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1. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M., Buijs-Gladdines, Jessica G.C.A.M., van de Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G., de Laat, Wouter, and Meijerink, Jules P.P.

Published
2023
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2. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, Meijerink, Jules P P, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, and Meijerink, Jules P P

Abstract

Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.

Published
2023

3. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Genetica Sectie Genoomdiagnostiek, Cancer, Genetica, CMM, CMM Groep Burgering, Hubrecht Institute with UMC, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, Meijerink, Jules P P, Genetica Sectie Genoomdiagnostiek, Cancer, Genetica, CMM, CMM Groep Burgering, Hubrecht Institute with UMC, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, and Meijerink, Jules P P

Published
2023

4. Trio-based whole exome sequencing in patients with suspected sporadic inborn errors of immunity: A retrospective cohort study

Author

Hebert, Anne, primary, Simons, Annet, additional, Schuurs-Hoeijmakers, Janneke HM, additional, Koenen, Hans JPM, additional, Zonneveld-Huijssoon, Evelien, additional, Henriet, Stefanie SV, additional, Schatorjé, Ellen JH, additional, Hoppenreijs, Esther PAH, additional, Leenders, Erika KSM, additional, Janssen, Etienne JM, additional, Santen, Gijs WE, additional, de Munnik, Sonja A, additional, van Reijmersdal, Simon V, additional, van Rijssen, Esther, additional, Kersten, Simone, additional, Netea, Mihai G, additional, Smeets, Ruben L, additional, van de Veerdonk, Frank L, additional, Hoischen, Alexander, additional, and van der Made, Caspar I, additional

Published
2022
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5. Author response: Trio-based whole exome sequencing in patients with suspected sporadic inborn errors of immunity: A retrospective cohort study

Author

Hebert, Anne, primary, Simons, Annet, additional, Schuurs-Hoeijmakers, Janneke HM, additional, Koenen, Hans JPM, additional, Zonneveld-Huijssoon, Evelien, additional, Henriet, Stefanie SV, additional, Schatorjé, Ellen JH, additional, Hoppenreijs, Esther PAH, additional, Leenders, Erika KSM, additional, Janssen, Etienne JM, additional, Santen, Gijs WE, additional, de Munnik, Sonja A, additional, van Reijmersdal, Simon V, additional, van Rijssen, Esther, additional, Kersten, Simone, additional, Netea, Mihai G, additional, Smeets, Ruben L, additional, van de Veerdonk, Frank L, additional, Hoischen, Alexander, additional, and van der Made, Caspar I, additional

Published
2022
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6. Prevalence of (Epi)genetic Predisposing Factors in a 5-Year Unselected National Wilms Tumor Cohort: A Comprehensive Clinical and Genomic Characterization

Author

Hol, Janna A., primary, Kuiper, Roland P., additional, van Dijk, Freerk, additional, Waanders, Esmé, additional, van Peer, Sophie E., additional, Koudijs, Marco J., additional, Bladergroen, Reno, additional, van Reijmersdal, Simon V., additional, Morgado, Lionel M., additional, Bliek, Jet, additional, Lombardi, Maria Paola, additional, Hopman, Saskia, additional, Drost, Jarno, additional, de Krijger, Ronald R., additional, van den Heuvel-Eibrink, Marry M., additional, and Jongmans, Marjolijn C.J., additional

Published
2022
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7. Independent prognostic value of BCR-ABL1-like signature and IKZF1 deletion, but not high CRLF2 expression, in children with B-cell precursor ALL

Author

van der Veer, Arian, Waanders, Esmé, Pieters, Rob, Willemse, Marieke E., Van Reijmersdal, Simon V., Russell, Lisa J., Harrison, Christine J., Evans, William E., van der Velden, Vincent H.J., Hoogerbrugge, Peter M., Van Leeuwen, Frank, Escherich, Gabriele, Horstmann, Martin A., Mohammadi Khankahdani, Leila, Rizopoulos, Dimitris, De Groot-Kruseman, Hester A., Sonneveld, Edwin, Kuiper, Roland P., and Den Boer, Monique L.

Published
2013
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8. Prevalence of (Epi)genetic Predisposing Factors in a 5-Year Unselected National Wilms Tumor Cohort: A Comprehensive Clinical and Genomic Characterization

Author

Genetica Klinische Genetica, Genetica, Genetica Sectie Genoomdiagnostiek, Child Health, Pathologie Pathologen staf, Speerpunt, Zorg en O&O, Cancer, Hol, Janna A., Kuiper, Roland P., Van Dijk, Freerk, Waanders, Esmé, Van Peer, Sophie E., Koudijs, Marco J., Bladergroen, Reno, Van Reijmersdal, Simon V., Morgado, Lionel M., Bliek, Jet, Lombardi, Maria Paola, Hopman, Saskia, Drost, Jarno, De Krijger, Ronald R., Van Den Heuvel-Eibrink, Marry M., Jongmans, Marjolijn C.J., Genetica Klinische Genetica, Genetica, Genetica Sectie Genoomdiagnostiek, Child Health, Pathologie Pathologen staf, Speerpunt, Zorg en O&O, Cancer, Hol, Janna A., Kuiper, Roland P., Van Dijk, Freerk, Waanders, Esmé, Van Peer, Sophie E., Koudijs, Marco J., Bladergroen, Reno, Van Reijmersdal, Simon V., Morgado, Lionel M., Bliek, Jet, Lombardi, Maria Paola, Hopman, Saskia, Drost, Jarno, De Krijger, Ronald R., Van Den Heuvel-Eibrink, Marry M., and Jongmans, Marjolijn C.J.

Published
2022

9. Clonal dynamics in pediatric B-cell precursor acute lymphoblastic leukemia with very early relapse

Author

PMC Medisch specialisten, Genetica Sectie Genoomdiagnostiek, Antić, Željko, Yu, Jiangyan, Bornhauser, Beat C, Lelieveld, Stefan H, van der Ham, Cedric G, van Reijmersdal, Simon V, Morgado, Lionel, Elitzur, Sarah, Bourquin, Jean-Pierre, Cazzaniga, Giovanni, Eckert, Cornelia, Camós, Mireia, Sutton, Rosemary, Cavé, Hélène, Moorman, Anthony V, Sonneveld, Edwin, Geurts van Kessel, Ad, van Leeuwen, Frank N, Hoogerbrugge, Peter M, Waanders, Esmé, Kuiper, Roland P, PMC Medisch specialisten, Genetica Sectie Genoomdiagnostiek, Antić, Željko, Yu, Jiangyan, Bornhauser, Beat C, Lelieveld, Stefan H, van der Ham, Cedric G, van Reijmersdal, Simon V, Morgado, Lionel, Elitzur, Sarah, Bourquin, Jean-Pierre, Cazzaniga, Giovanni, Eckert, Cornelia, Camós, Mireia, Sutton, Rosemary, Cavé, Hélène, Moorman, Anthony V, Sonneveld, Edwin, Geurts van Kessel, Ad, van Leeuwen, Frank N, Hoogerbrugge, Peter M, Waanders, Esmé, and Kuiper, Roland P

Published
2022

10. Clonal dynamics in pediatric B-cell precursor acute lymphoblastic leukemia with very early relapse

Author

Antić, Željko; https://orcid.org/0000-0001-9398-2637, Yu, Jiangyan, Bornhauser, Beat C, Lelieveld, Stefan H, van der Ham, Cedric G, van Reijmersdal, Simon V, Morgado, Lionel, Elitzur, Sarah, Bourquin, Jean-Pierre; https://orcid.org/0000-0001-6571-6227, Cazzaniga, Giovanni, Eckert, Cornelia; https://orcid.org/0000-0003-1039-2872, Camós, Mireia, Sutton, Rosemary, Cavé, Hélène, Moorman, Anthony V, Sonneveld, Edwin, Geurts van Kessel, Ad, van Leeuwen, Frank N, Hoogerbrugge, Peter M, Waanders, Esmé, Kuiper, Roland P, Antić, Željko; https://orcid.org/0000-0001-9398-2637, Yu, Jiangyan, Bornhauser, Beat C, Lelieveld, Stefan H, van der Ham, Cedric G, van Reijmersdal, Simon V, Morgado, Lionel, Elitzur, Sarah, Bourquin, Jean-Pierre; https://orcid.org/0000-0001-6571-6227, Cazzaniga, Giovanni, Eckert, Cornelia; https://orcid.org/0000-0003-1039-2872, Camós, Mireia, Sutton, Rosemary, Cavé, Hélène, Moorman, Anthony V, Sonneveld, Edwin, Geurts van Kessel, Ad, van Leeuwen, Frank N, Hoogerbrugge, Peter M, Waanders, Esmé, and Kuiper, Roland P

Abstract

INTRODUCTION One-quarter of the relapses in children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) occur very early (within 18 months, before completion of treatment), and prognosis in these patients is worse compared to cases that relapse after treatment has ended. METHODS In this study, we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy. RESULTS We observed a dynamic clonal evolution in all cases, with relapse almost exclusively originating from a subclone at diagnosis. We identified several driver mutations that may have influenced the outgrowth of a minor clone at diagnosis to become the major clone at relapse. For example, a minimal residual disease (MRD)-based standard-risk patient with ETV6-RUNX1-positive leukemia developed a relapse from a TP53-mutated subclone after loss of the wildtype allele. Furthermore, two patients with TCF3-PBX1-positive leukemia that developed a very early relapse carried E1099K WHSC1 mutations at diagnosis, a hotspot mutation that was recurrently encountered in other very early TCF3-PBX1-positive leukemia relapses as well. In addition to alterations in known relapse drivers, we found two cases with truncating mutations in the cohesin gene RAD21. CONCLUSION Comprehensive genomic characterization of diagnosis-relapse pairs shows that very early relapses in BCP-ALL frequently arise from minor subclones at diagnosis. A detailed understanding of the therapeutic pressure driving these events may aid the development of improved therapies.

Published
2022

12. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels By Recurrent CTCF inactivating Mutations in T Cell Acute Lymphoblastic Leukemia

Author

Smits, Willem K., primary, Vermeulen, Carlo, additional, Hagelaar, Rico, additional, Kimura, Shunsuke, additional, Vroegindeweij, Eric, additional, Buijs-Gladdines, Jessica G.C.A.M., additional, Van De Geer, Ellen, additional, Verstegen, Marjon J.A.M., additional, Splinter, Erik, additional, van Reijmersdal, Simon V., additional, Buijs, Arjan, additional, Galjart, Niels, additional, Van Eyndhoven, Winfried, additional, Van Min, Max Jan, additional, Kuiper, Roland P, additional, Kemmeren, Patrick, additional, Mullighan, Charles G., additional, De Laat, Wouter, additional, and Meijerink, Jules P.P., additional

Published
2021
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14. Genetic Screening for TLR7 Variants in Young and Previously Healthy Men With Severe COVID-19

Author

Solanich, Xavier, primary, Vargas-Parra, Gardenia, additional, van der Made, Caspar I., additional, Simons, Annet, additional, Schuurs-Hoeijmakers, Janneke, additional, Antolí, Arnau, additional, del Valle, Jesús, additional, Rocamora-Blanch, Gemma, additional, Setién, Fernando, additional, Esteller, Manel, additional, van Reijmersdal, Simon V., additional, Riera-Mestre, Antoni, additional, Sabater-Riera, Joan, additional, Capellá, Gabriel, additional, van de Veerdonk, Frank L., additional, van der Hoven, Ben, additional, Corbella, Xavier, additional, Hoischen, Alexander, additional, and Lázaro, Conxi, additional

Published
2021
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15. Genetic Screening for TLR7 Variants in Young and Previously Healthy Men With Severe COVID-19

Author

Solanich, Xavier, Vargas-Parra, Gardenia, van der Made, Caspar I., Simons, Annet, Schuurs-Hoeijmakers, Janneke, Antolí, Arnau, del Valle, Jesús, Rocamora-Blanch, Gemma, Setién, Fernando, Esteller, Manel, van Reijmersdal, Simon V., Riera-Mestre, Antoni, Sabater-Riera, Joan, Capellá, Gabriel, van de Veerdonk, Frank L., van der Hoven, Ben, Corbella, Xavier, Hoischen, Alexander, Lázaro, Conxi, Solanich, Xavier, Vargas-Parra, Gardenia, van der Made, Caspar I., Simons, Annet, Schuurs-Hoeijmakers, Janneke, Antolí, Arnau, del Valle, Jesús, Rocamora-Blanch, Gemma, Setién, Fernando, Esteller, Manel, van Reijmersdal, Simon V., Riera-Mestre, Antoni, Sabater-Riera, Joan, Capellá, Gabriel, van de Veerdonk, Frank L., van der Hoven, Ben, Corbella, Xavier, Hoischen, Alexander, and Lázaro, Conxi

Abstract

Introduction: Loss-of-function TLR7 variants have been recently reported in a small number of males to underlie strong predisposition to severe COVID-19. We aimed to determine the presence of these rare variants in young men with severe COVID-19. Methods: We prospectively studied males between 18 and 50 years-old without predisposing comorbidities that required at least high-flow nasal oxygen to treat COVID-19. The coding region of TLR7 was sequenced to assess the presence of potentially deleterious variants. Results: TLR7 missense variants were identified in two out of 14 patients (14.3%). Overall, the median age was 38 (IQR 30-45) years. Both variants were not previously reported in population control databases and were predicted to be damaging by in silico predictors. In a 30-year-old patient a maternally inherited variant [c.644A>G; p.(Asn215Ser)] was identified, co-segregating in his 27-year-old brother who also contracted severe COVID-19. A second variant [c.2797T>C; p.(Trp933Arg)] was found in a 28-year-old patient, co-segregating in his 24-year-old brother who developed mild COVID-19. Functional testing of this variant revealed decreased type I and II interferon responses in peripheral mononuclear blood cells upon stimulation with the TLR7 agonist imiquimod, confirming a loss-of-function effect. Conclusions: This study supports a rationale for the genetic screening for TLR7 variants in young men with severe COVID-19 in the absence of other relevant risk factors. A diagnosis of TLR7 deficiency could not only inform on treatment options for the patient, but also enables pre-symptomatic testing of at-risk male relatives with the possibility of instituting early preventive and therapeutic interventions.

Published
2021

16. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels by Recurrent CTCF Inactivating Mutations in Acute T Cell Leukemia

Author

Smits, Willem K., primary, Vermeulen, Carlo, additional, Hagelaar, Rico, additional, Kimura, Shunsuke, additional, Vroegiindeweij, Eric M., additional, Buijs-gladdines, Jessica G.C.A.M., additional, van de Geer-de Jong, Ellen, additional, Verstegen, Marjon J.A.M., additional, Splinter, Erik, additional, van Reijmersdal, Simon V., additional, Buijs, Arjan, additional, Galjart, Niels, additional, van Eijndhoven, Winfried, additional, van Min, Max, additional, Kuiper, Roland, additional, Kemmeren, Patrick, additional, Mullighan, Charles G., additional, de Laat, Wouter, additional, and Meijerink, Jules P.P., additional

Published
2021
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17. Multiclonal complexity of pediatric acute lymphoblastic leukemia and the prognostic relevance of subclonal mutations

Author

Antić, Željko, primary, Yu, Jiangyan, additional, Van Reijmersdal, Simon V., additional, Van Dijk, Anke, additional, Dekker, Linde, additional, Segerink, Wouter H., additional, Sonneveld, Edwin, additional, Fiocco, Marta, additional, Pieters, Rob, additional, Hoogerbrugge, Peter M., additional, Van Leeuwen, Frank N., additional, Van Kessel, Ad Geurts, additional, Waanders, Esme, additional, and Kuiper, Roland P., additional

Published
2020
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18. Presence of Genetic Variants Among Young Men With Severe COVID-19

Author

van der Made, Caspar I., primary, Simons, Annet, additional, Schuurs-Hoeijmakers, Janneke, additional, van den Heuvel, Guus, additional, Mantere, Tuomo, additional, Kersten, Simone, additional, van Deuren, Rosanne C., additional, Steehouwer, Marloes, additional, van Reijmersdal, Simon V., additional, Jaeger, Martin, additional, Hofste, Tom, additional, Astuti, Galuh, additional, Corominas Galbany, Jordi, additional, van der Schoot, Vyne, additional, van der Hoeven, Hans, additional, Hagmolen of ten Have, Wanda, additional, Klijn, Eva, additional, van den Meer, Catrien, additional, Fiddelaers, Jeroen, additional, de Mast, Quirijn, additional, Bleeker-Rovers, Chantal P., additional, Joosten, Leo A. B., additional, Yntema, Helger G., additional, Gilissen, Christian, additional, Nelen, Marcel, additional, van der Meer, Jos W. M., additional, Brunner, Han G., additional, Netea, Mihai G., additional, van de Veerdonk, Frank L., additional, and Hoischen, Alexander, additional

Published
2020
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19. Upfront Treatment Influences the Composition of Genetic Alterations in Relapsed Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia

Author

Yu, Jiangyan, primary, Waanders, Esmé, additional, van Reijmersdal, Simon V., additional, Antić, Željko, additional, van Bosbeek, Charlotte M., additional, Sonneveld, Edwin, additional, de Groot, Hester, additional, Fiocco, Marta, additional, van Kessel, Ad Geurts, additional, van Leeuwen, Frank N., additional, Pieters, Rob, additional, Hoogerbrugge, Peter M., additional, and Kuiper, Roland P., additional

Published
2020
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20. Clonal dynamics in pediatric B‐cell precursor acute lymphoblastic leukemia with very early relapse.

Author

Antić, Željko, Yu, Jiangyan, Bornhauser, Beat C., Lelieveld, Stefan H., van der Ham, Cedric G., van Reijmersdal, Simon V., Morgado, Lionel, Elitzur, Sarah, Bourquin, Jean‐Pierre, Cazzaniga, Giovanni, Eckert, Cornelia, Camós, Mireia, Sutton, Rosemary, Cavé, Hélène, Moorman, Anthony V., Sonneveld, Edwin, Geurts van Kessel, Ad, van Leeuwen, Frank N., Hoogerbrugge, Peter M., and Waanders, Esmé

Published
2022
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21. TRIM28 haploinsufficiency predisposes to Wilms tumor

Author

Diets, Illja J., Hoyer, Juliane, Ekici, Arif B., Popp, Bernt, Hoogerbrugge, Nicoline, van Reijmersdal, Simon V., Bhaskaran, Rajith, Hadjihannas, Michel, Vasileiou, Georgia, Thiel, Christian T., Seven, Didem, Uebe, Steffen, Ilencikova, Denisa, Waanders, Esmé, Mavinkurve-Groothuis, Annelies M.C., Roeleveld, Nel, de Krijger, Ronald R., Wegert, Jenny, Graf, Norbert, Vokuhl, Christian, Agaimy, Abbas, Gessler, Manfred, Reis, André, Kuiper, Roland P., Jongmans, Marjolijn C.J., Metzler, Markus, Diets, Illja J., Hoyer, Juliane, Ekici, Arif B., Popp, Bernt, Hoogerbrugge, Nicoline, van Reijmersdal, Simon V., Bhaskaran, Rajith, Hadjihannas, Michel, Vasileiou, Georgia, Thiel, Christian T., Seven, Didem, Uebe, Steffen, Ilencikova, Denisa, Waanders, Esmé, Mavinkurve-Groothuis, Annelies M.C., Roeleveld, Nel, de Krijger, Ronald R., Wegert, Jenny, Graf, Norbert, Vokuhl, Christian, Agaimy, Abbas, Gessler, Manfred, Reis, André, Kuiper, Roland P., Jongmans, Marjolijn C.J., and Metzler, Markus

Published
2019

22. TRIM28 haploinsufficiency predisposes to Wilms tumor

Author

Genetica Sectie Genoomdiagnostiek, Pathologie afdeling Cytologie, Pathologie Pathologen staf, Genetica, Genetica Klinische Genetica, Child Health, Cancer, Diets, Illja J., Hoyer, Juliane, Ekici, Arif B., Popp, Bernt, Hoogerbrugge, Nicoline, van Reijmersdal, Simon V., Bhaskaran, Rajith, Hadjihannas, Michel, Vasileiou, Georgia, Thiel, Christian T., Seven, Didem, Uebe, Steffen, Ilencikova, Denisa, Waanders, Esmé, Mavinkurve-Groothuis, Annelies M.C., Roeleveld, Nel, de Krijger, Ronald R., Wegert, Jenny, Graf, Norbert, Vokuhl, Christian, Agaimy, Abbas, Gessler, Manfred, Reis, André, Kuiper, Roland P., Jongmans, Marjolijn C.J., Metzler, Markus, Genetica Sectie Genoomdiagnostiek, Pathologie afdeling Cytologie, Pathologie Pathologen staf, Genetica, Genetica Klinische Genetica, Child Health, Cancer, Diets, Illja J., Hoyer, Juliane, Ekici, Arif B., Popp, Bernt, Hoogerbrugge, Nicoline, van Reijmersdal, Simon V., Bhaskaran, Rajith, Hadjihannas, Michel, Vasileiou, Georgia, Thiel, Christian T., Seven, Didem, Uebe, Steffen, Ilencikova, Denisa, Waanders, Esmé, Mavinkurve-Groothuis, Annelies M.C., Roeleveld, Nel, de Krijger, Ronald R., Wegert, Jenny, Graf, Norbert, Vokuhl, Christian, Agaimy, Abbas, Gessler, Manfred, Reis, André, Kuiper, Roland P., Jongmans, Marjolijn C.J., and Metzler, Markus

Published
2019

23. TRIM28 haploinsufficiency predisposes to Wilms tumor

Author

Diets, Illja J., primary, Hoyer, Juliane, additional, Ekici, Arif B., additional, Popp, Bernt, additional, Hoogerbrugge, Nicoline, additional, van Reijmersdal, Simon V., additional, Bhaskaran, Rajith, additional, Hadjihannas, Michel, additional, Vasileiou, Georgia, additional, Thiel, Christian T., additional, Seven, Didem, additional, Uebe, Steffen, additional, Ilencikova, Denisa, additional, Waanders, Esmé, additional, Mavinkurve‐Groothuis, Annelies M.C., additional, Roeleveld, Nel, additional, de Krijger, Ronald R., additional, Wegert, Jenny, additional, Graf, Norbert, additional, Vokuhl, Christian, additional, Agaimy, Abbas, additional, Gessler, Manfred, additional, Reis, André, additional, Kuiper, Roland P., additional, Jongmans, Marjolijn C.J., additional, and Metzler, Markus, additional

Published
2019
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28. Targeted Locus Amplification & Next Generation Sequencing for the Detection of Recurrent and Novel Gene Fusions for Improved Treatment Decisions in Pediatric Acute Lymphoblastic Leukemia

Author

Kuiper, Roland P., primary, van Reijmersdal, Simon V., additional, Simonis, Marieke, additional, Yu, Jiangyan, additional, Sonneveld, Edwin, additional, Scheijen, Blanca, additional, Boer, Judith M., additional, Boeree, Aurélie, additional, Klous, Petra, additional, Hoogerbrugge, Peter M, additional, Yilmaz, Mehmet, additional, van Leeuwen, Frank N., additional, Den Boer, Monique L., additional, and Splinter, Erik, additional

Published
2015
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29. Accurate detection of low-level mosaic mutations in pediatric acute lymphoblastic leukemia using single molecule tagging and deep-sequencing.

Author

Yu, Jiangyan, Antić, Željko, van Reijmersdal, Simon V., Hoischen, Alexander, Sonneveld, Edwin, Waanders, Esmé, and Kuiper, Roland P.

Subjects
MOSAICISM, LYMPHOBLASTIC leukemia, GENETIC mutation, NUCLEOTIDE sequencing, SINGLE molecules, PEDIATRICS, GENETICS
Abstract

Pathogenic mutations in relapse-associated genes in pediatric acute lymphoblastic leukemia may improve risk stratification when detected at subclonal levels at primary diagnosis. However, to detect subclonal mutations upfront, a deep-sequencing approach with high specificity and sensitivity is required. Here, we performed a proof-of-principle study to detect low-level mosaic RAS pathway mutations by deep sequencing using random tagging-based single molecule Molecular Inversion Probes (smMIPs). The smMIP-based approach could sensitively detect variants with allele frequency as low as 0.4%, which could all be confirmed by other techniques. In comparison, with standard deep-sequencing techniques we reached a detection threshold of only 2.5%, which hampered detection of seven low-level mosaic mutations representing 24% of all detected mutations. We conclude that smMIP-based deep-sequencing outperforms standard deep-sequencing techniques by showing lower background noise and high specificity, and is the preferred technology for detecting mutations upfront, particularly in genes in which mutations show limited clustering in hotspots. [ABSTRACT FROM AUTHOR]

Published
2018
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31. B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) Specific Copy Number Alterations Are Unique For Progressive Pediatric Chronic Myeloid Leukemia (CML): A Large Cohort Study

Author

van der Sligte, Naomi E, primary, Krumbholz, Manuela, additional, Pastorczak, Agata, additional, Scheijen, Blanca, additional, Tauer, Josephine T., additional, Nowasz, Christina, additional, Sonneveld, Edwin, additional, de Bock, Truuske H., additional, Meeuwsen - de Boer, Tiny G., additional, van Reijmersdal, Simon V., additional, Kuiper, Roland P., additional, Bradtke, Jutta, additional, Metzler, Markus, additional, Suttorp, Meinolf, additional, De Bont, Evelina S., additional, and van Leeuwen, Frank N., additional

Published
2013
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32. Identification of distinct protein Signatures Associated with genetic Abnormalities In Acute Lymphoblastic Leukemia

Author

Kuiper, Roland P., primary, Scheijen, Blanca, additional, Pastorczak, Agata, additional, van Reijmersdal, Simon V., additional, Thomas, Deborah A., additional, Zhang, Niangxiang, additional, Coombes, Kevin R., additional, Kantarjian, Hagop M., additional, Jabbour, Elias J., additional, De Bont, Eveline S.J.M, additional, van Leeuwen, Frank N., additional, and Kornblau, Steven M., additional

Published
2013
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34. Validation Study of Existing Gene Expression Signatures for Anti-TNF Treatment in Patients with Rheumatoid Arthritis

Author

Toonen, Erik J. M., primary, Gilissen, Christian, additional, Franke, Barbara, additional, Kievit, Wietske, additional, Eijsbouts, Agnes M., additional, den Broeder, Alfons A., additional, van Reijmersdal, Simon V., additional, Veltman, Joris A., additional, Scheffer, Hans, additional, Radstake, Timothy R. D. J., additional, van Riel, Piet L. C. M., additional, Barrera, Pilar, additional, and Coenen, Marieke J. H., additional

Published
2012
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35. The Origin and Nature of Tightly Clustered BTG1 Deletions in Precursor B-Cell Acute Lymphoblastic Leukemia Support a Model of Multiclonal Evolution

Author

Waanders, Esmé, primary, Scheijen, Blanca, additional, van der Meer, Laurens T., additional, van Reijmersdal, Simon V., additional, van Emst, Liesbeth, additional, Kroeze, Yvet, additional, Sonneveld, Edwin, additional, Hoogerbrugge, Peter M., additional, Geurts van Kessel, Ad, additional, van Leeuwen, Frank N., additional, and Kuiper, Roland P., additional

Published
2012
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36. Focal BTG1 Deletions Occur in Specific Precursor B-Cell Acute Lymphoblastic Leukemia Subtypes At Defined Hotspots Due to Aberrant V(D)J Recombination

Author

Scheijen, Blanca, primary, Waanders, Esmé, additional, van Reijmersdal, Simon V., additional, van der Meer, Laurens T., additional, van Emst, Liesbeth, additional, Verwiel, Eugene, additional, Kroeze, Yvet, additional, Sonneveld, Edwin, additional, Hoogerbrugge, Peter M., additional, van Kessel, Ad Geurts, additional, van Leeuwen, Frank N., additional, and Kuiper, Roland P., additional

Published
2011
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37. Exome Sequencing of Late Recurrence T-Cell Acute Lymphoblastic Leukemia in Children Confirms Second Leukemia and Exposes Predisposition Candidate Genes

Author

Waanders, Esmé, primary, van der Velden, Vincent H.J., additional, Szczepanski, Tomasz, additional, Vissers, Lisenka E.L.M., additional, de Ligt, Joep, additional, Gilissen, Christian, additional, van Dijk, Anke A.H., additional, van Reijmersdal, Simon V., additional, Hoogerbrugge, Peter M., additional, van Kessel, Ad Geurts, additional, van Dongen, Jacques J.M., additional, and Kuiper, Roland P., additional

Published
2011
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38. Integrated Use of Minimal Residual Disease Classification and IKZF1 Alteration Status Accurately Predicts 79% of Relapses In Pediatric Acute Lymphoblastic Leukemia

Author

Waanders, Esmé, primary, van der elden, Vincent H.J., additional, van der Schoot, Ellen, additional, van Leeuwen, Frank N., additional, van Reijmersdal, Simon V., additional, de Haas, Valerie, additional, Veerman, Anjo J., additional, van Kessel, Ad Geurts, additional, Hoogerbrugge, Peter M., additional, Kuiper, Roland P., additional, and van Dongen, Jacques J.M., additional

Published
2010
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39. BTG1, a Gene Frequently Deleted in Pre-B ALL, Controls Glucocorticoid Receptor-Mediated Gene Expression.

Author

van Leeuwen, Frank N., primary, van Galen, Joost Casper, additional, Kuiper, Roland P., additional, van Emst, Liesbeth, additional, Levers, Marloes R, additional, Tijchon, Esther, additional, Scheijen, Blanca, additional, Waanders, Esmee, additional, van Reijmersdal, Simon V, additional, Gillissen, Christian, additional, van Kessel, Ad Geurts, additional, and Hoogerbrugge, Peter M., additional

Published
2009
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40. Deletion of IKZF1 in Pediatric Precursor-B ALL Is a Strong Prognostic Marker for Relapse.

Author

Kuiper, Roland P., primary, Waanders, Esmee, additional, Van der Velden, Vincent H.J., additional, van Reijmersdal, Simon V, additional, Scheijen, Blanca, additional, Hehir-Kwa, Jayne, additional, Keijzers-Vloet, Suzanne T.M., additional, Sonneveld, Edwin, additional, van Dongen, Jacques JM, additional, van Leeuwen, Frank N., additional, van Kessel, Ad Geurts, additional, and Hoogerbrugge, Peter M., additional

Published
2009
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41. Ikaros Is a Frequently Affected Hematopoietic Differentiation Factor in Pediatric Relapse-Prone Precursor B-Cell Acute Lymphoblastic Leukemia

Author

Kuiper, Roland P., primary, van Leeuwen, Frank N., primary, van der Velden, Vincent, primary, van Reijmersdal, Simon V., primary, de Vries, Jeltje, primary, Keijzers-Vloet, Suzanne T.M., primary, Hehir-Kwa, Jayne, primary, van Wering, E., primary, van Dongen, Jacques JM, primary, Hoogerbrugge, Peter M., primary, and van Kessel, Ad Geurts, primary

Published
2008
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43. Detection of Genomic Lesions in Childhood Precursor-B Cell ALL in Diagnosis and Relapse Samples Using High Resolution Genomic Profiling.

Author

Kuiper, Roland P., primary, van Leeuwen, Frank N., additional, Keijzers-Vloet, Suzanne T.M., additional, van Reijmersdal, Simon V., additional, Hehir-Kwa, Jayne Y., additional, van Wering, Elisabeth R., additional, van der Velden, Vincent H.J., additional, van Dongen, Jacques J.M., additional, Schoenmakers, Eric F.P.M., additional, van Kessel, Ad Geurts, additional, and Hoogerbrugge, Peter M., additional

Published
2007
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44. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCFinactivating mutations in acute T cell leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M., Buijs-Gladdines, Jessica G.C.A.M., van de Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G., de Laat, Wouter, and Meijerink, Jules P.P.

Abstract

Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In T-ALL patients, we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5;14)(q35;q32.2) rearranged patients, and especially when CTCF bindings sites are preserved in between the BCL11B-enhancer and the TLX3oncogene. These solitary intervening sites insulate TLX3from the enhancer by inducing competitive looping to multiple binding sites near the TLX3promoter. Reduced CTCF levels, or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3promoter to BCL11B-enhancer looping that elevates oncogene expression levels and leukemia burden.

Published
2023
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45. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels By Recurrent CTCFinactivating Mutations in T Cell Acute Lymphoblastic Leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric, Buijs-Gladdines, Jessica G.C.A.M., Van De Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, Van Eyndhoven, Winfried, Van Min, Max Jan, Kuiper, Roland P, Kemmeren, Patrick, Mullighan, Charles G., De Laat, Wouter, and Meijerink, Jules P.P.

Abstract

Introduction.The CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops and forming the boundaries of structural domains. In addition, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCFinactivating events have been found in various human cancers. Loss-of-heterozygosity (LOH) or inactivating missense mutations in specific zinc- fingers have been identified in many human cancers including sporadic breast cancer, prostate cancer, Wilms-tumors and acute lymphoblastic leukemia (ALL). Heterozygous deletions or point mutations have been identified in over half of the patients with breast cancer or uterine endometrial cancers, deregulating global gene expression by altering methylated genomic states and poor survival. Here, we investigated the functional significance and molecular-cytogenetic associations of CTCFaberrations in T-cell acute lymphoblastic leukemia patients.

Published
2021
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48. Multiclonal complexity of pediatric acute lymphoblastic leukemia and the prognostic relevance of subclonal mutations

Author

Antić Ž, Yu J, Van Reijmersdal SV, Van Dijk A, Dekker L, Segerink WH, Sonneveld E, Fiocco M, Pieters R, Hoogerbrugge PM, Van Leeuwen FN, Van Kessel AG, Waanders E, and Kuiper RP

Subjects
Child, Clone Cells, Genomics, Humans, Mutation, Prognosis, Precursor Cell Lymphoblastic Leukemia-Lymphoma diagnosis, Precursor Cell Lymphoblastic Leukemia-Lymphoma genetics
Abstract

Genomic studies of pediatric acute lymphoblastic leukemia (ALL) have shown remarkable heterogeneity in initial diagnosis, with multiple (sub)clones harboring lesions in relapse-associated genes. However, the clinical relevance of these subclonal alterations remains unclear. We assessed the clinical relevance and prognostic value of subclonal alterations in the relapse-associated genes IKZF1, CREBBP, KRAS, NRAS, PTPN11, TP53, NT5C2, and WHSC1 in 503 ALL cases. Using Molecular Inversion Probe sequencing and breakpoint-spanning PCR we reliably detected alterations below 1% allele frequency. We identified 660 genomic alterations in 285 diagnosis samples of which 495 (75%) were subclonal. RAS pathway mutations were common, particularly in minor subclones, and comparisons between RAS hotspot mutations revealed differences in their capacity to drive clonal expansion in ALL. We did not find an association of subclonal alterations with unfavorable outcome. Particularly for IKZF1, an established prognostic marker in ALL, all clonal but none of the subclonal alterations were preserved at relapse. We conclude that, for the genes tested, there is no basis to consider subclonal alterations detected at diagnosis for risk group stratification of ALL treatment.

Published
2021
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