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4. The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses

Author

Föhse, Konstantin, Geckin, Büsra, Zoodsma, Martijn, Kilic, Gizem, Liu, Zhaoli, Röring, Rutger J., Overheul, Gijs J., van de Maat, Josephine, Bulut, Ozlem, Hoogerwerf, Jacobien J., ten Oever, Jaap, Simonetti, Elles, Schaal, Heiner, Adams, Ortwin, Müller, Lisa, Ostermann, Philipp Niklas, van de Veerdonk, Frank L., Joosten, Leo A.B., Haagmans, Bart L., van Crevel, Reinout, van Rij, Ronald P., GeurtsvanKessel, Corine, de Jonge, Marien I., Li, Yang, Domínguez-Andrés, Jorge, and Netea, Mihai G.

Published
2023
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5. Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A, Cosme, Luciano V, Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K, Krsticevic, Flavia, Johnston, J Spencer, Halbach, Rebecca, Crawford, Jacob E, Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A, Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V, Tu, Zhijian, Papathanos, Philippos A, Van Rij, Ronald P, Akbari, Omar S, Powell, Jeffrey, Phillippy, Adam M, and Bonizzoni, Mariangela

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Prevention, Infectious Diseases, Emerging Infectious Diseases, Rare Diseases, Human Genome, Vector-Borne Diseases, Biotechnology, Biodefense, 1.1 Normal biological development and functioning, 2.2 Factors relating to the physical environment, 3.2 Interventions to alter physical and biological environmental risks, Infection, Generic health relevance, Good Health and Well Being, Aedes, Animals, Arboviruses, Chromosome Mapping, Chromosomes, Genome, Genome Size, Immunity, Insect Vectors, Mosquito Vectors, RNA, Small Interfering, Transcriptome, Ae, albopictus, miRNAs, piRNA clusters, Viral integrations, Sex locus, Population differentiation, Developmental transcriptome, Ae. albopictus, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.ResultsWe use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.ConclusionThe AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Published
2020

8. The Hsf1-sHsp cascade has pan-antiviral activity in mosquito cells.

Author

Qu, Jieqiong, Schinkel, Michelle, Chiggiato, Lisa, Rosendo Machado, Samara, Overheul, Gijs J., Miesen, Pascal, and van Rij, Ronald P.

Subjects
AEDES aegypti, HEAT shock factors, CHIKUNGUNYA virus, MEDICAL sciences, HEAT shock proteins, ALPHAVIRUSES, ARBOVIRUSES
Abstract

Aedes mosquitoes transmit pathogenic arthropod-borne (arbo) viruses, putting nearly half the world's population at risk. Blocking virus replication in mosquitoes is a promising approach to prevent arbovirus transmission, the development of which requires in-depth knowledge of virus-host interactions and mosquito immunity. By integrating multi-omics data, we find that heat shock factor 1 (Hsf1) regulates eight small heat shock protein (sHsp) genes within one topologically associated domain in the genome of the Aedes aegypti mosquito. This Hsf1-sHsp cascade acts as an early response against chikungunya virus infection and shows pan-antiviral activity against chikungunya, Sindbis, and dengue virus as well as the insect-specific Agua Salud alphavirus in Ae. aegypti cells and against chikungunya virus and O'nyong-nyong virus in Aedes albopictus and Anopheles gambiae cells, respectively. Our comprehensive in vitro data suggest that Hsf1 could serve as a promising target for the development of novel intervention strategies to limit arbovirus transmission by mosquitoes. A multi-omics approach was used to identify a new antiviral cascade, Hsf1-sHsp, that exhibits broad antiviral activity against alphaviruses and a flavivirus in cells from three vector mosquito species. [ABSTRACT FROM AUTHOR]

Published
2025
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11. SARS-CoV-2 RNA in exhaled air of hospitalized COVID-19 patients

Author

Kurver, Lisa, van den Kieboom, Corné H., Lanke, Kjerstin, Diavatopoulos, Dimitri A., Overheul, Gijs J., Netea, Mihai G., ten Oever, Jaap, van Crevel, Reinout, Mulders-Manders, Karin, van de Veerdonk, Frank L., Wertheim, Heiman, Schouten, Jeroen, Rahamat-Langendoen, Janette, van Rij, Ronald P., Bousema, Teun, van Laarhoven, Arjan, and de Jonge, Marien I.

Published
2022
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18. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A., Cosme, Luciano V., Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K., Krsticevic, Flavia, Johnston, J. Spencer, Halbach, Rebecca, Crawford, Jacob E., Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A., Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V., Tu, Zhijian, Papathanos, Philippos A., Van Rij, Ronald P., Akbari, Omar S., Powell, Jeffrey, Phillippy, Adam M., and Bonizzoni, Mariangela

Published
2021
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29. Longitudinal proteomic profiling of the inflammatory response in dengue patients

Author

Garishah, Fadel Muhammad, primary, Boahen, Collins K., additional, Vadaq, Nadira, additional, Pramudo, Setyo G., additional, Tunjungputri, Rahajeng N., additional, Riswari, Silvita Fitri, additional, van Rij, Ronald P., additional, Alisjahbana, Bachti, additional, Gasem, Muhammad Hussein, additional, van der Ven, André J. A. M., additional, and de Mast, Quirijn, additional

Published
2023
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42. How the COVID-19 pandemic highlights the necessity of animal research

Author

Genzel, Lisa, Adan, Roger, Berns, Anton, van den Beucken, Jeroen, Blokland, Arjan, Boddeke, Erik H W G M, Bogers, Willy M, Bontrop, Ronald, Bulthuis, R, Bousema, Teun, Clevers, Hans, Coenen, Tineke C J J, Dam, Anne-Marie van, Deen, Peter M T, van Dijk, K W, Eggen, Bart J L, Elgersma, Ype, Erdogan, Izel, Englitz, Bernard, Fentener van Vlissingen, J Martje, la Fleur, Susanne, Fouchier, Ron, Fitzsimons, Carlos P, Frieling, Wilbert, Haagmans, Bart, Heesters, Balthasar A, Henckens, Marloes, Herfst, Sander, Hol, Elly, van den Hove, Daniel, de Jonge, Marien I, Jonkers, Jos, Joosten, Leo A B, Kalsbeek, Andries, Kamermans, Maarten, Kampinga, Harm H, Kas, Martien J, Keijer, J, Kersten, Sander, Kiliaan, Amanda J, Kooij, Taco W A, Kooijman, Sander, Koopman, Werner J H, Korosi, Aniko, Krugers, Harm J, Kuiken, Thijs, Kushner, Steven A, Langermans, Jan A M, Lesscher, Heidi, Lucassen, Paul J, Lutgens, Esther, Netea, Mihai G, Noldus, Lucas P J J, van der Meer, Jos W M, Meye, Frank J, Mul, Joram D, van Oers, Kees, Olivier, Jocelien D A, Pasterkamp, R Jeroen, Philippens, Ingrid H C H M, Prickaerts, Jos, Pullox, Bart J A, Rensen, Patrick C N, van Rheenen, Jacco, van Rij, Ronald P, Ritsma, Laila, Rockx, Barry H G, Roozendaal, Benno, van Schothorst, Evert M, Stittelaar, K, Stockhofe, Norbert, Swaab, Dick F, de Swart, Rik L, Vanderschuren, Louk J M J, de Vries, Taco, de Vrij, Femke, van Wezel, Richard, Wierenga, Corette J, Wiesmann, Maximilian, Willuhn, Ingo, de Zeeuw, Chris I, Homberg, Judith R, Celbiologie, Sub Theoretical Biology, Faculteit Diergeneeskunde, Afd Chemical Biology and Drug Discovery, AISS LAS/3'R Centre ULS, AISS Behaviour Neuroscience, dASS BW-1, Dep Farmaceutische wetenschappen, Sub General Pharmacology, Sub Cell Biology, Endocrinology, Laboratory for Endocrinology, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam Gastroenterology Endocrinology Metabolism, Biomedical Engineering and Physics, Paediatrics, Medical Biochemistry, ACS - Atherosclerosis & ischemic syndromes, Adult Psychiatry, Neurosciences, Virology, Psychiatry, Netherlands Institute for Neuroscience (NIN), Animal Ecology (AnE), Celbiologie, Sub Theoretical Biology, Faculteit Diergeneeskunde, Afd Chemical Biology and Drug Discovery, AISS LAS/3'R Centre ULS, AISS Behaviour Neuroscience, dASS BW-1, Dep Farmaceutische wetenschappen, Sub General Pharmacology, Sub Cell Biology, Anatomy and neurosciences, Amsterdam Movement Sciences, Internal medicine, Pediatric surgery, AMS - Tissue Function & Regeneration, Section Psychopharmacology, RS: FPN NPPP II, Psychiatrie & Neuropsychologie, RS: MHeNs - R3 - Neuroscience, Structural and Functional Plasticity of the nervous system (SILS, FNWI), Translational Immunology Groningen (TRIGR), Molecular Neuroscience and Ageing Research (MOLAR), Kas lab, Olivier lab, and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
0301 basic medicine, Alzheimer`s disease Donders Center for Medical Neuroscience [Radboudumc 1], Biomedical Research, Stress-related disorders Donders Center for Medical Neuroscience [Radboudumc 13], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Voeding, Metabolisme en Genomica, Behavioral Ecology, 0302 clinical medicine, Taverne, Pandemic, European commission, Animal testing, Experimental Zoology, Alternative methods, Bacteriologie, national, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Bacteriology, Host Pathogen Interaction & Diagnostics, Plan_S-Compliant_NO, Public relations, PE&RC, Genealogy, Metabolism and Genomics, Gedragsecologie, Reconstructive and regenerative medicine Radboud Institute for Molecular Life Sciences [Radboudumc 10], Human and Animal Physiology, Metabolisme en Genomica, Nutrition, Metabolism and Genomics, General Agricultural and Biological Sciences, Coronavirus Infections, Neuroinformatics, Animal Experimentation, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, Biophysics, Neurophysiology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Betacoronavirus, Voeding, Animal welfare, Life Science, Animals, Humans, Pandemics, VLAG, Nutrition, Host Pathogen Interaction & Diagnostics, business.industry, SARS-CoV-2, Correction, COVID-19, Bacteriology, Host Pathogen Interactie & Diagnostiek, Disease Models, Animal, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], 030104 developmental biology, Experimentele Zoologie, Bacteriologie, Host Pathogen Interactie & Diagnostiek, WIAS, Fysiologie van Mens en Dier, business, 030217 neurology & neurosurgery
Abstract

Recently, a petition was offered to the European Commission calling for an immediate ban on animal testing. Although a Europe-wide moratorium on the use of animals in science is not yet possible, there has been a push by the non-scientific community and politicians for a rapid transition to animal-free innovations. Although there are benefits for both animal welfare and researchers, advances on alternate methods have not progressed enough to be able to replace animal research in the foreseeable future. This trend has led first and foremost to a substantial increase in the administrative burden and hurdles required to make timely advances in research and treatments for human and animal diseases. The current COVID-19 pandemic clearly highlights how much we actually rely on animal research. COVID-19 affects several organs and systems, and various animal-free alternatives currently available do not even come close to this complexity. In this Essay we therefore argue that the use of animals is essential for the advancement of human and veterinary health., In this Essay, Genzel et al. make the case for animal research in light of the COVID-19 pandemic.

Published
2020
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43. Cationic Geminoid Peptide Amphiphiles Inhibit DENV2 Protease, Furin, and Viral Replication

Author

Damen, Mark, Izidoro, Mario A., Okamoto, Debora N., Oliveira, Lilian C.G., Amatdjais-Groenen, Helene I.V., van Dongen, Stijn F.M., van Cleef, Koen W.R., van Rij, Ronald P., Dieteren, Cindy E.J., Gironés, Daniel, van Buuren, Bernd N.M., Martina, Byron E.E., Osterhaus, Albert D.M.E., Juliano, Luiz, Scholte, Bob J., Feiters, Martin C., Damen, Mark, Izidoro, Mario A., Okamoto, Debora N., Oliveira, Lilian C.G., Amatdjais-Groenen, Helene I.V., van Dongen, Stijn F.M., van Cleef, Koen W.R., van Rij, Ronald P., Dieteren, Cindy E.J., Gironés, Daniel, van Buuren, Bernd N.M., Martina, Byron E.E., Osterhaus, Albert D.M.E., Juliano, Luiz, Scholte, Bob J., and Feiters, Martin C.

Abstract

Dengue is an important arboviral infectious disease for which there is currently no specific cure. We report gemini-like (geminoid) alkylated amphiphilic peptides containing lysines in combination with glycines or alanines (C15H31C(O)-Lys-(Gly or Ala)nLys-NHC16H33, shorthand notation C16-KXnK-C16 with X = A or G, and n = 0–2). The representatives with 1 or 2 Ala inhibit dengue protease and human furin, two serine proteases involved in dengue virus infection that have peptides with cationic amino acids as their preferred substrates, with IC50 values in the lower µM range. The geminoid C16-KAK-C16 combined inhibition of DENV2 protease (IC50 2.3 µM) with efficacy against replication of wildtype DENV2 in LLC-MK2 cells (EC50 4.1 µM) and an absence of toxicity. We conclude that the lysine-based geminoids have activity against dengue virus infection, which is based on their inhibition of the proteases involved in viral replication and are therefore promising leads to further developing antiviral therapeutics, not limited to dengue.

Published
2022

44. Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level

Author

Reimer, Katharina C., Jansen, Jitske, Overheul, Gijs J., Miesen, Pascal, van Rij, Ronald P., Triana, Sergio H., Smeets, Bart, Schneider, Rebekka K., Kramann, Rafael, Reimer, Katharina C., Jansen, Jitske, Overheul, Gijs J., Miesen, Pascal, van Rij, Ronald P., Triana, Sergio H., Smeets, Bart, Schneider, Rebekka K., and Kramann, Rafael

Abstract

We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds. For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022).

Published
2022

45. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Author

Achdout, Hagit, Aimon, Anthony, Bar-David, Elad, Barr, Haim, Ben-Shmuel, Amir, Bennett, James, Boby, Melissa L., Borden, Bruce, Bowman, Gregory R., Brun, Juliane, BVNBS, Sarma, Calmiano, Mark, Carbery, Anna, Cattermole, Emma, Chernychenko, Eugene, Choder, John D., Clyde, Austin, Coffland, Joseph E., Cohen, Galit, Cole, Jason, Contini, Alessandro, Cox, Lisa, Cvitkovic, Milan, Dias, Alex, Donckers, Kim, Dotson, David L., Douangamath, Alica, Duberstein, Shirly, Dudgeon, Tim, Dunnett, Louise, Eastman, Peter K., Erez, Noam, Eyermann, Charles J., Fairhead, Mike, Fate, Gwen, Fearon, Daren, Federov, Oleg, Ferla, Matteo, Fernandes, Rafaela S., Ferrins, Lori, Foster, Richard, Foster, Holly, Gabizon, Ronen, Garcia-Sastre, Adolfo, Gawriljuk, Victor O., Gehrtz, Paul, Gileadi, Carina, Giroud, Charline, Glass, William G., Glen, Robert, Itai glinert, Godoy, Andre S., Gorichko, Marian, Gorrie-Stone, Tyler, Griffen, Ed J., Hart, Storm Hassell, Heer, Jag, Henry, Micheal, Hill, Michelle, Horrell, Sam, Hurley, Matthew F.D., Israely, Tomer, Jajack, Andrew, Jnoff, Eric, Jochmans, Dirk, John, Tobias, De Jonghe, Steven, Kantsadi, Anastassia L., Kenny, Peter W., Kiappes, J.L., Koekemoer, Lizbe, Kovar, Boris, Krojer, Tobias, Lee, Alpha A., Lefker, Bruce A., Levy, Haim, London, Nir, Lukacik, Petra, Macdonald, Hannah Bruce, Maclean, Beth, Malla, Tika R., Matviiuk, Tatiana, McCorkindale, Willam, McGovern, Briana L., Melamed, Sharon, Michurin, Oleg, Mikolajek, Halina, Milne, Bruce F., Morris, Aaron, Morris, Garret M., Morwitzer, Melody Jane, Moustakas, Demetri, Nakamura, Aline M., Neto, Jose Brandao, Neyts, Johan, Nguyen, Luong, Noske, Gabriela D., Oleinikovas, Vladas, Oliva, Glaucius, Overheul, Gijs J., Owen, David, Psenak, Vladimir, Pai, Ruby, Pan, Jin, Paran, Nir, Perry, Benjamin, Pingle, Maneesh, Pinjari, Jakir, Politi, Boaz, Powell, Ailsa, Puni, Reut, Rangel, Victor L., Reddi, Ranbabu N., Reid, St Patrick, Resnick, Efrat, Ripka, Emily Grace, Robinson, Matthew C., Robinson, Ralph P., Rodriguez-Guerra, Jaime, Rosales, Romel, Rufa, Dominic, Schofield, Chris, Shafeev, Mikhail, Shaikh, Aarif, Shi, Jiye, Shurrush, Khriesto, Sing, Sukrit, Sittner, Assa, Skyner, Rachael, Smalley, Adam, Smilova, Mihaela D., Solmesky, Leonardo J., Spencer, John, Strain-Damarell, Claire, Swamy, Vishwanath, Tamir, Hadas, Tennant, Rachael, Thompson, Warren, Thompson, Andrew, Tomasia, Susana, Tumber, Anthony, Vakonakis, Ioannis, van Rij, Ronald P., van Geel, Laura, Varghese, Finny S., Vaschetto, Mariana, Vitner, Einat B., Voelz, Vincent, Volkamer, Andra, von Delft, Frank, von Delft, Annette, Walsh, Martin, Ward, Walter, Weatherall, Charlie, Weiss, Shay, White, Kris M., Wild, Conor Francis, Wittmann, Matthew, Wright, Nathan, Yahalom-Ronen, Yfat, Zaidmann, Daniel, Zidane, Hadeer, Zitzmann, Nicole, Jansen, Jitske, Reimer, Katharina C., Nagai, James S., de Beer, Marit, Roverts, Rona, Daviran, Deniz, Fermin, Liline A.S., Willemsen, Brigith, Beukenboom, Marcel, Djudjaj, Sonja, von Stillfried, Saskia, van Eijk, Larissa E., Mastik, Mirjam, Bulthuis, Marian, Dunnen, Wilfred den, van Goor, Harry, Hillebrands, Jan-Luuk, Triana, Sergio H., Alexandrov, Theodore, Timm, Marie-Cherelle, van den Berge, Bartholomeus T., van den Broek, Martijn, Nlandu, Quincy, Heijnert, Joelle, Bindels, Eric M.J., Hoogenboezem, Remco M., Mooren, Fieke, Kuppe, Christoph, Miesen, Pascal, Grünberg, Katrien, Ijzermans, Ties, Steenbergen, Eric J., Czogalla, Jan, Schreuder, Michiel F., Sommerdijk, Nico, Akiva, Anat, Boor, Peter, Puelles, Victor G., Floege, Jürgen, Huber, Tobias B., Costa, Ivan G., Schneider, Rebekka K., Smeets, Bart, and Kramann, Rafael

Published
2022
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47. Cationic Geminoid Peptide Amphiphiles Inhibit DENV2 Protease, Furin, and Viral Replication

Author

Damen, Mark, primary, Izidoro, Mario A., additional, Okamoto, Debora N., additional, Oliveira, Lilian C. G., additional, Amatdjais-Groenen, Helene I. V., additional, van Dongen, Stijn F. M., additional, Cleef, Koen W. R. van, additional, Rij, Ronald P. van, additional, Dieteren, Cindy E. J., additional, Gironés, Daniel, additional, Buuren, Bernd N. M. van, additional, Martina, Byron E. E., additional, Osterhaus, Albert D. M. E., additional, Juliano, Luiz, additional, Scholte, Bob, additional, and Feiters, Martin C., additional

Published
2022
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