Search Results - "FOEKENS, John A"

Gene expression-based classification of non-small cell lung carcinomas and survival prediction by Hou, Jun, Aerts, Joachim, den Hamer, Bianca, van Ijcken, Wilfred, den Bakker, Michael, Riegman, Peter, van der Leest, Cor, van der Spek, Peter, Foekens, John A, Hoogsteden, Henk C, Grosveld, Frank, Philipsen, Sjaak

“…Current clinical therapy of non-small cell lung cancer depends on histo-pathological classification. This approach poorly predicts clinical outcome for…”
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Selection of Bone Metastasis Seeds by Mesenchymal Signals in the Primary Tumor Stroma by Zhang, Xiang H.-F., Jin, Xin, Malladi, Srinivas, Zou, Yilong, Wen, Yong H., Brogi, Edi, Smid, Marcel, Foekens, John A., Massagué, Joan

“…How organ-specific metastatic traits arise in primary tumors remains unknown. Here, we show a role of the breast tumor stroma in selecting cancer cells that…”
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Efficacy of Cabazitaxel in Castration-resistant Prostate Cancer Is Independent of the Presence of AR-V7 in Circulating Tumor Cells by Onstenk, Wendy, Sieuwerts, Anieta M, Kraan, Jaco, Van, Mai, Nieuweboer, Annemieke J.M, Mathijssen, Ron H.J, Hamberg, Paul, Meulenbeld, Hielke J, De Laere, Bram, Dirix, Luc Y, van Soest, Robert J, Lolkema, Martijn P, Martens, John W.M, van Weerden, Wytske M, Jenster, Guido W, Foekens, John A, de Wit, Ronald, Sleijfer, Stefan

“…Abstract Background Androgen receptor splice variant 7 ( AR-V7 ) in circulating tumor cells (CTCs) from patients with metastatic castration-resistant prostate…”
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MicroRNAs as possible indicators of drug sensitivity in breast cancer cell lines by Uhr, Katharina, Prager-van der Smissen, Wendy J C, Heine, Anouk A J, Ozturk, Bahar, van Jaarsveld, Marijn T M, Boersma, Antonius W M, Jager, Agnes, Wiemer, Erik A C, Smid, Marcel, Foekens, John A, Martens, John W M

“…MicroRNAs (miRNAs) regulate gene expression post-transcriptionally. In this way they might influence whether a cell is sensitive or resistant to a certain…”
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A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer by Kloosterman, Wigard P, Coebergh van den Braak, Robert R J, Pieterse, Mark, van Roosmalen, Markus J, Sieuwerts, Anieta M, Stangl, Christina, Brunekreef, Ronne, Lalmahomed, Zarina S, Ooft, Salo, van Galen, Anne, Smid, Marcel, Lefebvre, Armel, Zwartkruis, Fried, Martens, John W M, Foekens, John A, Biermann, Katharina, Koudijs, Marco J, Ijzermans, Jan N M, Voest, Emile E

“…Genomic rearrangements that give rise to oncogenic gene fusions can offer actionable targets for cancer therapy. Here we present a systematic analysis of…”
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Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple-negative breast cancer progression by He, Jichao, McLaughlin, Ronan P., van der Beek, Lambert, Canisius, Sander, Wessels, Lodewyk, Smid, Marcel, Martens, John W. M., Foekens, John A., Zhang, Yinghui, van de Water, Bob

“…The genetically heterogeneous triple-negative breast cancer (TNBC) continues to be an intractable disease, due to lack of effective targeted therapies. Gene…”
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Subtypes of breast cancer show preferential site of relapse by Smid, Marcel, Wang, Yixin, Zhang, Yi, Sieuwerts, Anieta M, Yu, Jack, Klijn, Jan G M, Foekens, John A, Martens, John W M

“…We explored whether the five previously reported molecular subtypes in breast cancer show a preference for organ-specific relapse and searched for molecular…”
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Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons by Smid, Marcel, Coebergh van den Braak, Robert R J, van de Werken, Harmen J G, van Riet, Job, van Galen, Anne, de Weerd, Vanja, van der Vlugt-Daane, Michelle, Bril, Sandra I, Lalmahomed, Zarina S, Kloosterman, Wigard P, Wilting, Saskia M, Foekens, John A, IJzermans, Jan N M, Martens, John W M, Sieuwerts, Anieta M

“…Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for…”
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Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping by de Vree, Paula J P, de Wit, Elzo, Yilmaz, Mehmet, van de Heijning, Monique, Klous, Petra, Verstegen, Marjon J A M, Wan, Yi, Teunissen, Hans, Krijger, Peter H L, Geeven, Geert, Eijk, Paul P, Sie, Daoud, Ylstra, Bauke, Hulsman, Lorette O M, van Dooren, Marieke F, van Zutven, Laura J C M, van den Ouweland, Ans, Verbeek, Sjef, van Dijk, Ko Willems, Cornelissen, Marion, Das, Atze T, Berkhout, Ben, Sikkema-Raddatz, Birgit, van den Berg, Eva, van der Vlies, Pieter, Weening, Desiree, den Dunnen, Johan T, Matusiak, Magdalena, Lamkanfi, Mohamed, Ligtenberg, Marjolijn J L, ter Brugge, Petra, Jonkers, Jos, Foekens, John A, Martens, John W, van der Luijt, Rob, van Amstel, Hans Kristian Ploos, van Min, Max, Splinter, Erik, de Laat, Wouter

“…Chromatin crosslinking facilitates the detection in selected genomic regions of structural variants missed by existing approaches Despite developments in…”
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A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy by McLaughlin, Ronan P, He, Jichao, van der Noord, Vera E, Redel, Jevin, Foekens, John A, Martens, John W M, Smid, Marcel, Zhang, Yinghui, van de Water, Bob

“…The effective treatment of triple-negative breast cancer (TNBC) remains a profound clinical challenge. Despite frequent epidermal growth factor receptor (EGFR)…”
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Young Age at Diagnosis Correlates With Worse Prognosis and Defines a Subset of Breast Cancers With Shared Patterns of Gene Expression by ANDERS, Carey K, HSU, David S, NEVINS, Joseph R, POTTI, Anil, BLACKWELL, Kimberly L, BROADWATER, Gloria, ACHARYA, Chaitanya R, FOEKENS, John A, YI ZHANG, YIXIN WANG, MARCOM, P. Kelly, MARKS, Jeffrey R, FEBBO, Phillip G

“…Breast cancer arising in young women is correlated with inferior survival and higher incidence of negative clinicopathologic features. The biology driving this…”
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Anti-Epithelial Cell Adhesion Molecule Antibodies and the Detection of Circulating Normal-Like Breast Tumor Cells by Sieuwerts, Anieta M., Kraan, Jaco, Bolt, Joan, van der Spoel, Petra, Elstrodt, Fons, Schutte, Mieke, Martens, John W. M., Gratama, Jan-Willem, Sleijfer, Stefan, Foekens, John A.

“…Identification of specific subtypes of circulating tumor cells in peripheral blood of cancer patients can provide information about the biology of metastasis…”
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Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes by Koedoot, Esmee, Fokkelman, Michiel, Rogkoti, Vasiliki-Maria, Smid, Marcel, van de Sandt, Iris, de Bont, Hans, Pont, Chantal, Klip, Janna E., Wink, Steven, Timmermans, Mieke A., Wiemer, Erik A. C., Stoilov, Peter, Foekens, John A., Le Dévédec, Sylvia E., Martens, John W. M., van de Water, Bob

“…Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell…”
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Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer by He, Jichao, McLaughlin, Ronan P., van der Noord, Vera, Foekens, John A., Martens, John W. M., van Westen, Gerard, Zhang, Yinghui, van de Water, Bob

“…Purpose Owing to its genetic heterogeneity and acquired resistance, triple-negative breast cancer (TNBC) is not responsive to single-targeted therapy, causing…”
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Validation of a Radiosensitivity Molecular Signature in Breast Cancer by ESCHRICH, Steven A, FULP, William J, BERGH, Jonas, TORRES-ROCA, Javier F, PAWITAN, Yudi, FOEKENS, John A, SMID, Marcel, MARTENS, John W. M, ECHEVARRIA, Michelle, KAMATH, Vidya, LEE, Ji-Hyun, HARRIS, Eleanor E

“…Previously, we developed a radiosensitivity molecular signature [radiosensitivity index (RSI)] that was clinically validated in 3 independent datasets (rectal,…”
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Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation by Brinkman, Arie B., Nik-Zainal, Serena, Simmer, Femke, Rodríguez-González, F. Germán, Smid, Marcel, Alexandrov, Ludmil B., Butler, Adam, Martin, Sancha, Davies, Helen, Glodzik, Dominik, Zou, Xueqing, Ramakrishna, Manasa, Staaf, Johan, Ringnér, Markus, Sieuwerts, Anieta, Ferrari, Anthony, Morganella, Sandro, Fleischer, Thomas, Kristensen, Vessela, Gut, Marta, van de Vijver, Marc J., Børresen-Dale, Anne-Lise, Richardson, Andrea L., Thomas, Gilles, Gut, Ivo G., Martens, John W. M., Foekens, John A., Stratton, Michael R., Stunnenberg, Hendrik G.

“…Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially…”
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Definition of Clinically Distinct Molecular Subtypes in Estrogen Receptor–Positive Breast Carcinomas Through Genomic Grade by LOI, Sherene, HAIBE-KAINS, Benjamin, KLIJN, Jan G. M, LARSIMONT, Denis, BUYSE, Marc, BONTEMPI, Gianluca, DELORENZI, Mauro, PICCART, Martine J, SOTIRIOU, Christos, DESMEDT, Christine, LALLEMAND, Francoise, TUTT, Andrew M, GILLET, Cheryl, ELLIS, Paul, HARRIS, Adrian, BERGH, Jonas, FOEKENS, John A

“…A number of microarray studies have reported distinct molecular profiles of breast cancers (BC), such as basal-like, ErbB2-like, and two to three luminal-like…”
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miRNA expression profiling of 51 human breast cancer cell lines reveals subtype and driver mutation-specific miRNAs by Riaz, Muhammad, van Jaarsveld, Marijn T M, Hollestelle, Antoinette, Prager-van der Smissen, Wendy J C, Heine, Anouk A J, Boersma, Antonius W M, Liu, Jingjing, Helmijr, Jean, Ozturk, Bahar, Smid, Marcel, Wiemer, Erik A, Foekens, John A, Martens, John W M

“…Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression…”
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Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer by Foekens, John A, Sieuwerts, Anieta M, Smid, Marcel, Look, Maxime P, de Weerd, Vanja, Boersma, Antonius W.M, Klijn, Jan G.M, Wiemer, Erik A.C, Martens, John W.M

“…In this study, we quantified 249 mature micro-RNA (miRNA) transcripts in estrogen receptor-positive (ER⁺) primary breast tumors of patients with lymph…”
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Lung metastasis genes couple breast tumor size and metastatic spread by Minn, Andy J, Gupta, Gaorav P, Padua, David, Bos, Paula, Nguyen, Don X, Nuyten, Dimitry, Kreike, Bas, Zhang, Yi, Wang, Yixin, Ishwaran, Hemant, Foekens, John A, van de Vijver, Marc, Massagué, Joan

“…The association between large tumor size and metastatic risk in a majority of clinical cancers has led to questions as to whether these observations are…”
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