Recent publications

2023

Rawat S, Chatterjee D, Marwaha R, Charak G, Kumar G, Shaw S, Khatter D, Sharma S, de Heus C, Liv N, Klumperman J, Tuli A, Sharma M, RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes (2023) Journal of Cell Biology 222 (1): e202108001.
van der Beek J, Veenendaal T, de Heus C, van Dijk S, Ten Brink C, Liv N, Klumperman J, Ultrastructural Localization of Endogenous LC3 by On-Section Correlative Light-Electron Microscopy (2023) J Vis Exp (193) doi 10.3791/65067.
Liv N, Fermie J, Ten Brink CBM, de Heus C, Klumperman J, Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy (2023) Methods Cell Biology 2177:301-326.
de Heus C, Fermie J, Loginov S, Gerritsen HC, Klumperman J, Liv N, Correlative Live-cell-volume Electron Microscopy: Bridging Cellular Dynamics to 3D-Ultrastructure (2023) Microscopy and Microanalysis 29(29 Suppl 1):1188.
van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LL, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, Weingarth M, Vermeulen M, Klumperman J, Maurice MM, A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance (2023) Life Science Alliance 6(11):e202302058.
Bose S, de Heus C, Kennedy ME, Wang F, Jentsch TJ, Klumperman J, Stauber T, Impaired Autophagic Clearance with a Gain-of-Function Variant of the Lysosomal CI – /H + Exchanger CIC-7 (2023) Biomolecules 13(12):1799.
Katheder NS, Browder KC, Chang D, De Maziere A, Kujala P, van Dijk S, Klumperman J, Lu T-C, Li H, Lai Z, Sangaraju D, Jasper H, Nicotinic acetylcholine receptor signaling maintains epithelial barrier integrity (2023) Elife Dec 8:12e86381.

2022

Van der Beek J, De Heus C, Liv N & Klumperman J,
Quantitative correlative microscopy reveals the ultrastructural distribution of endogenous endosomal proteins (2022), Journal of Cell Biology 221 (1): e202106044.
Guo, Shanshan, Fernando Cázarez-Márquez, Han Jiao, Ewout Foppen, Nikita L. Korpel, Anita E. Grootemaat, Nalan Liv, Yuanqing Gao, Nicole van der Wel, Bing Zhou, Guangjun Nie, and Chun-Xia Yi. 2022. Specific Silencing of Microglial Gene Expression in the Rat Brain by Nanoparticle-Based Small Interfering RNA Delivery ACS Applied Materials & Interfaces 14(4):5066–79.
Zhang M, Chiozzi R Z, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms J B, Gadella BM & Bromfield EG, High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins (2022) Frontiers in Cell and Developmental Biology, 10, p. 836208.
Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC & Liv N, Correlative Organelle Microscopy Fluorescence Guided Volume Electron Microscopy of Intracellular Processes (2022), Frontiers in Cell and Developmental Biology 10, p. 829545.
Lehmann V, Schene IF, Ardisasmita AI, Liv N, Veenendaal T, Klumperman J, Van der Doef HPJ, Verkade HJ, Verstegen MMA, Van der Laan LJW Jans JJM, Verhoeven-Duif NM, Van Hasselt PM, Nieuwenhuis EES, Spee B & Fuchs SA, The potential and limitations of intrahepatic cholangiocyte organoids to study inborn errors of metabolism (2022), Journal of Inherited Metabolic Disease 45, (2) p. 353-365.
Van der Velden LM, Maas P, Van Amersfoort M, Timmermans-Sprang EPM, Mensinga A, Van der Vaart E, Malergue F, Viëtor H, Derksen PWB, Klumperman J, Van Agthoven A, Egan DA, Mol JA & Strous GJ, Small molecules to regulate the GH/IGF1 axis by inhibiting the growth hormone receptor synthesis (2022) Frontiers in Endocrinology, 13, 926210.
El Farissi, M., Buscone, S., Bax, N. A. M., van Rijswijk, J. W., Veenendaal, T., Keulards, D. C. J., Zelis, J. M., van Tuijl, S., Eerdekens, R., Demandt, J., Vervaat, F., Zimmermann, F. M., Bouwmeester, S., Rave, Y., Zhu, K. S., Conrad, C., van ‘t Veer, M., Pijls, N. H. J., Klumperman, J., Bouten, C. V. C. & 1 others, , Ultrastructural Characteristics of Myocardial Reperfusion Injury and Effect of Selective Intracoronary Hypothermia: An Observational Study in Isolated Beating Porcine Hearts ( 2022), Therapeutic hypothermia and temperature management. 12 (2) p.129-137
Fermie, J., de Jager, L., Foster, H. E., Veenendaal, T., de Heus, C., van Dijk, S., Ten Brink, C., Oorschot, V., Yang, L., Li, W., Müller, W. H., Howes, S., Carter, A. P., Förster, F., Posthuma, G., Gerritsen, H. C., Klumperman, J. & Liv, N., Bimodal endocytic probe for three-dimensional correlative light and electron microscopy (2022) Cell reports methods. 2, (5): p. 100220
De Mazière, A., van der Beek, J., van Dijk, S., de Heus, C., Reggiori, F., Koike, M. & Klumperman, J., . An optimized protocol for immuno-electron microscopy of endogenous LC3 (2022), (E-pub ahead of print) Autophagy. p. 1-19 19 p
Tavares, S., Liv, N., Pasolli, M., Opdam, M., Rätze, M. A. K., Saornil, M., Sluimer, L. M., Hengeveld, R. C. C., van Es, R., van Werkhoven, E., Vos, H., Rehmann, H., Burgering, B. M. T., Oosterkamp, H. M., Lens, S. M. A., Klumperman, J., Linn, S. C. & Derksen, P. W. B., FER regulates endosomal recycling and is a predictor for adjuvant taxane benefit in breast cancer (2022), Cell Reports. 39, (1):p. 110584

2021

Akiva, Anat, Johanna Melke, Sana Ansari, Nalan Liv, Robin van der Meijden, Merijn van Erp, Feihu Zhao, Merula Stout, Wouter H. Nijhuis, Cilia de Heus, Claudia Muñiz Ortera, Job Fermie, Judith Klumperman, Keita Ito, Nico Sommerdijk, and Sandra Hofmann. 2021. “An Organoid for Woven Bone.” Advanced Functional Materials 31(17):2010524.
Burns, Christian H., Belinda Yau, Anjelica Rodriguez, Jenna Triplett, Drew Maslar, You Sun An, Reini E. N. van der Welle, Ross G. Kossina, Max R. Fisher, Gregory W. Strout, Peter O. Bayguinov, Tineke Veenendaal, David Chitayat, James A. J. Fitzpatrick, Judith Klumperman, Melkam A. Kebede, and Cedric S. Asensio. 2021. “Pancreatic β-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion.” Diabetes 70(2):436–48.
Calandrini, Camilla, Sander R. van Hooff, Irene Paassen, Dilara Ayyildiz, Sepide Derakhshan, M. Emmy M. Dolman, Karin P. S. Langenberg, Marieke van de Ven, Cecilia de Heus, Nalan Liv, Marcel Kool, Ronald R. de Krijger, Godelieve A. M. Tytgat, Marry M. van den Heuvel-Eibrink, Jan J. Molenaar, and Jarno Drost. 2021. “Organoid-Based Drug Screening Reveals Neddylation as Therapeutic Target for Malignant Rhabdoid Tumors.” Cell Reports 36(8).
Dilsizoglu Senol, Aysegul, Maura Samarani, Sylvie Syan, Carlos M. Guardia, Takashi Nonaka, Nalan Liv, Patricia Latour-Lambert, Masato Hasegawa, Judith Klumperman, Juan S. Bonifacino, and Chiara Zurzolo. 2021. “α-Synuclein Fibrils Subvert Lysosome Structure and Function for the Propagation of Protein Misfolding between Cells through Tunneling Nanotubes.” PLoS Biology 19(7):e3001287.
El Farissi, Mohamed, Serena Buscone, Noortje A. M. Bax, Jan Willem van Rijswijk, Tineke Veenendaal, Danielle C. J. Keulards, Jo M. Zelis, Sjoerd van Tuijl, Rob Eerdekens, Jesse Demandt, Fabienne Vervaat, Frederik M. Zimmermann, Sjoerd Bouwmeester, Yahav Rave, Kwankwan S. Zhu, Cecile Conrad, Marcel van ’t Veer, Nico H. J. Pijls, Judith Klumperman, Carlijn V. C. Bouten, and Luuk C. Otterspoor. 2021. “Ultrastructural Characteristics of Myocardial Reperfusion Injury and Effect of Selective Intracoronary Hypothermia: An Observational Study in Isolated Beating Porcine Hearts.” Therapeutic Hypothermia and Temperature Management.
Gao, Xinxin, Ann De Mazière, Rhiannon Beard, Judith Klumperman, and Rami N. Hannoush. 2021. “Fatty Acylation Enhances the Cellular Internalization and Cytosolic Distribution of a Cystine-Knot Peptide.” iScience 24(11):103220.
Jamalpoor, Amer, Charlotte Agh van Gelder, Fjodor A. Yousef Yengej, Esther A. Zaal, Sante P. Berlingerio, Koenraad R. Veys, Carla Pou Casellas, Koen Voskuil, Khaled Essa, Carola ME Ammerlaan, Laura Rita Rega, Reini En van der Welle, Marc R. Lilien, Maarten B. Rookmaaker, Hans Clevers, Judith Klumperman, Elena Levtchenko, Celia R. Berkers, Marianne C. Verhaar, Maarten Altelaar, Rosalinde Masereeuw, and Manoe J. Janssen. 2021. “Cysteamine-Bicalutamide Combination Therapy Corrects Proximal Tubule Phenotype in Cystinosis.” EMBO Molecular Medicine 13(7):e13067.
Klumperman, Judith and Thomas Pucadyil. 2021. “Understanding Membrane Traffic from Molecular Ensemble, Energetics, and the Cell Biology of Participant Components.” Current Opinion in Cell Biology 71:III-VI.
Lane, Ryan, Yoram Vos, Anouk H. G. Wolters, Luc van Kessel, S. Elisa Chen, Nalan Liv, Judith Klumperman, Ben N. G. Giepmans, and Jacob P. Hoogenboom. 2021. “Optimization of Negative Stage Bias Potential for Faster Imaging in Large-Scale Electron Microscopy.” Journal of Structural Biology: X 5:100046.
Lehmann, Vivian, Imre F. Schene, Arif I. Ardisasmita, Nalan Liv, Tineke Veenendaal, Judith Klumperman, Hubert P. J. van der Doef, Henkjan J. Verkade, Monique M. A. Verstegen, Luc J. W. van der Laan, Judith J. M. Jans, Nanda M. Verhoeven-Duif, Peter M. van Hasselt, Edward E. S. Nieuwenhuis, Bart Spee, and Sabine A. Fuchs. 2021. “The Potential and Limitations of Intrahepatic Cholangiocyte Organoids to Study Inborn Errors of Metabolism.” Journal of Inherited Metabolic Disease.
Özkan, Nazmiye, Max Koppers, Inge van Soest, Alexandra van Harten, Daphne Jurriens, Nalan Liv, Judith Klumperman, Lukas C. Kapitein, Casper C. Hoogenraad, and Ginny G. Farías. 2021. “ER – Lysosome Contacts at a Pre-Axonal Region Regulate Axonal Lysosome Availability.” Nature Communications 12(1):4493.
Swinkels, Maurice, Ferdows Atiq, Petra E. Bürgisser, Johan A. Slotman, Adriaan B. Houtsmuller, Cilia de Heus, Judith Klumperman, Frank W. G. Leebeek, Jan Voorberg, Arend Jan Gerard Jansen, and Ruben Bierings. 2021. “Quantitative 3D Microscopy Highlights Altered von Willebrand Factor α-Granule Storage in Patients with von Willebrand Disease with Distinct Pathogenic Mechanisms.” Research and Practice in Thrombosis and Haemostasis 5(6):e12595.
Tran, Ngoc-Han, Stephen D. Carter, Ann De Mazière, Avi Ashkenazi, Judith Klumperman, Peter Walter, and Grant J. Jensen. 2021. “The Stress-Sensing Domain of Activated IRE1α Forms Helical Filaments in Narrow ER Membrane Tubes.” Science 374(6563):52–57.
van der Welle, Reini E. N., Rebekah Jobling, Christian Burns, Paolo Sanza, Jan A. van der Beek, Alfonso Fasano, Lan Chen, Fried J. Zwartkruis, Susan Zwakenberg, Edward F. Griffin, Corlinda Ten Brink, Tineke Veenendaal, Nalan Liv, Conny M. A. van Ravenswaaij-Arts, Henny H. Lemmink, Rolph Pfundt, Susan Blaser, Carolina Sepulveda, Andres M. Lozano, Grace Yoon, Teresa Santiago-Sim, Cedric S. Asensio, Guy A. Caldwell, Kim A. Caldwell, David Chitayat, and Judith Klumperman. 2021. “Neurodegenerative VPS41 Variants Inhibit HOPS Function and MTORC1-Dependent TFEB/TFE3 Regulation.” EMBO Molecular Medicine 13(5):e13258.
Zhang, M., E. G. Bromfield, T. Veenendaal, J. Klumperman, J. B. Helms, and B. M. Gadella. 2021. “Characterization of Different Oligomeric Forms of CRISP2 in the Perinuclear Theca versus the Fibrous Tail Structures of Boar Spermatozoa.” Biology of Reproduction 105(5):1160–70.

2020

Jain Goyal, Manu, Xiyan Zhao, Mariya Bozhinova, Karla Andrade-López, Cecilia de Heus, Sandra Schulze-Dramac, Michaela Müller-McNicoll, Judith Klumperman, and Julien Béthune. 2020. “A Paralog-Specific Role of COPI Vesicles in the Neuronal Differentiation of Mouse Pluripotent Cells.” Life Science Alliance 3(9):e202000714.
Jongsma, Marlieke LM, Jeroen Bakker, Birol Cabukusta, Nalan Liv, Daphne van Elsland, Job Fermie, Jimmy LL Akkermans, Coenraad Kuijl, Sabina Y. van der Zanden, Lennert Janssen, Denise Hoogzaad, Rik van der Kant, Ruud H. Wijdeven, Judith Klumperman, Ilana Berlin, and Jacques Neefjes. 2020. “SKIP-HOPS Recruits TBC1D15 for a Rab7-to-Arl8b Identity Switch to Control Late Endosome Transport.” The EMBO Journal 39(6):e102301.
Kuper, Willemijn F. E., Marlies Oostendorp, Brigitte T. A. van den Broek, Karin van Veghel, Lourens J. P. Nonkes, Edward E. S. Nieuwenhuis, Sabine A. Fuchs, Tineke Veenendaal, Judith Klumperman, Albert Huisman, Stefan Nierkens, and Peter M. van Hasselt. 2020. “Quantifying Lymphocyte Vacuolization Serves as a Measure of CLN3 Disease Severity.” JIMD Reports 54(1):87–97.
Ludikhuize, Marlies C., Maaike Meerlo, Marc Pages Gallego, Despina Xanthakis, Mar Burgaya Julià, Nguyen T. B. Nguyen, Eline C. Brombacher, Nalan Liv, Madelon M. Maurice, Ji hye Paik, Boudewijn M. T. Burgering, and Maria J. Rodriguez Colman. 2020. “Mitochondria Define Intestinal Stem Cell Differentiation Downstream of a FOXO/Notch Axis.” Cell Metabolism 32(5):889-900.e7.
Mohammadian, Sajjad, Alexandra V. Agronskaia, Gerhard A. Blab, Elly G. van Donselaar, Cecilia de Heus, Nalan Liv, Judith Klumperman, and Hans C. Gerritsen. 2020. “Integrated Super Resolution Fluorescence Microscopy and Transmission Electron Microscopy.” Ultramicroscopy 215:113007.
Nalle, Sam C., Rosa Barreira da Silva, Hua Zhang, Markus Decker, Cecile Chalouni, Min Xu, George Posthuma, Ann de Mazière, Judith Klumperman, Adriana Baz Morelli, Sebastian J. Fleire, Alan S. Verkman, E. Sergio Trombetta, Matthew L. Albert, and Ira Mellman. 2020. “Aquaporin-3 Regulates Endosome-to-Cytosol Transfer via Lipid Peroxidation for Cross Presentation.” PloS One 15(11):e0238484.
Omta, Wienand A., Roy G. van Heesbeen, Ian Shen, Jacob de Nobel, Desmond Robers, Lieke M. van der Velden, René H. Medema, Arno P. J. M. Siebes, Ad J. Feelders, Sjaak Brinkkemper, Judith S. Klumperman, Marco René Spruit, Matthieu J. S. Brinkhuis, and David A. Egan. 2020. “Combining Supervised and Unsupervised Machine Learning Methods for Phenotypic Functional Genomics Screening.” SLAS Discovery : Advancing Life Sciences R & D 25(6):655–64.
Piperno, Giulia Maria, Asma Naseem, Giulia Silvestrelli, Roberto Amadio, Nicoletta Caronni, Karla Evelia Cervantes-Luevano, Nalan Liv, Judith Klumperman, Andrea Colliva, Hashim Ali, Francesca Graziano, Philippe Benaroch, Hans Haecker, Richard N. Hanna, and Federica Benvenuti. 2020. “Wiskott-Aldrich Syndrome Protein Restricts CGAS/STING Activation by DsDNA Immune Complexes.” JCI Insight 5(17):e132857.
Scales, Suzie J., Nidhi Gupta, Ann M. De Mazière, George Posthuma, Cecilia P. Chiu, Andrew A. Pierce, Kathy Hötzel, Jianhua Tao, Oded Foreman, Georgios Koukos, Francesca Oltrabella, Judith Klumperman, WeiYu Lin, and Andrew S. Peterson. 2020. “Apolipoprotein L1-Specific Antibodies Detect Endogenous APOL1 inside the Endoplasmic Reticulum and on the Plasma Membrane of Podocytes.” Journal of the American Society of Nephrology : JASN 31(9):2044–64.

Van der Beek J, De Heus C, Liv N & Klumperman J,
Quantitative correlative microscopy reveals the ultrastructural distribution of endogenous endosomal proteins (2022), Journal of Cell Biology 221 (1): e202106044.
Guo, Shanshan, Fernando Cázarez-Márquez, Han Jiao, Ewout Foppen, Nikita L. Korpel, Anita E. Grootemaat, Nalan Liv, Yuanqing Gao, Nicole van der Wel, Bing Zhou, Guangjun Nie, and Chun-Xia Yi. 2022. Specific Silencing of Microglial Gene Expression in the Rat Brain by Nanoparticle-Based Small Interfering RNA Delivery ACS Applied Materials & Interfaces 14(4):5066–79.
Zhang M, Chiozzi R Z, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms J B, Gadella BM & Bromfield EG, High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins (2022) Frontiers in Cell and Developmental Biology, 10, p. 836208.
Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC & Liv N, Correlative Organelle Microscopy Fluorescence Guided Volume Electron Microscopy of Intracellular Processes (2022), Frontiers in Cell and Developmental Biology 10, p. 829545.
Lehmann V, Schene IF, Ardisasmita AI, Liv N, Veenendaal T, Klumperman J, Van der Doef HPJ, Verkade HJ, Verstegen MMA, Van der Laan LJW Jans JJM, Verhoeven-Duif NM, Van Hasselt PM, Nieuwenhuis EES, Spee B & Fuchs SA, The potential and limitations of intrahepatic cholangiocyte organoids to study inborn errors of metabolism (2022), Journal of Inherited Metabolic Disease 45, (2) p. 353-365.
Van der Velden LM, Maas P, Van Amersfoort M, Timmermans-Sprang EPM, Mensinga A, Van der Vaart E, Malergue F, Viëtor H, Derksen PWB, Klumperman J, Van Agthoven A, Egan DA, Mol JA & Strous GJ, Small molecules to regulate the GH/IGF1 axis by inhibiting the growth hormone receptor synthesis (2022) Frontiers in Endocrinology, 13, 926210.
El Farissi, M., Buscone, S., Bax, N. A. M., van Rijswijk, J. W., Veenendaal, T., Keulards, D. C. J., Zelis, J. M., van Tuijl, S., Eerdekens, R., Demandt, J., Vervaat, F., Zimmermann, F. M., Bouwmeester, S., Rave, Y., Zhu, K. S., Conrad, C., van ‘t Veer, M., Pijls, N. H. J., Klumperman, J., Bouten, C. V. C. & 1 others, , Ultrastructural Characteristics of Myocardial Reperfusion Injury and Effect of Selective Intracoronary Hypothermia: An Observational Study in Isolated Beating Porcine Hearts ( 2022), Therapeutic hypothermia and temperature management. 12 (2) p.129-137
Fermie, J., de Jager, L., Foster, H. E., Veenendaal, T., de Heus, C., van Dijk, S., Ten Brink, C., Oorschot, V., Yang, L., Li, W., Müller, W. H., Howes, S., Carter, A. P., Förster, F., Posthuma, G., Gerritsen, H. C., Klumperman, J. & Liv, N., Bimodal endocytic probe for three-dimensional correlative light and electron microscopy (2022) Cell reports methods. 2, (5): p. 100220
De Mazière, A., van der Beek, J., van Dijk, S., de Heus, C., Reggiori, F., Koike, M. & Klumperman, J., . An optimized protocol for immuno-electron microscopy of endogenous LC3 (2022), (E-pub ahead of print) Autophagy. p. 1-19 19 p
Tavares, S., Liv, N., Pasolli, M., Opdam, M., Rätze, M. A. K., Saornil, M., Sluimer, L. M., Hengeveld, R. C. C., van Es, R., van Werkhoven, E., Vos, H., Rehmann, H., Burgering, B. M. T., Oosterkamp, H. M., Lens, S. M. A., Klumperman, J., Linn, S. C. & Derksen, P. W. B., FER regulates endosomal recycling and is a predictor for adjuvant taxane benefit in breast cancer (2022), Cell Reports. 39, (1):p. 110584