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2. Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

Author

Pogorelov, Dimitrii, Bode, Sebastian Felix Nepomuk, He, Xin, Ramiro-Garcia, Javier, Hedin, Fanny, Ammerlaan, Wim, Konstantinou, Maria, Capelle, Christophe M., Zeng, Ni, Poli, Aurélie, Domingues, Olivia, Montamat, Guillem, Hunewald, Oliver, Ciré, Séverine, Baron, Alexandre, Longworth, Joseph, Demczuk, Agnieszka, Bazon, Murilo Luiz, Casper, Ingrid, Klimek, Ludger, Neuberger-Castillo, Lorie, Revets, Dominique, Guyonnet, Lea, Delhalle, Sylvie, Zimmer, Jacques, Benes, Vladimir, Codreanu-Morel, Françoise, Lehners-Weber, Christiane, Weets, Ilse, Alper, Pinar, Brenner, Dirk, Gutermuth, Jan, Guerin, Coralie, Morisset, Martine, Hentges, François, Schneider, Reinhard, Shamji, Mohamed H., Betsou, Fay, Wilmes, Paul, Glaab, Enrico, Cosma, Antonio, Goncalves, Jorge, Hefeng, Feng Q., and Ollert, Markus

Published
2024
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3. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress

Author

de Jaime-Soguero, Anchel, Hattemer, Janina, Bufe, Anja, Haas, Alexander, van den Berg, Jeroen, van Batenburg, Vincent, Das, Biswajit, di Marco, Barbara, Androulaki, Stefania, Böhly, Nicolas, Landry, Jonathan J. M., Schoell, Brigitte, Rosa, Viviane S., Villacorta, Laura, Baskan, Yagmur, Trapp, Marleen, Benes, Vladimir, Chabes, Andrei, Shahbazi, Marta, Jauch, Anna, Engel, Ulrike, Patrizi, Annarita, Sotillo, Rocio, van Oudenaarden, Alexander, Bageritz, Josephine, Alfonso, Julieta, Bastians, Holger, and Acebrón, Sergio P.

Published
2024
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8. Treatment of Brain Arteriovenous Malformations

Author

Beneš, Vladimír, Bubeníková, Adéla, Skalický, Petr, Bradáč, Ondřej, Di Rocco, Concezio, Series Editor, Arraez, Miguel A., Editorial Board Member, Boop, Frederick A., Editorial Board Member, Froelich, Sebastien, Editorial Board Member, Kato, Yoko, Editorial Board Member, Pang, Dachling, Editorial Board Member, and Tu, Yong-Kwang, Editorial Board Member

Published
2024
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10. Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 – 07/2023

Author

Bundschuh, Christian, Weidner, Niklas, Klein, Julian, Rausch, Tobias, Azevedo, Nayara, Telzerow, Anja, Mallm, Jan-Philipp, Kim, Heeyoung, Steiger, Simon, Seufert, Isabelle, Börner, Kathleen, Bauer, Katharina, Hübschmann, Daniel, Jost, Katharina Laurence, Parthé, Sylvia, Schnitzler, Paul, Boutros, Michael, Rippe, Karsten, Müller, Barbara, Bartenschlager, Ralf, Kräusslich, Hans-Georg, and Benes, Vladimir

Published
2024
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11. Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics

Author

Pryszlak, Anna, Wenzel, Tobias, Seitz, Kiley West, Hildebrand, Falk, Kartal, Ece, Cosenza, Marco Raffaele, Benes, Vladimir, Bork, Peer, and Merten, Christoph

Subjects
Quantitative Biology - Genomics, Physics - Biological Physics, Quantitative Biology - Quantitative Methods
Abstract

We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples, and to prepare these cells for bulk whole genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de-novo assembly of high-quality genomes. While microbiome strains are increasingly demanded for biomedical applications, the vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplify a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing., Comment: 18 pages incl. references, 4 main figures and one supplementary figure

Published
2021
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15. Interferon-Driven Immune Dysregulation in Common Variable Immunodeficiency–Associated Villous Atrophy and Norovirus Infection

Author

Strohmeier, Valentina, Andrieux, Geoffroy, Unger, Susanne, Pascual-Reguant, Anna, Klocperk, Adam, Seidl, Maximilian, Marques, Otavio Cabral, Eckert, Marleen, Gräwe, Katja, Shabani, Michelle, von Spee-Mayer, Caroline, Friedmann, David, Harder, Ina, Gutenberger, Sylvia, Keller, Baerbel, Proietti, Michele, Bulashevska, Alla, Grimbacher, Bodo, Provaznik, Jan, Benes, Vladimir, Goldacker, Sigune, Schell, Christoph, Hauser, Anja E., Boerries, Melanie, Hasselblatt, Peter, and Warnatz, Klaus

Published
2023
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16. Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Author

Beneyto-Calabuig, Sergi, Merbach, Anne Kathrin, Kniffka, Jonas-Alexander, Antes, Magdalena, Szu-Tu, Chelsea, Rohde, Christian, Waclawiczek, Alexander, Stelmach, Patrick, Gräßle, Sarah, Pervan, Philip, Janssen, Maike, Landry, Jonathan J.M., Benes, Vladimir, Jauch, Anna, Brough, Michaela, Bauer, Marcus, Besenbeck, Birgit, Felden, Julia, Bäumer, Sebastian, Hundemer, Michael, Sauer, Tim, Pabst, Caroline, Wickenhauser, Claudia, Angenendt, Linus, Schliemann, Christoph, Trumpp, Andreas, Haas, Simon, Scherer, Michael, Raffel, Simon, Müller-Tidow, Carsten, and Velten, Lars

Published
2023
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19. High‐resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD

Author

Schwartz, Uwe, Llamazares Prada, Maria, Pohl, Stephanie T, Richter, Mandy, Tamas, Raluca, Schuler, Michael, Keller, Corinna, Mijosek, Vedrana, Muley, Thomas, Schneider, Marc A, Quast, Karsten, Hey, Joschka, Heußel, Claus P, Warth, Arne, Winter, Hauke, Serçin, Özdemirhan, Karmouty‐Quintana, Harry, Jyothula, Soma SK, Patel, Manish K, Herth, Felix, Koch, Ina, Petrosino, Giuseppe, Titimeaua, Alexandru, Mardin, Balca R, Weichenhan, Dieter, Jurkowski, Tomasz P, Imbusch, Charles D, Brors, Benedikt, Benes, Vladimir, Jung, Birgit, Wyatt, David, Stahl, Heiko F, Plass, Christoph, and Jurkowska, Renata Z

Published
2023
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20. Drivers and determinants of strain dynamics following fecal microbiota transplantation

Author

Schmidt, Thomas S. B., Li, Simone S., Maistrenko, Oleksandr M., Akanni, Wasiu, Coelho, Luis Pedro, Dolai, Sibasish, Fullam, Anthony, Glazek, Anna M., Hercog, Rajna, Herrema, Hilde, Jung, Ferris, Kandels, Stefanie, Orakov, Askarbek, Thielemann, Roman, von Stetten, Moritz, Van Rossum, Thea, Benes, Vladimir, Borody, Thomas J., de Vos, Willem M., Ponsioen, Cyriel Y., Nieuwdorp, Max, and Bork, Peer

Published
2022
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21. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Author

Cossarizza, Andrea, Chang, Hyun-Dong, Radbruch, Andreas, Acs, Andreas, Adam, Dieter, Adam-Klages, Sabine, Agace, William W, Aghaeepour, Nima, Akdis, Mübeccel, Allez, Matthieu, Almeida, Larissa Nogueira, Alvisi, Giorgia, Anderson, Graham, Andrä, Immanuel, Annunziato, Francesco, Anselmo, Achille, Bacher, Petra, Baldari, Cosima T, Bari, Sudipto, Barnaba, Vincenzo, Barros-Martins, Joana, Battistini, Luca, Bauer, Wolfgang, Baumgart, Sabine, Baumgarth, Nicole, Baumjohann, Dirk, Baying, Bianka, Bebawy, Mary, Becher, Burkhard, Beisker, Wolfgang, Benes, Vladimir, Beyaert, Rudi, Blanco, Alfonso, Boardman, Dominic A, Bogdan, Christian, Borger, Jessica G, Borsellino, Giovanna, Boulais, Philip E, Bradford, Jolene A, Brenner, Dirk, Brinkman, Ryan R, Brooks, Anna ES, Busch, Dirk H, Büscher, Martin, Bushnell, Timothy P, Calzetti, Federica, Cameron, Garth, Cammarata, Ilenia, Cao, Xuetao, Cardell, Susanna L, Casola, Stefano, Cassatella, Marco A, Cavani, Andrea, Celada, Antonio, Chatenoud, Lucienne, Chattopadhyay, Pratip K, Chow, Sue, Christakou, Eleni, Čičin-Šain, Luka, Clerici, Mario, Colombo, Federico S, Cook, Laura, Cooke, Anne, Cooper, Andrea M, Corbett, Alexandra J, Cosma, Antonio, Cosmi, Lorenzo, Coulie, Pierre G, Cumano, Ana, Cvetkovic, Ljiljana, Dang, Van Duc, Dang-Heine, Chantip, Davey, Martin S, Davies, Derek, De Biasi, Sara, Del Zotto, Genny, Dela Cruz, Gelo Victoriano, Delacher, Michael, Della Bella, Silvia, Dellabona, Paolo, Deniz, Günnur, Dessing, Mark, Di Santo, James P, Diefenbach, Andreas, Dieli, Francesco, Dolf, Andreas, Dörner, Thomas, Dress, Regine J, Dudziak, Diana, Dustin, Michael, Dutertre, Charles-Antoine, Ebner, Friederike, Eckle, Sidonia BG, Edinger, Matthias, Eede, Pascale, Ehrhardt, Götz RA, Eich, Marcus, Engel, Pablo, Engelhardt, Britta, and Erdei, Anna

Subjects
1.1 Normal biological development and functioning, Underpinning research, Inflammatory and immune system, Allergy and Immunology, Cell Separation, Consensus, Flow Cytometry, Humans, Phenotype, Immunology
Abstract

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

Published
2019

22. Integrated genomic analysis reveals actionable targets in pediatric spinal cord low-grade gliomas

Author

Misove Adela, Vicha Ales, Broz Petr, Vanova Katerina, Sumerauer David, Stolova Lucie, Sramkova Lucie, Koblizek Miroslav, Zamecnik Josef, Kyncl Martin, Holubova Zuzana, Liby Petr, Taborsky Jakub, Benes Vladimir, Pernikova Ivana, Jones T. W. David, Sill Martin, Stancokova Terezia, Krskova Lenka, and Zapotocky Michal

Subjects
Spinal cord, Low-grade glioma, KIAA1549:BRAF fusion, NTRK fusion, Methylation profiling, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Gliomas are the most common central nervous tumors in children and adolescents. However, spinal cord low-grade gliomas (sLGGs) are rare, with scarce information on tumor genomics and epigenomics. To define the molecular landscape of sLGGs, we integrated clinical data, histology, and multi-level genetic and epigenetic analyses on a consecutive cohort of 26 pediatric patients. Driver molecular alteration was found in 92% of patients (24/26). A novel variant of KIAA1549:BRAF fusion (ex10:ex9) was identified using RNA-seq in four cases. Importantly, only one-third of oncogenic drivers could be revealed using standard diagnostic methods, and two-thirds of pediatric patients with sLGGs required extensive molecular examination. The majority (23/24) of detected alterations were potentially druggable targets. Four patients in our cohort received targeted therapy with MEK or NTRK inhibitors. Three of those exhibited clinical improvement (two with trametinib, one with larotrectinib), and two patients achieved partial response. Methylation profiling was implemented to further refine the diagnosis and revealed intertumoral heterogeneity in sLGGs. Although 55% of tumors clustered with pilocytic astrocytoma, other rare entities were identified in this patient population. In particular, diffuse leptomeningeal glioneuronal tumors (n = 3) and high-grade astrocytoma with piloid features (n = 1) and pleomorphic xanthoastrocytoma (n = 1) were present. A proportion of tumors (14%) had no match with the current version of the classifier. Complex molecular genetic sLGGs characterization was invaluable to refine diagnosis, which has proven to be essential in such a rare tumor entity. Moreover, identifying a high proportion of drugable targets in sLGGs opened an opportunity for new treatment modalities.

Published
2022
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24. Molecular Biology of CCM

Author

Mládek, Arnošt, Skalický, Petr, Beneš, Vladimír, Bradáč, Ondřej, Bradáč, Ondřej, editor, and Beneš, Vladimír, editor

Published
2020
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29. Neutralizing antibody response against the B.1.617.2 (delta) and the B.1.1.529 (omicron) variants after a third mRNA SARS-CoV-2 vaccine dose in kidney transplant recipients

Author

Benning, Louise, Morath, Christian, Bartenschlager, Marie, Kim, Heeyoung, Reineke, Marvin, Beimler, Jörg, Buylaert, Mirabel, Nusshag, Christian, Kälble, Florian, Reichel, Paula, Töllner, Maximilian, Schaier, Matthias, Klein, Katrin, Benes, Vladimir, Rausch, Tobias, Rieger, Susanne, Stich, Maximilian, Tönshoff, Burkhard, Weidner, Niklas, Schnitzler, Paul, Zeier, Martin, Süsal, Caner, Hien Tran, Thuong, Bartenschlager, Ralf, and Speer, Claudius

Published
2022
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33. Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

Author

Petrosino, Giuseppe, Ponte, Giovanna, Volpe, Massimiliano, Zarrella, Ilaria, Ansaloni, Federico, Langella, Concetta, Di Cristina, Giulia, Finaurini, Sara, Russo, Monia T., Basu, Swaraj, Musacchia, Francesco, Ristoratore, Filomena, Pavlinic, Dinko, Benes, Vladimir, Ferrante, Maria I., Albertin, Caroline, Simakov, Oleg, Gustincich, Stefano, Fiorito, Graziano, and Sanges, Remo

Published
2022
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38. Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

Author

Triana, Sergio, Vonficht, Dominik, Jopp-Saile, Lea, Raffel, Simon, Lutz, Raphael, Leonce, Daniel, Antes, Magdalena, Hernández-Malmierca, Pablo, Ordoñez-Rueda, Diana, Ramasz, Beáta, Boch, Tobias, Jann, Johann-Christoph, Nowak, Daniel, Hofmann, Wolf-Karsten, Müller-Tidow, Carsten, Hübschmann, Daniel, Alexandrov, Theodore, Benes, Vladimir, Trumpp, Andreas, Paulsen, Malte, Velten, Lars, and Haas, Simon

Published
2021
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42. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress

Author

CMM Sectie Molecular Cancer Research, Cancer, Hubrecht Institute with UMC, de Jaime-Soguero, Anchel, Hattemer, Janina, Bufe, Anja, Haas, Alexander, van den Berg, Jeroen, van Batenburg, Vincent, Das, Biswajit, di Marco, Barbara, Androulaki, Stefania, Böhly, Nicolas, Landry, Jonathan J.M., Schoell, Brigitte, Rosa, Viviane S., Villacorta, Laura, Baskan, Yagmur, Trapp, Marleen, Benes, Vladimir, Chabes, Andrei, Shahbazi, Marta, Jauch, Anna, Engel, Ulrike, Patrizi, Annarita, Sotillo, Rocio, van Oudenaarden, Alexander, Bageritz, Josephine, Alfonso, Julieta, Bastians, Holger, Acebrón, Sergio P., CMM Sectie Molecular Cancer Research, Cancer, Hubrecht Institute with UMC, de Jaime-Soguero, Anchel, Hattemer, Janina, Bufe, Anja, Haas, Alexander, van den Berg, Jeroen, van Batenburg, Vincent, Das, Biswajit, di Marco, Barbara, Androulaki, Stefania, Böhly, Nicolas, Landry, Jonathan J.M., Schoell, Brigitte, Rosa, Viviane S., Villacorta, Laura, Baskan, Yagmur, Trapp, Marleen, Benes, Vladimir, Chabes, Andrei, Shahbazi, Marta, Jauch, Anna, Engel, Ulrike, Patrizi, Annarita, Sotillo, Rocio, van Oudenaarden, Alexander, Bageritz, Josephine, Alfonso, Julieta, Bastians, Holger, and Acebrón, Sergio P.

Published
2024

43. Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells

Author

Fuentes, Manuel [0000-0002-7305-3766], Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Staniek, Julian, Kalina, Tomas, Andrieux, Geoffroy, Boerries, Melanie, Janowska, Iga, Fuentes, Manuel, Díez, Paula, Bakardjieva, Marina, Stancikova, Jitka, Raabe, Jan, Neumann, Julika, Schwenk, Sabine, Arpesella, Leonardo, Stuchly, Jan, Benes, Vladimir, García-Valiente, Rodrigo, Fernández-García, Jonatan, Carsetti, Rita, Piano Mortari, Eva, Catala, Albert, Calle, Oscar de la, Sogkas, Georgios, Neven, Bénédicte, Rieux-Laucat, Frédéric, Magerus, Aude, Neth, Olaf, Olbrich, Peter, Voll, Reinhard E., Alsina, Laia, Allende, Luis, González-Granado, Luis, Böhler, Chiara, Thiel, Jens, Venhoff, Nils, Lorenzetti, Raquel, Warnatz, Klaus, Unger, Susanne, Seidl, Maximilian, Mielenz, Dirk, Schneider, Pascal, Ehl, Stephan, Rensing-Ehl, Anne, Smulski, Cristian Roberto, Rizzi, Marta, Fuentes, Manuel [0000-0002-7305-3766], Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Staniek, Julian, Kalina, Tomas, Andrieux, Geoffroy, Boerries, Melanie, Janowska, Iga, Fuentes, Manuel, Díez, Paula, Bakardjieva, Marina, Stancikova, Jitka, Raabe, Jan, Neumann, Julika, Schwenk, Sabine, Arpesella, Leonardo, Stuchly, Jan, Benes, Vladimir, García-Valiente, Rodrigo, Fernández-García, Jonatan, Carsetti, Rita, Piano Mortari, Eva, Catala, Albert, Calle, Oscar de la, Sogkas, Georgios, Neven, Bénédicte, Rieux-Laucat, Frédéric, Magerus, Aude, Neth, Olaf, Olbrich, Peter, Voll, Reinhard E., Alsina, Laia, Allende, Luis, González-Granado, Luis, Böhler, Chiara, Thiel, Jens, Venhoff, Nils, Lorenzetti, Raquel, Warnatz, Klaus, Unger, Susanne, Seidl, Maximilian, Mielenz, Dirk, Schneider, Pascal, Ehl, Stephan, Rensing-Ehl, Anne, Smulski, Cristian Roberto, and Rizzi, Marta

Abstract

Defective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS with FAS mutations (ALPS-FAS), but paradoxically, fewer conventional memory cells differentiate from FAS-expressing germinal center (GC) B cells. Resistance to FAS-induced apoptosis does not explain this phenotype. We tested the hypothesis that defective non-apoptotic FAS signaling may contribute to impaired B cell differentiation in ALPS. We analyzed secondary lymphoid organs of patients with ALPS-FAS and found low numbers of memory B cells, fewer GC B cells, and an expanded extrafollicular (EF) B cell response. Enhanced mTOR activity has been shown to favor EF versus GC fate decision, and we found enhanced PI3K/mTOR and BCR signaling in ALPS-FAS splenic B cells. Modeling initial T-dependent B cell activation with CD40L in vitro, we showed that FAS competent cells with transient FAS ligation showed specifically decreased mTOR axis activation without apoptosis. Mechanistically, transient FAS engagement with involvement of caspase-8 induced nuclear exclusion of PTEN, leading to mTOR inhibition. In addition, FASL-dependent PTEN nuclear exclusion and mTOR modulation were defective in patients with ALPS-FAS. In the early phase of activation, FAS stimulation promoted expression of genes related to GC initiation at the expense of processes related to the EF response. Hence, our data suggest that non-apoptotic FAS signaling acts as molecular switch between EF versus GC fate decisions via regulation of the mTOR axis and transcription. The defect of this modulatory circuit may explain the observed hypergammaglobulinemia and low memory B cell numbers in ALPS.

Published
2024

47. Clinical and molecular study of radiation-induced gliomas

Author

Trkova, Katerina, primary, Sumerauer, David, additional, Bubenikova, Adela, additional, Krskova, Lenka, additional, Vicha, Ales, additional, Koblizek, Miroslav, additional, Zamecnik, Josef, additional, Jurasek, Bruno, additional, Kyncl, Martin, additional, Malinova, Bela, additional, Ondrova, Barbora, additional, Jones, David T. W., additional, Sill, Martin, additional, Strnadova, Martina, additional, Stolova, Lucie, additional, Misove, Adela, additional, Benes, Vladimir, additional, and Zapotocky, Michal, additional

Published
2024
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50. AVM Grading Schemes

Author

Bradáč, Ondřej, Beneš, Vladimír, Štekláčová, Anna, Beneš, Vladimír, editor, and Bradáč, Ondřej, editor

Published
2017
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