Valérie Wouters    
PhD student
Ynze van Cleef    
Bioinformatician
  
Joep Grootjans Group

The role of the immune system in cancer development and progression

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Our Focus

My research focusses on the interplay between cancer and inflammation. We have three major research lines in the lab:  

  1. Colitis-associated cancer (CAC) is the most feared complication of Inflammatory Bowel Disease (IBD). We investigate how chronic intestinal inflammation in IBD patients induces immune-cell adaptations that promote CAC development. In particular, we study intrinsic anti-inflammatory mechanisms emerging during cycles of inflammation, which are beneficial to dampen inflammation but simultaneously promote CAC by decreasing immunosurveillance.  

  

  1. Next to inflammation-induced cancer, we also investigate how cancer treatment (immunotherapy) results in intestinal inflammation. Immune-checkpoint blockade (anti-PD1, anti-CTLA4) has shown unprecedented responses in selected patients with metastasized cancer, yet it also has considerable side-effects, such as the development of immune-checkpoint inhibitor-induced (ICI) colitis. In the DECIPHER study, we aim to develop predictive algorithms for susceptibility to develop such immune-related side effects. This is key to select patients in which prophylactic colon-specific anti-inflammatory therapy should be started concomitant with immunotherapy, to avoid cessation of anti-cancer therapy in these patients.  

  

  1. Third, we study the role of the peritoneal immune system in peritoneal metastasized disease, a disease entity for which no therapies are available, and thus with a large unmet clinical need. We recently discovered that the human peritoneal immune system is immunosuppressive in nature, as for example demonstrated by the large amounts of suppressive macrophages. In pre-clinical in vivo and in vitro models, we test immunomodulatory treatments. With the help of Oncode, we are currently setting up a clinical proof of concept study to target intraperitoneal suppressive macrophages as a treatment option of peritoneal metastasized gastric- and colorectal cancer. 

About Joep Grootjans

Members

Joep Grootjans
Oncode Investigator
Rosalia Franco Fernandez    
PhD student
Dalia Lartey    
PhD student
Dennis Poel    
PostDoc
Fabienne Verburg    
PhD Student
Hina Naz Khan    
PostDoc
Job Saris    
PhD student
Jurriaan Romano    
PhD Student
Kelly van Wijnbergen    
PhD student
Maaike Jong    
Postdoc
Nina Mezgec Mrzlikar    
PhD student
Rose Leijdesdorff    
PhD student
Sofía Frigerio    
PhD student
Stephanie de Wit    
Research technician
 
   
Sarah Derks Group

GEA, genome-immunome interactions, intratumor heterogeneity, targeted-immunotherapy

Kép

Our Focus

My research focus is finding better therapies for patients with gastroesophageal cancer (GEA) by studying the biological foundation of the disease. Using 1) clinically relevant patient cohorts, 2) patient-derived cancer models, and 3) in vivo mouse models we aim to understand resistance to conventional therapies and find methods to improve those.   

My group currently focusses on the following research lines:  

  1.  Identification of cancer-cell derived immune suppressive mechanisms. Using our GEA biobank we have analysed the immune infiltrate and secretum of cancer and immune cells and use this data to understand how cancer cells suppress tumour infiltrating immune cells and use this knowledge to reinstate the antitumor immune response.  
  1. Establishing a patient-derived cancer immune coculture system to test novel immunotherapeutic strategies. This co-culture model is optimized and currently the foundation of multiple inter-institutional collaborations.  
  1. Study the role of VEGFA in resistance to immunotherapy using a recently established immunogenic GEA mouse model.  
  1. Perform a drug-repurposing screen to find better therapies for chemotherapy-resistant GEAs.  

    As a physician-scientist I play a key role in different investigator-initiated trials to test novel immune stimulating treatment strategies such a the AUSPICIOUS-trial, LOAD-study and MEMENTO trial.  

About Sarah Derks

My Research

Sarah Derks is a medical oncologist at Amsterdam UMC in Amsterdam, the Netherlands. She did her PhD at the pathology department of the Maastricht University Medical Center and residency training Internal Medicine and Medical Oncology Fellowship at the VU University Medical Center in Amsterdam. After acquiring a translational research fellowship from the Dutch Cancer Society, she carried out post-doctoral training (2014-2017) in the laboratory of Dr. Adam Bass at Dana-Farber Harvard Cancer Center in Boston, MA, USA, working on a variety of genome and immune oriented studies in gastroesophageal adenocarcinomas (GEA).

Having returned to the Netherlands Dr Derks started her own research group with a focus on how GEA cells shape their immune microenvironment and how a pre-existing immune infiltrate influences response to standard therapy with the ultimate goal to identify novel targeted immunomodulatory strategies and improve survival of patients with this deadly disease. Her lab currently focusses on how genome features such chromosomal instability, intratumor heterogeneity and upregulation of oncogenic or immunomodulatory genes influences the immune microenvironment and thereby response to therapy. As a physician scientist she has the unique opportunity to use fresh tumor specimen to study the disease that is actually living in the patient and use this tissue to test new therapeutic approaches. Besides laboratory oriented studies she is a PI on 2 investigator initiated trials testing novel GEA treatment strategies.

Sarah Derks is member of the Gastro-Intestinal Faculty group from the European Society of Medical Oncology, member of the Research board of the Amsterdam UMC, and Executive Board member of the Immuno-Oncology Center at Amsterdam UMC.

Awards
  • 2017 NWO veni

  • 2016 Young investigator award American Society of Clinical Oncology

  • 2015 Wong Familiy Award in Translational Oncology

  • 2012 Translational Research Fellowship Dutch Cancer Society

  • 2004 Kootstra Talent Fellowship

Key Publications
  1. van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022. doi:10.3390/CANCERS14204986.

  2. de Klerk LK, Goedegebuure RSA, van Grieken NCT et al. Molecular profiles of response to neoadjuvant chemoradiotherapy in oesophageal cancers to develop personalized treatment strategies. Mol Oncol 2021; 154:901–914

  3. Goedegebuure RSA, Harrasser M, de Klerk LK et al. Pre-treatment tumor-infiltrating T cells influence response to neoadjuvant chemoradiotherapy in esophageal adenocarcinoma. Oncoimmunology 2021. doi:10.1080/2162402X.2021.1954807.

  4. de Klerk LK, Patel AK, Derks S et al. Original research: Phase II study of pembrolizumab in refractory esophageal cancer with correlates of response and survival. J Immunother Cancer 2021; 99:2472.

  5. Derks S, de Klerk LK, Xu X et al. Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas. Annals of Oncology 2020; 31:1011–1020.

  6. Pectasides E, Stachler MD, Derks S et al. Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma. CANCER DISCOVERY | 2018. doi:10.1158/2159-8290.CD-17-0395.

  7. Kim J, Bowlby R, Mungall AJ et al. Integrated genomic characterization of oesophageal carcinoma. Nature 2017 541:7636 2017; 5417636:169–175.

  8. Derks S, Nason KS, Liao X et al. Epithelial PD-L2 expression marks Barrett’s esophagus and esophageal Adenocarcinoma. Cancer Immunol Res 2015; 310:1123–1129.

Members

Sarah Derks    
Group leader
Daniëlle Polling    
PhD
Jasper Sanders    
Phd student
Jens Seidel    
Research Associate
Julia Myrda    
PhD
Kayla Brugman    
Phd student
Maryam Akbarzadeh    
Postdoctoral researcher
Rok Žiberna    
Phd student
Sterre Kruize    
PhD