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3. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

Middelkamp, Sjors, Manders, Freek, Peci, Flavia, van Roosmalen, Markus J., González, Diego Montiel, Bertrums, Eline J.M., van der Werf, Inge, Derks, Lucca L.M., Groenen, Niels M., Verheul, Mark, Trabut, Laurianne, Pleguezuelos-Manzano, Cayetano, Brandsma, Arianne M., Antoniou, Evangelia, Reinhardt, Dirk, Bierings, Marc, Belderbos, Mirjam E., and van Boxtel, Ruben

Published
2023
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4. A multi-platform reference for somatic structural variation detection

Author

Espejo Valle-Inclan, Jose, Besselink, Nicolle J.M., de Bruijn, Ewart, Cameron, Daniel L., Ebler, Jana, Kutzera, Joachim, van Lieshout, Stef, Marschall, Tobias, Nelen, Marcel, Priestley, Peter, Renkens, Ivo, Roemer, Margaretha G.M., van Roosmalen, Markus J., Wenger, Aaron M., Ylstra, Bauke, Fijneman, Remond J.A., Kloosterman, Wigard P., and Cuppen, Edwin

Published
2022
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7. Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Author

Bollen, Yannik, Stelloo, Ellen, van Leenen, Petra, van den Bos, Myrna, Ponsioen, Bas, Lu, Bingxin, van Roosmalen, Markus J., Bolhaqueiro, Ana C. F., Kimberley, Christopher, Mossner, Maximilian, Cross, William C. H., Besselink, Nicolle J. M., van der Roest, Bastiaan, Boymans, Sander, Oost, Koen C., de Vries, Sippe G., Rehmann, Holger, Cuppen, Edwin, Lens, Susanne M. A., Kops, Geert J. P. L., Kloosterman, Wigard P., Terstappen, Leon W. M. M., Barnes, Chris P., Sottoriva, Andrea, Graham, Trevor A., and Snippert, Hugo J. G.

Published
2021
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8. Direct detection of 8-oxo-dG using nanopore sequencing

Author

Pagès-Gallego, Marc, primary, van Soest, Daan M. K., additional, Besselink, Nicolle J. M., additional, Straver, Roy, additional, Keijer, Janneke P., additional, Vermeulen, Carlo, additional, Marcozzi, Alessio, additional, van Roosmalen, Markus J., additional, van Boxtel, Ruben, additional, Burgering, Boudewijn M. T., additional, Dansen, Tobias B., additional, and de Ridder, Jeroen, additional

Published
2024
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9. Transient Differentiation-State Plasticity Occurs during Acute Lymphoblastic Leukemia Initiation

Author

Cardiopulmonale Chirurgie pat. zorg, Poort, Vera M., Hagelaar, Rico, van Roosmalen, Markus J., Trabut, Laurianne, Buijs-Gladdines, Jessica G.C.A.M., van Wijk, Bram, Meijerink, Jules, van Boxtel, Ruben, Cardiopulmonale Chirurgie pat. zorg, Poort, Vera M., Hagelaar, Rico, van Roosmalen, Markus J., Trabut, Laurianne, Buijs-Gladdines, Jessica G.C.A.M., van Wijk, Bram, Meijerink, Jules, and van Boxtel, Ruben

Published
2024

10. Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms

Author

Bertrums, Eline J.M., de Kanter, Jurrian K., Derks, Lucca L.M., Verheul, Mark, Trabut, Laurianne, van Roosmalen, Markus J., Hasle, Henrik, Antoniou, Evangelia, Reinhardt, Dirk, Dworzak, Michael N., Mühlegger, Nora, van den Heuvel-Eibrink, Marry M., Zwaan, C. Michel, Goemans, Bianca F., van Boxtel, Ruben, Bertrums, Eline J.M., de Kanter, Jurrian K., Derks, Lucca L.M., Verheul, Mark, Trabut, Laurianne, van Roosmalen, Markus J., Hasle, Henrik, Antoniou, Evangelia, Reinhardt, Dirk, Dworzak, Michael N., Mühlegger, Nora, van den Heuvel-Eibrink, Marry M., Zwaan, C. Michel, Goemans, Bianca F., and van Boxtel, Ruben

Abstract

Therapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.

Published
2024

11. Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA.

Author

CMM Groep Dansen, Cancer, CMM Groep Kloosterman, CMM Groep De Keizer, CMM Groep Burgering, CMM Groep Cuppen, CMM Sectie Molecular Cancer Research, van Soest, Daan M K, Polderman, Paulien E, den Toom, Wytze T F, Keijer, Janneke P, van Roosmalen, Markus J, Leyten, Tim M F, Lehmann, Johannes, Zwakenberg, Susan, De Henau, Sasha, van Boxtel, Ruben, Burgering, Boudewijn M T, Dansen, Tobias B, CMM Groep Dansen, Cancer, CMM Groep Kloosterman, CMM Groep De Keizer, CMM Groep Burgering, CMM Groep Cuppen, CMM Sectie Molecular Cancer Research, van Soest, Daan M K, Polderman, Paulien E, den Toom, Wytze T F, Keijer, Janneke P, van Roosmalen, Markus J, Leyten, Tim M F, Lehmann, Johannes, Zwakenberg, Susan, De Henau, Sasha, van Boxtel, Ruben, Burgering, Boudewijn M T, and Dansen, Tobias B

Published
2024

12. Characteristics of de novo structural changes in the human genome

Author

Kloosterman, Wigard P, Francioli, Laurent C, Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y, Abdellaoui, Abdel, Lameijer, Eric-Wubbo, Moed, Matthijs H, Koval, Vyacheslav, Renkens, Ivo, van Roosmalen, Markus J, Arp, Pascal, Karssen, Lennart C, Coe, Bradley P, Handsaker, Robert E, Suchiman, Eka D, Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C, Consortium, Genome of the Netherlands, Uitterlinden, André, van Duijn, Cornelia M, Swertz, Morris A, Wijmenga, Cisca, van Ommen, GertJan B, Slagboom, P Eline, Boomsma, Dorret I, Schönhuth, Alexander, Eichler, Evan E, de Bakker, Paul IW, Ye, Kai, and Guryev, Victor

Subjects
Genetics, Human Genome, Alleles, Amino Acid Sequence, Female, Genetic Variation, Genome, Human, Genomics, Haplotypes, Humans, INDEL Mutation, Male, Molecular Sequence Data, Mutation Rate, Polymorphism, Single Nucleotide, Retroelements, Sequence Alignment, Sequence Analysis, DNA, Genome of Netherlands Consortium, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (1-20 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations.

Published
2015

13. Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Author

Valle-Inclan, Jose Espejo, Stangl, Christina, de Jong, Anouk C., van Dessel, Lisanne F., van Roosmalen, Markus J., Helmijr, Jean C. A., Renkens, Ivo, Janssen, Roel, de Blank, Sam, de Witte, Chris J., Martens, John W. M., Jansen, Maurice P. H. M., Lolkema, Martijn P., and Kloosterman, Wigard P.

Published
2021
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14. An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity

Author

Kopper, Oded, de Witte, Chris J., Lõhmussaar, Kadi, Valle-Inclan, Jose Espejo, Hami, Nizar, Kester, Lennart, Balgobind, Anjali Vanita, Korving, Jeroen, Proost, Natalie, Begthel, Harry, van Wijk, Lise M., Revilla, Sonia Aristín, Theeuwsen, Rebecca, van de Ven, Marieke, van Roosmalen, Markus J., Ponsioen, Bas, Ho, Victor W. H., Neel, Benjamin G., Bosse, Tjalling, Gaarenstroom, Katja N., Vrieling, Harry, Vreeswijk, Maaike P. G., van Diest, Paul J., Witteveen, Petronella O., Jonges, Trudy, Bos, Johannes L., van Oudenaarden, Alexander, Zweemer, Ronald P., Snippert, Hugo J. G., Kloosterman, Wigard P., and Clevers, Hans

Published
2019
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16. Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA.

Author

van Soest, Daan M. K., Polderman, Paulien E., den Toom, Wytze T. F., Keijer, Janneke P., van Roosmalen, Markus J., Leyten, Tim M. F., Lehmann, Johannes, Zwakenberg, Susan, De Henau, Sasha, van Boxtel, Ruben, Burgering, Boudewijn M. T., and Dansen, Tobias B.

Subjects
NUCLEAR DNA, MITOCHONDRIA, CELL cycle, REACTIVE oxygen species, DNA damage
Abstract

Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of chromosomal DNA mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondria can directly damage nuclear DNA is largely lacking. In this study, we investigated the effects of H2O2 released by mitochondria or produced at the nucleosomes using a titratable chemogenetic approach. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2. Nuclear H2O2 gives rise to DNA damage and mutations and a subsequent p53 dependent cell cycle arrest. Mitochondrial H2O2 release shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. We conclude that H2O2 released from mitochondria is unlikely to directly damage nuclear genomic DNA, limiting its contribution to oncogenic transformation and aging. Nuclear DNA damage downstream of mitochondrial ROS is often cited to contribute to cancer initiation and aging. However, here the authors show that although H2O2 induces DNA mutations when produced near DNA, it does not when released by mitochondria. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Identification of human D lactate dehydrogenase deficiency

Author

Monroe, Glen R., van Eerde, Albertien M., Tessadori, Federico, Duran, Karen J., Savelberg, Sanne M. C., van Alfen, Johanna C., Terhal, Paulien A., van der Crabben, Saskia N., Lichtenbelt, Klaske D., Fuchs, Sabine A., Gerrits, Johan, van Roosmalen, Markus J., van Gassen, Koen L., van Aalderen, Mirjam, Koot, Bart G., Oostendorp, Marlies, Duran, Marinus, Visser, Gepke, de Koning, Tom J., Calì, Francesco, Bosco, Paolo, Geleijns, Karin, de Sain-van der Velden, Monique G. M., Knoers, Nine V., Bakkers, Jeroen, Verhoeven-Duif, Nanda M., van Haaften, Gijs, and Jans, Judith J.

Published
2019
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19. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

CMM Groep Snippert, CMM Groep Kloosterman, CTI Leusen, SCT patientenzorg, Child Health, Infection & Immunity, Regenerative Medicine and Stem Cells, Arts-assistenten Kinderen, CMM Groep Cuppen, Middelkamp, Sjors, Manders, Freek, Peci, Flavia, van Roosmalen, Markus J., González, Diego Montiel, Bertrums, Eline J.M., van der Werf, Inge, Derks, Lucca L.M., Groenen, Niels M., Verheul, Mark, Trabut, Laurianne, Pleguezuelos-Manzano, Cayetano, Brandsma, Arianne M., Antoniou, Evangelia, Reinhardt, Dirk, Bierings, Marc, Belderbos, Mirjam E., van Boxtel, Ruben, CMM Groep Snippert, CMM Groep Kloosterman, CTI Leusen, SCT patientenzorg, Child Health, Infection & Immunity, Regenerative Medicine and Stem Cells, Arts-assistenten Kinderen, CMM Groep Cuppen, Middelkamp, Sjors, Manders, Freek, Peci, Flavia, van Roosmalen, Markus J., González, Diego Montiel, Bertrums, Eline J.M., van der Werf, Inge, Derks, Lucca L.M., Groenen, Niels M., Verheul, Mark, Trabut, Laurianne, Pleguezuelos-Manzano, Cayetano, Brandsma, Arianne M., Antoniou, Evangelia, Reinhardt, Dirk, Bierings, Marc, Belderbos, Mirjam E., and van Boxtel, Ruben

Published
2023

21. Supplementary Table from Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms

Author

Bertrums, Eline J.M., primary, Rosendahl Huber, Axel K.M., primary, de Kanter, Jurrian K., primary, Brandsma, Arianne M., primary, van Leeuwen, Anaïs J.C.N., primary, Verheul, Mark, primary, van den Heuvel-Eibrink, Marry M., primary, Oka, Rurika, primary, van Roosmalen, Markus J., primary, de Groot-Kruseman, Hester A., primary, Zwaan, C. Michel, primary, Goemans, Bianca F., primary, and van Boxtel, Ruben, primary

Published
2023
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24. Data from Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms

Author

Bertrums, Eline J.M., primary, Rosendahl Huber, Axel K.M., primary, de Kanter, Jurrian K., primary, Brandsma, Arianne M., primary, van Leeuwen, Anaïs J.C.N., primary, Verheul, Mark, primary, van den Heuvel-Eibrink, Marry M., primary, Oka, Rurika, primary, van Roosmalen, Markus J., primary, de Groot-Kruseman, Hester A., primary, Zwaan, C. Michel, primary, Goemans, Bianca F., primary, and van Boxtel, Ruben, primary

Published
2023
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25. Supplementary Figure from Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms

Author

Bertrums, Eline J.M., primary, Rosendahl Huber, Axel K.M., primary, de Kanter, Jurrian K., primary, Brandsma, Arianne M., primary, van Leeuwen, Anaïs J.C.N., primary, Verheul, Mark, primary, van den Heuvel-Eibrink, Marry M., primary, Oka, Rurika, primary, van Roosmalen, Markus J., primary, de Groot-Kruseman, Hester A., primary, Zwaan, C. Michel, primary, Goemans, Bianca F., primary, and van Boxtel, Ruben, primary

Published
2023
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27. Supplementary Materials and Methods from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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28. Supplementary Figures 1-11 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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30. Supplementary Table 4 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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31. Supplementary Figure Legends from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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32. Supplementary Table 2 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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33. Supplementary Table 3 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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34. Supplementary Table 1 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity

Author

Stangl, Christina, primary, Post, Jasmin B., primary, van Roosmalen, Markus J., primary, Hami, Nizar, primary, Verlaan-Klink, Ingrid, primary, Vos, Harmjan R., primary, van Es, Robert M., primary, Koudijs, Marco J., primary, Voest, Emile E., primary, Snippert, Hugo J.G., primary, and Kloosterman, W.P., primary

Published
2023
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35. Supplementary Table S3 from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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36. Supplementary Data file from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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37. Data from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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38. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

Middelkamp, Sjors, primary, Manders, Freek, additional, Peci, Flavia, additional, van Roosmalen, Markus J., additional, González, Diego Montiel, additional, Bertrums, Eline J.M., additional, van der Werf, Inge, additional, Derks, Lucca L.M., additional, Groenen, Niels M., additional, Verheul, Mark, additional, Trabut, Laurianne, additional, Brandsma, Arianne M., additional, Antoniou, Evangelia, additional, Reinhardt, Dirk, additional, Bierings, Marc, additional, Belderbos, Mirjam E., additional, and van Boxtel, Ruben, additional

Published
2023
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39. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease

Author

van der Crabben, Saskia N., Hennus, Marije P., McGregor, Grant A., Ritter, Deborah I., Nagamani, Sandesh C.S., Wells, Owen S., Harakalova, Magdalena, Chinn, Ivan K., Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M., Terheggen-Lagro, Suzanne W., van Lieshout, Stef, van Roosmalen, Markus J., Renkens, Ivo, Duran, Karen, Nijman, Isaac J., Kloosterman, Wigard P., Hennekam, Eric, Orange, Jordan S., van Hasselt, Peter M., Wheeler, David A., Palecek, Jan J., Lehmann, Alan R., Oliver, Antony W., Pearl, Laurence H., Plon, Sharon E., Murray, Johanne M., and van Haaften, Gijs

Subjects
Complications and side effects, Development and progression, Genetic aspects, Health aspects, Chromosome abnormalities -- Complications and side effects, Pediatric diseases -- Genetic aspects -- Development and progression, Gene mutation -- Health aspects, Adult respiratory distress syndrome -- Genetic aspects -- Development and progression, Gene mutations -- Health aspects, Children -- Diseases, Acute respiratory distress syndrome -- Genetic aspects -- Development and progression
Abstract

Introduction Chromosome dynamics in eukaryotes are controlled by the structural maintenance of the chromosome complex (SMC) family of proteins, which form 3 highly conserved and functional complexes: cohesin (SMC1/SMC3), condensin [...], The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.

Published
2016
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40. Retrospective Lineage Tracing of Pediatric Acute Myeloid Leukemia Using Single-Cell Whole Genome Sequencing

Author

Bertrums, Eline J.M., primary, Middelkamp, Sjors, additional, van der Werf, Inge M., additional, Manders, Freek, additional, Brandsma, Arianne M., additional, Groenen, Niels M., additional, Verheul, Mark, additional, van Roosmalen, Markus J., additional, Zwaan, C. Michel, additional, van den Heuvel-Eibrink, Marry M., additional, Goemans, Bianca F., additional, and Van Boxtel, Ruben, additional

Published
2022
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41. Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms

Author

Bertrums, Eline J.M., primary, Rosendahl Huber, Axel K.M., additional, de Kanter, Jurrian K., additional, Brandsma, Arianne M., additional, van Leeuwen, Anaïs J.C.N., additional, Verheul, Mark, additional, van den Heuvel-Eibrink, Marry M., additional, Oka, Rurika, additional, van Roosmalen, Markus J., additional, de Groot-Kruseman, Hester A., additional, Zwaan, C. Michel, additional, Goemans, Bianca F., additional, and van Boxtel, Ruben, additional

Published
2022
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42. A multi-platform reference for somatic structural variation detection

Author

CMM Groep Cuppen, CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Child Health, Espejo Valle-Inclan, Jose, Besselink, Nicolle J M, de Bruijn, Ewart, Cameron, Daniel L, Ebler, Jana, Kutzera, Joachim, van Lieshout, Stef, Marschall, Tobias, Nelen, Marcel, Priestley, Peter, Renkens, Ivo, Roemer, Margaretha G M, van Roosmalen, Markus J, Wenger, Aaron M, Ylstra, Bauke, Fijneman, Remond J A, Kloosterman, Wigard P, Cuppen, Edwin, CMM Groep Cuppen, CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Child Health, Espejo Valle-Inclan, Jose, Besselink, Nicolle J M, de Bruijn, Ewart, Cameron, Daniel L, Ebler, Jana, Kutzera, Joachim, van Lieshout, Stef, Marschall, Tobias, Nelen, Marcel, Priestley, Peter, Renkens, Ivo, Roemer, Margaretha G M, van Roosmalen, Markus J, Wenger, Aaron M, Ylstra, Bauke, Fijneman, Remond J A, Kloosterman, Wigard P, and Cuppen, Edwin

Published
2022

43. Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to TherapyRelated Myeloid Neoplasms

Author

Bertrums, Eline J.M., Rosendahl Huber, Axel K.M., de Kanter, Jurrian K., Brandsma, Arianne M., van Leeuwen, Anaïs J.C.N., Verheul, Mark, van den Heuvel-Eibrink, Marry M., Oka, Rurika, van Roosmalen, Markus J., de Groot-Kruseman, Hester A., Michel Zwaan, C., Goemans, Bianca F., van Boxtel, Ruben, Bertrums, Eline J.M., Rosendahl Huber, Axel K.M., de Kanter, Jurrian K., Brandsma, Arianne M., van Leeuwen, Anaïs J.C.N., Verheul, Mark, van den Heuvel-Eibrink, Marry M., Oka, Rurika, van Roosmalen, Markus J., de Groot-Kruseman, Hester A., Michel Zwaan, C., Goemans, Bianca F., and van Boxtel, Ruben

Abstract

Childhood cancer survivors are confronted with various chronic health conditions like therapy-related malignancies. However, it is unclear how exposure to chemotherapy contributes to the mutation burden and clonal composition of healthy tissues early in life. Here, we studied mutation accumulation in hematopoietic stem and progenitor cells (HSPC) before and after cancer treatment of 24 children. Of these children, 19 developed therapy-related myeloid neoplasms (t-MN). Posttreatment HSPCs had an average mutation burden increase comparable to what treatment-naïve cells accumulate during 16 years of life, with excesses up to 80 years. In most children, these additional mutations were induced by clock-like processes, which are also active during healthy aging. Other patients harbored mutations that could be directly attributed to treatments like platinum-based drugs and thiopurines. Using phylogenetic inference, we demonstrate that most t-MN in children originate after the start of treatment and that leukemic clones become dominant during or directly after chemotherapy exposure. SIGNIFICANCE: Our study shows that chemotherapy increases the mutation burden of normal blood cells in cancer survivors. Only few drugs damage the DNA directly, whereas in most patients, chemotherapy-induced mutations are caused by processes similar to those present during normal aging.

Published
2022

44. Article Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo

Author

CMM Groep Cuppen, CMM Groep Kloosterman, Cancer, Hasaart, Karlijn A L, Manders, Freek, Ubels, Joske, Verheul, Mark, van Roosmalen, Markus J, Groenen, Niels M, Oka, Rurika, Kuijk, Ewart, Lopes, Susana M Chuva de Sousa, Boxtel, Ruben van, CMM Groep Cuppen, CMM Groep Kloosterman, Cancer, Hasaart, Karlijn A L, Manders, Freek, Ubels, Joske, Verheul, Mark, van Roosmalen, Markus J, Groenen, Niels M, Oka, Rurika, Kuijk, Ewart, Lopes, Susana M Chuva de Sousa, and Boxtel, Ruben van

Published
2022

45. MutationalPatterns: the one stop shop for the analysis of mutational processes

Author

CTI Leusen, CMM Groep Kloosterman, Epi Infectieziekten Team 2, Infection & Immunity, CMM Groep Cuppen, Cancer, Manders, Freek, Brandsma, Arianne M, de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J, van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, van Boxtel, Ruben, CTI Leusen, CMM Groep Kloosterman, Epi Infectieziekten Team 2, Infection & Immunity, CMM Groep Cuppen, Cancer, Manders, Freek, Brandsma, Arianne M, de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J, van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, and van Boxtel, Ruben

Published
2022

46. Additional file 2 of MutationalPatterns: the one stop shop for the analysis of mutational processes

Author

Manders, Freek, Brandsma, Arianne M., de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J., van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, and van Boxtel, Ruben

Abstract

Additional file 2. Description of the wet-lab generation and sequencing analysis of the knockout lines. These lines were used to illustrate the functions of the MutationalPatterns package on novel real-world data and provide new biological conclusions.

Published
2022
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47. Additional file 1 of MutationalPatterns: the one stop shop for the analysis of mutational processes

Author

Manders, Freek, Brandsma, Arianne M., de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J., van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, and van Boxtel, Ruben

Abstract

Additional file 1: Additional figures, which help to illustrate the data present in this work and provide the reader with a more comprehensive understanding of the manuscript. Figure S1. Removing the DBSs and MBSs results in an improved SBS profile. Figure S2. Mutation contexts can be visualized with a river plot. Figure S3. Lesion segregation can be visualized. Figure S4. Variational Bayes NMF can be used to predict the optimal number of signatures to extract. Figure S5. Strict refitting iteratively removes signatures. Figure S6. Bootstrapped signature refitting can be visualized with a jitter plot. Figure S7. TT[C > T]CT is the most common substitution type in metastatic melanomas. Figure S8. The matrix generating functions have O(n) or better scaling. Figure S9. Benchmark of the ���mut_matrix��� function. Figure S10. Recall-precision plot of different refitting methods in MutationalPatterns. Figure S11. Western blot analysis of AHH-1 CRISPR-Cas9 edited clonal lines. Figure S12. Uncropped original version of the western blots in Fig. S11. Figure S13. SBS profiles of knockout samples.

Published
2022
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48. Additional file 3 of MutationalPatterns: the one stop shop for the analysis of mutational processes

Author

Manders, Freek, Brandsma, Arianne M., de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J., van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, and van Boxtel, Ruben

Abstract

Additional file 3: Additional tables containing extra data that can help the reader better understand the manuscript. Table S1. List of new features and bugfixes. Table S2. The potential damage of mutational signatures. Table S3. The genes used for the signature potential damage analysis. Table S4. Overview of the source of the replication timing data.

Published
2022
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50. Deregulation of Splicing in Pediatric Acute Myeloid Stem and Progenitor Cells

Author

Mondala, Phoebe, primary, Van Der Werf, Inge, additional, Balaian, Larisa, additional, Steel, Kathleen, additional, Ladel, Luisa, additional, Mason, Cayla, additional, Diep, Raymond, additional, Cloos, Jacqueline, additional, Kaspers, Gertjan, additional, van Roosmalen, Markus J, additional, Van Boxtel, Ruben, additional, Chan, Warren, additional, Mark, Adam, additional, Donohoe, Mary, additional, La Clair, James, additional, Wentworth, Peggy, additional, Fisch, Kathleen, additional, Crews, Leslie A, additional, Whisenant, Thomas, additional, Burkart, Michael, additional, and Jamieson, Catriona, additional

Published
2021
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