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51. Data from Chromosomal and MicroRNA Expression Patterns Reveal Biologically Distinct Subgroups of 11q− Neuroblastoma

Author

Buckley, Patrick G., primary, Alcock, Leah, primary, Bryan, Kenneth, primary, Bray, Isabella, primary, Schulte, Johannes H., primary, Schramm, Alexander, primary, Eggert, Angelika, primary, Mestdagh, Pieter, primary, De Preter, Katleen, primary, Vandesompele, Jo, primary, Speleman, Frank, primary, and Stallings, Raymond L., primary

Published
2023
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52. Table S3 from LDHA in Neuroblastoma Is Associated with Poor Outcome and Its Depletion Decreases Neuroblastoma Growth Independent of Aerobic Glycolysis

Author

Dorneburg, Carmen, primary, Fischer, Matthias, primary, Barth, Thomas F.E., primary, Mueller-Klieser, Wolfgang, primary, Hero, Barbara, primary, Gecht, Judith, primary, Carter, Daniel R., primary, de Preter, Katleen, primary, Mayer, Benjamin, primary, Christner, Lisa, primary, Speleman, Frank, primary, Marshall, Glenn M., primary, Debatin, Klaus-Michael, primary, and Beltinger, Christian, primary

Published
2023
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53. Supplemental Data 9 from Upregulation of MAPK Negative Feedback Regulators and RET in Mutant ALK Neuroblastoma: Implications for Targeted Treatment

Author

Lambertz, Irina, primary, Kumps, Candy, primary, Claeys, Shana, primary, Lindner, Sven, primary, Beckers, Anneleen, primary, Janssens, Els, primary, Carter, Daniel R., primary, Cazes, Alex, primary, Cheung, Belamy B., primary, De Mariano, Marilena, primary, De Bondt, An, primary, De Brouwer, Sara, primary, Delattre, Olivier, primary, Gibbons, Jay, primary, Janoueix-Lerosey, Isabelle, primary, Laureys, Geneviève, primary, Liang, Chris, primary, Marchall, Glenn M., primary, Porcu, Michael, primary, Takita, Junko, primary, Trujillo, David Camacho, primary, Van Den Wyngaert, Ilse, primary, Van Roy, Nadine, primary, Van Goethem, Alan, primary, Van Maerken, Tom, primary, Zabrocki, Piotr, primary, Cools, Jan, primary, Schulte, Johannes H., primary, Vialard, Jorge, primary, Speleman, Frank, primary, and De Preter, Katleen, primary

Published
2023
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54. Supplementary Table 2 from Meta-analysis of Neuroblastomas Reveals a Skewed ALK Mutation Spectrum in Tumors with MYCN Amplification

Author

De Brouwer, Sara, primary, De Preter, Katleen, primary, Kumps, Candy, primary, Zabrocki, Piotr, primary, Porcu, Michaël, primary, Westerhout, Ellen M., primary, Lakeman, Arjan, primary, Vandesompele, Jo, primary, Hoebeeck, Jasmien, primary, Van Maerken, Tom, primary, De Paepe, Anne, primary, Laureys, Geneviève, primary, Schulte, Johannes H., primary, Schramm, Alexander, primary, Van Den Broecke, Caroline, primary, Vermeulen, Joëlle, primary, Van Roy, Nadine, primary, Beiske, Klaus, primary, Renard, Marleen, primary, Noguera, Rosa, primary, Delattre, Olivier, primary, Janoueix-Lerosey, Isabelle, primary, Kogner, Per, primary, Martinsson, Tommy, primary, Nakagawara, Akira, primary, Ohira, Miki, primary, Caron, Huib, primary, Eggert, Angelika, primary, Cools, Jan, primary, Versteeg, Rogier, primary, and Speleman, Frank, primary

Published
2023
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55. Supplementary Data from Accurate Outcome Prediction in Neuroblastoma across Independent Data Sets Using a Multigene Signature

Author

De Preter, Katleen, primary, Vermeulen, Joëlle, primary, Brors, Benedikt, primary, Delattre, Olivier, primary, Eggert, Angelika, primary, Fischer, Matthias, primary, Janoueix-Lerosey, Isabelle, primary, Lavarino, Cinzia, primary, Maris, John M., primary, Mora, Jaume, primary, Nakagawara, Akira, primary, Oberthuer, André, primary, Ohira, Miki, primary, Schleiermacher, Gudrun, primary, Schramm, Alexander, primary, Schulte, Johannes H., primary, Wang, Qun, primary, Westermann, Frank, primary, Speleman, Frank, primary, and Vandesompele, Jo, primary

Published
2023
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57. Supplementary Information from LDHA in Neuroblastoma Is Associated with Poor Outcome and Its Depletion Decreases Neuroblastoma Growth Independent of Aerobic Glycolysis

Author

Dorneburg, Carmen, primary, Fischer, Matthias, primary, Barth, Thomas F.E., primary, Mueller-Klieser, Wolfgang, primary, Hero, Barbara, primary, Gecht, Judith, primary, Carter, Daniel R., primary, de Preter, Katleen, primary, Mayer, Benjamin, primary, Christner, Lisa, primary, Speleman, Frank, primary, Marshall, Glenn M., primary, Debatin, Klaus-Michael, primary, and Beltinger, Christian, primary

Published
2023
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58. Supplemental Data from Upregulation of MAPK Negative Feedback Regulators and RET in Mutant ALK Neuroblastoma: Implications for Targeted Treatment

Author

Lambertz, Irina, primary, Kumps, Candy, primary, Claeys, Shana, primary, Lindner, Sven, primary, Beckers, Anneleen, primary, Janssens, Els, primary, Carter, Daniel R., primary, Cazes, Alex, primary, Cheung, Belamy B., primary, De Mariano, Marilena, primary, De Bondt, An, primary, De Brouwer, Sara, primary, Delattre, Olivier, primary, Gibbons, Jay, primary, Janoueix-Lerosey, Isabelle, primary, Laureys, Geneviève, primary, Liang, Chris, primary, Marchall, Glenn M., primary, Porcu, Michael, primary, Takita, Junko, primary, Trujillo, David Camacho, primary, Van Den Wyngaert, Ilse, primary, Van Roy, Nadine, primary, Van Goethem, Alan, primary, Van Maerken, Tom, primary, Zabrocki, Piotr, primary, Cools, Jan, primary, Schulte, Johannes H., primary, Vialard, Jorge, primary, Speleman, Frank, primary, and De Preter, Katleen, primary

Published
2023
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59. Supplementary Figure 5. from Targeting MYCN-Driven Transcription By BET-Bromodomain Inhibition

Author

Henssen, Anton, primary, Althoff, Kristina, primary, Odersky, Andrea, primary, Beckers, Anneleen, primary, Koche, Richard, primary, Speleman, Frank, primary, Schäfers, Simon, primary, Bell, Emma, primary, Nortmeyer, Maike, primary, Westermann, Frank, primary, De Preter, Katleen, primary, Florin, Alexandra, primary, Heukamp, Lukas, primary, Spruessel, Annika, primary, Astrahanseff, Kathy, primary, Lindner, Sven, primary, Sadowski, Natalie, primary, Schramm, Alexander, primary, Astorgues-Xerri, Lucile, primary, Riveiro, Maria E., primary, Eggert, Angelika, primary, Cvitkovic, Esteban, primary, and Schulte, Johannes H., primary

Published
2023
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60. Supplementary Data from Chromosomal and MicroRNA Expression Patterns Reveal Biologically Distinct Subgroups of 11q− Neuroblastoma

Author

Buckley, Patrick G., primary, Alcock, Leah, primary, Bryan, Kenneth, primary, Bray, Isabella, primary, Schulte, Johannes H., primary, Schramm, Alexander, primary, Eggert, Angelika, primary, Mestdagh, Pieter, primary, De Preter, Katleen, primary, Vandesompele, Jo, primary, Speleman, Frank, primary, and Stallings, Raymond L., primary

Published
2023
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61. Supplementary Figure Legend from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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62. Supplementary Methods from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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63. Supplementary Table 3 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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64. Supplementary Figure 1 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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65. Supplementary Figure 2 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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66. Supplementary Figure 4 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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67. Supplementary Table 1 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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68. Supplementary Table 2 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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69. Supplementary Figure 3 from Histone Chaperone CHAF1A Inhibits Differentiation and Promotes Aggressive Neuroblastoma

Author

Barbieri, Eveline, primary, De Preter, Katleen, primary, Capasso, Mario, primary, Chen, Zaowen, primary, Hsu, Danielle M., primary, Tonini, Gian Paolo, primary, Lefever, Steve, primary, Hicks, John, primary, Versteeg, Rogier, primary, Pession, Andrea, primary, Speleman, Frank, primary, Kim, Eugene S., primary, and Shohet, Jason M., primary

Published
2023
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70. Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma

Author

Hastings, Jordan F., primary, Latham, Sharissa L., additional, Kamili, Alvin, additional, Wheatley, Madeleine S., additional, Han, Jeremy Z. R., additional, Wong-Erasmus, Marie, additional, Phimmachanh, Monica, additional, Nobis, Max, additional, Pantarelli, Chiara, additional, Cadell, Antonia L., additional, O’Donnell, Yolande E. I., additional, Leong, King Ho, additional, Lynn, Sophie, additional, Geng, Fan-Suo, additional, Cui, Lujing, additional, Yan, Sabrina, additional, Achinger-Kawecka, Joanna, additional, Stirzaker, Clare, additional, Norris, Murray D., additional, Haber, Michelle, additional, Trahair, Toby N., additional, Speleman, Frank, additional, De Preter, Katleen, additional, Cowley, Mark J., additional, Bogdanovic, Ozren, additional, Timpson, Paul, additional, Cox, Thomas R., additional, Kolch, Walter, additional, Fletcher, Jamie I., additional, Fey, Dirk, additional, and Croucher, David R., additional

Published
2023
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71. MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma

Author

Beckers, Anneleen, Van Peer, Gert, Carter, Daniel R., Gartlgruber, Moritz, Herrmann, Carl, Agarwal, Saurabh, Helsmoortel, Hetty H., Althoff, Kristina, Molenaar, Jan J., Cheung, Belamy B., Schulte, Johannes H., Benoit, Yves, Shohet, Jason M., Westermann, Frank, Marshall, Glenn M., Vandesompele, Jo, De Preter, Katleen, and Speleman, Frank

Published
2015
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72. Additional file 5 of Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

Author

Deleu, Jill, Schoofs, Kathleen, Decock, Anneleen, Verniers, Kimberly, Roelandt, Sofie, Denolf, Angie, Verreth, Joke, De Wilde, Bram, Van Maerken, Tom, De Preter, Katleen, and Vandesompele, Jo

Abstract

Additional file 5: Figure S2. Overview of TapeStation results. Results from TapeStation of all cfDNA samples purified with one of the six (co-)purification kits. There are 13/46 samples that have concentrations below LOD (20 pg/µl), and 2/46 samples without any peaks (flat profiles). For 1/46 samples there was not enough material left for TapeStation.

Published
2023
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73. Additional file 6 of Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

Author

Deleu, Jill, Schoofs, Kathleen, Decock, Anneleen, Verniers, Kimberly, Roelandt, Sofie, Denolf, Angie, Verreth, Joke, De Wilde, Bram, Van Maerken, Tom, De Preter, Katleen, and Vandesompele, Jo

Abstract

Additional file 6: Figure S3. Detailed description of laboratory workflow. Workflow used to determine co-purification performance of each kit and subsequent calculations to determine the concentrations in each eluate: (A) MIRA and CCF, (B) MIR, (C) CAT, (D) MAX, and (E) MAP.

Published
2023
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74. Additional file 7 of Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

Author

Deleu, Jill, Schoofs, Kathleen, Decock, Anneleen, Verniers, Kimberly, Roelandt, Sofie, Denolf, Angie, Verreth, Joke, De Wilde, Bram, Van Maerken, Tom, De Preter, Katleen, and Vandesompele, Jo

Abstract

Additional file 7: Figure S4. Experimental overview of a combined cfDNA/cfRNA quantification and a parallel quantification of cfDNA and cfRNA.

Published
2023
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76. TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets

Author

Decaesteker, Bieke, Denecker, Geertrui, Van Neste, Christophe, Dolman, Emmy M., Van Loocke, Wouter, Gartlgruber, Moritz, Nunes, Carolina, De Vloed, Fanny, Depuydt, Pauline, Verboom, Karen, Rombaut, Dries, Loontiens, Siebe, De Wyn, Jolien, Kholosy, Waleed M., Koopmans, Bianca, Essing, Anke H. W., Herrmann, Carl, Dreidax, Daniel, Durinck, Kaat, Deforce, Dieter, Van Nieuwerburgh, Filip, Henssen, Anton, Versteeg, Rogier, Boeva, Valentina, Schleiermacher, Gudrun, van Nes, Johan, Mestdagh, Pieter, Vanhauwaert, Suzanne, Schulte, Johannes H., Westermann, Frank, Molenaar, Jan J., De Preter, Katleen, and Speleman, Frank

Published
2018
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80. RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

Author

Nunes, Carolina, primary, Depestel, Lisa, additional, Mus, Liselot, additional, Keller, Kaylee M., additional, Delhaye, Louis, additional, Louwagie, Amber, additional, Rishfi, Muhammad, additional, Whale, Alex, additional, Kara, Neesha, additional, Andrews, Simon R., additional, Dela Cruz, Filemon, additional, You, Daoqi, additional, Siddiquee, Armaan, additional, Cologna, Camila Takeno, additional, De Craemer, Sam, additional, Dolman, Emmy, additional, Bartenhagen, Christoph, additional, De Vloed, Fanny, additional, Sanders, Ellen, additional, Eggermont, Aline, additional, Bekaert, Sarah-Lee, additional, Van Loocke, Wouter, additional, Bek, Jan Willem, additional, Dewyn, Givani, additional, Loontiens, Siebe, additional, Van Isterdael, Gert, additional, Decaesteker, Bieke, additional, Tilleman, Laurentijn, additional, Van Nieuwerburgh, Filip, additional, Vermeirssen, Vanessa, additional, Van Neste, Christophe, additional, Ghesquiere, Bart, additional, Goossens, Steven, additional, Eyckerman, Sven, additional, De Preter, Katleen, additional, Fischer, Matthias, additional, Houseley, Jon, additional, Molenaar, Jan, additional, De Wilde, Bram, additional, Roberts, Stephen S., additional, Durinck, Kaat, additional, and Speleman, Frank, additional

Published
2022
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82. RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

Author

Nunes, Carolina, Depestel, Lisa, Mus, Liselot, Keller, Kaylee M., Delhaye, Louis, Louwagie, Amber, Rishfi, Muhammad, Whale, Alex, Kara, Neesha, Andrews, Simon R., Cruz, Filemon Dela, You, Daoqi, Siddiquee, Armaan, Cologna, Camila Takeno, De Craemer, Sam, Dolman, Emmy, Bartenhagen, Christoph, De Vloed, Fanny, Sanders, Ellen, Eggermont, Aline, Bekaert, Sarah Lee, Van Loocke, Wouter, Bek, Jan Willem, Dewyn, Givani, Loontiens, Siebe, Van Isterdael, Gert, Decaesteker, Bieke, Tilleman, Laurentijn, Van Nieuwerburgh, Filip, Vermeirssen, Vanessa, Van Neste, Christophe, Ghesquiere, Bart, Goossens, Steven, Eyckerman, Sven, De Preter, Katleen, Fischer, Matthias, Houseley, Jon, Molenaar, Jan, De Wilde, Bram, Roberts, Stephen S., Durinck, Kaat, Speleman, Frank, Nunes, Carolina, Depestel, Lisa, Mus, Liselot, Keller, Kaylee M., Delhaye, Louis, Louwagie, Amber, Rishfi, Muhammad, Whale, Alex, Kara, Neesha, Andrews, Simon R., Cruz, Filemon Dela, You, Daoqi, Siddiquee, Armaan, Cologna, Camila Takeno, De Craemer, Sam, Dolman, Emmy, Bartenhagen, Christoph, De Vloed, Fanny, Sanders, Ellen, Eggermont, Aline, Bekaert, Sarah Lee, Van Loocke, Wouter, Bek, Jan Willem, Dewyn, Givani, Loontiens, Siebe, Van Isterdael, Gert, Decaesteker, Bieke, Tilleman, Laurentijn, Van Nieuwerburgh, Filip, Vermeirssen, Vanessa, Van Neste, Christophe, Ghesquiere, Bart, Goossens, Steven, Eyckerman, Sven, De Preter, Katleen, Fischer, Matthias, Houseley, Jon, Molenaar, Jan, De Wilde, Bram, Roberts, Stephen S., Durinck, Kaat, and Speleman, Frank

Abstract

High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upon in vitro knockdown and accelerated tumor formation in a neuroblastoma zebrafish model coexpressing human RRM2 with MYCN. Forced RRM2 induction alleviates excessive replicative stress induced by CHK1 inhibition, while high RRM2 expression in human neuroblastomas correlates with high CHK1 activity. MYCN-driven zebrafish tumors with RRM2 co-overexpression exhibit differentially expressed DNA repair genes in keeping with enhanced ATR-CHK1 signaling activity. In vitro, RRM2 inhibition enhances intrinsic replication stress checkpoint addiction. Last, combinatorial RRM2-CHK1 inhibition acts synergistic in high-risk neuroblastoma cell lines and patient-derived xenograft models, illustrating the therapeutic potential.

Published
2022

83. RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

Author

Afd Pharmaceutics, Pharmaceutics, Nunes, Carolina, Depestel, Lisa, Mus, Liselot, Keller, Kaylee M., Delhaye, Louis, Louwagie, Amber, Rishfi, Muhammad, Whale, Alex, Kara, Neesha, Andrews, Simon R., Cruz, Filemon Dela, You, Daoqi, Siddiquee, Armaan, Cologna, Camila Takeno, De Craemer, Sam, Dolman, Emmy, Bartenhagen, Christoph, De Vloed, Fanny, Sanders, Ellen, Eggermont, Aline, Bekaert, Sarah Lee, Van Loocke, Wouter, Bek, Jan Willem, Dewyn, Givani, Loontiens, Siebe, Van Isterdael, Gert, Decaesteker, Bieke, Tilleman, Laurentijn, Van Nieuwerburgh, Filip, Vermeirssen, Vanessa, Van Neste, Christophe, Ghesquiere, Bart, Goossens, Steven, Eyckerman, Sven, De Preter, Katleen, Fischer, Matthias, Houseley, Jon, Molenaar, Jan, De Wilde, Bram, Roberts, Stephen S., Durinck, Kaat, Speleman, Frank, Afd Pharmaceutics, Pharmaceutics, Nunes, Carolina, Depestel, Lisa, Mus, Liselot, Keller, Kaylee M., Delhaye, Louis, Louwagie, Amber, Rishfi, Muhammad, Whale, Alex, Kara, Neesha, Andrews, Simon R., Cruz, Filemon Dela, You, Daoqi, Siddiquee, Armaan, Cologna, Camila Takeno, De Craemer, Sam, Dolman, Emmy, Bartenhagen, Christoph, De Vloed, Fanny, Sanders, Ellen, Eggermont, Aline, Bekaert, Sarah Lee, Van Loocke, Wouter, Bek, Jan Willem, Dewyn, Givani, Loontiens, Siebe, Van Isterdael, Gert, Decaesteker, Bieke, Tilleman, Laurentijn, Van Nieuwerburgh, Filip, Vermeirssen, Vanessa, Van Neste, Christophe, Ghesquiere, Bart, Goossens, Steven, Eyckerman, Sven, De Preter, Katleen, Fischer, Matthias, Houseley, Jon, Molenaar, Jan, De Wilde, Bram, Roberts, Stephen S., Durinck, Kaat, and Speleman, Frank

Published
2022

86. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples

Author

Van Paemel, Ruben, primary, Vandeputte, Charlotte, additional, Raman, Lennart, additional, Van Thorre, Jolien, additional, Willems, Leen, additional, Van Dorpe, Jo, additional, Van Der Linden, Malaïka, additional, De Wilde, Jilke, additional, De Koker, Andries, additional, Menten, Björn, additional, Devalck, Christine, additional, Vicha, Ales, additional, Grega, Marek, additional, Schleiermacher, Gudrun, additional, Iddir, Yasmine, additional, Chicard, Mathieu, additional, van Zogchel, Lieke, additional, Stutterheim, Janine, additional, Lak, Nathalie S.M., additional, Tytgat, G.A.M., additional, Laureys, Geneviève, additional, Speleman, Frank, additional, De Wilde, Bram, additional, Lammens, Tim, additional, De Preter, Katleen, additional, and Van Roy, Nadine, additional

Published
2022
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89. Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study

Author

Vermeulen, Joëlle, De Preter, Katleen, Naranjo, Arlene, Vercruysse, Liesbeth, Van Roy, Nadine, Hellemans, Jan, Swerts, Katrien, Bravo, Sophie, Scaruffi, Paola, Tonini, Gian Paolo, De Bernardi, Bruno, Noguera, Rosa, Piqueras, Marta, Cañete, Adela, Castel, Victoria, Janoueix-Lerosey, Isabelle, Delattre, Olivier, Schleiermacher, Gudrun, Michon, Jean, Combaret, Valérie, Fischer, Matthias, Oberthuer, André, Ambros, Peter F, Beiske, Klaus, Bénard, Jean, Marques, Bárbara, Rubie, Hervé, Kohler, Janice, Pötschger, Ulrike, Ladenstein, Ruth, Hogarty, Michael D, McGrady, Patrick, London, Wendy B, Laureys, Geneviève, Speleman, Frank, and Vandesompele, Jo

Published
2009
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90. Frequency and Prognostic Impact of ALK Amplifications and Mutations in the European Neuroblastoma Study Group (SIOPEN) High-Risk Neuroblastoma Trial (HR-NBL1)

Author

Bellini, Angela, primary, Pötschger, Ulrike, additional, Bernard, Virginie, additional, Lapouble, Eve, additional, Baulande, Sylvain, additional, Ambros, Peter F., additional, Auger, Nathalie, additional, Beiske, Klaus, additional, Bernkopf, Marie, additional, Betts, David R., additional, Bhalshankar, Jaydutt, additional, Bown, Nick, additional, de Preter, Katleen, additional, Clément, Nathalie, additional, Combaret, Valérie, additional, Font de Mora, Jaime, additional, George, Sally L., additional, Jiménez, Irene, additional, Jeison, Marta, additional, Marques, Barbara, additional, Martinsson, Tommy, additional, Mazzocco, Katia, additional, Morini, Martina, additional, Mühlethaler-Mottet, Annick, additional, Noguera, Rosa, additional, Pierron, Gaelle, additional, Rossing, Maria, additional, Taschner-Mandl, Sabine, additional, Van Roy, Nadine, additional, Vicha, Ales, additional, Chesler, Louis, additional, Balwierz, Walentyna, additional, Castel, Victoria, additional, Elliott, Martin, additional, Kogner, Per, additional, Laureys, Geneviève, additional, Luksch, Roberto, additional, Malis, Josef, additional, Popovic-Beck, Maja, additional, Ash, Shifra, additional, Delattre, Olivier, additional, Valteau-Couanet, Dominique, additional, Tweddle, Deborah A., additional, Ladenstein, Ruth, additional, and Schleiermacher, Gudrun, additional

Published
2021
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91. MEIS2 Is an Adrenergic Core Regulatory Transcription Factor Involved in Early Initiation of TH-MYCN-Driven Neuroblastoma Formation

Author

De Wyn, Jolien, primary, Zimmerman, Mark W., additional, Weichert-Leahey, Nina, additional, Nunes, Carolina, additional, Cheung, Belamy B., additional, Abraham, Brian J., additional, Beckers, Anneleen, additional, Volders, Pieter-Jan, additional, Decaesteker, Bieke, additional, Carter, Daniel R., additional, Look, Alfred Thomas, additional, De Preter, Katleen, additional, Van Loocke, Wouter, additional, Marshall, Glenn M., additional, Durbin, Adam D., additional, Speleman, Frank, additional, and Durinck, Kaat, additional

Published
2021
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92. Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions

Author

Schoofs, Kathleen, Philippron, Annouck, Avila Cobos, Francisco, Koster, Jan, Lefever, Steve, Anckaert, Jasper, De Looze, Danny, Vandesompele, Jo, Pattyn, Piet, De Preter, Katleen, Center of Experimental and Molecular Medicine, and CCA - Cancer biology and immunology

Subjects
Statistics and Probability, Esophageal Neoplasms, PROGRESSION, Library and Information Sciences, Adenocarcinoma, UP-REGULATION, DIAGNOSIS, Education, Barrett Esophagus, Plasma, Medicine and Health Sciences, Humans, SIGNATURES, MICRORNA EXPRESSION, Statistics, ADENOCARCINOMA, PROFILES, GENE, Computer Science Applications, MicroRNAs, HIGH-GRADE DYSPLASIA, BARRETTS-ESOPHAGUS, Disease Progression, Probability and Uncertainty, Statistics, Probability and Uncertainty, Biomarkers, Information Systems
Abstract

In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy and disease esophageal tissue sample were included. In total, this comprehensive dataset consists of 102 sequenced libraries from 51 samples. Based on this data, 119 expression profiles are available for three biotypes, including miRNA (51), mRNA (51) and circRNA (17). This unique resource allows for discovery of novel biomarkers and disease mechanisms, comparison of tissue and liquid biopsy profiles, integration of coding and non-coding RNA patterns, and can serve as a validation dataset in other RNA landscaping studies. Moreover, structural RNA differences can be identified in this dataset, including protein coding mutations, fusion genes, and circular RNAs.

Published
2021

94. Abstract 2481: Time-resolved transcriptome analysis of murine TH-MYCN driven neuroblastoma identifies MEIS2 as early initiating factor and novel core gene regulatory circuitry constituent

Author

Durinck, Kaat, primary, Zimmerman, Mark, additional, Weichert-Leahey, Nina, additional, Dewyn, Jolien, additional, Van Loocke, Wouter, additional, Nunes, Carolina, additional, Beckers, Anneleen, additional, Decaesteker, Bieke, additional, Volders, Pieter-Jan, additional, Van Neste, Christophe, additional, Cheung, Belamy, additional, Carter, Daniel, additional, Look, Thomas A., additional, Marshall, Glenn, additional, De Preter, Katleen, additional, Durbin, Adam, additional, and Speleman, Franki, additional

Published
2021
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95. Correction to: The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: as review (European Journal of Pediatrics, (2020), 179, 2, (191-202), 10.1007/s00431-019-03545-y)

Author

van Paemel, Ruben, Vlug, Roos, de Preter, Katleen, van Roy, Nadine, Speleman, Frank, Willems, Leen, Lammens, Tim, Laureys, Geneviève, Schleiermacher, Gudrun, Tytgat, Godelieve A. M., Astrahantseff, Kathy, Deubzer, Hedwig, de Wilde, Bram, and CCA - Imaging and biomarkers

Subjects
genetic structures, education, sense organs, skin and connective tissue diseases, eye diseases
Abstract

In the original version of this article, a reader pointed out that there was a mistake in the phrasing in a paragraph. This could potentially be harmful to children. The authors agree to change the wording. “vitreous fluid” will be changed to “aqueous humor”.

Published
2020

96. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples

Author

Van Paemel, Ruben, Vandeputte, Charlotte, Raman, Lennart, Van Thorre, Jolien, Willems, Leen, Van Dorpe, Jo, Van Der Linden, Malaïka, De Wilde, Jilke, De Koker, Andries, Menten, Björn, Devalck, Christine, Vicha, Ales, Grega, Marek, Schleiermacher, Gudrun, Iddir, Yasmine, Chicard, Mathieu, van Zogchel, Lieke, Stutterheim, Janine, Lak, Nathalie N.S.M., Tytgat, Godelieve G.A.M., Laureys, Geneviève, Speleman, Frank, De Wilde, Bram, Lammens, Tim, De Preter, Katleen, Van Roy, Nadine, Van Paemel, Ruben, Vandeputte, Charlotte, Raman, Lennart, Van Thorre, Jolien, Willems, Leen, Van Dorpe, Jo, Van Der Linden, Malaïka, De Wilde, Jilke, De Koker, Andries, Menten, Björn, Devalck, Christine, Vicha, Ales, Grega, Marek, Schleiermacher, Gudrun, Iddir, Yasmine, Chicard, Mathieu, van Zogchel, Lieke, Stutterheim, Janine, Lak, Nathalie N.S.M., Tytgat, Godelieve G.A.M., Laureys, Geneviève, Speleman, Frank, De Wilde, Bram, Lammens, Tim, De Preter, Katleen, and Van Roy, Nadine

Abstract

Background: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. Procedure: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. Results: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. Conclusion: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

97. Frequency and prognostic impact of alk amplifications and mutations in the european neuroblastoma study group (siopen) high-risk neuroblastoma trial (hr-nbl1)

Author

Bellini, Angela, Potschger, Ulrike, Bernard, Virginie, Lapouble, Eve, Baulande, Sylvain, Ambros, Peter F., Auger, Nathalie, Beiske, Klaus, Bernkopf, Marie, Betts, David R., Bhalshankar, Jaydutt, Bown, Nick, De Preter, Katleen, Clement, Nathalie, Combaret, Valerie, De Mora, Jaime Font, George, Sally L., Jimenez, Irene, Jeison, Marta, Marques, Barbara, Martinsson, Tommy, Mazzocco, Katia, Morini, Martina, Muhlethaler-Mottet, Annick, Noguera, Rosa, Pierron, Gaelle, Rossing, Maria, Taschner-Mandl, Sabine, Van Roy, Nadine, Vicha, Ales, Chesler, Louis, Balwierz, Walentyna, Castel, Victoria, Elliott, Martin, Kogner, Per, Laureys, Genevieve, Luksch, Roberto, Malis, Josef, Popovic-Beck, Maja, Ash, Shifra, Delattre, Olivier, Valteau-Couanet, Dominique, Tweddle, Deborah A., Ladenstein, Ruth, Schleiermacher, Gudrun, Bellini, Angela, Potschger, Ulrike, Bernard, Virginie, Lapouble, Eve, Baulande, Sylvain, Ambros, Peter F., Auger, Nathalie, Beiske, Klaus, Bernkopf, Marie, Betts, David R., Bhalshankar, Jaydutt, Bown, Nick, De Preter, Katleen, Clement, Nathalie, Combaret, Valerie, De Mora, Jaime Font, George, Sally L., Jimenez, Irene, Jeison, Marta, Marques, Barbara, Martinsson, Tommy, Mazzocco, Katia, Morini, Martina, Muhlethaler-Mottet, Annick, Noguera, Rosa, Pierron, Gaelle, Rossing, Maria, Taschner-Mandl, Sabine, Van Roy, Nadine, Vicha, Ales, Chesler, Louis, Balwierz, Walentyna, Castel, Victoria, Elliott, Martin, Kogner, Per, Laureys, Genevieve, Luksch, Roberto, Malis, Josef, Popovic-Beck, Maja, Ash, Shifra, Delattre, Olivier, Valteau-Couanet, Dominique, Tweddle, Deborah A., Ladenstein, Ruth, and Schleiermacher, Gudrun

Abstract

PURPOSE In neuroblastoma (NB), the ALK receptor tyrosine kinase can be constitutively activated through activating point mutations or genomic amplification. We studied ALK genetic alterations in high-risk (HR) patients on the HR-NBL1/SIOPEN trial to determine their frequency, correlation with clinical parameters, and prognostic impact. MATERIALS AND METHODS Diagnostic tumor samples were available from 1,092 HR-NBL1/SIOPEN patients to determine ALK amplification status (n 5 330), ALK mutational profile (n 5 191), or both (n 5 571). RESULTS Genomic ALK amplification (ALKa) was detected in 4.5% of cases (41 out of 901), all except one with MYCN amplification (MNA). ALKa was associated with a significantly poorer overall survival (OS) (5-year OS: ALKa [n 5 41] 28% [95% CI, 15 to 42]; no-ALKa [n 5 860] 51% [95% CI, 47 to 54], [P , .001]), particularly in cases with metastatic disease. ALK mutations (ALKm) were detected at a clonal level (. 20% mutated allele fraction) in 10% of cases (76 out of 762) and at a subclonal level (mutated allele fraction 0.1%-20%) in 3.9% of patients (30 out of 762), with a strong correlation between the presence of ALKm and MNA (P , .001). Among 571 cases with known ALKa and ALKm status, a statistically significant difference in OS was observed between cases with ALKa or clonal ALKm versus subclonal ALKm or no ALK alterations (5-year OS: ALKa [n 5 19], 26% [95% CI, 10 to 47], clonal ALKm[n565] 33% [95% CI, 21 to 44], subclonal ALKm(n522) 48% [95% CI, 26 to 67], and no alteration [n 5 465], 51% [95% CI, 46 to 55], respectively; P 5 .001). Importantly, in a multivariate model, involvement of more than one metastatic compartment (hazard ratio [HR], 2.87; P , .001), ALKa (HR, 2.38; P 5 .004), and clonal ALKm (HR, 1.77; P 5 .001) were independent predictors of poor outcome. CONCLUSION Genetic alterations of ALK (clonal mutations and amplifications) in HR-NB are independent predictors of poorer survival. These data provide a rationale for integr

Published
2021

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