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Hoekstra, Mirjam E. (author), Slagter, Maarten (author), Urbanus, Jos (author), Toebes, Mireille (author), Slingerland, Nadine (author), de Rink, Iris (author), Kluin, Roelof J.C. (author), Nieuwland, Marja (author), Wessels, L.F.A. (author)Cells in the tumor microenvironment (TME) influence each other through secretion and sensing of soluble mediators, such as cytokines and chemokines. While signaling of interferon γ (IFNγ) and tumor necrosis factor α (TNFα) is integral to anti-tumor immune responses, our understanding of the spatiotemporal behavior of these cytokines is...journal article 2024
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Gil Jimenez, A. (author), van Dijk, Nick (author), Vos, Joris L. (author), Lubeck, Yoni (author), van Montfoort, Maurits L. (author), Peters, Dennis (author), Hooijberg, Erik (author), Broeks, Annegien (author), Wessels, L.F.A. (author)Immune checkpoint inhibitors (ICI) can achieve remarkable responses in urothelial cancer (UC), which may depend on tumor microenvironment (TME) characteristics. However, the relationship between the TME, usually characterized by immune cell density, and response to ICI is unclear. Here, we quantify the TME immune cell densities and spatial...journal article 2024
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van de Haar, Joris (author), Mankor, Joanne M. (author), Hummelink, Karlijn (author), Monkhorst, Kim (author), Smit, Egbert F. (author), Wessels, L.F.A. (author), Cuppen, Edwin (author), Aerts, Joachim G.J.V. (author), Voest, Emile E. (author)PURPOSE: The clinical value of STK11, KEAP1, and EGFR alterations for guiding immune checkpoint blockade (ICB) therapy in non-small cell lung cancer (NSCLC) remains controversial, as some patients with these proposed resistance biomarkers show durable ICB responses. More specific combinatorial biomarker approaches are urgently needed for this...journal article 2024
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van Nee, Mirrelijn M. (author), Wessels, L.F.A. (author), van de Wiel, Mark A. (author)BACKGROUND: High-dimensional prediction considers data with more variables than samples. Generic research goals are to find the best predictor or to select variables. Results may be improved by exploiting prior information in the form of co-data, providing complementary data not on the samples, but on the variables. We consider adaptive ridge...journal article 2023
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de Vries, Natasja L. (author), van de Haar, Joris (author), Veninga, Vivien (author), Chalabi, Myriam (author), Ijsselsteijn, Marieke E. (author), van der Ploeg, Manon (author), van den Bulk, Jitske (author), Ruano, Dina (author), Wessels, L.F.A. (author)DNA mismatch repair-deficient (MMR-d) cancers present an abundance of neoantigens that is thought to explain their exceptional responsiveness to immune checkpoint blockade (ICB)<sup>1,2</sup>. Here, in contrast to other cancer types<sup>3–5</sup>, we observed that 20 out of 21 (95%) MMR-d cancers with genomic inactivation of β2-microglobulin ...journal article 2023
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Liefaard, Marte C. (author), Moore, Kat S. (author), Mulder, Lennart (author), van den Broek, Daan (author), Wesseling, Jelle (author), Sonke, Gabe S. (author), Wessels, L.F.A. (author), Rookus, Matti (author), Lips, Esther H. (author)In this article the data availability statement was incorrectly given. “EGAS0000100682” should have been “EGAS00001006821”. The correct statement as follows. The datasets generated during and/or analysed during the current study are deposited at the European Genome-phenome Archive (EGA) under the accession numbers EGAS00001006821 and...journal article 2023
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Lefrère, Hanne (author), Moore, Kat (author), Floris, Giuseppe (author), Sanders, Joyce (author), Seignette, Iris M. (author), Bismeijer, Tycho (author), Peters, Dennis (author), Broeks, Annegien (author), Wessels, L.F.A. (author)PURPOSE: Patients with postpartum breast cancer diagnosed after cessation of breastfeeding (postweaning, PP-BCPW) have a particularly poor prognosis compared with patients diagnosed during lactation (PP-BCDL), or to pregnant (Pr-BC) and nulliparous (NP-BC) patients, regardless of standard prognostic characteristics. Animal studies point to a...journal article 2023
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Mourragui, S.M.C. (author), Loog, M. (author), van Nee, Mirrelijn (author), de Wiel, Mark A.van (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)Motivation: Anti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard...conference paper 2023
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Gil Jimenez, A. (author), van Dorp, Jeroen (author), Contreras-Sanz, Alberto (author), van der Vos, Kristan (author), Vis, Daniel J. (author), Braaf, Linde (author), Broeks, Annegien (author), Alcaraz, Antonio (author), Wessels, L.F.A. (author)The authors regret that the following statement regarding author contributions was missed: Kristan van der Vos is currently a Scientific Editor for Cell Reports Medicine, which is published by Elsevier. Dr van der Vos was not involved in the peer-review process or editorial discussions about this manuscript. The authors would like to...journal article 2023
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Gil Jimenez, A. (author), van Dorp, Jeroen (author), Contreras-Sanz, Alberto (author), van der Vos, Kristan (author), Vis, Daniel J. (author), Braaf, Linde (author), Broeks, Annegien (author), Kerkhoven, Ron (author), van Kessel, Kim E.M. (author), Wessels, L.F.A. (author)Cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy is recommended for patients with muscle-invasive bladder cancer (MIBC). It has been shown that somatic deleterious mutations in ERCC2, gain-of-function mutations in ERBB2, and alterations in ATM, RB1, and FANCC are correlated with pathological response to NAC in...journal article 2023
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Liefaard, Marte C. (author), Moore, Kat S. (author), Mulder, Lennart (author), van den Broek, Daan (author), Wesseling, Jelle (author), Sonke, Gabe S. (author), Wessels, L.F.A. (author), Rookus, Matti (author), Lips, Esther H. (author)Background: Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. Methods: Platelet mRNA was sequenced from 266 women with stage I–IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised...journal article 2023
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van de Haar, Joris (author), Ma, Xuhui (author), Ooft, Salo N. (author), van der Helm, Pim W. (author), Hoes, Louisa R. (author), Mainardi, Sara (author), Pinato, David J. (author), Sun, Kristi (author), Wessels, L.F.A. (author)Genomics has greatly improved how patients with cancer are being treated; however, clinical-grade genomic biomarkers for chemotherapies are currently lacking. Using whole-genome analysis of 37 patients with metastatic colorectal cancer (mCRC) treated with the chemotherapy trifluridine/tipiracil (FTD/TPI), we identified KRAS codon G12 (KRAS...journal article 2023
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Lips, Esther H. (author), Kumar, Tapsi (author), Megalios, Anargyros (author), Visser, Lindy L. (author), Sheinman, Michael (author), Fortunato, Angelo (author), Shah, Vandna (author), Hoogstraat, Marlous (author), Wessels, L.F.A. (author)Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5–10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address...journal article 2022
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Grinkevitch, Vera (author), Wappett, Mark (author), Crawford, Nyree (author), Price, Stacey (author), Lees, Andrea (author), McCann, Christopher (author), McAllister, Katherine (author), Prehn, Jochen (author), Wessels, L.F.A. (author)Multivalent second-generation TRAIL-R2 agonists are currently in late preclinical development and early clinical trials. Herein, we use a representative second-generation agent, MEDI3039, to address two major clinical challenges facing these agents: lack of predictive biomarkers to enable patient selection and emergence of resistance. Genome...journal article 2022
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Jaaks, Patricia (author), Coker, Elizabeth A. (author), Vis, Daniel J. (author), Edwards, Olivia (author), Carpenter, Emma F. (author), Leto, Simonetta M. (author), Dwane, Lisa (author), Sassi, Francesco (author), Wessels, L.F.A. (author)Combinations of anti-cancer drugs can overcome resistance and provide new treatments<sup>1,2</sup>. The number of possible drug combinations vastly exceeds what could be tested clinically. Efforts to systematically identify active combinations and the tissues and molecular contexts in which they are most effective could accelerate the...journal article 2022
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Hoogstraat, Marlous (author), Lips, Esther H. (author), Mayayo-Peralta, Isabel (author), Mulder, Lennart (author), Kristel, Petra (author), van der Heijden, Ingrid (author), Annunziato, Stefano (author), van Seijen, Maartje (author), Wessels, L.F.A. (author)When locally advanced breast cancer is treated with neoadjuvant chemotherapy, the recurrence risk is significantly higher if no complete pathologic response is achieved. Identification of the underlying resistance mechanisms is essential to select treatments with maximal efficacy and minimal toxicity. Here we employed gene expression profiles...journal article 2022
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Linder, Simon (author), Hoogstraat, Marlous (author), Stelloo, Suzan (author), Eickhoff, Nils (author), Schuurman, Karianne (author), de Barros, Hilda (author), Alkemade, Maartje (author), Bekers, Elise M. (author), Wessels, L.F.A. (author)In prostate cancer, androgen receptor (AR)–targeting agents are very effective in various disease stages. However, therapy resistance inevitably occurs, and little is known about how tumor cells adapt to bypass AR suppression. Here, we performed integrative multiomics analyses on tissues isolated before and after 3 months of AR-targeting...journal article 2022
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Jochems, Fleur (author), Thijssen, Bram (author), De Conti, Giulia (author), Jansen, Robin (author), Pogacar, Ziva (author), Groot, Kelvin (author), Wang, Liqin (author), Schepers, Arnout (author), Wessels, L.F.A. (author)Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in...journal article 2021
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Pijnenburg, R. (author), Laumann, S.J. (author), Wessels, R. (author), Maat, G. Ter (author), Armstrong, L.S. (author), Vardon, P.J. (author), Bruhn, D.F. (author), Barnhoorn, A. (author), Wapenaar, C.P.A. (author)The European Plate Observing System - Netherlands (EPOS-NL) is the Dutch research infrastructure for solid Earth sciences. EPOS-NL is a cluster of large-scale geophysical facilities for research on georesources and geohazards. It is a partnership between Delft University of Technology (TU Delft), the Royal Netherlands Meteorological Institute...conference paper 2021
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Ragusi, Max A.A. (author), Bismeijer, Tycho (author), van der Velden, Bas H.M. (author), Loo, Claudette E. (author), Canisius, Sander (author), Wesseling, Jelle (author), Wessels, L.F.A. (author), Elias, Sjoerd G. (author), Gilhuijs, Kenneth G.A. (author)Purpose: To assess whether contralateral parenchymal enhancement (CPE) on MRI is associated with gene expression pathways in ER+/HER2-breast cancer, and if so, whether such pathways are related to survival. Methods: Preoperative breast MRIs were analyzed of early ER+/HER2-breast cancer patients eligible for breast-conserving surgery included...journal article 2021