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973 results on '"Brakenhoff, Ruud H"'

2. Hallmarks of a genomically distinct subclass of head and neck cancer

Author

Muijlwijk, Tara, Nauta, Irene H., van der Lee, Anabel, Grünewald, Kari J. T., Brink, Arjen, Ganzevles, Sonja H., Baatenburg de Jong, Robert J., Atanesyan, Lilit, Savola, Suvi, van de Wiel, Mark A., Peferoen, Laura A. N., Bloemena, Elisabeth, van de Ven, Rieneke, Leemans, C. René, Poell, Jos B., and Brakenhoff, Ruud H.

Published
2024
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5. Immune-based classification of HPV-associated oropharyngeal cancer with implications for biomarker-driven treatment de-intensification

Author

Zeng, Peter YF, Cecchini, Matthew J, Barrett, John W, Shammas-Toma, Matthew, De Cecco, Loris, Serafini, Mara S, Cavalieri, Stefano, Licitra, Lisa, Hoebers, Frank, Brakenhoff, Ruud H, Leemans, C René, Scheckenbach, Kathrin, Poli, Tito, Wang, Xiaowei, Liu, Xinyi, Laxague, Francisco, Prisman, Eitan, Poh, Catherine, Bose, Pinaki, Dort, Joseph C, Shaikh, Mushfiq H, Ryan, Sarah EB, Dawson, Alice, Khan, Mohammed I, Howlett, Christopher J, Stecho, William, Plantinga, Paul, da Silva, Sabrina Daniela, Hier, Michael, Khan, Halema, MacNeil, Danielle, Mendez, Adrian, Yoo, John, Fung, Kevin, Lang, Pencilla, Winquist, Eric, Palma, David A, Ziai, Hedyeh, Amelio, Antonio L, Li, Shawn S-C, Boutros, Paul C, Mymryk, Joe S, and Nichols, Anthony C

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer, Prevention, Infectious Diseases, Precision Medicine, Radiation Oncology, Digestive Diseases, Sexually Transmitted Infections, Dental/Oral and Craniofacial Disease, Good Health and Well Being, Humans, Papillomavirus Infections, Retrospective Studies, Neoplasm Recurrence, Local, Oropharyngeal Neoplasms, Squamous Cell Carcinoma of Head and Neck, Prognosis, Biomarkers, Human Papillomavirus Viruses, Head and Neck Neoplasms, Papillomaviridae, Head and neck squamous cell carcinoma, Transcriptomics, Cancer immunology, HPV, De-escalation, Clinical Sciences, Public Health and Health Services, Clinical sciences, Epidemiology
Abstract

BackgroundThere is significant interest in treatment de-escalation for human papillomavirus-associated (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) patients given the generally favourable prognosis. However, 15-30% of patients recur after primary treatment, reflecting a need for improved risk-stratification tools. We sought to develop a molecular test to risk stratify HPV+ OPSCC patients.MethodsWe created an immune score (UWO3) associated with survival outcomes in six independent cohorts comprising 906 patients, including blinded retrospective and prospective external validations. Two aggressive radiation de-escalation cohorts were used to assess the ability of UWO3 to identify patients who recur. Multivariate Cox models were used to assess the associations between the UWO3 immune class and outcomes.FindingsA three-gene immune score classified patients into three immune classes (immune rich, mixed, or immune desert) and was strongly associated with disease-free survival in six datasets, including large retrospective and prospective datasets. Pooled analysis demonstrated that the immune rich group had superior disease-free survival compared to the immune desert (HR = 9.0, 95% CI: 3.2-25.5, P = 3.6 × 10-5) and mixed (HR = 6.4, 95% CI: 2.2-18.7, P = 0.006) groups after adjusting for age, sex, smoking status, and AJCC8 clinical stage. Finally, UWO3 was able to identify patients from two small treatment de-escalation cohorts who remain disease-free after aggressive de-escalation to 30 Gy radiation.InterpretationWith additional prospective validation, the UWO3 score could enable biomarker-driven clinical decision-making for patients with HPV+ OPSCC based on robust outcome prediction across six independent cohorts. Prospective de-escalation and intensification clinical trials are currently being planned.FundingCIHR, European Union, and the NIH.

Published
2022

6. TNM 8 staging system beyond p16: Double HPV/p16 status is superior to p16 alone in predicting outcome in oropharyngeal squamous cell carcinoma

Author

von Buchwald, Christian, Jakobsen, Kathrine Kronberg, Carlander, Amanda-Louise Fenger, Tous, Sara, Grønhøj, Christian, Rasmussen, Jacob H., Brooks, Jill, Taberna, Miren, Mena, Marisa, Morey, Francisca, Bruni, Laia, Batis, Nikolaos, Brakenhoff, Ruud H., René Leemans, C., Jong, Robert J.Baatenburg de, Klussmann, Jens Peter, Wuerdemann, Nora, Wagner, Steffen, Dalianis, Tina, Marklund, Linda, Mirghani, Haïtham, Schache, Andrew, James, Jaqueline A., Huang, Shao Hui, O’Sullivan, Brian, Nankivell, Paul, Broglie, Martina A., Hoffmann, Markus, Quabius, Elgar Susanne, Anderson, Lesley A., Craig, Stephanie G., Alemany, Laia, and Mehanna, Hisham

Published
2024
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8. Genome-wide siRNA screens identify RBBP9 function as a potential target in Fanconi anaemia-deficient head-and-neck squamous cell carcinoma

Author

Pai, Govind, Roohollahi, Khashayar, Rockx, Davy, de Jong, Yvonne, Stoepker, Chantal, Pennings, Charlotte, Rooimans, Martin, Vriend, Lianne, Piersma, Sander, Jimenez, Connie R., De Menezes, Renee X., Van Beusechem, Victor W., Brakenhoff, Ruud H., Te Riele, Hein, Wolthuis, Rob M. F., and Dorsman, Josephine C.

Published
2023
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10. HeNeCOn: An ontology for integrative research in Head and Neck cancer

Author

Poli, Tito, Rossi, Silvia, Martinelli, Elena, Licitra, Lisa, Cavalieri, Stefano, De Cecco, Loris, Canevari, Silvana, Scheckenbach, Kathrin, Brakenhoff, Ruud H., Nauta, Irene, Hoebers, Frank J.P., Wesseling, Frederik W.R., Trama, Annalisa, Gatta, Gemma, Hernández, Liss, Estévez-Priego, Estefanía, López-Pérez, Laura, Fernanda Cabrera-Umpiérrez, María, Arredondo, María Teresa, and Fico, Giuseppe

Published
2024
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11. The course of health-related quality of life in the first 2 years after a diagnosis of head and neck cancer: the role of personal, clinical, psychological, physical, social, lifestyle, disease-related, and biological factors

Author

Verdonck-de Leeuw, Irma M., Korsten, Laura H.A., van Nieuwenhuizen, Annette, Baatenburg de Jong, Rob J., Brakenhoff, Ruud H., Buffart, Laurien M., Lamers, Femke, Langendijk, Johannes A., Leemans, C. René, Smit, Jan H., Sprangers, Mirjam A., Takes, Robert P., Terhaard, Chris H. J., Lissenberg-Witte, Birgit I., and Jansen, Femke

Published
2023
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13. Study retention and attrition in a longitudinal cohort study including patient-reported outcomes, fieldwork and biobank samples: results of the Netherlands quality of life and Biomedical cohort study (NET-QUBIC) among 739 head and neck cancer patients and 262 informal caregivers

Author

Jansen, Femke, Brakenhoff, Ruud H., Baatenburg de Jong, Rob J., Langendijk, Johannes A., Leemans, C. René, Takes, Robert P., Terhaard, Chris H. J., Smit, Jan H., and Verdonck-de Leeuw, Irma M.

Published
2022
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15. Improved high-dimensional prediction with Random Forests by the use of co-data

Author

Beest, Dennis E. te, Mes, Steven W., Brakenhoff, Ruud H., and van de Wiel, Mark A.

Subjects
Statistics - Applications
Abstract

Prediction in high dimensional settings is difficult due to large by number of variables relative to the sample size. We demonstrate how auxiliary "co-data" can be used to improve the performance of a Random Forest in such a setting. Co-data are incorporated in the Random Forest by replacing the uniform sampling probabilities (used to draw candidate variables, the default for a Random Forest) by co-data moderated sampling probabilities. Co-data here is defined as any type information that is available on the variables of the primary data, but does not use its response labels. These moderated sampling probabilities are, inspired by empirical Bayes, learned from the data at hand. We demonstrate this co-data moderated Random Forest (CoRF) with one example. In the example we aim to predict a lymph node metastasis with gene expression data. We demonstrate how a set of external p-values, a gene signature, and the correlation between gene expression and DNA copy number can improve the predictive performance., Comment: 17 pages, 4 figures, to be published

Published
2017

16. Architectural dysplasia in surgical margins and the risk of local relapse in oral cancer.

Author

Nauta, Irene H., Peferoen, Laura A. N., Brakenhoff, Ruud H., Leemans, C. René, and Bloemena, Elisabeth

Subjects
SQUAMOUS cell carcinoma, CANCER relapse, SURGICAL margin, DYSPLASIA, ORAL cancer
Abstract

Background: A major challenge in the clinical management of oral cavity squamous cell carcinoma is local relapse. Even when surgical margins are tumor‐free, local relapses occur frequently, and relapse prediction by histology remains suboptimal. In leukoplakia, an oral potentially malignant disorder, the presence of architectural dysplasia is a critical risk factor for malignant transformation. This study aimed to investigate whether the presence of architectural dysplasia in oral cavity squamous cell carcinoma surgical margins is a risk factor for local relapse. Methods: Hematoxylin and eosin‐stained slides of resection margins from a consecutive cohort of surgically treated patients diagnosed with stage I–IV oral cavity squamous cell carcinoma between 2008 and 2014 were assessed for the presence of architectural dysplasia (N = 311). Five‐year local relapse‐free survival rates of oral cavity squamous cell carcinoma with architectural dysplasia were compared to those of oral cavity squamous cell carcinoma without architectural dysplasia. Results: In total, 92 of 311 (29.6%) of oral cavity squamous cell carcinoma displayed architectural dysplasia in the margins. The presence of architectural dysplasia was associated with higher patient age, female sex, less pack years, lower cT‐stage, and a cohesive tumor growth pattern. In oral cavity squamous cell carcinomas with architectural dysplasia, postoperative (chemo)radiotherapy was less often indicated compared with oral cavity squamous cell carcinoma without architectural dysplasia (19.5% vs. 36.1%, p = 0.009). Five‐year local relapse‐free survival was significantly lower in oral cavity squamous cell carcinoma with architectural dysplasia than in oral cavity squamous cell carcinoma without architectural dysplasia (83.1% vs. 94.9%, p = 0.017). Conclusions: Oral cavity squamous cell carcinoma arising in the background of architectural dysplasia displays relatively favorable clinical and histopathological characteristics. Nonetheless, the presence of architectural dysplasia in oral cavity squamous cell carcinoma surgical margins is associated with a higher risk of local relapse, indicating its clinical relevance. [ABSTRACT FROM AUTHOR]

Published
2024
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19. The value of regular follow‐up of oral leukoplakia for early detection of malignant transformation.

Author

Evren, Ilkay, Najim, Ahmad M., Poell, Jos B., Brouns, Elisabeth R., Wils, Leon J., Peferoen, Laura A. N., Brakenhoff, Ruud H., Bloemena, Elisabeth, van der Meij, Erik H., and de Visscher, Jan G. A. M.

Subjects
SQUAMOUS cell carcinoma, PEARSON correlation (Statistics), MOUTH tumors, T-test (Statistics), DATA analysis, EARLY detection of cancer, FISHER exact test, ORAL leukoplakia, RETROSPECTIVE studies, MANN Whitney U Test, CHI-squared test, DESCRIPTIVE statistics, MEDICAL records, ACQUISITION of data, STATISTICS, DATA analysis software, PATIENT aftercare, DISEASE progression
Abstract

Objectives: Evaluate whether regular follow‐up of oral leukoplakia (OL) resulted in early detection of malignant transformation (MT). Method: Two hundred and twenty‐two consecutive patients with OL (147 females, 75 males); median follow‐up period of 64 months (range: 12–300). Three groups were distinguished: group A (n = 92) follow‐up at the hospital; group B (n = 84) follow‐up by their dentist; group C (n = 46) lost to follow‐up. Results: OLs in group B compared to group A, were smaller in size (<2 cm; p < 0.001), showed more hyperkeratosis (p < 0.001) and less moderate/severe dysplasia (p < 0.001). MT occurred in 45 (20%) patients: 32 (35%) in group A, five (6%) in group B and eight (17%) in group C. There was no significant difference in clinical tumour size between group A (median: 15 mm, range: 1–40) and group B (median: 10 mm, range: 3–25; p = 0.496). Tumour size was smaller for patients in groups A and B (median: 10 mm, range 1–40) compared to group C (median: 33 mm, range: 3–100; p = 0.003). There was a positive correlation between tumour size and interval between the last visit in all patients (p = 0.022). Conclusion: Regular follow‐up of OL resulted in early detection of MT. If properly selected, follow‐up of OL performed by the dentist seems feasible. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Supplementary Table 1 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, primary, Harris, Jeffrey R., primary, Ganzevles, Sonja H., primary, Muthuswamy, Anantharaman, primary, Houtkamp, Mischa, primary, Plantinga, Theo S., primary, Bloemena, Elisabeth, primary, Brakenhoff, Ruud H., primary, Breij, Esther C.W., primary, and van de Ven, Rieneke, primary

Published
2024
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25. Supplementary Figure S3 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, primary, Harris, Jeffrey R., primary, Ganzevles, Sonja H., primary, Muthuswamy, Anantharaman, primary, Houtkamp, Mischa, primary, Plantinga, Theo S., primary, Bloemena, Elisabeth, primary, Brakenhoff, Ruud H., primary, Breij, Esther C.W., primary, and van de Ven, Rieneke, primary

Published
2024
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26. Supplementary Table 2 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, primary, Harris, Jeffrey R., primary, Ganzevles, Sonja H., primary, Muthuswamy, Anantharaman, primary, Houtkamp, Mischa, primary, Plantinga, Theo S., primary, Bloemena, Elisabeth, primary, Brakenhoff, Ruud H., primary, Breij, Esther C.W., primary, and van de Ven, Rieneke, primary

Published
2024
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27. Data from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, primary, Harris, Jeffrey R., primary, Ganzevles, Sonja H., primary, Muthuswamy, Anantharaman, primary, Houtkamp, Mischa, primary, Plantinga, Theo S., primary, Bloemena, Elisabeth, primary, Brakenhoff, Ruud H., primary, Breij, Esther C.W., primary, and van de Ven, Rieneke, primary

Published
2024
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28. Supplementary Table 3 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, primary, Harris, Jeffrey R., primary, Ganzevles, Sonja H., primary, Muthuswamy, Anantharaman, primary, Houtkamp, Mischa, primary, Plantinga, Theo S., primary, Bloemena, Elisabeth, primary, Brakenhoff, Ruud H., primary, Breij, Esther C.W., primary, and van de Ven, Rieneke, primary

Published
2024
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35. Genomic Engineering of Oral Keratinocytes to Establish In Vitro Oral Potentially Malignant Disease Models as a Platform for Treatment Investigation.

Author

Wils, Leon J., Buijze, Marijke, Stigter-van Walsum, Marijke, Brink, Arjen, van Kempen, Britt E., Peferoen, Laura, Brouns, Elisabeth R., de Visscher, Jan G. A. M., van der Meij, Erik H., Bloemena, Elisabeth, Poell, Jos B., and Brakenhoff, Ruud H.

Subjects
KERATINOCYTE differentiation, DYSPLASIA, KERATINOCYTES, ORAL leukoplakia, ORAL mucosa, SMALL molecules, CELL lines, CELL culture
Abstract

Precancerous cells in the oral cavity may appear as oral potentially malignant disorders, but they may also present as dysplasia without visual manifestation in tumor-adjacent tissue. As it is currently not possible to prevent the malignant transformation of these oral precancers, new treatments are urgently awaited. Here, we generated precancer culture models using a previously established method for the generation of oral keratinocyte cultures and incorporated CRISPR/Cas9 editing. The generated cell lines were used to investigate the efficacy of a set of small molecule inhibitors. Tumor-adjacent mucosa and oral leukoplakia biopsies were cultured and genetically characterized. Mutations were introduced in CDKN2A and TP53 using CRISPR/Cas9 and combined with the ectopic activation of telomerase to generate cell lines with prolonged proliferation. The method was tested in normal oral keratinocytes and tumor-adjacent biopsies and subsequently applied to a large set of oral leukoplakia biopsies. Finally, a subset of the immortalized cell lines was used to assess the efficacy of a set of small molecule inhibitors. Culturing and genomic engineering was highly efficient for normal and tumor-adjacent oral keratinocytes, but success rates in oral leukoplakia were remarkably low. Knock-out of CDKN2A in combination with either the activation of telomerase or knock-out of TP53 seemed a prerequisite for immortalization. Prolonged culturing was accompanied by additional genetic aberrations in these cultures. The generated cell lines were more sensitive than normal keratinocytes to small molecule inhibitors of previously identified targets. In conclusion, while very effective for normal keratinocytes and tumor-adjacent biopsies, the success rate of oral leukoplakia cell culturing methods was very low. Genomic engineering enabled the prolonged culturing of OL-derived keratinocytes but was associated with acquired genetic changes. Further studies are required to assess to what extent the immortalized cultures faithfully represent characteristics of the cells in vivo. [ABSTRACT FROM AUTHOR]

Published
2024
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37. 940 High plasma cell presence in oral cancers with high frequencies of tumor-infiltrating B cells identified by transcriptional, flow cytometric and spatial profiling

Author

Nijenhuis, Dennis NLM, primary, Muijlwijk, Tara, additional, Ganzevles, Sonja H, additional, Hansson, Stina Lie, additional, Lee, Anabel van der, additional, Nauta, Irene, additional, Rene Leemans, C, additional, Brakenhoff, Ruud H, additional, and Ven, Rieneke van de, additional

Published
2023
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38. Cover Image

Author

Wils, Leon J., primary, Poell, Jos B., additional, Peferoen, Laura A. N., additional, Evren, Ilkay, additional, Brouns, Elisabeth R., additional, de Visscher, Jan G. A. M., additional, van der Meij, Erik H., additional, Brakenhoff, Ruud H., additional, and Bloemena, Elisabeth, additional

Published
2023
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40. An antibody-drug conjugate directed to tissue factor shows preclinical anti-tumor activity in head and neck cancer as a single agent and in combination with chemoradiotherapy

Author

Bakema, Jantine E., primary, Stigter-van Walsum, Marijke, additional, Harris, Jeffrey R., additional, Ganzevles, Sonja H., additional, Muthuswamy, Anantharaman, additional, Houtkamp, Mischa, additional, Plantinga, Theo S., additional, Bloemena, Elisabeth, additional, Brakenhoff, Ruud H., additional, Breij, Esther C.W., additional, and van de Ven, Rieneke, additional

Published
2023
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42. Discovery of Salivary Gland Tumors’ Biomarkers via Co-Regularized Sparse-Group Lasso

Author

Imangaliyev, Sultan, Matse, Johannes H., Bolscher, Jan G. M., Brakenhoff, Ruud H., Wong, David T. W., Bloemena, Elisabeth, Veerman, Enno C. I., Levin, Evgeni, 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, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Yamamoto, Akihiro, editor, Kida, Takuya, editor, Uno, Takeaki, editor, and Kuboyama, Tetsuji, editor

Published
2017
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46. Clinical Validity of a Prognostic Gene Expression Cluster-Based Model in Human Papillomavirus–Positive Oropharyngeal Carcinoma

Author

Cavalieri, Stefano, Serafini, Mara S., Carenzo, Andrea, Canevari, Silvana, Brakenhoff, Ruud H., Leemans, C. René, Nauta, Irene H., Hoebers, Frank, van den Hout, Mari F. C. M., Scheckenbach, Kathrin, Hoffmann, Thomas K., Ardighieri, Laura, Poli, Tito, Quattrone, Pasquale, Locati, Laura D., Licitra, Lisa, and De Cecco, Loris

Published
2021
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47. Privacy-preserving distributed learning of radiomics to predict overall survival and HPV status in head and neck cancer

Author

Bogowicz, Marta, Jochems, Arthur, Deist, Timo M., Tanadini-Lang, Stephanie, Huang, Shao Hui, Chan, Biu, Waldron, John N., Bratman, Scott, O’Sullivan, Brian, Riesterer, Oliver, Studer, Gabriela, Unkelbach, Jan, Barakat, Samir, Brakenhoff, Ruud H., Nauta, Irene, Gazzani, Silvia E., Calareso, Giuseppina, Scheckenbach, Kathrin, Hoebers, Frank, Wesseling, Frederik W. R., Keek, Simon, Sanduleanu, Sebastian, Leijenaar, Ralph T. H., Vergeer, Marije R., Leemans, C. René, Terhaard, Chris H. J., van den Brekel, Michiel W. M., Hamming-Vrieze, Olga, van der Heijden, Martijn A., Elhalawani, Hesham M., Fuller, Clifton D., Guckenberger, Matthias, and Lambin, Philippe

Published
2020
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49. MRI-based radiomic prognostic signature for locally advanced oral cavity squamous cell carcinoma:development, testing and comparison with genomic prognostic signatures

Author

Corti, Anna, De Cecco, Loris, Cavalieri, Stefano, Lenoci, Deborah, Pistore, Federico, Calareso, Giuseppina, Mattavelli, Davide, de Graaf, Pim, Leemans, C René, Brakenhoff, Ruud H, Ravanelli, Marco, Poli, Tito, Licitra, Lisa, Corino, Valentina, and Mainardi, Luca

Abstract

BACKGROUND: . At present, the prognostic prediction in advanced oral cavity squamous cell carcinoma (OCSCC) is based on the tumor-node-metastasis (TNM) staging system, and the most used imaging modality in these patients is magnetic resonance image (MRI). With the aim to improve the prediction, we developed an MRI-based radiomic signature as a prognostic marker for overall survival (OS) in OCSCC patients and compared it with published gene expression signatures for prognosis of OS in head and neck cancer patients, replicated herein on our OCSCC dataset.METHODS: For each patient, 1072 radiomic features were extracted from T1 and T2-weighted MRI (T1w and T2w). Features selection was performed, and an optimal set of five of them was used to fit a Cox proportional hazard regression model for OS. The radiomic signature was developed on a multi-centric locally advanced OCSCC retrospective dataset (n = 123) and validated on a prospective cohort (n = 108).RESULTS: The performance of the signature was evaluated in terms of C-index (0.68 (IQR 0.66-0.70)), hazard ratio (HR 2.64 (95% CI 1.62-4.31)), and high/low risk group stratification (log-rank p CONCLUSIONS: Overall, the present study suggests that MRI signatures, containing non-invasive and cost-effective remarkable information, could be exploited as prognostic tools.

Published
2023

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