Immunology: Ton Schumacher
Research interest: Cancer Immunology
The aim of our research is straightforward 1). To design novel technologies that can be used to examine and modify antigen-specific T cell immunity 2). To use these tools to unravel and manipulate the molecular processes underlying immune recognition by T lymphocytes. Within these projects, a main focus is on the design and testing of novel concepts for adoptive immunotherapy of cancer.
Dissecting antigen-specific T cell immunity in human cancer
There is now substantial evidence that therapeutic manipulation of immune reactivity can result in clinically meaningful effects on human cancer. For example, T cell responses induced by T cell checkpoint blockade, or infusion of ex vivo expanded tumor-infiltrating T cells (TIL therapy), has shown substantial activity in metastatic melanoma. Importantly, at present it is largely unknown which cytotoxic T cell reactivities mediate such cancer regressions. Furthermore, knowledge of such reactivities would be of obvious use, both to monitor current therapies and to design more targeted strategies that selectively aim to enhance immune reactivity against these antigens.
To address this issue, we have developed a broadly applicable "MHC-based toolkit" for the parallel detection of many different T cell populations within a single sample. In many ongoing projects we are now using this platform to understand the effects of for instance TIL therapy and T cell checkpoint blockade in cancer patients.
A particularly intriguing twist to this research line is the
notion that mutated 'neo-antigens' that could serve as regression
antigens in patients may be identified on the basis of cancer exome
data. Towards this purpose, we generate maps of all tumor-specific
mutations within human cancer lesions and use this information to
analyze reactivity against predicted mutated peptides by T cells
from the same patient. Interestingly, the first evidence for
the feasibility of this exome-based approach to identify human
neo-antigens has recently been obtained. In the coming years, this
approach should offer the possibility to determine to what extent
the mutational landscape in human tumors is recognized by cytotoxic
T cells. In addition, this link between cancer genomics and T cell
immunology may allow one to address fundamental questions about
cancer immune editing, and may suggest novel ways to harness the T
cell repertoire in human disease.
(Selected references: Toebes et al., Nat Med 2006; Hadrup et al., Nat Methods 2009, Heemskerk et al., EMBO J 2012, Kvistborg et al., Curr Opin Immunol 2013, van Rooij et al., J Clin Oncol 2013)
Dissection of cellular immunity through single cell tracing
To also allow the tracing of cell fate at the single cell level, we have developed technologies with which individual cells can be tagged with genetic barcodes. This tagging technology relies on the use of oncoretroviral and lentiviral libraries containing thousands of different DNA 'barcodes'. Infection of progenitor cells of interest by these libraries of viral vectors and subsequent analysis of the barcodes present within the cell populations that arise from them can then be utilized to reveal lineage relationships. In recent projects, we have for instance used this barcode labeling strategy, together with second generation sequencing, to measure the output of individual antigen-specific T cells, and to address which (types of) progeny are generated by individual multipotent hematopoietic progenitors in vivo. In addition to this in vivo single cell tracing work, we have become highly interested in a specialized subset of tissue-resident memory T cells. In recent work we have demonstrated the existence of a population of "skin patrolling memory T cells" that cruise through former sites of infection, and in ongoing work we are evaluating how this T cell population can form a possible link between renewed antigen production and the development of a state of 'pathogen alert'.
(Selected references: van Heijst et al., Science 2009; Schumacher et al., Nat Rev immunol 2010, Ariotti et al., PNAS 2012, Gerlach et al., Science 2013, Naik et al., Nature 2013)
Adoptive T cell therapy (collaboration with Haanen lab)
The cornerstone of our translational work is the development and
evaluation of adoptive T cell therapies for human cancer. The
MHC-based monitoring strategies described above form a very useful
starting point for the further clinical development of TCR
engineered T cell therapy, an area of research that is of special
interest to the lab. In the coming years we aim to prepare for a
large clinical program in which we will test the clinical value of
a series of different T cell receptors that target various
tumor-associated antigens. Towards this goal, we have developed
technology that allows rapid TCR gene identification from many
samples, and have utilized it to isolate a library of TCR genes
that target many different cancer/germline antigens. In parallel
work, we aim to evaluate the potential of non-viral gene transfer
strategies and would like to evaluate the potential of more
personalized strategies for TCR gene therapy, in which the
tumor-specific TCR repertoire of individual patients is
(Selected references: Kessels et al., Nat Immunol 2001; Bendle et al., Nat Med 2010, Linnemann et al., Nat Med 2013)
- Ferenc A. Scheeren, Dr.Senior Postdoctoral fellow
- Francesca Amicarella, Dr. Postdoctoral fellow
- Telma Lança, Ph.D.Postdoctoral fellow
- Wouter Scheper, Dr.Postdoctoral fellow
- Chong SunPostdoctoral Fellow
- Kaspar BresserPh.D. Student
- Feline Dijkgraaf, MScPh.D. Student
- Lorenzo Fanchi, MScPh.D. Student
- Mirjam Hoekstra, MScPh.D. student
- Anne van der Leun, MScPh.D. Student
- Meike Logtenberg, MScPh.D. Student
- Riccardo Mezzadra, MScPh.D. Student
- Ali Can SahilliogluPh.D. Student
- Maarten SlagterPh.D. Student
- Marlous van den BraberTechnician
- Marjolein de BruijnTechnician
- Daisy Philips, MScTechnician
- Mireille ToebesResearch Technician
- Jos UrbanusResearch Technician
- Georgi ApriamashviliMaster Student
- Chris KweekelMaster Student
- Pieter Lindenbergh, BScMaster Student
- Sanne ReijmMaster Student
Ferenc A. Scheeren, Dr.
Senior Postdoctoral fellow
I was trained in human B cell immunology at the NKI and AMC. As a KWF fellow I went to Stanford University (California USA) to work in the lab of Michael Clarke. He was the first to describe cancer stem cells in solid tumors (breast cancer). Currently I am doing my second part of my KWF fellowship in the department of Immunology.
The focus of my work is solid tumor heterogeneity, stemness and sterile inflammation, with the purpose to find new therapeutic targets.
Francesca Amicarella, Dr.
I obtained my masters degree in Medical Biotechnology at the University of Florence. I then moved to Basel, where I started my PhD training at the cancer immunotherapy laboratory of the Department of Biomedicine. During these years, I studied the impact of IL-17-releasing CD4+ T cells in human colorectal cancer.
Due to my strong interest in tumor immunology, I decided to join Ton Schumacher's group on a Swiss National Science Foundation fellowship. My current research aims to improve our understanding of the role played by different T cell subsets in immune responses that develop in human colorectal cancer.
Telma Lança, Ph.D.
I did my PhD in the lab of Bruno Silva-Santos, at the Molecular Medicine Institute, Lisboa, where I studied the immune responses of gd T cells to tumors. As a Postdoctoral fellow in the Schumacher lab, I am studying the role of different immunosuppressive molecules in melanoma recognition by T cells.
Wouter Scheper, Dr.
After completing a PhD in tumor immunology at the UMC Utrecht, I started working as a postdoc in the Schumacher lab in November 2014. Here, my research aims to (a) dissect the specificities and functionalities of tumor-infiltrating T cells, and (b) develop novel approaches for the production of highly tumor-reactive, patient-specific clinical T cell products.
I received my PhD cum laude from Utrecht University in 2015, under the mentorship of Prof. René Bernards at the Netherlands Cancer institute. During the study, I used systematic approaches, primarily function-based genetic screens, to investigate resistance mechanisms of cancer to targeted therapies and designed effective therapeutic approaches that overcome such resistance.
After graduation, I chose to stay at the NKI because of the world-class research groups and state-of-the-art facilities. I joined the group of Prof. Ton Schumacher at the end of 2015. Here I work on the development and application of high-throughput functional genetic tools to improve cancer immunotherapy and discover novel therapeutic targets.
During my bachelor's (HLO at the Hogeschool Leiden) and master's (Biomedical Sciences at the University of Amsterdam) programs I received training while working in multiple labs at the LUMC, NKI and Whitehead Institute. During these internships I worked on various projects in the fields of tumor immunology, gene regulation and bioengineering.
My current research focuses on two subjects. First, to dissect the recognition of tumor cells by T cells, mainly from the tumor cell perspective. Second, to develop and engineer systems that allow one to address various subjects in tumor biology and immunology.
Feline Dijkgraaf, MSc
After finishing the broad Bachelor Bèta-gamma, I enrolled in the Master Biomedical Sciences at the University of Amsterdam. During this training, I specifically focused on cancer immunology at various research institutes such as the University of Cambridge, UK, the Amsterdam Medical Center and finally the Netherlands Cancer Institute (NKI-AVL).
Currently, I am working on a PhD-project in the stimulating work environment of the NKI-AVL, in which I aim to study the behavior of tissue-resident memory T cells using live imaging.
Lorenzo Fanchi, MSc
I'm Lorenzo Fanchi, PhD student in the Schumacher lab. I graduated at Wageningen University specializing in Medical Biotechnology. After working for a year in vaccine technology at Crucell, I was looking for a new challenge and had the opportunity to start my PhD at the NKI. I'm particularly interested in translational research in the field of cancer immunotherapy, specifically the role and therapeutic application of T cells in tumor infiltrating lymphocytes (TIL).
Mirjam Hoekstra, MSc
I studied Life Science (Bio-exact, BSc) and Immunology (MSc) at the University of Amsterdam. During my studies, I performed research internships at the Netherlands Cancer Institute, Utrecht University and Massachusetts Institute of Technology, focusing on innate and adaptive immunity.
I'm mostly interested in fundamental immunology, specifically the role of T cells in immune responses. I have been working in the Schumacher lab as a PhD student since February 2014, and my work focuses on the behavior of tissue-resident memory T cells in the skin and the development of (reporter) technologies to study this.
Anne van der Leun, MSc
After finishing my Master "Cancer
Genomics and Developmental
Biology" at Utrecht University, I joined
the Schumacher and Zuur labs as a PhD student in June
2015. Here, my main focus is on the dissection of T cell reactivity
in head and neck cancer. I aim to better understand the
functionality of tumor infiltrating lymphocytes at the single cell
level, with the ultimate goal to improve current immunotherapeutic
approaches and make immunotherapy applicable to a broader range of
Meike Logtenberg, MSc
After finishing my Bachelor's degree at University College Utrecht, I enrolled in the 'Cancer, Stem Cells and Developmental Biology' Master program at the Utrecht University. During this program, I was trained at the Hubrecht Institute (Utrecht) and at the Centre of Stem Cells and Regenerative Medicine (London) in cancer and stem cell biology. I started my PhD at the group of Ton Schumacher in October 2015. I am interested in identifying and understanding tumor escape mechanisms from the immune system, and how these mechanisms can be targeted to improve effective tumor cell killing.
Riccardo Mezzadra, MSc
I got my master degree in Medical Biotechnology in Milan, Italy, with an experimental thesis aimed at exploring potential genotoxic risks associated with gene therapy.
After that I started my PhD in Ton Schumacher's lab, where I am mainly involved in the development of novel gene transfer system and novel receptors for lymphocyte gene modification.
Ali Can Sahillioglu
The rate of scientific progress is limited by scientists' imagination, and their research tools. My research interest is to develop novel methods for single cell tracing and then use these to reveal the underlying mechanisms of cellular heterogeneity in T-cell populations and cancer.
I received my B.Sc. and M.Sc. degrees from Bogazici University, Istanbul, and I have been working in the Schumacher Lab since October 2013.
My training consisted of a Bsc in Biomedical sciences and a Msc in Bioinformatics & Systems Biology at the University of Amsterdam and VU University Amsterdam. The internships I did revolved around data analysis and mathematical modelling in various biological contexts: Huntington's disease, synthetic (prokaryotic) biology and GPCR signalling. My current goal is to improve our quantitative understanding of T-cell mediated tumor regression and its dependence on other cells/factors in the local microenvironment, by computational analysis of experimental data generated here at the NKI and elsewhere. Hopefully this will contribute to more effective T-cell based immunotherapeutic strategies.
Marlous van den Braber
After finishing my bachelor's degree, I joined Ton Schumacher's group as a Technician. In my work I mostly focus on MHC multimer-based immune monitoring. This includes not only the production and extension of our MHC based toolbox but also the monitoring of immune responses in patients treated with cancer immunotherapy.
Marjolein de Bruijn
After finishing my Bachelor (BASc), I started working as a technician in the group of Ton Schumacher with the main focus of my work at the project of my internship period. As part of my study 'Biology and Medical Laboratory Research' at the Hogeschool Leiden I was given the opportunity to do my internship at the NKI, where we investigated cell death mechanisms induced after T cell recognition.
Daisy Philips, MSc
After finishing my Master at the Free University of Amsterdam, I started working as a technician in the group of Ton Schumacher. The main focus of my work is the immunomonitoring of patients who received immunotherapy. This involves the analysis of patient material by combinatorial coding for the detection of tumor reactive T cells and the analysis of patient material to assess the functionality of tumor reactive T cells.
In September 1996, I started as a technician in the lab of Ton Schumacher: setting up the lab was a challenging job. During the following years, I developed my own projects, specializing myself in protein biochemistry, and in particular MHC multimer-based tools for immune monitoring (Toebes et al, Nat Med. 2006). In addition to this work, currently I am training and assisting technicians, post-docs and PhD students, and have collaborations with groups in other disciplines, such as chemistry. This variation makes this job exciting: I can express my creative mind.
In 2001 I joined the Schumacher lab as a technician and since then I worked on several challenging projects (not all of them equally successful). A large part of my job is to design constructs and cloning strategies, of which the creation of the barcode mouse certainly was the most ambitious cloning project I was ever involved in. At the moment I am also managing the barcode mouse project. Over the years I have acquired quite some experience in developing gene designs and am now helping out many people in their efforts (as a one-eyed king in the land of the blind..)
Most of all I like the diversity in the research projects and the great support there is among colleagues.
The possibility to mobilizethe immune system for cancer treatment has gained enormous momentum in recent years and yielded impressive success stories. Under the supervision of Ali Can Sahillioglu I am working on possible improvements for cancer immunotherapy, which are needed to make the treatment more successful and bearable for patients.
As a second year masters student at the University of Amsterdam, I aimed for a challenging internship at the NKI in the group of prof. Ton Schumacher. Under supervision of Lianne Kok, I'm studying the kinetics, differentiation and clonality of CD8+ T cells during an influenza infection using the DNA barcoding system.
Pieter Lindenbergh, BSc
For my first master (History and Philosophy of Science, UU) I studied the relation between immunological and molecular cancer research from the 1980s until now. Taking the NKI as a case study, I employed anthropological and historical methods to identify how and why these two branches of cancer research converge over time. Currently I am doing my major internship for my second master (Cancer and Stem Cell Biology, UU). Together with my supervisor Telma Lança, I aim to study the contribution of the mutational load to a tumor's immunogenicity in vivo.
I'm a masterstudent Biomedical Sciences at the Leiden University focusing on oncology and immunology. The last internship of my study, I perform at the NKI. Under supervision of Lorenzo Fanchi, I study TCR gene therapy for individual patients in vivo.
Key publications View All Publications
Heterogeneous Differentiation Patterns of Individual CD8+ T Cells
Science 2013 May 3;340(6132):635-9.
Gerlach C, Rohr JC, Perié L, van Rooij N, van Heijst JW, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TN. et al.Link to pubmed
Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma
J Clin Oncol. 2013 Nov 10;31(32):e439-42
van Rooij1* N, van Buuren1* MM, Philips1 D, Velds2 A, Toebes1 M, Heemskerk1 B, van Dijk1 LJA, Behjati3 S, Hilkmann4 H, el Atmioui4 et al.Link to publication
Recent publications View All Publications
The branching point in erythro-myeloid differentiation.
Cell. 2015 Dec 17;163(7):1655-62. doi: 10.1016/j.cell.2015.11.059.
Perié L, Duffy KR, Kok L, de BoerRJ, Schumacher TN.Link to pubmed
Subtle CXCR3-dependent chemotaxis of CTLs within infected tissue allows efficient target localization.
J Immunol. 2015;195:5285-95.
Ariotti S, Beltman JB, Borsje R, Hoekstra ME, Halford WP, Haanen JB, de Boer RJ, Schumacher TN.Link to pubmed
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