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UMC Repository: Recent submissions

  • Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist 
    Salas-Leiva, Dayana E.; Tromer, Eelco C.; Curtis, Bruce A.; Jerlström-Hultqvist, Jon; Kolisko, Martin; Yi, Zhenzhen; Salas-Leiva, Joan S.; Gallot-Lavallée, Lucie; Williams, Shelby K.; Kops, Geert J.P.L.; Archibald, John M.; Simpson, Alastair G.B.; Roger, Andrew J. (Nature Publishing Group, 2021-12)
    Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved ...
  • Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions 
    Andersson, Alma; Larsson, Ludvig; Stenbeck, Linnea; Salmén, Fredrik; Ehinger, Anna; Wu, Sunny Z.; Al-Eryani, Ghamdan; Roden, Daniel; Swarbrick, Alex; Borg, Åke; Frisén, Jonas; Engblom, Camilla; Lundeberg, Joakim (Nature Publishing Group, 2021-10-14)
    In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions ...
  • A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses 
    Beumer, Joep; Geurts, Maarten H.; Lamers, Mart M.; Puschhof, Jens; Zhang, Jingshu; van der Vaart, Jelte; Mykytyn, Anna Z.; Breugem, Tim I.; Riesebosch, Samra; Schipper, Debby; van den Doel, Petra B.; de Lau, Wim; Pleguezuelos-Manzano, Cayetano; Busslinger, Georg; Haagmans, Bart L.; Clevers, Hans (Nature Publishing Group, 2021-12)
    Rapid identification of host genes essential for virus replication may expedite the generation of therapeutic interventions. Genetic screens are often performed in transformed cell lines that poorly represent viral target ...
  • Phospholamban antisense oligonucleotides improve cardiac function in murine cardiomyopathy 
    Grote Beverborg, Niels; Später, Daniela; Knöll, Ralph; Hidalgo, Alejandro; Yeh, Steve T.; Elbeck, Zaher; Silljé, Herman H.W.; Eijgenraam, Tim R.; Siga, Humam; Zurek, Magdalena; Palmér, Malin; Pehrsson, Susanne; Albery, Tamsin; Bomer, Nils; Hoes, Martijn F.; Boogerd, Cornelis J.; Frisk, Michael; van Rooij, Eva; Damle, Sagar; Louch, William E.; Wang, Qing Dong; Fritsche-Danielson, Regina; Chien, Kenneth R.; Hansson, Kenny M.; Mullick, Adam E.; de Boer, Rudolf A.; van der Meer, Peter (Nature Publishing Group, 2021-12)
    Heart failure (HF) is a major cause of morbidity and mortality worldwide, highlighting an urgent need for novel treatment options, despite recent improvements. Aberrant Ca2+ handling is a key feature of HF pathophysiology. ...
  • Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease 
    Chu, Xiaojing; Jaeger, Martin; Beumer, Joep; Bakker, Olivier B.; Aguirre-Gamboa, Raul; Oosting, Marije; Smeekens, Sanne P.; Moorlag, Simone; Mourits, Vera P.; Koeken, Valerie A.C.M.; de Bree, Charlotte; Jansen, Trees; Mathews, Ian T.; Dao, Khoi; Najhawan, Mahan; Watrous, Jeramie D.; Joosten, Irma; Sharma, Sonia; Koenen, Hans J.P.M.; Withoff, Sebo; Jonkers, Iris H.; Netea-Maier, Romana T.; Xavier, Ramnik J.; Franke, Lude; Xu, Cheng Jian; Joosten, Leo A.B.; Sanna, Serena; Jain, Mohit; Kumar, Vinod; Clevers, Hans; Wijmenga, Cisca; Netea, Mihai G.; Li, Yang (BioMed Central, 2021-12)
    Background: Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors. Result: We systematically investigate ...
  • Unexpected contribution of fibroblasts to muscle lineage as a mechanism for limb muscle patterning 
    Esteves de Lima, Joana; Blavet, Cédrine; Bonnin, Marie Ange; Hirsinger, Estelle; Comai, Glenda; Yvernogeau, Laurent; Delfini, Marie Claire; Bellenger, Léa; Mella, Sébastien; Nassari, Sonya; Robin, Catherine; Schweitzer, Ronen; Fournier-Thibault, Claire; Jaffredo, Thierry; Tajbakhsh, Shahragim; Relaix, Frédéric; Duprez, Delphine (Nature Publishing Group, 2021-12)
    Positional information driving limb muscle patterning is contained in connective tissue fibroblasts but not in myogenic cells. Limb muscles originate from somites, while connective tissues originate from lateral plate ...
  • BCL-XL is crucial for progression through the adenoma-to-carcinoma sequence of colorectal cancer 
    Ramesh, Prashanthi; Lannagan, Tamsin R.M.; Jackstadt, Rene; Atencia Taboada, Lidia; Lansu, Nico; Wirapati, Pratyaksha; van Hooff, Sander R.; Dekker, Danielle; Pritchard, Jessica; Kirov, Aleksandar B.; van Neerven, Sanne M.; Tejpar, Sabine; Kops, Geert J.P.L.; Sansom, Owen J.; Medema, Jan Paul (Springer Nature, 2021-12)
    Evasion of apoptosis is a hallmark of cancer, which is frequently mediated by upregulation of the antiapoptotic BCL-2 family proteins. In colorectal cancer (CRC), previous work has highlighted differential antiapoptotic ...
  • Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development 
    Sen, Maya; Mooijman, Dylan; Chialastri, Alex; Boisset, Jean Charles; Popovic, Mina; Heindryckx, Björn; Chuva de Sousa Lopes, Susana M.; Dey, Siddharth S.; van Oudenaarden, Alexander (Nature Publishing Group, 2021-12)
    DNA methylation (5mC) is central to cellular identity. The global erasure of 5mC from the parental genomes during preimplantation mammalian development is critical to reset the methylome of gametes to the cells in the ...
  • Safety and biodegradability of a synthetic dural sealant patch (Liqoseal) in a porcine cranial model 
    Kinaci, Ahmet; Bergmann, Wilhelmina; van Thoor, Sander; Redegeld, Saskia; van der Zwan, Albert; van Doormaal, Tristan P C (John Wiley & Sons Inc., 2021-12)
    Background: Liqoseal consists of a watertight layer of poly(ester)ether urethane and an adhesive layer containing polyethylene glycol-N-hydroxysuccinimide (PEG-NHS). It is designed to prevent cerebrospinal fluid (CSF) ...
  • Author Correction: Establishment of patient-derived cancer organoids for drug-screening applications (Nature Protocols, (2020), 15, 10, (3380-3409), 10.1038/s41596-020-0379-4) 
    Driehuis, Else; Kretzschmar, Kai; Clevers, Hans (Springer Nature, 2021-12)
    A Correction to this paper has been published: https://doi.org/10.1038/s41596-021-00494-5
  • Recent Advances in Developmental Hematopoiesis: Diving Deeper With New Technologies 
    Weijts, Bart; Yvernogeau, Laurent; Robin, Catherine (Frontiers Media S. A., 2021-11-24)
    The journey of a hematopoietic stem cell (HSC) involves the passage through successive anatomical sites where HSCs are in direct contact with their surrounding microenvironment, also known as niche. These spatial and ...
  • Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions 
    Bobone, Sara; Pannone, Luca; Biondi, Barbara; Solman, Maja; Flex, Elisabetta; Canale, Viviana Claudia; Calligari, Paolo; De Faveri, Chiara; Gandini, Tommaso; Quercioli, Andrea; Torini, Giuseppe; Venditti, Martina; Lauri, Antonella; Fasano, Giulia; Hoeksma, Jelmer; Santucci, Valerio; Cattani, Giada; Bocedi, Alessio; Carpentieri, Giovanna; Tirelli, Valentina; Sanchez, Massimo; Peggion, Cristina; Formaggio, Fernando; Den Hertog, Jeroen; Martinelli, Simone; Bocchinfuso, Gianfranco; Tartaglia, Marco; Stella, Lorenzo (American Chemical Society, 2021-11-11)
    We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently ...
  • The H3.3K27M oncohistone affects replication stress outcome and provokes genomic instability in pediatric glioma 
    Bočkaj, Irena; Martini, Tosca E.I.; De Camargo Magalhães, Eduardo S.; Bakker, Petra L.; Meeuwsen-De Boer, Tiny G.J.; Armandari, Inna; Meuleman, Saskia L.; Mondria, Marin T.; Stok, Colin; Kok, Yannick P.; Bakker, Bjorn; Wardenaar, René; Seiler, Jonas; Broekhuis, Mathilde J.C.; Van Den Bos, Hilda; Spierings, Diana C.J.; Ringnalda, Femke C.A.; Clevers, Hans; Schüller, Ulrich; Van Vugt, Marcel A.T.M.; Foijer, Floris; Bruggeman, Sophia W.M. (Public Library of Science, 2021-11-09)
    While comprehensive molecular profiling of histone H3.3 mutant pediatric high-grade glioma has revealed extensive dysregulation of the chromatin landscape, the exact mechanisms driving tumor formation remain poorly understood. ...
  • Oxidative Stress Leads to β-Cell Dysfunction Through Loss of β-Cell Identity 
    Leenders, Floris; Groen, Nathalie; de Graaf, Natascha; Engelse, Marten A; Rabelink, Ton J.; de Koning, Eelco J.P.; Carlotti, Françoise (Frontiers Media S. A., 2021-11-04)
    Pancreatic β-cell failure is a critical event in the onset of both main types of diabetes mellitus but underlying mechanisms are not fully understood. β-cells have low anti-oxidant capacity, making them more susceptible ...
  • Protein Aggregation Is an Early Manifestation of Phospholamban p.(Arg14del)-Related Cardiomyopathy: Development of PLN-R14del-Related Cardiomyopathy 
    Eijgenraam, Tim R.; Boogerd, Cornelis J.; Stege, Nienke M.; Oliveira Nunes Teixeira, Vivian; Dokter, Martin M.; Schmidt, Lukas E.; Yin, Xiaoke; Theofilatos, Konstantinos; Mayr, Manuel; van der Meer, Peter; van Rooij, Eva; van der Velden, Jolanda; Silljé, Herman H.W.; de Boer, Rudolf A. (Lippincott Williams & Wilkins, 2021-11-01)
    BACKGROUND: The p.(Arg14del) pathogenic variant (R14del) of the PLN (phospholamban) gene is a prevalent cause of cardiomyopathy with heart failure. The exact underlying pathophysiology is unknown, and a suitable therapy ...
  • Epigenetic state changes underlie metabolic switch in mouse post-infarction border zone cardiomyocytes 
    Günthel, Marie; Duijvenboden, Karel van; de Bakker, Dennis E.M.; Hooijkaas, Ingeborg B.; Bakkers, Jeroen; Barnett, Phil; Christoffels, Vincent M. (MDPI AG, 2021-11)
    Myocardial infarction causes ventricular muscle loss and formation of scar tissue. The surviving myocardium in the border zone, located adjacent to the infarct, undergoes profound changes in function, structure and ...
  • H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity 
    Methot, Stephen P.; Padeken, Jan; Brancati, Giovanna; Zeller, Peter; Delaney, Colin E.; Gaidatzis, Dimos; Kohler, Hubertus; van Oudenaarden, Alexander; Großhans, Helge; Gasser, Susan M. (Nature Research, 2021-11)
    The developmental role of histone H3K9 methylation (H3K9me), which typifies heterochromatin, remains unclear. In Caenorhabditis elegans, loss of H3K9me leads to a highly divergent upregulation of genes with tissue and ...
  • The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 function 
    Koltowska, Katarzyna; Okuda, Kazuhide S.; Gloger, Marleen; Rondon-Galeano, Maria; Mason, Elizabeth; Xuan, Jiachen; Dudczig, Stefanie; Chen, Huijun; Arnold, Hannah; Skoczylas, Renae; Bower, Neil I.; Paterson, Scott; Lagendijk, Anne Karine; Baillie, Gregory J.; Leshchiner, Ignaty; Simons, Cas; Smith, Kelly A.; Goessling, Wolfram; Heath, Joan K.; Pearson, Richard B.; Sanij, Elaine; Schulte-Merker, Stefan; Hogan, Benjamin M. (Nature Research, 2021-11)
    The development of a functional vasculature requires the coordinated control of cell fate, lineage differentiation and network growth. Cellular proliferation is spatiotemporally regulated in developing vessels, but how ...
  • The prognostic potential of human prostate cancer-associated macrophage subtypes as revealed by single-cell transcriptomics 
    Siefert, Joseph C.; Cioni, Bianca; Muraro, Mauro J.; Alshalalfa, Mohammed; Vivie, Judith; van der Poel, Henk G.; Schoots, Ivo G.; Bekers, Elise; Feng, Felix Y.; Wessels, Lodewyk F.A.; Zwart, Wilbert; Bergman, Andries M. (American Association for Cancer Research Inc., 2021-10)
    Macrophages in the tumor microenvironment are causally linked with prostate cancer development and progression, yet little is known about their composition in neoplastic human tissue. By performing single cell transcriptomic ...
  • Disease modeling following organoid-based expansion of airway epithelial cells 
    Eenjes, Evelien; van Riet, Sander; Kroon, Andre A.; Slats, Annelies M.; Khedoe, P. Padmini S.J.; Boerema-De Munck, Anne; Buscop-Van Kempen, Marjon; Ninaber, Dennis K.; Reiss, Irwin K.M.; Clevers, Hans; Rottier, Robbert J.; Hiemstra, Pieter S. (American Physiological Society, 2021-10)
    Air-liquid interface (ALI) cultures are frequently used in lung research but require substantial cell numbers that cannot readily be obtained from patients. We explored whether organoid expansion [three-dimensional (3D)] ...