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8 results on '"Zwaan, Kenn"'

1. Platelet RNA sequencing for cancer screening in patients with unprovoked venous thromboembolism: a prospective cohort study

Author

Mulder, Frits I., Kraaijpoel, Noémie, Carrier, Marc, Guman, Noori A., Jara-Palomares, Luis, Di Nisio, Marcello, Ageno, Walter, Beyer-Westendorf, Jan, Klok, Frederikus A., Vanassche, Thomas, Otten, Hans-Martin B., Cosmi, Benilde, Wolde, Marije ten, In ‘t Veld, Sjors G.J. G., Post, Edward, Ramaker, Jip, Zwaan, Kenn, Peters, Mike, Delluc, Aurélien, Kamphuisen, Pieter W., Sanchez-Lopez, Veronica, Porreca, Ettore, Bossuyt, Patrick M.M., Büller, Harry R., Wurdinger, Thomas, Best, Myron G., and van Es, Nick

Published
2023
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2. Detection and localization of early- and late-stage cancers using platelet RNA

Author

In ’t Veld, Sjors G.J.G., Arkani, Mohammad, Post, Edward, Antunes-Ferreira, Mafalda, D’Ambrosi, Silvia, Vessies, Daan C.L., Vermunt, Lisa, Vancura, Adrienne, Muller, Mirte, Niemeijer, Anna-Larissa N., Tannous, Jihane, Meijer, Laura L., Le Large, Tessa Y.S., Mantini, Giulia, Wondergem, Niels E., Heinhuis, Kimberley M., van Wilpe, Sandra, Smits, A. Josien, Drees, Esther E.E., Roos, Eva, Leurs, Cyra E., Tjon Kon Fat, Lee-Ann, van der Lelij, Ewoud J., Dwarshuis, Govert, Kamphuis, Maarten J., Visser, Lisanne E., Harting, Romee, Gregory, Annemijn, Schweiger, Markus W., Wedekind, Laurine E., Ramaker, Jip, Zwaan, Kenn, Verschueren, Heleen, Bahce, Idris, de Langen, Adrianus J., Smit, Egbert F., van den Heuvel, Michel M., Hartemink, Koen J., Kuijpers, Marijke J.E., oude Egbrink, Mirjam G.A., Griffioen, Arjan W., Rossel, Rafael, Hiltermann, T. Jeroen N., Lee-Lewandrowski, Elizabeth, Lewandrowski, Kent B., De Witt Hamer, Philip C., Kouwenhoven, Mathilde, Reijneveld, Jaap C., Leenders, William P.J., Hoeben, Ann, Verdonck-de Leeuw, Irma M., Leemans, C. René, Baatenburg de Jong, Robert J., Terhaard, Chris H.J., Takes, Robert P., Langendijk, Johannes A., de Jager, Saskia C., Kraaijeveld, Adriaan O., Pasterkamp, Gerard, Smits, Minke, Schalken, Jack A., Łapińska-Szumczyk, Sylwia, Łojkowska, Anna, Żaczek, Anna J., Lokhorst, Henk, van de Donk, Niels W.C.J., Nijhof, Inger, Prins, Henk-Jan, Zijlstra, Josée M., Idema, Sander, Baayen, Johannes C., Teunissen, Charlotte E., Killestein, Joep, Besselink, Marc G., Brammen, Lindsay, Bachleitner-Hofmann, Thomas, Mateen, Farrah, Plukker, John T.M., Heger, Michal, de Mast, Quirijn, Lisman, Ton, Pegtel, D. Michiel, Bogaard, Harm-Jan, Jassem, Jacek, Supernat, Anna, Mehra, Niven, Gerritsen, Winald, de Kroon, Cornelis D., Lok, Christianne A.R., Piek, Jurgen M.J., Steeghs, Neeltje, van Houdt, Winan J., Brakenhoff, Ruud H., Sonke, Gabe S., Verheul, Henk M., Giovannetti, Elisa, Kazemier, Geert, Sabrkhany, Siamack, Schuuring, Ed, Sistermans, Erik A., Wolthuis, Rob, Meijers-Heijboer, Hanne, Dorsman, Josephine, Oudejans, Cees, Ylstra, Bauke, Westerman, Bart A., van den Broek, Daan, Koppers-Lalic, Danijela, Wesseling, Pieter, Nilsson, R. Jonas A., Vandertop, W. Peter, Noske, David P., Tannous, Bakhos A., Sol, Nik, Best, Myron G., and Wurdinger, Thomas

Published
2022
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3. Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management

Author

Antunes-Ferreira, Mafalda, D’Ambrosi, Silvia, Arkani, Mohammad, Post, Edward, in ‘t Veld, Sjors G. J. G., Ramaker, Jip, Zwaan, Kenn, Kucukguzel, Ece Demirel, Wedekind, Laurine E., Griffioen, Arjan W., Oude Egbrink, Mirjam, Kuijpers, Marijke J. E., van den Broek, Daan, Noske, David P., Hartemink, Koen J., Sabrkhany, Siamack, Bahce, Idris, Sol, Nik, Bogaard, Harm-Jan, Koppers-Lalic, Danijela, Best, Myron G., Wurdinger, Thomas, Neurosurgery, Pulmonary medicine, Medical oncology laboratory, AII - Cancer immunology, CCA - Cancer biology and immunology, CCA - Cancer Treatment and quality of life, ACS - Pulmonary hypertension & thrombosis, CCA - Imaging and biomarkers, and CCA - Cancer immunology

Abstract

Liquid biopsy approaches offer a promising technology for early and minimally invasive cancer detection. Tumor-educated platelets (TEPs) have emerged as a promising liquid biopsy biosource for the detection of various cancer types. In this study, we processed and analyzed the TEPs collected from 466 Non-small Cell Lung Carcinoma (NSCLC) patients and 410 asymptomatic individuals (controls) using the previously established thromboSeq protocol. We developed a novel particle-swarm optimization machine learning algorithm which enabled the selection of an 881 RNA biomarker panel (AUC 0.88). Herein we propose and validate in an independent cohort of samples (n = 558) two approaches for blood samples testing: one with high sensitivity (95% NSCLC detected) and another with high specificity (94% controls detected). Our data explain how TEP-derived spliced RNAs may serve as a biomarker for minimally-invasive clinical blood tests, complement existing imaging tests, and assist the detection and management of lung cancer patients.

Published
2023
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4. Supplementary table S1 from Combined Therapy of AXL and HDAC Inhibition Reverses Mesenchymal Transition in Diffuse Intrinsic Pontine Glioma

Author

Meel, Michaël H., primary, de Gooijer, Mark C., primary, Metselaar, Dennis S., primary, Sewing, A. Charlotte P., primary, Zwaan, Kenn, primary, Waranecki, Piotr, primary, Breur, Marjolein, primary, Buil, Levi C.M., primary, Lagerweij, Tonny, primary, Wedekind, Laurine E., primary, Twisk, Jos W.R., primary, Koster, Jan, primary, Hashizume, Rintaro, primary, Raabe, Eric H., primary, Montero Carcaboso, Ángel, primary, Bugiani, Marianna, primary, Phoenix, Timothy N., primary, van Tellingen, Olaf, primary, van Vuurden, Dannis G., primary, Kaspers, Gertjan J.L., primary, and Hulleman, Esther, primary

Published
2023
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5. Supplementary Data Legends from Combined Therapy of AXL and HDAC Inhibition Reverses Mesenchymal Transition in Diffuse Intrinsic Pontine Glioma

Author

Meel, Michaël H., primary, de Gooijer, Mark C., primary, Metselaar, Dennis S., primary, Sewing, A. Charlotte P., primary, Zwaan, Kenn, primary, Waranecki, Piotr, primary, Breur, Marjolein, primary, Buil, Levi C.M., primary, Lagerweij, Tonny, primary, Wedekind, Laurine E., primary, Twisk, Jos W.R., primary, Koster, Jan, primary, Hashizume, Rintaro, primary, Raabe, Eric H., primary, Montero Carcaboso, Ángel, primary, Bugiani, Marianna, primary, Phoenix, Timothy N., primary, van Tellingen, Olaf, primary, van Vuurden, Dannis G., primary, Kaspers, Gertjan J.L., primary, and Hulleman, Esther, primary

Published
2023
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6. Supplementary figures from Combined Therapy of AXL and HDAC Inhibition Reverses Mesenchymal Transition in Diffuse Intrinsic Pontine Glioma

Author

Meel, Michaël H., primary, de Gooijer, Mark C., primary, Metselaar, Dennis S., primary, Sewing, A. Charlotte P., primary, Zwaan, Kenn, primary, Waranecki, Piotr, primary, Breur, Marjolein, primary, Buil, Levi C.M., primary, Lagerweij, Tonny, primary, Wedekind, Laurine E., primary, Twisk, Jos W.R., primary, Koster, Jan, primary, Hashizume, Rintaro, primary, Raabe, Eric H., primary, Montero Carcaboso, Ángel, primary, Bugiani, Marianna, primary, Phoenix, Timothy N., primary, van Tellingen, Olaf, primary, van Vuurden, Dannis G., primary, Kaspers, Gertjan J.L., primary, and Hulleman, Esther, primary

Published
2023
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7. Distinct Platelet Ribonucleic Acid Signatures in Patients with Pulmonary Hypertension

Author

Smits, A. Josien, primary, Arkani, Mohammad, additional, In ’t Veld, Sjors G.J.G., additional, Huis in ‘t Veld, Anna E., additional, Sol, Nik, additional, Groeneveldt, Joanne A., additional, Botros, Liza, additional, Braams, Natalia J., additional, Jansen, Samara M.A., additional, Ramaker, Jip, additional, Zwaan, Kenn, additional, Post, Edward, additional, Nossent, Esther J., additional, Boonstra, Anco, additional, de Man, Frances S., additional, Noordegraaf, Anton Vonk, additional, Gomez-Arroyo, Jose, additional, Best, Myron G., additional, Wurdinger, Tom, additional, and Bogaard, Harm Jan, additional

Published
2022
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8. Distinct Platelet RNA Signatures in Patients with Pulmonary Hypertension

Author

Smits, A Josien, Arkani, Mohammad, In 't Veld, Sjors G J G, Huis In 't Veld, Anna E, Sol, Nik, Groeneveldt, Joanne A, Botros, Liza, Braams, Natalia J, Jansen, Samara Ma, Ramaker, Jip, Zwaan, Kenn, Post, Edward, Nossent, Esther J, Boonstra, Anco, de Man, Frances S, Vonk Noordegraaf, Anton, Gomez-Arroyo, Jose, Best, Myron G, Wurdinger, Tom, Bogaard, Harm Jan, Pulmonology, and Neurosurgery

Abstract

RATIONALE: Pulmonary hypertension encompasses progressive disorders leading to right ventricular dysfunction and early death. Late detection is an important cause of poor clinical outcomes. However, biomarkers that accurately predict the presence of pulmonary hypertension are currently lacking. OBJECTIVES: In this study we provide evidence that blood platelets contain a distinctive RNA profile that may be exploited for detection of pulmonary hypertension. METHODS: Blood platelet RNA was isolated prospectively from 177 prevalent patients with different subtypes of pulmonary hypertension as well as 195 controls clinically not suspected of pulmonary hypertension. Sequencing libraries were created using SMARTer cDNA amplification, and sequenced on the Illumina HiSeq platform. RNA-sequencing reads were mapped to the human reference genome, and intron-spanning spliced RNA reads were selected. Differential spliced RNA panels were calculated by ANOVA-statistics. A particle swarm optimisation (PSO)-enhanced classification algorithm was built employing a development (n=213 samples) and independent validation series (n=159 samples). RESULTS: We detected a total of 4014 different RNAs in blood platelets from pulmonary hypertension patients (n=177) and asymptomatic controls (n=195). GSEA gene ontology analysis revealed enriched RNA levels for genes related to RNA-processing, translation and mitochondrial function. A PSO-selected RNA panel of 408 distinctive differentially spliced RNAs mediated detection of pulmonary hypertension with 93% sensitivity, 62% specificity, 77% accuracy, 0.89 (95%CI 0.83-0.93) area under the curve and a negative predictive value of 91% in the independent validation series. Prediction score was independent of age, sex, smoking, pulmonary hypertension subtype, and the use of pulmonary hypertension-specific medication or anti-coagulants. CONCLUSION: A platelet RNA-panel may accurately discriminate patients with pulmonary hypertension from asymptomatic controls. In the light of current diagnostic delays, this study is the starting point for further development and evaluation of a platelet RNA-based blood test, to ultimately improve early diagnosis and clinical outcomes in patients with pulmonary hypertension.

Published
2022

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