Erasmus MC

Nitika Taneja Group

3-D chromatin remodeling and replication

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Our Focus

Chemoresistance poses a significant challenge in cancer treatment, allowing cancer cells to continue proliferating despite chemotherapy-induced replication stress and DNA damage. My research focuses on investigating the underlying molecular mechanisms that modify chromatin at replication forks, enabling cells to cope with replication stress. My expertise lies in chromatin biology, replication stress, and chemoresistance.  

  

In my lab, we have developed novel tools and technologies to study chromatin dynamics at replication forks, ranging from single-molecule chromatin fibers to kb-resolution analysis of nascent genome under replication stress through high-throughput genomics. Using various mammalian systems, including tumour models, we aim to uncover how chromatin dynamics and histone modifiers regulate replication fork stability and genome integrity during stress and how these mechanisms contribute to chemotherapy resistance in cancer cells.  

  

Main Research Questions:  

  • How do local histone/RNA modifications at replication forks drive spatial chromatin reorganization, including chromatin loop stabilization and phase separation, to promote replication fork stability under replication stress?  
  • How do differences in spatial chromatin organization, including chromatin loop stabilization and phase separation, distinguish chemo resistant cancer cells from chemo sensitive ones and which key factors enable this adaptation, offering potential targets to resensitize chemo resistant tumours effectively?  

About Nitika Taneja

My Research

Nitika Taneja is an Associate Professor and Principal Investigator at Erasmus MC, focusing her research on understanding the intricate molecular mechanisms of chromatin remodeling during DNA replication and replication stress to maintain genome stability. During her PhD work under Prof. Christian Lehner at the University of Zurich, Switzerland, she demonstrated the transgenerational propagation of histones/epigenetic marks from fathers to progeny. This research highlighted the essential role of a retained centromere histone variant in male gametes, inherited during the first zygotic DNA replication, crucial for embryonic development.

During her postdoctoral tenure at the National Cancer Institute, NIH, USA, with Dr. Shiv Grewal, Dr. Taneja designed specialized genetic screens to identify factors critical for genome and epigenome stability during DNA replication. In 2018, she established her research program at the Department of Molecular Genetics, Erasmus MC, Netherlands. Her research program explores the role of 3-D chromatin architecture in mediating replication fork stability under replication stress. By uncovering these connections and identifying key factors, her work unveils potential mechanisms and strategies to sensitize cancer cells to chemotherapy. Her team also develops innovative tools and technologies to investigate transient chromatin changes at replication fork sites and genome-wide chromatin spatial reorganization in response to replication stress.

Awards
  • 2025: ERC Proof of Concept Grant
  • 2025: Marie Skłodowska-Curie Postdoctoral Fellowship (Horizon Europe), awarded to a postdoctoral researcher
  • 2024: Oncode Technology Development Award
  • 2024: Junior Oncode Investigator Award
  • 2023: ERC Starting Grant
  • 2023: NWO Aspasia Premium
  • 2022: NWO Vidi Grant
  • 2021: NWO Women in STEM Incentive Grant
  • 2021: Convergence Health & Technology – Open Mind Grant
  • 2020: Erasmus+ Grant
  • 2018: Daniel den Hoed Foundation Young Investigator Award
  • 2017: Fellows Award for Research Excellence
  • 2012: Sri AsaNanda Young Scientific Talent Award
Key Publications
  • 2025 | Fencing the genome: ubiquitin signaling restricts heterochromatin spread | Collin Bakker et al. | Signal Transduction and Targeted Therapy | View publication
  • 2025 | H2BK120ub and its reader RNF169 differentially regulate replication fork remodeling and stability | Filip D. Duzanic et al. | EMBO Reports | View publication
  • 2025 | Nucleoplasmic Lamin A/C controls replication fork restart upon stress by modulating local H3K9me3 and ADP-ribosylation levels | Veronica Cherdyntseva et al. | Nature Communications | View publication
  • 2025 | Ubiquitination of the histone variant mH2A1.2 prevents toxic RAD18 accumulation at a subset of genomic loci upon replication stress | Maxime Galloy et al. | Molecular Cell | View publication
  • 2024 | Enhancing quantitative imaging to study DNA damage response: A guide to automated liquid handling and imaging | Calvin Shun Yu Lo et al. | DNA Repair | View publication
  • 2024 | SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots | Sidrit Uruci et al. | bioRxiv (preprint) | View publication
  • 2023 | Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination | Carlota Davó-Martínez et al. | Nucleic Acids Research | View publication
  • 2023 | Dynamic de novo heterochromatin assembly and disassembly at replication forks ensure fork stability | Vincent Gaggioli et al. | Nature Cell Biology | View publication
  • 2022 | A microfluidic cancer-on-chip platform predicts drug response using organotypic tumor slice culture | Sanjiban Chakrabarty et al. | Cancer Research | View publication
  • 2021 | R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde | Sidrit Uruci et al. | International Journal of Molecular Sciences | View publication
  • 2021 | SMARCAD1 Mediated Active Replication Fork Stability Maintains Genome Integrity | Calvin Shun Yu Lo et al. | Science Advances | View publication

Members

Nitika Taneja
Oncode Investigator
Ashutosh Choudhury    
PhD student
Collin Bakker    
PhD student
Jialin Li    
PhD
Joanna Paulson    
PhD student
Kaustav Sengupta    
Postdoc
Vincent Gaggioli    
PostDoc
Xingde Wang    
PhD
 
Rebekka Schneider Group

Hematopoietic stem cells; leukemia; bone marrow failure; myelodysplastic syndrome; myeloproliferative neoplasms; genetic fate tracing; CRISPR-Cas9; scRNA sequencing

Kép

Our Focus

My research focuses on understanding how blood cancers actively reshape their environment to support their own growth and progression—and how this process can be therapeutically disrupted. I demonstrated that bone marrow damage and scarring in cancer are not passive consequences of disease but are driven by cancer cells through inflammatory signals and pathological interactions with surrounding support cells, creating a self-reinforcing niche that fuels tumor persistence and evolution.  

 

By identifying key cellular players and cancer-induced signaling pathways, my work revealed exploitable weaknesses that allow selective targeting of malignant cells while preserving normal blood formation. These insights have directly enabled the development of novel, mechanism-based therapies, including treatments now being tested in clinical trials and advanced through a biotech company I co-founded. Overall, my research reframes bone marrow cancers as diseases sustained by dynamic, druggable cancer–microenvironment interactions and provides a clear path toward more effective and less toxic cancer therapies. 

About Rebekka Schneider

My Research

I am a pathologist by training with a strong background in clinical hematopathology and basic research. In my MD thesis (RWTH Aachen, Germany), I focused on cellular plasticity and tissue engineering of skin and continued independent research projects in parallel to my residency/fellowship in Pathology with focus on the role of the microenvironment in myeloid malignancies but also chronic kidney disease (2008-2012). I performed my post-doc (after MD qualification) in Ben Ebert‘s lab at Harvard Medical School from 2012-2015. After my postdoctoral fellowship, I returned to Aachen to finish my fellowship in Pathology, and started my own independent research laboratory at Erasmus MC. In parallel to running my laboratory at Erasmus MC, I finalized my PhD (conducted at Harvard Medical School, Boston, USA and Erasmus MC, Rotterdam).

My primary focus is disease-oriented laboratory investigation of clonal myeloid neoplasms, employing a range of genomic technologies as well as classical cellular and molecular biology experimental approaches. My central goal is to translate my research directly into development of novel targeted therapeutics for the vast and growing patient population suffering from fibrosis and organ failure due to chronic blood cancer or even cancer more broadly. I made significant discoveries for improved diagnosis and treatments for blood cancers. In summary, the major achievements of my lab have been the identification of fibrosis-driving cells in primary myelofibrosis (PMF) and the identification of their activating mechanisms. This work has led to the initiation of a clinical trial for which we just received funding for and which will be started in 2023. I have filed a priority patent (application # 20187323.9; date of filing: 23/07/2020) to protect the new use of Tasquinimod for MPN after preclinical proof-of-concept was demonstrated. I have received an ERC proof-of-concept grant beginning of 2021 to translate our preclinical findings into a clinical trial. Active Biotech (NASDAQ STOCKHOLM: ACTI) has entered into an exclusive license agreement with us (Oncode Institute) for the global rights to patents relating to the use of tasquinimod and other inhibitors of S100 for use in treatment of myelofibrosis (MF).

As a post-doctoral research fellow, I was the first to discover recurrent mutations in a blood cancer called del(5q) MDS. Importantly, we identified a mechanism in the mutated, disease-causing cells that is an “Achilles Heel” and can be used to specifically eliminate the disease-causing cells without affecting normal blood formation – one of the main challenges in cancer research. In my laboratory at Erasmus MC, we now thrive to identify novel therapeutic strategies to eradicate disease-initiating in myeloid blood cancers. Additionally, I identified that inflammation and activation of the innate immune system are central mechanisms in the development of not of myeloid malignancies. Using CRISPR/Cas9-gene editing, I showed that targeting activated mechanisms can restore the normal function of diseased hematopoietic cells. In my lab, we now focus on understanding the underlying mechanisms for the inflammation in the bone marrow (protein synthesis, aging etc) and are searching for novel therapeutic targets to block inflammation and inhibit disease progression.

In the next 5-10 years I want to focus on identifying novel druggable targets in myeloid malignancies by using the multitude of cellular and molecular assays established in my group. I furthermore intend to bring together scientists, societies and companies working in the abovementioned areas of research, in order to intensify their interaction, and to thereby foster the translation of several innovative treatment concepts into the clinic.

Awards
  • 2022: Gerhard Domagk Award for Excellence in Cancer Research, Gerhard Domagk Foundation, Germany
  • 2022: NWO Vidi Grant
  • 2021: ERC Proof of Concept Grant
  • 2019: Swammerdam Award, Dutch Society for Haematology (NVvH)
  • 2018: KWF Bas Mulder Award – Dissecting the mechanisms of malignant transformation in del(5q) myelodysplastic syndrome to selectively target disease-initiating haematopoietic stem cells
  • 2017: ERC Starting Grant (deFIBER) – Dissecting the cellular and molecular dynamics of bone marrow fibrosis for improved diagnostics and treatment
  • 2017: Erasmus MC Fellowship – Functional and molecular dissection of clonal selection in myeloproliferative neoplasms
  • 2017: International MPN Foundation Grant – Dissecting the cellular and molecular dynamics of bone marrow fibrosis for improved diagnostics and treatment
  • 2017: European Hematology Association (EHA) John Goldman Clinical Research Grant – Functional dissection of abnormal protein translation in the erythroid differentiation defect in del(5q) MDS
  • 2017: Johann Georg Zimmermann Award for Excellence in Cancer Research
  • 2016: Innovation Award for German Academic Medicine (Innovationspreis Deutsche Hochschulmedizin)
  • 2016: Artur Pappenheim Award, German Society for Haematology and Medical Oncology (DGHO)
  • 2015: Abstract Achievement Award, American Society of Hematology Annual Meeting
  • 2015: Best Abstract Award, FASEB Meeting on Haematological Malignancies
  • 2015: Year's Best in Hematology 2014, American Society of Hematology – Recognition of the publication Role of casein kinase 1A1 in the biology and targeted therapy of del(5q) MDS
  • 2014: Abstract Achievement Award, American Society of Hematology Annual Meeting
  • 2013: Abstract Achievement Award, American Society of Hematology Annual Meeting
  • 2011: Travel Award, 61st Lindau Nobel Laureate Meeting
  • 2010: Travel Award, International Consortium of Stem Cell Networks Symposium for Outstanding Young Researchers
  • 2010: Best Abstract Award, German Society of Pathology – Differential matrix remodelling of adult bone marrow and perinatal umbilical cord mesenchymal stem cells on 3D collagen scaffolds for bone tissue engineering
  • 2010: Best Abstract Award, German Society of Pathology – Epigenetic reprogramming of haematopoietic stem cells by fusion with embryonic stem cells
  • 2009: First Prize, Best Abstract and Presentation Award, German Society of Stem Cell Research
  • 2009: Borchers Award for Excellence in Medical Thesis
Key Publications
  • 2025 | Inhibiting the alarmin-driven hematopoiesis-stromal cell crosstalk in primary myelofibrosis ameliorates bone marrow fibrosis | Hélène F. E. Gleitz et al. | HemaSphere | View publication
  • 2025 | Non-Invasive Detection of Bone Marrow Fibrosis in Myeloproliferative Neoplasms Using Cell-Free RNA | Mohamed Saad et al. | iScience | View publication
  • 2025 | Wnt-dependent spatiotemporal reprogramming of bone marrow niches drives fibrosis | Bella Banjanin et al. | HemaSphere | View publication
  • 2024 | Collaborative effect of Csnk1a1 haploinsufficiency and mutant p53 in Myc induction can promote leukemic transformation | Stijn N. R. Fuchs et al. | Blood Advances | View publication
  • 2024 | Endothelial LATS2 is a suppressor of bone marrow fibrosis | Kishor K. Sivaraj et al. | Nature Cardiovascular Research | View publication
  • 2024 | Non-canonical Hedgehog signaling mediates profibrotic hematopoiesis-stroma crosstalk in myeloproliferative neoplasms | Jessica E. Pritchard et al. | Cell Reports | View publication
  • 2022 | Genetic barcoding systematically compares genes in del(5q) MDS and reveals a central role for CSNK1A1 in clonal expansion | Ursula S. A. Stalmann et al. | Blood Advances | View publication
  • 2022 | SARS-CoV-2 infects kidney cells and causes kidney fibrosis | J. Jansen et al. | Cell Stem Cell | View publication
  • 2022 | Single-cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situ | Ursula S. A. Stalmann et al. | Experimental Hematology | View publication
  • 2021 | Heterogeneous bone marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis | Nils B. Leimkühler et al. | Cell Stem Cell | View publication
  • 2021 | Decoding myofibroblast origins in human kidney fibrosis | C. Kuppe et al. | Nature | View publication
  • 2020 | Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN | Hélène F. E. Gleitz et al. | Blood | View publication
  • 2019 | Rps14, Csnk1a1 and miRNA145/miRNA146a deficiency cooperate in the clinical phenotype and activation of the innate immune system in the 5q- syndrome | F. Ribezzo et al. | Leukemia | View publication
  • 2018 | Gli1+ mesenchymal stromal cells are a key driver of bone marrow fibrosis and an important cellular therapeutic target | Rebekka K. Schneider et al. | Cell Stem Cell | View publication
  • 2016 | Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8/S100A9 | Rebekka K. Schneider et al. | Nature Medicine | View publication
  • 2014 | Role of casein kinase 1A1 in the biology and targeted therapy of del(5q) MDS | Rebekka K. Schneider et al. | Cancer Cell | View publication

Members

Rebekka Schneider
Group leader
Aurelie Boeree    
Technician
Hector Tejeda Mora    
PostDoc
Hélène Gleitz    
Post-doctoral research fellow
Stephani Schmitz    
PhD student
Stijn Fuchs    
Research technician
   
Jurgen Marteijn Group

Transcription Stress & Genome Stability

Kép

Our Focus

The goal of my lab is to mechanistically dissect the DNA damage response (DDR), as defects in this pathway are frequently observed in cancer and create vulnerabilities that can be exploited for anti-cancer therapies. Our central focus is on how cells cope with transcription-blocking DNA lesions (TBLs).  

 

Accurate regulation of gene expression is essential for proper cell function and tissue homeostasis. However, the DNA template transcribed by RNA polymerase II (Pol II) is continuously challenged by DNA-damaging agents of environmental origin, such as UV light, dietary chemicals, and chemotherapeutics, as well as endogenous sources including reactive oxygen species and aldehydes. If TBLs are not resolved efficiently, prolonged stalling of Pol II severely disrupts cellular function due to loss of newly synthesized RNA or production of aberrant RNA transcripts. Persistent Pol II stalling also promotes R-loop formation and can lead to transcription–replication conflicts and genome instability. 

 

Our research focuses on how TBLs are detected and repaired by distinct transcription-coupled repair (TCR) pathways, and how these lesions impact transcription dynamics, genome stability, and DDR signaling. We further investigate whether targeting TCR pathways can be exploited to enhance the efficacy of cancer therapies. In parallel, we study how DNA damage affects transcription in non-dividing cells and contributes to chemotherapy-induced neurotoxicity, a major dose-limiting side effect of cancer treatment. 

About Jurgen Marteijn

My Research

Jurgen Marteijn started his career as a PhD student in the Central Hematology Laboratory at the Radboud University Medical Center, Nijmegen where he studied the role of the ubiquitin proteasome pathway during haematopoiesis. In 2006 he became a postdoc in the department of Genetics, were he subsequently started his independent research line to study the role of the post-translation modification ubiquitin during DNA-repair and DNA damage-associated signaling (Marteijn, JCB,2009 and van Cuijk, Nat.Com,2015). Using a quantitative proteomics approach to identify DNA damage induced ubiquitylation events, his research group identified UVSSA. This novel identified Transcription-Coupled Repair factor (TCR) is mutated in the UV-sensitive syndrome (Schwertman, Nat.Gen, 2012).

This finding enabled his lab to further dissect the regulation and molecular mechanism of TCR and to understand the severe clinical consequences associated with inherited TCR-defects. Using a combination of live-cell imaging and quantitative proteomics, his research group showed that chromatin remodeling is an essential process during the restart of transcription upon removal of transcription blocking lesions by TCR (Dinant, Mol.Cel, 2013). Furhtermore, his team revealed that the spliceosome is a key target of the DDR and defines a R-loop-dependent, non-canonical ATM activation by transcription-blocking lesions as an important event in the DNA damage response upon transcriptional stress (Tresini, Nature,2015).

Awards
  • 2020:Ammodo Science Award for groundbreaking team research in the life sciences

  • 2018: VICI Grant of Netherlands Organisation for Scientific Research

  • 2014: VIDI Grant of Netherlands Organisation for Scientific Research

  • 2011: Erasmus MC Fellowship

  • 2008: Veni Grant of Netherlands Organisation for Scientific Research

Key Publications
  • 2025 | Mechanisms of transcription-coupled repair and DNA damage surveillance in health and disease | Marjolein van Sluis et al. | Nature Reviews Molecular Cell Biology | View publication
  • 2024 | Differential processing of RNA polymerase II at DNA damage correlates with transcription-coupled repair syndrome severity | Camila Gonzalo-Hansen et al. | Nucleic Acids Research | View publication
  • 2024 | STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment | Anisha R. Ramadhin et al. | Molecular Cell | View publication
  • 2024 | Transcription-coupled DNA-protein crosslink repair by CSB and CRL4CSA-mediated degradation | Marjolein van Sluis et al. | Nature Cell Biology | View publication
  • 2022 | Active DNA damage eviction by HLTF stimulates nucleotide excision repair | Marvin van Toorn et al. | Molecular Cell | View publication
  • 2022 | DNA damage-induced transcription stress triggers the genome-wide degradation of promoter-bound Pol II | Barbara Steurer et al. | Nature Communications | View publication
  • 2021 | Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability | Marit E. Geijer et al. | Nature Cell Biology | View publication
  • 2019 | The DNA damage response to transcription stress | Hannes Lans et al. | Nature Reviews Molecular Cell Biology | View publication
  • 2018 | Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II | Barbara Steurer et al. | Proceedings of the National Academy of Sciences | View publication
  • 2015 | SUMO and ubiquitin-dependent XPC exchange drives nucleotide excision repair | Loes van Cuijk et al. | Nature Communications | View publication
  • 2015 | The core spliceosome as target and effector of non-canonical ATM signalling | Maria Tresini et al. | Nature | View publication
  • 2014 | Understanding nucleotide excision repair and its roles in cancer and ageing | Jurgen A. Marteijn et al. | Nature Reviews Molecular Cell Biology | View publication
  • 2013 | Enhanced chromatin dynamics by FACT promotes transcriptional restart after UV-induced DNA damage | Christoffel Dinant et al. | Molecular Cell | View publication
  • 2012 | UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair | Petra Schwertman et al. | Nature Genetics | View publication

Members

Jurgen Marteijn
Group leader
Roel Janssens    
Technician
Camila Gonzalo Hansen    
Phd student
Cindy Blom    
PhD student
Daria Repkina    
Phd student
Georgia Avramidou    
PhD student
Marjolein van Sluis    
Postdoctoral Researcher
Qing Yu    
Phd student
Emilio Gomez Vazquez
PhD student
Julia Haerkens  
Roland Kanaar Group

Molecular radiation biology

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Our Focus

We define and dissect the molecular circuits of the DNA damage response (DDR) to identify molecular targets for designing novel mechanism-based anti-cancer interventions.  

 
We address fundamental mechanistic aspects of the DDR with special attention to homologous recombination, DNA mismatch repair and DNA replication stress. We study the dynamic molecular interactions that are responsible for the assembly and disassembly of the molecular factories that guard and repair the genome both at the biochemical and cellular level.  

  

Our translational research involves proton therapy and cancer-on-chip studies. We are characterizing the proton DNA damage response and testing hypotheses on combination therapies. Our cancer-on-chip studies are aimed at making chips compatible with optical imaging such that functional probes, for biological pathways, can be imaged in ex vivo tumour slices from patients.  

About Roland Kanaar

Name

Roland Kanaar

Position
Oncode Investigator at Erasmus MC
My Research

Roland Kanaar studied chemistry at Leiden University. He performed his PhD research (1984-1988) in the lab of Piet van de Putte on the mechanism of site-specific DNA recombination. His post-doctoral work at the University of California, Berkeley, with Nick Cozzarelli and Don Rio aimed at understanding the molecular mechanisms of homologous DNA recombination and RNA splicing, respectively. In 1995 he moved to the Erasmus University Medical Center to become professor of Molecular Genetics in 2000.

His current research addresses the mechanisms and biological relevance of the DNA damage response (DDR). Defects in the DDR lead to the accumulation of DNA lesions and mutations, which causes hereditary diseases, cancer, cell decay and aging. A central theme in the lab concerns the mechanisms of DNA double-strand break metabolism.

A breakthrough discovery was the revelation that homologous recombination in mammalian organisms contributes to repair of ionizing radiation-induced DNA double-strands. This was contrary to the existing dogma, which held that in mammals DNA double strand breaks were repaired almost exclusively by non-homologous DNA end-joining. Importantly, using mouse reverse genetics his team demonstrated that homologous recombination and non-homologous DNA end-joining pathway have overlapping, as well as specialized roles. Furthermore, his team discovered that hyperthermia augments DNA damage based anti-cancer treatments by degrading BRCA2, a mechanistic insight with direct clinical implications.

Awards
  • 2013: Elected member of the KNAW (Royal Netherlands Academy of Arts and Sciences)

  • 2012: Cozzarelli Prize, National Academy of Sciences, USA

  • 2002: Elected member of EMBO

Key Publications
  1. Modesti, M., Budzowska, M., Baldeyron, C., Demmers, J. A., Ghirlando, R., & Kanaar, R. (2007). RAD51AP1 is a structure-specific DNA binding protein that stimulates joint molecule formation during RAD51-mediated homologous recombination. Molecular cell, 28(3), 468-481.

  2. Kanaar, R., & Wyman, C. (2008). DNA repair by the MRN complex: break it to make it. Cell, 135(1), 14-16.

  3. Agarwal, S., van Cappellen, W. A., Guénolé, A., Eppink, B., Linsen, S. E., Meijering, E., ... & Essers, J. (2011). ATP-dependent and independent functions of Rad54 in genome maintenance. The Journal of cell biology, 192(5), 735-750.

  4. Krawczyk, P. M., Eppink, B., Essers, J., Stap, J., Rodermond, H., Odijk, H., ... & Soullié, T. (2011). Mild hyperthermia inhibits homologous recombination, induces BRCA2 degradation, and sensitizes cancer cells to poly (ADP-ribose) polymerase-1 inhibition. Proceedings of the National Academy of Sciences, 108(24), 9851-9856.

  5. Tham, K. C., Hermans, N., Winterwerp, H. H., Cox, M. M., Wyman, C., Kanaar, R., & Lebbink, J. H. (2013). Mismatch repair inhibits homeologous recombination via coordinated directional unwinding of trapped DNA structures. Molecular cell, 51(3), 326-337.

  6. Zelensky, A. N., Schimmel, J., Kool, H., Kanaar, R., & Tijsterman, M. (2017). Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA. Nature communications, 8(1), 66.

Members

Roland Kanaar
Group leader
Alex Zelensky    
Assistant Professor
Arnab Ray Chaudhuri    
Associate Professor
Charlie Laffeber    
Technician
Dik van Gent    
Senior Investigator
Joyce Lebbink    
Associate professor
Julie Nonnekens    
Assistant Professor
Kelly de Koning    
Technician
Maayke Kuijten    
Postdoc fellow
Nina Becx    
PhD student
Raviprasad Kuthethur Vittala Das    
PostDoc
Romano van Genderen    
PhD student
Sari van Rossum Fikkert    
Research technician
Tim Heemskerk    
PhD student
 
   
Ruud Delwel Group

Molecular genetics of AML

Kép

Our Focus

Introduction: We study the mechanisms of defective gene regulation in acute myeloid leukemia (AML), with a specific focus on a unique subtype for which currently no cure is available. This subtype carries chromosomal abnormalities involving chr:3q26 causing overexpression of a gene called EVI1 (also designated MECOM). In “The New Yorker”, Tatiana Schlossberg, the granddaughter of JFK wrote a heartbreaking article about her fight against this currently incurable form of leukemia. She died on December 30th (https://archive.ph/eUmQV). Due to this  tragic story, 3q26 rearranged leukemia received worldwide attention. This story illustrates the severity of this type of cancer and that, even though progress has been made in cancer treatment in the past decennia, there are still subtypes of cancer that are incurable. In my group we decided to focus our research on understanding the biology of this subtype of leukemia and hope to find leads to cure this dreadful disease. 

 

Enhancer targeting: The overexpression of the EVI1 gene, which is located at chr:3q26, is caused by so called enhancer hijacking as the result of the chromosomal rearrangements. More than ten types of 3q26 rearrangements, hijacking the same numbers of enhancers from distinct “donor-genes” have been discovered that activate EVI1 expression in AML cells in various patients. The question that we address is: Can we inhibit EVI1 expression by interfering with the enhancer activity? We identified a number of compounds, among which drugs that specifically target so called CBP/p300 proteins. Those proteins are enzymes that bind to enhancers but their activity appears to be different when bound to distinct enhancers.  To our surprise were the effects of the p300/CBP inhibitors particularly strong and showed a certain level of selectivity for the hijacked enhancers. Consequently we demonstrated that  those drugs inhibit oncogene EVI1 expression and consequently interfere with leukaemia growth in vitro. An in vivo study, investigating the effects of those drugs on leukemic outgrowth, is currently being conducted. Together with the group of Bas van Steensel we are now planning experiments to understand why certain enhancers are hijacked so frequently, what they have in common at the nucleotide level and which protein complexes are predicted to be involved in this action. We anticipate on the discovery of more specific targets. 

 

Targeting EVI1 function: Another approach to interfere with oncogenes, is to target their function or activity. Therefore, targeting EVI1 protein in AMLs with aberrant expression may be another way to find cures for the disease. We found that EVI1 interacts with a nuclear protein called CTBP. This interaction was found to be essential for leukemic transformation. In fact we found an experimental approach to break EVI1/CTBP interaction and demonstrated inhibition of  tumor growth in a humanized mouse model. These findings hava been published in 2024 in  ScienceAdvances. We uncovered and published a month ago what the target gene is for EVI1/CTBP. The EVI1/CTBP repressor complex binds to regulatory elements of the gene for CEBPalpha (CEBPA). CEBPA is essential for the development of healthy neutrophils. When CEBPA is mutated, absent or repressed  neutrophils cannot be generated and the chances of leukemia development  are high. Our findings that CEBPA expression is blocked by EVI1/CTBP have been published in Blood in December 2025. In collaboration with Sebastian Pomplun, we are developing now small peptide-compounds to inhibit leukemic growth in patients with a chr.3q26 rearrangement. More importantly, this work, that we carried out with Oncode support has now been used to apply for external funds. I am proud to announce that this work is now in part funded by the World Wide Cancer Foundation.  

 

We have now developed more models to test the effects of compounds on either the expression of EVI1 or the function by EVI1 in leukemia.  

 

Finally, our program has now also affected another malignancy. We have found that  EVI1 overexpression due to genetic defects occurs with high frequency in Ovarian Cancer. A manuscript is now under review. 

About Ruud Delwel

My Research

Ruud Delwel started his career in 1983 in the lab of Bob Lowenberg, studying the in vitro behaviour of human acute myeloid leukemia cells in vitro. He obtained his PhD in 1990 (Cum Laude) and became a post doctoral fellow in the group of Dr. James Ihly, at the St. Jude’s Children’s Research Hospital in Memphis, Tennessee Leiden, and carried out retroviral insertional mutagenesis to discover novel disease genes in AML. He discovered the EVI1 gene to be one of the most severe disease genes in mouse leukemia’s and in human. When back in the Netherlands, ErasmusMC, he moved on studying the biological consequences of altered gene expression in human and murine AML.

His two major breakthrough studies are 1) The discovery that human AML can be classified based on unique gene expression signatures and on specific gene methylation profiles. These studies led to the uncover of a subset of unique AML cases with aberrant expression of the EVI1 gene. Further in depth analysis revealed a unique mechanism of enhancer deregulation in a subset of human EVI1-AMLs. Ruud Delwel and his team have been able to combine patient analysis with molecular studies using in vitro and in vivo modelling to improve our insight into molecular aspects of acute myeloid leukemia. These studies and the proposal that followed on these studies have been awarded by the Dutch Cancer Society or "Koningin Wilhelmina Fonds” with the "Koningin Wilhelmina Onderzoek prijs", or KWO Award.

Our research now focusses on the mechanisms of aberrant gene (EVI1) control by hijacked enhancers and how we may interfere with the aberrant expression of those genes. Applying sophisticated in vitro models we screened for compounds, using the drug repurposing library obtained by Oncode, to uncover ways to interfere with oncogene expression. We obtained several interesting hits, which are investigated further in the next five years within Oncode.

Awards
  • 2017: José Carreras Lecture and Award
  • 2015: KWO Research Award
  • 1994–1998: Fellowship, Royal Netherlands Academy of Arts and Sciences (KNAW)
  • 1991–1992: NWO-NATO Fellowship, St. Jude Children's Research Hospital, Memphis, USA
Key Publications
  • 2025 | MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia | Dorien Pastoors et al. | Blood | View publication
  • 2025 | Oncogenic Enhancers in Leukemia | Roger Mulet-Lazaro et al. | Blood Cancer Discovery | View publication
  • 2024 | Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia | Roger Mulet-Lazaro et al. | Nature Communications | View publication
  • 2024 | Oncogene EVI1 drives acute myeloid leukemia via a targetable interaction with CTBP2 | Dorien Pastoors et al. | Science Advances | View publication
  • 2021 | Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia | Leonie Smeenk et al. | Cancer Discovery | View publication
  • 2021 | The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops | Sophie Ottema et al. | Nature Communications | View publication
  • 2021 | Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML | Roger Mulet-Lazaro et al. | Blood | View publication
  • 2020 | Atypical 3q26/MECOM rearrangements genocopy inv(3)/t(3;3) in acute myeloid leukemia | Sophie Ottema et al. | Blood | View publication
  • 2017 | Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers | Jacob L. Glass et al. | Cancer Discovery | View publication
  • 2015 | Mutational spectrum of myeloid malignancies with inv(3)/t(3;3) reveals a predominant involvement of RAS/RTK signaling pathways | Stefan Gröschel et al. | Blood | View publication
  • 2014 | A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia | Stefan Gröschel et al. | Cell | View publication

Members

Ruud Delwel
Group leader
Bas Wouters    
Senior Investigator
Claudia Erpelinck    
Technician
Dorien Pastoors    
PhD student
Emma Boertjes    
PhD student
Leonie Smeenk    
Postdoc fellow
Marije Havermans    
Technician
Stanley van Herk    
Technician
Shivani Rajhansa
PhD
Juliette Engelberts
PhD Student
  
   
Miao-Ping Chien Group

Single cell technology, advanced imaging & quantitative analysis, cancer-driving cells, target discovery

Kép

Our Focus

Our research aims to uncover the mechanisms driving tumor metastasis, tumor progression, and therapy resistance by developing and applying imaging-guided single-cell and spatial omics technologies. By integrating advanced microscopy, computational analysis, and omics profiling, we link dynamic cellular behaviors and morphological phenotypes to their underlying molecular programs. 

 

We develop proprietary platforms, such as FUNseq, BC-seq, and CIN-seq, that enable behavior- and phenotype-coupled sequencing, allowing rare but clinically relevant subpopulations (e.g., migratory, chromosomally unstable, immune-evasive, or drug-resistant cells) to be identified, isolated, and profiled. Using these approaches, we have discovered predictive metastasis signatures and novel mechanisms in head and neck squamous cell carcinoma, and identified actionable pathways associated with chromosomal instability and tumor progression. 

 

To capture tumor-microenvironment interactions, we develop spatial and in situ FUNseq technologies to profile immune niches and dynamic cell states within live tissues and 3D organoid models. In parallel, we apply deep learning models to prospectively predict cell fate decisions, enabling causal dissection of disease-driving processes. 

Our work on therapy resistance focuses on DNA damage response dynamics and cancer cell plasticity, including the development of FUN-TRACE and PAINT-seq to uncover epigenetic and pre-existing resistance mechanisms. Together, our integrative approach provides a dynamic, single-cell view of cancer biology with direct translational potential.

About Miao-Ping Chien

My Research

Miao-Ping Chien is a multidisciplinary scientist. She obtained her PhD in chemistry and biochemistry at University of California, San Diego, where she successfully invented a nanomaterial that can specifically be targeted to and deposited in tumor tissues for a long period of time, through which the tumor can be detected with conjugated probes (fluorescent or MRI contrast agents) and treated with attached drugs (Doxorubicin). After that, she pursued her postdoctoral training in optical engineering and computational biology with Dr. Adam Cohen at Harvard University, where she developed technologies that are applicable to single cell biology and high-throughput measurements.

In 2017 June, Miao-Ping joined Erasmus MC as a group leader. Her research focuses on developing and applying multidisciplinary technologies (advanced microscopy and imaging, computation, single cell technology and bioinformatics) to investigate the underlying mechanisms of tumorigenesis, particularly of rare cancer-driving cells. Her main research goals are: the creation and application of technology for (early) detection and treatment of tumors, and the creation and application of single cell technology to facilitate the discovery and interpretation of genetic, transcriptomic and proteomic profiles of aberrant (single) cancer cells, with the aim of translating the knowledge gained to clinical applications. She is a founder of UFO Biosciences, which aims to profile rare & cancer-driving cells and identify actionable targets driving clinically relevant tumorigenic phenotypes.

Awards
  • 2025: KWF Proof-of-Concept Grant
  • 2025: NWO Perspectief Grant
  • 2024: ERC Consolidator Grant
  • 2024: NWO XL Grant
  • 2023: EMC2 Synergy Grant
  • 2023: Aspasia Award
  • 2022: NWO Vidi Award
  • 2022: KWF Public-Private-Partnership Grant, TKI
  • 2022: Two Flagship Consortium Grants
  • 2022: Computable Award
  • 2022: Inspiring Fifty Deep Tech
  • 2020: Ammodo Science Award
  • 2020: Josephine Nefkens Foundation Grant
  • 2020: Erasmus MC-TU Delft Convergence Grant
  • 2018: Erasmus MC Fellowship
  • 2017: CancerGenomiCs.nl Junior Fellowship
  • 2017: NWO Veni Award
Key Publications
  • 2025 | Functional Single-Cell Proteomics: Technology and Biological Applications | Pin-Rui Su | Methods in Molecular Biology | View publication
  • 2025 | Unraveling the molecular mechanisms underlying spontaneous chromosomal instability through CIN-seq | Pin-Rui Su et al. | bioRxiv | View publication
  • 2024 | Investigating the Metabolic Heterogeneity of Cancer Cells Using Functional Single-Cell Selection and nLC Combined with Multinozzle Emitter Mass Spectrometry | Kai-Wen Cheng et al. | Analytical Chemistry | View publication
  • 2023 | Instant processing of large-scale image data with FACT, a real-time cell segmentation and tracking algorithm | Ting-Chun Chou et al. | Cell Reports Methods | View publication
  • 2023 | Protocol for profiling intratumor heterogeneity using spatially annotated single cell sequencing | Myrthe M. Smit et al. | STAR Protocols | View publication
  • 2023 | Spatial Transcriptomic Technologies | Tsai-Ying Chen et al. | Cells | View publication
  • 2022 | Linking the genotypes and phenotypes of cancer cells in heterogenous populations via real-time optical tagging and image analysis | Li You et al. | Nature Biomedical Engineering | View publication
  • 2022 | Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics | Pin-Rui Su et al. | Cell Reports Methods | View publication
  • 2022 | Functional single-cell sequencing links dynamic phenotypes to their genotypes | Daan Brinks | Nature Biomedical Engineering | View publication
  • 2021 | A Comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis | Li Li et al. | Genome Biology | View publication
  • 2021 | Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter | M. P. Chien et al. | Science Advances | View publication

Members

Miao-Ping Chien
Group Leader
Cecile Beerens    
Technician
Jelle Storteboom    
Post Doc
Johanna Vliet    
Scientist
Junfeng Huang    
Phd student
Lars van Roemburg    
PhD student
Li You    
Postdoc fellow
Maria Teresa López Cascales    
Postdoctoral researcher
Oluwatoba Ajani    
Phd student
Pierangela Chiafele    
Research Analyst
Reza Ghadiri Rad    
PhD student
Ting-Chun Chou    
PhD student
Tsai- Ying Chen    
Phd Student
Swati Garg
Project Manager