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202 results on '"Gillis, A. J. M."'

1. Integrated genomic analysis reveals aberrations in WNT signaling in germ cell tumors of childhood and adolescence

Author

Xu, Lin, Pierce, Joshua L., Sanchez, Angelica, Chen, Kenneth S., Shukla, Abhay A., Fustino, Nicholas J., Stuart, Sarai H., Bagrodia, Aditya, Xiao, Xue, Guo, Lei, Krailo, Mark D., Shaikh, Furqan, Billmire, Deborah F., Pashankar, Farzana, Bestrashniy, Jessica, Oosterhuis, J. Wolter, Gillis, Ad J. M., Xie, Yang, Teot, Lisa, Mora, Jaume, Poynter, Jenny N., Rakheja, Dinesh, Looijenga, Leendert H. J., Draper, Bruce W., Frazier, A. Lindsay, and Amatruda, James F.

Published
2023
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8. Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection

Author

Pathologie Groep Van Diest, Loehr, Amanda R, Timmerman, Dennis M, Liu, Michelle, Gillis, Ad J M, Matthews, Melia, Bloom, Jordana C, Nicholls, Peter K, Page, David C, Miller, Andrew D, Looijenga, Leendert H J, Weiss, Robert S, Pathologie Groep Van Diest, Loehr, Amanda R, Timmerman, Dennis M, Liu, Michelle, Gillis, Ad J M, Matthews, Melia, Bloom, Jordana C, Nicholls, Peter K, Page, David C, Miller, Andrew D, Looijenga, Leendert H J, and Weiss, Robert S

Published
2023

9. A Type System for DNAQL

Author

Brijder, Robert, Gillis, Joris J. M., Van den Bussche, Jan, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Stefanovic, Darko, editor, and Turberfield, Andrew, editor

Published
2012
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10. Expressive Power of Safe First-Order Logical Decision Trees

Author

Gillis, Joris J. M., Van den Bussche, Jan, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Muggleton, Stephen H., editor, Tamaddoni-Nezhad, Alireza, editor, and Lisi, Francesca A., editor

Published
2012
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11. A Formal Model for Databases in DNA

Author

Gillis, Joris J. M., Van den Bussche, Jan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Horimoto, Katsuhisa, editor, Nakatsui, Masahiko, editor, and Popov, Nikolaj, editor

Published
2012
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12. Graph-Theoretic Formalization of Hybridization in DNA Sticker Complexes

Author

Brijder, Robert, Gillis, Joris J. M., Van den Bussche, Jan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cardelli, Luca, editor, and Shih, William, editor

Published
2011
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13. Induction of Relational Algebra Expressions

Author

Gillis, Joris J. M., Van den Bussche, Jan, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, and De Raedt, Luc, editor

Published
2010
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14. The Relation between Order of Acquisition, Segmental Frequency and Function: The Case of Word-Initial Consonants in Dutch

Author

van Severen, Lieve, Gillis, Joris J. M., and Molemans, Inge

Abstract

The impact of input frequency (IF) and functional load (FL) of segments in the ambient language on the acquisition order of word-initial consonants is investigated. Several definitions of IF/FL are compared and implemented. The impact of IF/FL and their components are computed using a longitudinal corpus of interactions between thirty Dutch-speaking children (age range: 0 ; 6-2 ; 0) and their primary caretaker(s). The corpus study reveals significant correlations between IF/FL and acquisition order. The highest predictive values are found for the token frequency of segments, and for FL computed on minimally different word types in child-directed speech. Although IF and FL significantly correlate, they do have a different impact on the order of acquisition of word-initial consonants. When the impact of IF is partialed out, FL still has a significant correlation with acquisition order. The reverse is not true, suggesting that the acquisition of word-initial consonants is mainly influenced by their discriminating function.

Published
2013
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16. A Genetic Screen Implicates miRNA-372 and miRNA-373 as Oncogenes in Testicular Germ Cell Tumors

Author

Voorhoeve, P. Mathijs, Sage, Carlos le, Schrier, Mariette, Gillis, Ad J. M., Stoop, Hans, Nagel, Remco, Liu, Ying-Poi, Duijse, Josyanne van, Drost, Jarno, Griekspoor, Alexander, Zlotorynski, Eitan, Yabuta, Norikazu, Vita, Gabriella De, Nojima, Hiroshi, Looijenga, Leendert H. J., Agami, Reuven, Back, Nathan, editor, Cohen, Irun R., editor, Lajtha, Abel, editor, Lambris, John D., editor, Paoletti, Rodolfo, editor, Fagagna, Fabrizio d'Adda di, editor, Chiocca, Susanna, editor, McBlane, Fraser, editor, and Cavallaro, Ugo, editor

Published
2007
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17. Chromosome 3p25.3 Gain Is Associated With Cisplatin Resistance and Is an Independent Predictor of Poor Outcome in Male Malignant Germ Cell Tumors

Author

Timmerman, Dennis M., Eleveld, Thomas F., Sriram, Sruthi, Dorssers, Lambert C. J., Gillis, Ad J. M., Schmidtova, Silvia, Kalavska, Katarina, van de Werken, Harmen J. G., Oing, Christoph, Honecker, Friedemann, Mego, Michal, Looijenga, Leendert H. J., Timmerman, Dennis M., Eleveld, Thomas F., Sriram, Sruthi, Dorssers, Lambert C. J., Gillis, Ad J. M., Schmidtova, Silvia, Kalavska, Katarina, van de Werken, Harmen J. G., Oing, Christoph, Honecker, Friedemann, Mego, Michal, and Looijenga, Leendert H. J.

Abstract

PURPOSE Cisplatin is the main systemic treatment modality for male type II germ cell tumors (GCTs). Although generally very effective, 5%-10% of patients suffer from cisplatin-resistant disease. Identification of the driving mechanisms of resistance will enable improved risk stratification and development of alternative treatments. METHODS We developed and characterized cisplatin-resistant GCT cell line models and compared their molecular characteristics with patient samples with cisplatin resistance and/or a poor clinical outcome. Subsequently, the association between the overlapping genetic features and clinical data was assessed. Finally, we used Cox regression to determine the prognostic relevance of these features within the currently used risk classification. RESULTS Gain of chromosome 3p25.3 was detected in all cisplatin-resistant cell lines, and copy number of this region correlated with the level of resistance (R = 0.96, P = 1.5e-04). Gain of this region was detected at low frequencies in primary tumors and at higher frequencies in relapsed and/or cisplatin-resistant tumors. Chromosome 3p25.3 gain was associated with shorter progression-free survival and overall survival, with the strongest association observed in nonseminomas excluding pure teratomas. 3p25.3 gain was more frequently observed in tumors with yolk sac tumor histology and predicted adverse outcome independent of the International Germ Cell Cancer Collaborative Group risk classification and the presence of TP53/MDM2 alterations. CONCLUSION On the basis of both in vitro analyses and clinical data, we found 3p25.3 to be strongly associated with cisplatin resistance and poor clinical outcome in male type II GCTs. Using genomic profiling, 3p25.3 status could help to improve risk stratification in male patients with type II GCT. Further characterization of this locus and underlying mechanisms of resistance is warranted to guide development of novel treatment approaches for cisplatin-resist

Published
2022

25. Recurrence of a Mediastinal Germ-Cell Tumor as a Somatic-Type Malignancy: A Complex Case Report

Author

Zorgeenheid Kinderchirurgie Medisch, Pathologie Pathologen staf, Cancer, PMC Medisch specialisten, CTC, Circulatory Health, Pathologie Groep Van Diest, Hulsker, Caroline C C, Kranendonk, Mariëtte E G, Eleveld, Thomas F, Gillis, Ad J M, van de Ven, Cornelis P, van Eijkelenburg, Natasha K A, van der Kaaij, Niels P, van der Steeg, Alida F W, Looijenga, Leendert H J, Zorgeenheid Kinderchirurgie Medisch, Pathologie Pathologen staf, Cancer, PMC Medisch specialisten, CTC, Circulatory Health, Pathologie Groep Van Diest, Hulsker, Caroline C C, Kranendonk, Mariëtte E G, Eleveld, Thomas F, Gillis, Ad J M, van de Ven, Cornelis P, van Eijkelenburg, Natasha K A, van der Kaaij, Niels P, van der Steeg, Alida F W, and Looijenga, Leendert H J

Published
2021

26. Additional file 1 of Napabucasin overcomes cisplatin resistance in ovarian germ cell tumor-derived cell line by inhibiting cancer stemness

Author

Schmidtova, Silvia, Dorssers, Lambert C. J., Kalavska, Katarina, Gillis, Ad J. M., J. Wolter Oosterhuis, Stoop, Hans, Miklikova, Svetlana, Kozovska, Zuzana, Burikova, Monika, Gercakova, Katarina, Durinikova, Erika, Chovanec, Michal, Mego, Michal, Kucerova, Lucia, and Looijenga, Leendert H. J.

Subjects
Data_FILES
Abstract

Additional file 1: Additional methods

Published
2020
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28. Additional file 4 of Napabucasin overcomes cisplatin resistance in ovarian germ cell tumor-derived cell line by inhibiting cancer stemness

Author

Schmidtova, Silvia, Dorssers, Lambert C. J., Kalavska, Katarina, Gillis, Ad J. M., J. Wolter Oosterhuis, Stoop, Hans, Miklikova, Svetlana, Kozovska, Zuzana, Burikova, Monika, Gercakova, Katarina, Durinikova, Erika, Chovanec, Michal, Mego, Michal, Kucerova, Lucia, and Looijenga, Leendert H. J.

Abstract

Additional file 2: Table S1 Sequences of primers used for expression analysis.

Published
2020
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40. Heterogeneous X inactivation in trophoblastic cells of human full-term female placentas

Author

Looijenga, Leendert H. J., Gillis, Ad J. M., Verkerk, Annemieke J.M.H., Putten, Wim L.J. van, and Oosterhuis, J. Wolter

Subjects
Dosage compensation (Genetics) -- Research, Trophoblast -- Genetic aspects, Placenta -- Genetic aspects, Biological sciences
Abstract

Methylation of the androgen receptor in a human full-term placenta is specific for trophoblastic cells, and the X chromosome can be of paternal origin or maternal origin. Methylation status of the polymorphic androgen-receptor gene has been studied using PCR in full-term human female placentas. Sites investigated are methylated specifically on the inactive X chromosome. No methylation was seen in microdissected stromal tissue of the placenta or umbilical cord. X inactivation was preferentially maternal in three of nine placentas for which two closely apposed samples were studied. In one it was preferentially paternal and in five heterogeneous. Two others had regions with balanced preferentially maternal and preferentially paternal X inactivation.

Published
1999

44. JKT-1 is not a human seminoma cell line

Author

de Jong, Jeroen, Stoop, Hans, Gillis, Ad J. M., van Gurp, Ruud J. H. L. M., van Drunen, Ellen, Beverloo, H. Berna, Lau, Yun-Fai Chris, Schneider, Dominik T., Sherlock, Jon K., Baeten, John, Hatakeyama, Shingo, Ohyama, Chikara, Oosterhuis, J. Wolter, and Looijenga, Leendert H. J.

Published
2007

45. Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data

Author

Lobo, João, Gillis, Ad J M, van den Berg, Annette, Dorssers, Lambert C J, Belge, Gafanzer, Dieckmann, Klaus-Peter, Roest, Henk P, van der Laan, Luc J W, Gietema, Jourik, Hamilton, Robert J, Jerónimo, Carmen, Henrique, Rui, Salvatori, Daniela, Looijenga, Leendert H J, Lobo, João, Gillis, Ad J M, van den Berg, Annette, Dorssers, Lambert C J, Belge, Gafanzer, Dieckmann, Klaus-Peter, Roest, Henk P, van der Laan, Luc J W, Gietema, Jourik, Hamilton, Robert J, Jerónimo, Carmen, Henrique, Rui, Salvatori, Daniela, and Looijenga, Leendert H J

Abstract

Liquid biopsy-based biomarkers, such as microRNAs, represent valuable tools for patient management, but often do not make it to integration in the clinic. We aim to explore issues impeding this transition, in the setting of germ cell tumors, for which novel biomarkers are needed. We describe a model for identifying and validating clinically relevant microRNAs for germ cell tumor patients, using both in vitro, in vivo (mouse model) and patient-derived data. Initial wide screening of candidate microRNAs is performed, followed by targeted profiling of potentially relevant biomarkers. We demonstrate the relevance of appropriate (negative) controls, experimental conditions (proliferation), and issues related to sample origin (serum, plasma, cerebral spinal fluid) and pre-analytical variables (hemolysis, contaminants, temperature), all of which could interfere with liquid biopsy-based studies and their conclusions. Finally, we show the value of our identification model in a specific scenario, contradicting the presumed role of miR-375 as marker of teratoma histology in liquid biopsy setting. Our findings indicate other putative microRNAs (miR-885-5p, miR-448 and miR-197-3p) fulfilling this clinical need. The identification model is informative to identify the best candidate microRNAs to pursue in a clinical setting.

Published
2019

46. Role of gain of 12p in germ cell tumour development

Author

LOOIJENGA, LEENDERT H. J., ZAFARANA, GAETANO, GRYGALEWICZ, BEATA, SUMMERSGILL, BRENDA, DEBIEC-RYCHTER, MARIA, VELTMAN, JORIS, SCHOENMAKERS, ERIC F. P. M., RODRIGUEZ, SANDRINE, JAFER, OSMAN, CLARK, JEREMY, VAN KESSEL, AD GEURTS, SHIPLEY, JANET, VAN GURP, RUUD J. H. L. M., GILLIS, AD J. M., and OOSTERHUIS, J. WOLTER

Published
2003

49. Whole-genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline

Author

Giannoulatou, Eleni, Maher, Geoffrey J., Ding, Zhihao, Gillis, Ad J. M., Dorssers, Lambert C. J., Hoischen, Alexander, Rajpert-De Meyts, Ewa, McVean, Gilean, Wilkie, Andrew O. M., Looijenga, Leendert H. J., Goriely, Anne, and Pathology

Subjects
Male, Cell biology, DNA Copy Number Variations, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biochemistry, Chromosomes, Chromosomal Disorders, Cancer Genomics, Genomic Medicine, Testicular Neoplasms, Animal Cells, Spermatocytes, Basic Cancer Research, Genetics, Medicine and Health Sciences, Biomarkers, Tumor, Point Mutation, Humans, Receptor, Fibroblast Growth Factor, Type 3, Sexual Maturation, Germ-Line Mutation, Clinical Genetics, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], DNA methylation, Genome, Human, Biology and Life Sciences, High-Throughput Nucleotide Sequencing, DNA, Genomics, Chromatin, Sperm, Spermatogonia, Nucleic acids, Germ Cells, Oncology, Mutation, Somatic Mutation, Epigenetics, Gene expression, Cellular Types, DNA modification, Chromatin modification, Research Article, Chromosome biology
Abstract

Contains fulltext : 174702.pdf (Publisher’s version ) (Open Access) Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases. To gain insights in the etiology of SpT and into properties of the male germline, we performed whole-genome sequencing of five tumors (4/5 with matched normal tissue). The acquired single nucleotide variant load was extremely low (~0.2 per Mb), with an average of 6 (2-9) non-synonymous variants per tumor, none of which is likely to be oncogenic. The observed mutational signature of SpTs is strikingly similar to that of germline de novo mutations, mostly involving C>T transitions with a significant enrichment in the ACG trinucleotide context. The tumors exhibited extensive aneuploidy (50-99 autosomes/tumor) involving whole-chromosomes, with recurrent gains of chr9 and chr20 and loss of chr7, suggesting that aneuploidy itself represents the initiating oncogenic event. We propose that SpT etiology recapitulates the unique properties of male germ cells; because of evolutionary constraints to maintain low point mutation rate, rare tumorigenic driver events are caused by a combination of gene imbalance mediated via whole-chromosome aneuploidy. Finally, we propose a general framework of male germ cell tumor pathology that accounts for their mutational landscape, timing and cellular origin.

Published
2017
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50. Serum microRNA profiles in athyroid patients on and off levothyroxine therapy

Author

Massolt, Elske T., primary, Chaker, Layal, additional, Visser, Theo J., additional, Gillis, Ad J. M., additional, Dorssers, Lambert C. J., additional, Beukhof, Carolien M., additional, Kam, Boen L. R., additional, Franssen, Gaston J., additional, Brigante, Giulia, additional, van Ginhoven, Tessa M., additional, Visser, W. Edward, additional, Looijenga, Leendert H. J., additional, and Peeters, Robin P., additional

Published
2018
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