Searched for: author:"Wessels, L.F.A."
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Singh, Abhishek A. (author), Schuurman, Karianne (author), Nevedomskaya, Ekaterina (author), Stelloo, Suzan (author), Linder, Simon (author), Droog, Marjolein (author), Kim, Yongsoo (author), Sanders, Joyce (author), van der Poel, Henk (author), Bergman, Andries M. (author), Wessels, L.F.A. (author), Zwart, Wilbert (author)
Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human...
journal article 2019
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Gisler, Santiago (author), de Pinho Goncalves, J.S. (author), Akhtar, Waseem (author), de Jong, Johann (author), Pindyurin, Alexey V. (author), Wessels, L.F.A. (author), van Lohuizen, Maarten (author)
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic...
journal article 2019
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Bosdriesz, Evert (author), Prahallad, Anirudh (author), Klinger, Bertram (author), Sieber, Anja (author), Bosma, Astrid (author), Bernards, René (author), Blüthgen, Nils (author), Wessels, L.F.A. (author)
Motivation Signal-transduction networks are often aberrated in cancer cells, and new anti-cancer drugs that specifically target oncogenes involved in signaling show great clinical promise. However, the effectiveness of such targeted treatments is often hampered by innate or acquired resistance due to feedbacks, crosstalks or network...
journal article 2018
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Aben, N.N. (author), Westerhuis, Johan A. (author), Song, Yipeng (author), Kiers, Henk A.L. (author), Michaut, Magali (author), Smilde, Age K. (author), Wessels, L.F.A. (author)
Motivation In biology, we are often faced with multiple datasets recorded on the same set of objects, such as multi-omics and phenotypic data of the same tumors. These datasets are typically not independent from each other. For example, methylation may influence gene expression, which may, in turn, influence drug response. Such relationships...
journal article 2018
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Komor, Malgorzata A. (author), Bosch, Linda J.W. (author), Bounova, Gergana (author), Bolijn, Anne S. (author), Delis‐van Diemen, Pien M. (author), Rausch, Christian (author), Hoogstrate, Youri (author), Stubbs, Andrew P. (author), de Jong, Mark (author), Wessels, L.F.A. (author), More Authors (author)
Consensus molecular subtyping is an RNA expression-based classification system for colorectal cancer (CRC). Genomic alterations accumulate during CRC pathogenesis, including the premalignant adenoma stage, leading to changes in RNA expression. Only a minority of adenomas progress to malignancies, a transition that is associated with specific...
journal article 2018
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Bismeijer, Tycho (author), Canisius, Sander (author), Wessels, L.F.A. (author)
Effective cancer treatment is crucially dependent on the identification of the biological processes that drive a tumor. However, multiple processes may be active simultaneously in a tumor. Clustering is inherently unsuitable to this task as it assigns a tumor to a single cluster. In addition, the wide availability of multiple data types per...
journal article 2018
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Vossen, David M. (author), Verhagen, Caroline V.M. (author), Grénman, Reidar (author), Kluin, Roelof J.C. (author), Verheij, Marcel (author), van den Brekel, Michiel W.M. (author), Wessels, L.F.A. (author), Vens, Conchita (author)
Background Large cancer genome studies continue to reveal new players in treatment response and tumorigenesis. The discrimination of functional alterations from the abundance of passenger genetic alterations still poses challenges and determines DNA sequence variant selection procedures. Here we evaluate variant selection strategies that...
journal article 2018
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Severson, Tesa M. (author), Kim, Yongsoo (author), Joosten, Stacey E.P. (author), Schuurman, Karianne (author), Van Der Groep, Petra (author), Moelans, Cathy B. (author), ter Hoeve, Natalie D. (author), Manson, Quirine F. (author), Martens, J.W.M. (author), Wessels, L.F.A. (author), More Authors (author)
journal article 2018
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Stelloo, Suzan (author), Nevedomskaya, Ekaterina (author), Kim, Yongsoo (author), Schuurman, Karianne (author), Valle-Encinas, Eider (author), Lobo, João (author), Krijgsman, Oscar (author), Peeper, Daniel Simon (author), Chang, Seiwon Laura (author), Wessels, L.F.A. (author), More Authors (author)
The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. Here, to comprehensively study the epigenetic landscape, we perform RNA-seq with ChIP-seq for AR and histone...
journal article 2018
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Weeber, Fleur (author), Cirkel, Geert A. (author), Hoogstraat, Marlous (author), Bins, Sander (author), Gadellaa-van Hooijdonk, Christa G.M. (author), Ooft, Salo (author), van Werkhoven, Erik (author), Willems, Stefan M. (author), van Stralen, Marijn (author), Veldhuis, Wouter B. (author), Besselink, Nicolle J.M. (author), Horlings, Hugo M. (author), Steeghs, Neeltje (author), de Jonge, Maja J. (author), Langenberg, Marlies H.G. (author), Wessels, L.F.A. (author), Cuppen, Edwin P.J.G. (author), Cuppen, Edwin P.J.G. (author), Schellens, J.H. (author), Sleijfer, Stefan (author), Lolkema, Martijn P. (author), Voest, Emile E. (author)
Background: In this study, our aim was to identify molecular aberrations predictive for response to everolimus, an mTOR inhibitor, regardless of tumor type. Methods: To generate hypotheses about potential markers for sensitivity to mTOR inhibition, drug sensitivity and genomic profiles of 835 cell lines were analyzed. Subsequently, a...
journal article 2017
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Gallenne, Tristan (author), Ross, Kenneth N. (author), Visser, Nils L. (author), Salony (author), Desmet, Christian J. (author), Wittner, Ben S. (author), Wessels, L.F.A. (author), Ramaswamy, Sridhar (author), Peeper, Daniel Ss (author)
Prognostic classifiers conceivably comprise biomarker genes that functionally contribute to the oncogenic and metastatic properties of cancer, but this has not been investigated systematically. The transcription factor Fra-1 not only has an essential role in breast cancer, but also drives the expression of a highly prognostic gene set. Here,...
journal article 2017
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Roumeliotis, Theodoros I. (author), Williams, Steven P. (author), Gonçalves, Emanuel (author), Alsinet, Clara (author), Del Castillo Velasco-Herrera, Martin (author), Aben, N.N. (author), Zamanzad Ghavidel, Fatemeh (author), Michaut, Magali (author), Schubert, Michael (author), Price, Stacey (author), Wessels, L.F.A. (author), More Authors (author)
Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust...
journal article 2017
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Severson, Tesa M. (author), Wolf, Denise M. (author), Yau, Christina (author), Peeters, Justine (author), Wehkam, Diederik (author), Schouten, Philip C. (author), Chin, Suet-Feung (author), Majewski, Ian J. (author), Michaut, Magali (author), Bosma, Astrid (author), Pereira, Bernard (author), Bismeijer, Tycho (author), Wessels, L.F.A. (author), Caldas, Carlos (author), Bernards, Rene (author), Simon, Iris M. (author), Glas, Annuska M. (author), Linn, Sabine C. (author), van 't Veer, Laura (author)
Background: Patients with BRCA1-like tumors correlate with improved response to DNA double-strand break-inducing therapy. A gene expression-based classifier was developed to distinguish between BRCA1-like and non-BRCA1-like tumors. We hypothesized that these tumors may also be more sensitive to PARP inhibitors than standard treatments. Methods:...
journal article 2017
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Kersten, Kelly (author), Coffelt, Seth B. (author), Hoogstraat, Marlous (author), Verstegen, Niels J.M. (author), Vrijland, Kim (author), Ciampricotti, Metamia (author), Doornebal, Chris W. (author), Hau, Cheei-Sing (author), Wellenstein, Max D. (author), Salvagno, Camilla (author), Doshi, Parul (author), Lips, Esther H. (author), Wessels, L.F.A. (author), de Visser, Karin E. (author)
Patients with primary solid malignancies frequently exhibit signs of systemic inflammation. Notably, elevated levels of neutrophils and their associated soluble mediators are regularly observed in cancer patients, and correlate with reduced survival and increased metastasis formation. Recently, we demonstrated a mechanistic link between...
journal article 2017
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Koppens, Martijn A.J. (author), Bounova, Gergana (author), Cornelissen-Steijger, Paulien (author), de Vries, Nienke (author), Sansom, Owen J. (author), Wessels, L.F.A. (author), van Lohuizen, Maarten (author)
EZH2 inhibitors have gained great interest for their use as anti-cancer therapeutics. However, most research has focused on EZH2 mutant cancers and recently adverse effects of EZH2 inactivation have come to light. To determine whether colorectal cancer cells respond to EZH2 inhibition and to explore which factors influence the degree of response...
journal article 2016
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Knijnenburg, Theo A. (author), Klau, Gunnar W (author), Lorio, Francesco (author), Garnett, Mathew J. (author), McDermott, Ultan (author), Shmulevich, I (author), Wessels, L.F.A. (author)
Mining large datasets using machine learning approaches often leads to models that are hard to interpret and not amenable to the generation of hypotheses that can be experimentally tested. We present ‘Logic Optimization for Binary Input to Continuous Output’ (LOBICO), a computational approach that infers small and easily interpretable logic...
journal article 2016
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Canisius, Sander (author), Wessels, L.F.A. (author), Martens, John W. M. (author)
In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration probabilities across tumors. We present Discrete Independence Statistic Controlling for Observations with Varying Event Rates (DISCOVER),...
journal article 2016
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Iorio, Francesco (author), Knijnenburg, Theo A. (author), Vis, Daniel J. (author), Bignell, Graham R. (author), Menden, Michael P. (author), Schubert, Michael (author), Aben, N.N. (author), Gonçalves, Emanuel (author), Barthorpe, Syd (author), Wessels, L.F.A. (author), More Authors (author)
Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancerdriven alterations identified in 11,289 tumors from 29 tissues (integrating somatic mutations, copy...
journal article 2016
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Michaut, M (author), Chin, Suet-Feung (author), Majewski, Ian J. (author), Severson, Tesa M. (author), Bismeijer, Tycho (author), de Koning, L (author), Peeters, JK (author), Schouten, Philip C. (author), Rueda, OM (author), Bosma, AJ (author), Wessels, L.F.A. (author), More Authors (author)
Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for around 10% of all breast cancers. The molecular processes that drive the development of ILC are still largely unknown. We have performed a comprehensive genomic, transcriptomic and...
journal article 2016
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Thijssen, B. (author), Dijkstra, Tjeerd M.H. (author), Heskes, Tom (author), Wessels, L.F.A. (author)
Background
Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and...
journal article 2016
Searched for: author:"Wessels, L.F.A."
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