Cancer Etiology, Mutagenesis and Clonal Evolution

Our Focus
Our research group focuses on understanding the origins of cancer by decoding and recoding DNA. We address two main questions: 1) why do children develop cancer even though their cells are largely free from damage caused by aging, and 2) what processes cause the DNA mutations that drive carcinogenesis?
To answer these questions, we analyse the DNA of individual cells isolated from patient samples. The DNA code can serve as an historical record, allowing us to trace back and study the moment cancer began. We have developed single-cell DNA analysis methods to decode these archives and uncover critical insights into the life history of cancer.
In parallel, we use genetic modification technologies to recode DNA in stem cells, simulating cancer-driving mutations, or expose these cells to potential carcinogens to study their effects. Together, our work sheds light on preventable causes of cancer and provides unique insights into how cancer arises and sometimes evades treatment.
About Ruben van Boxtel

Ruben van Boxtel
My Research
The research group of Ruben van Boxtel has pioneered the development of experimental and computational approaches to study the genomes of human stem cells. Using these methods, his group showed that mutation accumulation varies across different tissues throughout human life. In 2017, Ruben was appointed as a group leader at the Princess Máxima Center for Pediatric Oncology, where he focusses on studying why children get leukemia and lymphoma, and what the genotoxic effects of treatment are in the hematopoietic system. Using in-depth mutational analyses, the group of Ruben has discovered mutational cancer signatures caused by a genotoxic gut bacterium and an antiviral drug.
Ruben received an NWO Vidi award in 2017 by the Netherlands Organization for Scientific Research, which is a prestigious personal Dutch grant for starting group leaders, for his research on studying genomic integrity of human stem cells throughout life. In addition, Ruben received an ERC Consolidator award by the European Research Council in 2019, which is the most prestigious grant for established young research leaders in Europe, to study the causes of therapy-related myeloid neoplasms in childhood cancer survivors. In the same year, he was selected as an Oncode Investigator, which a collective institute bringing together the best fundamental cancer researchers in the Netherlands. In 2022, Ruben received the NYSCF Robertson Stem Cell Investigator Award for his work on studying long-term toxicity in the hematopoietic system of childhood cancer survivors.
Awards
2022: New York Stem Cell Foundation Robertson Stem Cell Investigator Award
2022: Ammodo Science Award for ground-breaking research (team award with Omnes Pro Uno)
2019: ERC Consolidator grant
2019: Selected Oncode member
2017: NWO VIDI Award
Key Publications
Bertrums EJM, Rosendahl Huber AKM, de Kanter JK, Brandsma AM, van Leeuwen AJCN, Verheul M, van den Heuvel-Eibrink MM, Oka R, van Roosmalen MJ, de Groot-Kruseman HA, Zwaan CM, Goemans BF, van Boxtel R. Elevated mutational age in blood of children treated for cancer contributes to therapy-related myeloid neoplasms. Cancer Discovery (2022) 12:1860-1872.
de Kanter JK, Peci F, Bertrums E, Rosendahl Huber A, van Leeuwen A, van Roosmalen MJ, Manders F, Verheul M, Oka R, Brandsma AM, Bierings M, Belderbos M, van Boxtel R. Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients. Cell Stem Cell (2021) 28:1726-1739.e6.
Brandsma AM, Bertrums EJM, van Roosmalen MJ, Hofman DA, Oka R, Verheul M, Manders F, Ubels J, Belderbos ME, van Boxtel R. Mutation signatures of pediatric acute myeloid leukemia and normal blood progenitors associated with differential patient outcomes. Blood Cancer Discovery (2021) 2:484-499.
Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F, Dalmasso G, Stege PB, Paganelli FL, Geurts MH, Beumer J, Mizutani T, van der Linden R, van Elst S; Genomics England Research Consortium, Top J, Willems RJL, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R*,Clevers H*. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature (2020) 580:269-273. *co-corresponding authors
Osorio FG, Rosendahl Huber A, Oka R, Verheul M, Patel SH, Karlijn Hasaart K, de la Fonteijne L, Varela I, Camargo FD, van Boxtel R. Somatic Mutations Reveal Lineage Relationships
and Age-Related Mutagenesis in Human Hematopoiesis. Cell Reports (2018) 25: 2308-2316Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EE, Verstegen MM, van der Laan LJ, de Jonge J, IJzermans JN, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R. Tissue-specific mutation accumulation in human adult stem cells during life. Nature (2016) 538:260-264.
Members
Ruben van Boxtel Group leader | Alexander Steemers PhD student | Anaïs van Leeuwen |
Annemarie Rietman | Diego Montiel González Bioinformatician | Bo Scherer PostDoc |
Eirini Daskalaki PhD student | Elizaveta Kulaeva PhD student | Laurianne Trabut Research Technician |
Lucca Derks Phd candidate | Maarten Geurts | Mark van Roosmalen Bio informaticus |
Mark Verheul | Matteo Boretto PostDoc | Menno Tooren PhD Student |
Rico Hagelaar Bioinformatician |