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UMC Repository: Recent submissions

  • Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration 
    de Bakker, Dennis E.M.; Bouwman, Mara; Dronkers, Esther; Simões, Filipa C.; Riley, Paul R.; Goumans, Marie José; Smits, Anke M.; Bakkers, Jeroen (Company of Biologists Ltd, 2021-10)
    Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms, such as zebrafish, cardiac ...
  • A public–private partnership model for COVID-19 diagnostics 
    Krijger, Peter H.L.; Hoek, Tim A.; Boersma, Sanne; Donders, Lieke I.P.M.; Broeders, Maaike M.C.; Pieterse, Mark; Toonen, Pim W.; Logister, Ive; Verhagen, Bram M.P.; Verstegen, Marjon J.A.M.; van Ravesteyn, Thomas W.; Roymans, Rene J.T.M.; Mattiroli, Francesca; Vandesompele, Jo; Nijhuis, Monique; Meijer, Stefan; van Weert, Anton; Dekker, Edwin; Dom, Fred J.; Ruijtenbeek, Rob; van der Velden, Lieven B.J.; van de Bovenkamp, Jeroen H.B.; Bosch, Martijn; de Laat, Wouter; Tanenbaum, Marvin E. (Nature Research, 2021-10)
  • Intestinal organoid cocultures with microbes 
    Puschhof, Jens; Pleguezuelos-Manzano, Cayetano; Martinez-Silgado, Adriana; Akkerman, Ninouk; Saftien, Aurelia; Boot, Charelle; de Waal, Amy; Beumer, Joep; Dutta, Devanjali; Heo, Inha; Clevers, Hans (Springer Nature, 2021-10)
    Adult-stem-cell-derived organoids model human epithelial tissues ex vivo, which enables the study of host–microbe interactions with great experimental control. This protocol comprises methods to coculture organoids with ...
  • Single-cell Ribo-seq reveals cell cycle-dependent translational pausing 
    VanInsberghe, Michael; van den Berg, Jeroen; Andersson-Rolf, Amanda; Clevers, Hans; van Oudenaarden, Alexander (Nature Research, 2021-09-23)
    Single-cell sequencing methods have enabled in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These tools focus predominantly on sequencing the genomes1, epigenomes2 and ...
  • Troy/Tnfrsf19 marks epidermal cells that govern interfollicular epidermal renewal and cornification 
    Kretzschmar, Kai; Boonekamp, Kim E.; Bleijs, Margit; Asra, Priyanca; Koomen, Mandy; Chuva de Sousa Lopes, Susana M.; Giovannone, Barbara; Clevers, Hans (Cell Press, 2021-09-14)
    The skin epidermis is a highly compartmentalized tissue consisting of a cornifying epithelium called the interfollicular epidermis (IFE) and associated hair follicles (HFs). Several stem cell populations have been described ...
  • Promises and challenges of organoid-guided precision medicine 
    Bose, Shree; Clevers, Hans; Shen, Xiling (Cell Press, 2021-09-10)
    Organoids are self-organizing, expanding 3D cultures derived from stem cells. Using tissue derived from patients, these miniaturized models recapitulate various aspects of patient physiology and disease phenotypes, including ...
  • Evidence generation and reproducibility in cell and gene therapy research: A call to action 
    Abou-el-Enein, Mohamed; Angelis, Aris; Appelbaum, Frederick R.; Andrews, Nancy C.; Bates, Susan E.; Bierman, Arlene S.; Brenner, Malcolm K.; Cavazzana, Marina; Caligiuri, Michael A.; Clevers, Hans; Cooke, Emer; Daley, George Q.; Dzau, Victor J.; Ellis, Lee M.; Fineberg, Harvey V.; Goldstein, Lawrence S.B.; Gottschalk, Stephen; Hamburg, Margaret A.; Ingber, Donald E.; Kohn, Donald B.; Krainer, Adrian R.; Maus, Marcela V.; Marks, Peter; Mummery, Christine L.; Pettigrew, Roderic I.; Rutter, Joni L.; Teichmann, Sarah A.; Terzic, Andre; Urnov, Fyodor D.; Williams, David A.; Wolchok, Jedd D.; Lawler, Mark; Turtle, Cameron J.; Bauer, Gerhard; Ioannidis, John P.A. (Cell Press, 2021-09-10)
  • Oxidized low-density lipoproteins as a novel risk factor and therapeutic target for ACM 
    Tsui, Hoyee; Han, Su Ji; van Rooij, Eva (Springer Science and Business Media Deutschland GmbH, 2021-09-07)
    Arrhythmogenic cardiomyopathy (ACM) is an inherited heart disease involving arrhythmia in young adults accompanied by structural changes at later stages. In this issue of EMBO Molecular Medicine, Sommariva et al (2021) ...
  • Multistep mechanism of G-quadruplex resolution during DNA replication 
    Sato, Koichi; Martin-Pintado, Nerea; Post, Harm; Altelaar, Maarten; Knipscheer, Puck (American Association for the Advancement of Science, 2021-09)
    G-quadruplex (or G4) structures form in guanine-rich DNA sequences and threaten genome stability when not properly resolved. G4 unwinding occurs during S phase via an unknown mechanism. Using Xenopus egg extracts, we define ...
  • Host phospholipid peroxidation fuels ExoU-dependent cell necrosis and supports Pseudomonas aeruginosa-driven pathology 
    Bagayoko, Salimata; Leon-Icaza, Stephen Adonai; Pinilla, Miriam; Hessel, Audrey; Santoni, Karin; Péricat, David; Bordignon, Pierre Jean; Moreau, Flavie; Eren, Elif; Boyancé, Aurélien; Naser, Emmanuelle; Lefèvre, Lise; Berrone, Céline; Iakobachvili, Nino; Metais, Arnaud; Rombouts, Yoann; Lugo-Villarino, Geanncarlo; Coste, Agnès; Attrée, Ina; Frank, Dara W.; Clevers, Hans; Peters, Peter J.; Cougoule, Céline; Planès, Rémi; Meunier, Etienne (Public Library of Science, 2021-09)
    Regulated cell necrosis supports immune and anti-infectious strategies of the body; however, dysregulation of these processes drives pathological organ damage. Pseudomonas aeruginosa expresses a phospholipase, ExoU that ...
  • Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression 
    Vos, Erica S.M.; Valdes-Quezada, Christian; Huang, Yike; Allahyar, Amin; Verstegen, Marjon J.A.M.; Felder, Anna Karina; van der Vegt, Floor; Uijttewaal, Esther C.H.; Krijger, Peter H.L.; de Laat, Wouter (Cell Press, 2021-08-05)
    To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage ...
  • Twisting of the zebrafish heart tube during cardiac looping is a tbx5-dependent and tissue-intrinsic process 
    Tessadori, Federico; Tsingos, Erika; Colizzi, Enrico Sandro; Kruse, Fabian; Van Den Brink, Susanne C.; Van Den Boogaard, Malou; Christoffels, Vincent M.; Merks, Roeland M.H.; Bakkers, Jeroen (eLife Sciences Publications, 2021-08)
    Organ laterality refers to the left-right asymmetry in disposition and conformation of internal organs and is established during embryogenesis. The heart is the first organ to display visible left-right asymmetries through ...
  • Genetic analysis of plasmid-encoded mcr-1 resistance in Enterobacteriaceae derived from poultry meat in the Netherlands 
    Jamin, Casper; Sanders, Bazante K; Zhou, Miaomiao; Costessi, Adalberto; Duijsings, Danny; Kluytmans, Jan A J W; van Alphen, Lieke B; Schrauwen, Eefje J A (Oxford, 2021-12)
    Background: Colistin is classified as the highest priority and critically important antimicrobial for human medicine by WHO as it is the last resort agent for treatment of carbapenem-resistant Enterobacteriaceae in humans. ...
  • Experimental and field investigations of exposure, replication and transmission of SARS-CoV-2 in pigs in the Netherlands 
    Sikkema, Reina S.; Tobias, Tijs; Oreshkova, Nadia; de Bruin, Erwin; Okba, Nisreen; Chandler, Felicity; Hulst, Marcel M.; Rodon, Jordi; Houben, Manon; van Maanen, Kees; Bultman, Hans; Meester, Marina; Gerhards, Nora M.; Bouwknegt, Martijn; Urlings, Bert; Haagmans, Bart; Kluytmans, Jan; GeurtsvanKessel, Corine H.; van der Poel, Wim H.M.; Koopmans, Marion P.G.; Stegeman, Arjan (Taylor and Francis Ltd., 2022-12-31)
    In order to assess the risk of SARS-CoV-2 infection, transmission and reservoir development in swine, we combined results of an experimental and two observational studies. First, intranasal and intratracheal challenge of ...
  • CRISPR base editing lowers cholesterol in monkeys 
    van Kampen, Sebastiaan Johannes; van Rooij, Eva (Nature Research, 2021-08)
  • Consensus Paper: Experimental Neurostimulation of the Cerebellum 
    Miterko, Lauren N; Baker, Kenneth B; Beckinghausen, Jaclyn; Bradnam, Lynley V; Cheng, Michelle Y; Cooperrider, Jessica; DeLong, Mahlon R; Gornati, Simona V; Hallett, Mark; Heck, Detlef H; Hoebeek, Freek E; Kouzani, Abbas Z; Kuo, Sheng-Han; Louis, Elan D; Machado, Andre; Manto, Mario; McCambridge, Alana B; Nitsche, Michael A; Taib, Nordeyn Oulad Ben; Popa, Traian; Tanaka, Masaki; Timmann, Dagmar; Steinberg, Gary K; Wang, Eric H; Wichmann, Thomas; Xie, Tao; Sillitoe, Roy V (Springer New York, 2019-12)
    The cerebellum is best known for its role in controlling motor behaviors. However, recent work supports the view that it also influences non-motor behaviors. The contribution of the cerebellum towards different brain ...
  • Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model 
    Sharma, Kunal; Thacker, Vivek V.; Dhar, Neeraj; Clapés Cabrer, Maria; Dubois, Anaëlle; Signorino-Gelo, François; Mullenders, Jasper; Knott, Graham W.; Clevers, Hans; McKinney, John D. (Cell Press, 2021-07-20)
    Recurrence of uropathogenic Escherichia coli (UPEC) infections has been attributed to reactivation of quiescent intracellular reservoirs (QIRs) in deep layers of the bladder wall. QIRs are thought to arise late during ...
  • Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma 
    De Crignis, Elisa; Hossain, Tanvir; Romal, Shahla; Carofiglio, Fabrizia; Moulos, Panagiotis; Khalid, Mir Mubashir; Rao, Shringar; Bazrafshan, Ameneh; Verstegen, Monique M.A.; Pourfarzad, Farzin; Koutsothanassis, Christina; Gehart, Helmuth; Kan, Tsung Wai; Palstra, Robert Jan; Boucher, Charles; Ijzermans, Jan M.N.; Huch, Meritxell; Boj, Sylvia F.; Vries, Robert; Clevers, Hans; van der Laan, Luc; Hatzis, Pantelis; Mahmoudi, Tokameh (eLife Sciences Publications, 2021-07)
    The molecular events that drive Hepatitis B virus (HBV)-mediated transformation and tumorigenesis have remained largely unclear, due to the absence of a relevant primary model system. Here we propose the use of human liver ...
  • Building bridges between fields: Bringing together development and homeostasis 
    Weterings, Sonja D.C.; van Oostrom, Marek J.; Sonnen, Katharina F. (Company of Biologists Ltd, 2021-07)
    Despite striking parallels between the fields of developmental biology and adult tissue homeostasis, these are disconnected in contemporary research. Although development describes tissue generation and homeostasis describes ...
  • Exploring the human lacrimal gland using organoids and single-cell sequencing 
    Bannier-Hélaouët, Marie; Post, Yorick; Korving, Jeroen; Trani Bustos, Marc; Gehart, Helmuth; Begthel, Harry; Bar-Ephraim, Yotam E.; van der Vaart, Jelte; Kalmann, Rachel; Imhoff, Saskia M.; Clevers, Hans (Cell Press, 2021-07-01)
    The lacrimal gland is essential for lubrication and protection of the eye. Disruption of lacrimal fluid production, composition, or release results in dry eye, causing discomfort and damage to the ocular surface. Here, we ...