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UMC Repository: Recent submissions

  • Sports participation is not associated with adherence to prophylaxis in Dutch patients with haemophilia 
    Haemophilia in the Netherlands 6 Steering Group (Wiley-Blackwell, 2021-05)
  • Cytokine Output of Adipocyte-iNKT Cell Interplay Is Skewed by a Lipid-Rich Microenvironment 
    van Eijkeren, Robert J; Morris, Imogen; Borgman, Anouska; Markovska, Angela; Kalkhoven, Eric (Frontiers Media S. A., 2020-07-31)
    The complex direct and indirect interplay between adipocytes and various adipose tissue (AT)-resident immune cells plays an important role in maintaining local and whole-body insulin sensitivity. Adipocytes can directly ...
  • FXR Isoforms Control Different Metabolic Functions in Liver Cells via Binding to Specific DNA Motifs 
    Ramos Pittol, Jose Miguel; Milona, Alexandra; Morris, Imogen; Willemsen, Ellen C L; van der Veen, Suzanne W; Kalkhoven, Eric; van Mil, Saskia W C (W.B. Saunders, 2020-11)
    BACKGROUND & AIMS: The nuclear receptor subfamily 1 group H member 4 (NR1H4, also called FXR) is a ligand-activated transcription factor that, upon binding of bile acids, regulates the expression of genes involved in bile ...
  • DeepDose: a robust deep learning-based dose engine for abdominal tumours in a 1.5 T MRI radiotherapy system 
    Tsekas, Georgios; Bol, Gijsbert H; Raaymakers, Bas W; Kontaxis, Charis (IOP Publishing Ltd., 2021-03-21)
    We present a robust deep learning-based framework for dose calculations of abdominal tumours in a 1.5 T MRI radiotherapy system. For a set of patient plans, a convolutional neural network is trained on the dose of individual ...
  • Interaction between gad65 antibodies and dietary fish intake or plasma phospholipid n-3 polyunsaturated fatty acids on incident adult-onset diabetes: The epic-interact study 
    Löfvenborg, Josefin E.; Carlsson, Sofia; Andersson, Tomas; Hampe, Christiane S.; Koulman, Albert; Lopez, María Dolores Chirlaque; Jakszyn, Paula; Katzke, Verena A.; Kühn, Tilman; Kyrø, Cecilie; Masala, Giovanna; Nilsson, Peter M.; Overvad, Kim; Panico, Salvatore; Sánchez, Maria Jose; Van Der Schouw, Yvonne; Schulze, Matthias B.; Tjønneland, Anne; Weiderpass, Elisabete; Riboli, Elio; Forouhi, Nita G.; Sharp, Stephen J.; Rolandsson, Olov; Wareham, Nicholas J. (American Diabetes Association Inc., 2021-02-01)
    OBJECTIVE: Islet autoimmunity is associated with diabetes incidence. We investigated whether there was an interaction between dietary fish intake or plasma phospholipid n-3 polyunsaturated fatty acid (PUFA) concentration ...
  • Author Correction: Fasting-mimicking diet and hormone therapy induce breast cancer regression 
    Caffa, Irene; Spagnolo, Vanessa; Vernieri, Claudio; Valdemarin, Francesca; Becherini, Pamela; Wei, Min; Brandhorst, Sebastian; Zucal, Chiara; Driehuis, Else; Ferrando, Lorenzo; Piacente, Francesco; Tagliafico, Alberto; Cilli, Michele; Mastracci, Luca; Vellone, Valerio G; Piazza, Silvano; Cremonini, Anna Laura; Gradaschi, Raffaella; Mantero, Carolina; Passalacqua, Mario; Ballestrero, Alberto; Zoppoli, Gabriele; Cea, Michele; Arrighi, Annalisa; Odetti, Patrizio; Monacelli, Fiammetta; Salvadori, Giulia; Cortellino, Salvatore; Clevers, Hans; De Braud, Filippo; Sukkar, Samir G; Provenzani, Alessandro; Longo, Valter D; Nencioni, Alessio (Nature Research, 2020-12-24)
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.
  • Calorie Restriction Increases the Number of Competing Stem Cells and Decreases Mutation Retention in the Intestine 
    Bruens, Lotte; Ellenbroek, Saskia Inge Johanna; Suijkerbuijk, Saskia Jacoba Elisabeth; Azkanaz, Maria; Hale, Alexander James; Toonen, Pim; Flanagan, Dustin James; Sansom, Owen James; Snippert, Hugo Johannes; van Rheenen, Jacco (Cell Press, 2020-07-21)
    Calorie restriction (CR) extends lifespan through several intracellular mechanisms, including increased DNA repair, leading to fewer DNA mutations that cause age-related pathologies. However, it remains unknown how CR acts ...
  • High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells 
    Beumer, Joep; Puschhof, Jens; Bauzá-Martinez, Julia; Martínez-Silgado, Adriana; Elmentaite, Rasa; James, Kylie R; Ross, Alexander; Hendriks, Delilah; Artegiani, Benedetta; Busslinger, Georg A; Ponsioen, Bas; Andersson-Rolf, Amanda; Saftien, Aurelia; Boot, Charelle; Kretzschmar, Kai; Geurts, Maarten H; Bar-Ephraim, Yotam E; Pleguezuelos-Manzano, Cayetano; Post, Yorick; Begthel, Harry; van der Linden, Franka; Lopez-Iglesias, Carmen; van de Wetering, Willine J; van der Linden, Reinier; Peters, Peter J; Heck, Albert J R; Goedhart, Joachim; Snippert, Hugo; Zilbauer, Matthias; Teichmann, Sarah A; Wu, Wei; Clevers, Hans (Elsevier, 2020-06-11)
    Enteroendocrine cells (EECs) sense intestinal content and release hormones to regulate gastrointestinal activity, systemic metabolism, and food intake. Little is known about the molecular make-up of human EEC subtypes and ...
  • LGR5 in breast cancer and ductal carcinoma in situ: a diagnostic and prognostic biomarker and a therapeutic target 
    Hagerling, Catharina; Owyong, Mark; Sitarama, Vaishnavi; Wang, Chih-Yang; Lin, Charlene; van den Bijgaart, Renske J E; Koopman, Charlotte D; Brenot, Audrey; Nanjaraj, Ankitha; Wärnberg, Fredrik; Jirström, Karin; Klein, Ophir D; Werb, Zena; Plaks, Vicki (BioMed Central, 2020-06-10)
    BACKGROUND: Novel biomarkers are required to discern between breast tumors that should be targeted for treatment from those that would never become clinically apparent and/or life threatening for patients. Moreover, ...
  • LKB1 Represses ATOH1 via PDK4 and Energy Metabolism and Regulates Intestinal Stem Cell Fate 
    Gao, Yajing; Yan, Yan; Tripathi, Sushil; Pentinmikko, Nalle; Amaral, Ana; Päivinen, Pekka; Domènech-Moreno, Eva; Andersson, Simon; Wong, Iris P L; Clevers, Hans; Katajisto, Pekka; Mäkelä, Tomi P (W.B. Saunders, 2020-04)
    BACKGROUND & AIMS: In addition to the Notch and Wnt signaling pathways, energy metabolism also regulates intestinal stem cell (ISC) function. Tumor suppressor and kinase STK11 (also called LKB1) regulates stem cells and ...
  • Eleven grand challenges in single-cell data science 
    all co-authors (BioMed Central, 2020-02-07)
    The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment ...
  • Cellulose Nanofibril Hydrogel Promotes Hepatic Differentiation of Human Liver Organoids 
    Krüger, Melanie; Oosterhoff, Loes A; van Wolferen, Monique E; Schiele, Simon A; Walther, Andreas; Geijsen, Niels; De Laporte, Laura; van der Laan, Luc J W; Kock, Linda M; Spee, Bart (John Wiley & Sons Inc., 2020-03)
    To replicate functional liver tissue in vitro for drug testing or transplantation, 3D tissue engineering requires representative cell models as well as scaffolds that not only promote tissue production but also are applicable ...
  • Barriers and facilitators for treatment-seeking for mental health conditions and substance misuse: multi-perspective focus group study within the military (vol 6, e146, 2020): Barriers and facilitators for treatment-seeking for mental health conditions and substance misuse: Multi-perspective focus group study within the military (BJPsych Open (2020) 6 (e146) DOI: 10.1192/bjo.2020.136) 
    Bogaers, Rebecca; Geuze, Elbert; van Weeghel, Jaap; Leijten, Fenna; van de Mheen, Dike; Varis, Piia; Rozema, Andrea; Brouwers, Evelien (Cambridge University Press, 2021-02-08)
    This article refers incorrectly to the affiliation of author Evelien Brouwers. The correct affiliation for this author is Tranzo, Scientific Center for Care and Wellfare, Tilburg School of Social and Behavioral Sciences, ...
  • Fast and efficient generation of knock-in human organoids using homology-independent CRISPR-Cas9 precision genome editing 
    Artegiani, Benedetta; Hendriks, Delilah; Beumer, Joep; Kok, Rutger; Zheng, Xuan; Joore, Indi; Chuva de Sousa Lopes, Susana; van Zon, Jeroen; Tans, Sander; Clevers, Hans (Nature Research, 2020-03)
    CRISPR-Cas9 technology has revolutionized genome editing and is applicable to the organoid field. However, precise integration of exogenous DNA sequences into human organoids is lacking robust knock-in approaches. Here, ...
  • Cyclin B1 scaffolds MAD1 at the kinetochore corona to activate the mitotic checkpoint 
    Allan, Lindsey A; Camacho Reis, Magda; Ciossani, Giuseppe; Huis In 't Veld, Pim J; Wohlgemuth, Sabine; Kops, Geert Jpl; Musacchio, Andrea; Saurin, Adrian T (Springer Science and Business Media Deutschland GmbH, 2020-06-17)
    Cyclin B:CDK1 is the master kinase regulator of mitosis. We show here that, in addition to its kinase functions, mammalian Cyclin B also scaffolds a localised signalling pathway to help preserve genome stability. Cyclin ...
  • Organoid cultures of early-onset colorectal cancers reveal distinct and rare genetic profiles 
    Yan, Helen H N; Siu, Hoi Cheong; Ho, Siu Lun; Yue, Sarah S K; Gao, Yang; Tsui, Wai Yin; Chan, Dessy; Chan, April S; Wong, Jason W H; Man, Alice H Y; Lee, Bernard C H; Chan, Annie S Y; Chan, Anthony K W; Hui, Ho Sang; Cheung, Arthur K L; Law, Wai Lun; Lo, Oswens S H; Yuen, Siu Tsan; Clevers, Hans; Leung, Suet Yi (BMJ Publishing Group, 2020-12)
    OBJECTIVE: Sporadic early-onset colorectal cancer (EOCRC) has bad prognosis, yet is poorly represented by cell line models. We examine the key mutational and transcriptomic alterations in an organoid biobank enriched in ...
  • XPF-ERCC1 protects liver, kidney and blood homeostasis outside the canonical excision repair pathways 
    Mulderrig, Lee; Garaycoechea, Juan I (Public Library of Science, 2020-04)
    Loss of the XPF-ERCC1 endonuclease causes a dramatic phenotype that results in progeroid features associated with liver, kidney and bone marrow dysfunction. As this nuclease is involved in multiple DNA repair transactions, ...
  • Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq 
    Markodimitraki, Corina M; Rang, Franka J; Rooijers, Koos; de Vries, Sandra S; Chialastri, Alex; de Luca, Kim L; Lochs, Silke J A; Mooijman, Dylan; Dey, Siddharth S; Kind, Jop (Springer Nature, 2020-06)
    Protein-DNA interactions are essential for establishing cell type-specific chromatin architecture and gene expression. We recently developed scDam&T-seq, a multi-omics method that can simultaneously quantify protein-DNA ...
  • Author Correction: A structural model for microtubule minus-end recognition and protection by CAMSAP proteins 
    Atherton, Joseph; Jiang, Kai; Stangier, Marcel M; Luo, Yanzhang; Hua, Shasha; Houben, Klaartje; van Hooff, Jolien J E; Joseph, Agnel-Praveen; Scarabelli, Guido; Grant, Barry J; Roberts, Anthony J; Topf, Maya; Steinmetz, Michel O; Baldus, Marc; Moores, Carolyn A; Akhmanova, Anna (Nature Research, 2020-06)
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.
  • Patient-derived pancreatic tumour organoids identify therapeutic responses to oncolytic adenoviruses 
    Raimondi, Giulia; Mato-Berciano, Ana; Pascual-Sabater, Silvia; Rovira-Rigau, Maria; Cuatrecasas, Miriam; Fondevila, Constantino; Sánchez-Cabús, Santiago; Begthel, Harry; Boj, Sylvia F; Clevers, Hans; Fillat, Cristina (Elsevier, 2020-06)
    BACKGROUND: Pancreatic patient-derived organoids (PDOs) are a well-established model for studying pancreatic ductal adenocarcinoma (PDAC) carcinogenesis and are potential predictors of clinical responses to chemotherapy. ...